################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 2351519 Genus_species: Desulfitobacterium hafniense DCB-2 Taxid: 49338 Genome size: 4600 Libraries: KYR, KVE, LGY, AAZH, AIZS, TAN, WTA ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 2351519 ------------------------------------------------------------------- ID=2351519 ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 6372309 # phrap: 5565474 # db: 4600000 5512594 +/- 724507 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s KYR 12 4 83.85 440.25 8 66.28 334.75 KVE 0 0 0.00 0.00 0 0.00 0.00 AAZH 164 82 98.71 646.80 82 98.99 648.74 TAN 80 40 95.50 637.10 40 96.20 653.15 AIZS 330 165 97.59 732.88 165 96.78 717.99 WTA 248 124 98.50 666.11 124 98.24 669.58 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 2351519_fasta.screen -new_ace -minmatch 30 -maxmatch 55 -minscore 55 -revise_greedy -max_subclone_size 50000 -vector_bound 20 > phrap.out /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 2351519_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.2351519.out /home/copeland/scripts/librariesInfoTxt.sh 2351519 phrap.out > librariesInfo.txt ################################################################### Library vector screening AAZH.000001.000100 screen.out 2351519_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351519_fasta.screen /sequences/LRS.fasta AAZH.000101.000200 screen.out.1 2351519_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta AIZS.000001.000100 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta AIZS.000101.000200 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta AIZS.000201.000300 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KVE.000001.000100 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KVE.000101.000200 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KYR.000001.000100 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KYR.000101.000200 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KYR.000201.000300 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KYR.000301.000400 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KYR.000401.000500 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta TAN.000001.000100 screen.out 2351519_fasta.screen /sequences/pCC1FOS.fasta screen.out.std 2351519_fasta.screen /sequences/LRS.fasta WTA.000001.000100 screen.out 2351519_fasta.screen /sequences/p21.fasta screen.out.std 2351519_fasta.screen /sequences/LRS.fasta WTA.000101.000200 screen.out 2351519_fasta.screen /sequences/p21.fasta screen.out.std 2351519_fasta.screen /sequences/LRS.fasta AAZH.000001.000100 screen.out 2351519_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351519_fasta.screen /sequences/LRS.fasta AAZH.000101.000200 screen.out.1 2351519_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta AIZS.000001.000100 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta AIZS.000101.000200 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta AIZS.000201.000300 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KVE.000001.000100 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KVE.000101.000200 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KYR.000001.000100 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KYR.000101.000200 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KYR.000201.000300 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KYR.000301.000400 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta KYR.000401.000500 screen.out.1 2351519_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351519_fasta.screen /sequences/LRS.fasta TAN.000001.000100 screen.out 2351519_fasta.screen /sequences/pCC1FOS.fasta screen.out.std 2351519_fasta.screen /sequences/LRS.fasta WTA.000001.000100 screen.out 2351519_fasta.screen /sequences/p21.fasta screen.out.std 2351519_fasta.screen /sequences/LRS.fasta WTA.000101.000200 screen.out 2351519_fasta.screen /sequences/p21.fasta screen.out.std 2351519_fasta.screen /sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 2351519_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 150702 total values totalling 91266821.0000. <605.611213 +/- 183.399251> #Range: [ 22 - 901 ] #Most likely bin: [ 650 - 700 ] 27749 counts #Median bin: [ 650 - 700 ] 27749 counts |X 0 - 50 : [ 593 0.00 0.00 ] |XXXX 50 - 100 : [ 2625 0.02 0.02 ] |XXXXX 100 - 150 : [ 3343 0.02 0.04 ] |XXXX 150 - 200 : [ 2840 0.02 0.06 ] |XXXX 200 - 250 : [ 2805 0.02 0.08 ] |XXXX 250 - 300 : [ 2835 0.02 0.10 ] |XXXX 300 - 350 : [ 3017 0.02 0.12 ] |XXXXX 350 - 400 : [ 3319 0.02 0.14 ] |XXXXX 400 - 450 : [ 3753 0.02 0.17 ] |XXXXXXX 450 - 500 : [ 4560 0.03 0.20 ] |XXXXXXXXXX 500 - 550 : [ 7250 0.05 0.25 ] |XXXXXXXXXXXXXXXXX 550 - 600 : [ 11896 0.08 0.32 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 21421 0.14 0.47 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 27749 0.18 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 24019 0.16 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 20930 0.14 0.95 ] |XXXXXXXXXX 800 - 850 : [ 7167 0.05 1.00 ] |X 850 - 900 : [ 579 0.00 1.00 ] | 900 - 950 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for AAZH Command: /usr/xpg4/bin/grep AAZH 2351519_fasta.screen.screen.ids > reads.trim15.AAZH.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAZH.rl 2 50 #Found 17593 total values totalling 10690712.0000. <607.668505 +/- 127.634460> #Range: [ 27 - 901 ] #Most likely bin: [ 550 - 600 ] 4274 counts #Median bin: [ 600 - 650 ] 3593 counts | 0 - 50 : [ 21 0.00 0.00 ] |X 50 - 100 : [ 77 0.00 0.01 ] |X 100 - 150 : [ 103 0.01 0.01 ] |X 150 - 200 : [ 106 0.01 0.02 ] |X 200 - 250 : [ 115 0.01 0.02 ] |X 250 - 300 : [ 160 0.01 0.03 ] |X 300 - 350 : [ 152 0.01 0.04 ] |XX 350 - 400 : [ 242 0.01 0.06 ] |XXX 400 - 450 : [ 303 0.02 0.07 ] |XXXXXX 450 - 500 : [ 601 0.03 0.11 ] |XXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 2187 0.12 0.23 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 4274 0.24 0.47 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3593 0.20 0.68 ] |XXXXXXXXXXXXXXXXXX 650 - 700 : [ 1887 0.11 0.79 ] |XXXXXXXXXXXX 700 - 750 : [ 1282 0.07 0.86 ] |XXXXXXXXXXXXXX 750 - 800 : [ 1520 0.09 0.94 ] |XXXXXXXX 800 - 850 : [ 861 0.05 0.99 ] |X 850 - 900 : [ 108 0.01 1.00 ] | 900 - 950 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for KVE Command: /usr/xpg4/bin/grep KVE 2351519_fasta.screen.screen.ids > reads.trim15.KVE.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.KVE.rl 2 50 #Found 14005 total values totalling 6917025.0000. <493.896823 +/- 202.794488> #Range: [ 23 - 773 ] #Most likely bin: [ 650 - 700 ] 3165 counts #Median bin: [ 550 - 600 ] 1226 counts |XX 0 - 50 : [ 171 0.01 0.01 ] |XXXXXXXX 50 - 100 : [ 635 0.05 0.06 ] |XXXXXXXX 100 - 150 : [ 646 0.05 0.10 ] |XXXXXX 150 - 200 : [ 498 0.04 0.14 ] |XXXXXXX 200 - 250 : [ 573 0.04 0.18 ] |XXXXXX 250 - 300 : [ 513 0.04 0.22 ] |XXXXXXX 300 - 350 : [ 521 0.04 0.25 ] |XXXXXXX 350 - 400 : [ 564 0.04 0.29 ] |XXXXXXX 400 - 450 : [ 571 0.04 0.34 ] |XXXXXXXXX 450 - 500 : [ 678 0.05 0.38 ] |XXXXXXXXXX 500 - 550 : [ 794 0.06 0.44 ] |XXXXXXXXXXXXXXX 550 - 600 : [ 1226 0.09 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2727 0.19 0.72 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3165 0.23 0.95 ] |XXXXXXXXX 700 - 750 : [ 693 0.05 1.00 ] | 750 - 800 : [ 30 0.00 1.00 ] JAZZ trim 15 readlength histogram for KYR Command: /usr/xpg4/bin/grep KYR 2351519_fasta.screen.screen.ids > reads.trim15.KYR.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.KYR.rl 2 50 #Found 45565 total values totalling 22521831.0000. <494.279184 +/- 195.697812> #Range: [ 22 - 787 ] #Most likely bin: [ 650 - 700 ] 9853 counts #Median bin: [ 550 - 600 ] 4172 counts |X 0 - 50 : [ 269 0.01 0.01 ] |XXXXXXX 50 - 100 : [ 1637 0.04 0.04 ] |XXXXXXXXX 100 - 150 : [ 2267 0.05 0.09 ] |XXXXXXXX 150 - 200 : [ 1893 0.04 0.13 ] |XXXXXXX 200 - 250 : [ 1748 0.04 0.17 ] |XXXXXXX 250 - 300 : [ 1699 0.04 0.21 ] |XXXXXXX 300 - 350 : [ 1785 0.04 0.25 ] |XXXXXXX 350 - 400 : [ 1846 0.04 0.29 ] |XXXXXXXX 400 - 450 : [ 2061 0.05 0.33 ] |XXXXXXXXXX 450 - 500 : [ 2353 0.05 0.39 ] |XXXXXXXXXXXX 500 - 550 : [ 2955 0.06 0.45 ] |XXXXXXXXXXXXXXXXX 550 - 600 : [ 4172 0.09 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 9209 0.20 0.74 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 9853 0.22 0.96 ] |XXXXXXX 700 - 750 : [ 1785 0.04 1.00 ] | 750 - 800 : [ 33 0.00 1.00 ] JAZZ trim 15 readlength histogram for WTA Command: /usr/xpg4/bin/grep WTA 2351519_fasta.screen.screen.ids > reads.trim15.WTA.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.WTA.rl 2 50 #Found 22684 total values totalling 15578404.0000. <686.757362 +/- 86.667798> #Range: [ 31 - 843 ] #Most likely bin: [ 700 - 750 ] 7031 counts #Median bin: [ 650 - 700 ] 6552 counts | 0 - 50 : [ 18 0.00 0.00 ] | 50 - 100 : [ 27 0.00 0.00 ] | 100 - 150 : [ 33 0.00 0.00 ] | 150 - 200 : [ 40 0.00 0.01 ] | 200 - 250 : [ 43 0.00 0.01 ] | 250 - 300 : [ 76 0.00 0.01 ] | 300 - 350 : [ 86 0.00 0.01 ] |X 350 - 400 : [ 132 0.01 0.02 ] |X 400 - 450 : [ 110 0.00 0.02 ] |X 450 - 500 : [ 159 0.01 0.03 ] |XX 500 - 550 : [ 268 0.01 0.04 ] |XXXX 550 - 600 : [ 713 0.03 0.08 ] |XXXXXXXXXXXXXXXXXX 600 - 650 : [ 3133 0.14 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 6552 0.29 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7031 0.31 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3976 0.18 0.99 ] |XX 800 - 850 : [ 287 0.01 1.00 ] JAZZ trim 15 readlength histogram for LGY JAZZ trim 15 readlength histogram for TAN Command: /usr/xpg4/bin/grep TAN 2351519_fasta.screen.screen.ids > reads.trim15.TAN.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.TAN.rl 2 50 #Found 7178 total values totalling 4765871.0000. <663.955280 +/- 129.765655> #Range: [ 23 - 826 ] #Most likely bin: [ 700 - 750 ] 2592 counts #Median bin: [ 700 - 750 ] 2592 counts |X 0 - 50 : [ 37 0.01 0.01 ] |X 50 - 100 : [ 54 0.01 0.01 ] |X 100 - 150 : [ 58 0.01 0.02 ] |X 150 - 200 : [ 34 0.00 0.03 ] |X 200 - 250 : [ 36 0.01 0.03 ] |X 250 - 300 : [ 57 0.01 0.04 ] |X 300 - 350 : [ 47 0.01 0.04 ] |X 350 - 400 : [ 56 0.01 0.05 ] |X 400 - 450 : [ 78 0.01 0.06 ] |XX 450 - 500 : [ 111 0.02 0.08 ] |XX 500 - 550 : [ 159 0.02 0.10 ] |XXXXX 550 - 600 : [ 329 0.05 0.15 ] |XXXXXXXXXX 600 - 650 : [ 675 0.09 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1847 0.26 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2592 0.36 0.86 ] |XXXXXXXXXXXXXXX 750 - 800 : [ 969 0.13 0.99 ] |X 800 - 850 : [ 39 0.01 1.00 ] JAZZ trim 15 readlength histogram for AIZS Command: /usr/xpg4/bin/grep AIZS 2351519_fasta.screen.screen.ids > reads.trim15.AIZS.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIZS.rl 2 50 #Found 43677 total values totalling 30792978.0000. <705.015866 +/- 137.439092> #Range: [ 24 - 897 ] #Most likely bin: [ 750 - 800 ] 14402 counts #Median bin: [ 700 - 750 ] 10636 counts | 0 - 50 : [ 77 0.00 0.00 ] |X 50 - 100 : [ 195 0.00 0.01 ] |X 100 - 150 : [ 236 0.01 0.01 ] |X 150 - 200 : [ 269 0.01 0.02 ] |X 200 - 250 : [ 290 0.01 0.02 ] |X 250 - 300 : [ 330 0.01 0.03 ] |X 300 - 350 : [ 426 0.01 0.04 ] |X 350 - 400 : [ 479 0.01 0.05 ] |XX 400 - 450 : [ 630 0.01 0.07 ] |XX 450 - 500 : [ 658 0.02 0.08 ] |XX 500 - 550 : [ 887 0.02 0.10 ] |XXX 550 - 600 : [ 1182 0.03 0.13 ] |XXXXXX 600 - 650 : [ 2084 0.05 0.18 ] |XXXXXXXXXXXX 650 - 700 : [ 4445 0.10 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 10636 0.24 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 14402 0.33 0.85 ] |XXXXXXXXXXXXXXXXX 800 - 850 : [ 5980 0.14 0.99 ] |X 850 - 900 : [ 471 0.01 1.00 ] ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.2351519_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.2351519_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 150168 total values totalling 73202.6650. <0.487472 +/- 0.068517> #Range: [ 0.0645 - 0.8889 ] #Most likely bin: [ 0.5 - 0.505 ] 6180 counts #Median bin: [ 0.485 - 0.49 ] 5675 counts | 0.06 - 0.065 : [ 1 0.00 0.00 ] #... | 0.165 - 0.17 : [ 1 0.00 0.00 ] | 0.17 - 0.175 : [ 2 0.00 0.00 ] #... | 0.185 - 0.19 : [ 2 0.00 0.00 ] #... | 0.195 - 0.2 : [ 2 0.00 0.00 ] | 0.2 - 0.205 : [ 3 0.00 0.00 ] | 0.205 - 0.21 : [ 1 0.00 0.00 ] | 0.21 - 0.215 : [ 2 0.00 0.00 ] | 0.215 - 0.22 : [ 6 0.00 0.00 ] | 0.22 - 0.225 : [ 1 0.00 0.00 ] | 0.225 - 0.23 : [ 4 0.00 0.00 ] | 0.23 - 0.235 : [ 3 0.00 0.00 ] | 0.235 - 0.24 : [ 3 0.00 0.00 ] | 0.24 - 0.245 : [ 9 0.00 0.00 ] | 0.245 - 0.25 : [ 4 0.00 0.00 ] | 0.25 - 0.255 : [ 19 0.00 0.00 ] | 0.255 - 0.26 : [ 12 0.00 0.00 ] | 0.26 - 0.265 : [ 18 0.00 0.00 ] | 0.265 - 0.27 : [ 16 0.00 0.00 ] | 0.27 - 0.275 : [ 14 0.00 0.00 ] | 0.275 - 0.28 : [ 24 0.00 0.00 ] | 0.28 - 0.285 : [ 31 0.00 0.00 ] | 0.285 - 0.29 : [ 34 0.00 0.00 ] | 0.29 - 0.295 : [ 47 0.00 0.00 ] | 0.295 - 0.3 : [ 48 0.00 0.00 ] | 0.3 - 0.305 : [ 76 0.00 0.00 ] | 0.305 - 0.31 : [ 70 0.00 0.00 ] | 0.31 - 0.315 : [ 75 0.00 0.00 ] |X 0.315 - 0.32 : [ 110 0.00 0.00 ] |X 0.32 - 0.325 : [ 153 0.00 0.01 ] |X 0.325 - 0.33 : [ 179 0.00 0.01 ] |XX 0.33 - 0.335 : [ 245 0.00 0.01 ] |XX 0.335 - 0.34 : [ 281 0.00 0.01 ] |XX 0.34 - 0.345 : [ 323 0.00 0.01 ] |XX 0.345 - 0.35 : [ 370 0.00 0.01 ] |XXX 0.35 - 0.355 : [ 496 0.00 0.02 ] |XXXX 0.355 - 0.36 : [ 579 0.00 0.02 ] |XXXX 0.36 - 0.365 : [ 676 0.00 0.03 ] |XXXXX 0.365 - 0.37 : [ 807 0.01 0.03 ] |XXXXXX 0.37 - 0.375 : [ 861 0.01 0.04 ] |XXXXXXX 0.375 - 0.38 : [ 1050 0.01 0.04 ] |XXXXXXXX 0.38 - 0.385 : [ 1262 0.01 0.05 ] |XXXXXXXX 0.385 - 0.39 : [ 1263 0.01 0.06 ] |XXXXXXXXXX 0.39 - 0.395 : [ 1477 0.01 0.07 ] |XXXXXXXXXX 0.395 - 0.4 : [ 1534 0.01 0.08 ] |XXXXXXXXXXXX 0.4 - 0.405 : [ 1904 0.01 0.09 ] |XXXXXXXXXXXXX 0.405 - 0.41 : [ 2054 0.01 0.11 ] |XXXXXXXXXXXXXX 0.41 - 0.415 : [ 2148 0.01 0.12 ] |XXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 2504 0.02 0.14 ] |XXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 2618 0.02 0.16 ] |XXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 2810 0.02 0.17 ] |XXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 3111 0.02 0.20 ] |XXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 3323 0.02 0.22 ] |XXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 3565 0.02 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 3785 0.03 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 4234 0.03 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 4355 0.03 0.32 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 4561 0.03 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 4849 0.03 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 4967 0.03 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 5283 0.04 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 5446 0.04 0.49 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 5675 0.04 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 5585 0.04 0.57 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 5086 0.03 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 6180 0.04 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 5291 0.04 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 4991 0.03 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 4783 0.03 0.74 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 4585 0.03 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 4064 0.03 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 3804 0.03 0.82 ] |XXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 3389 0.02 0.85 ] |XXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 3041 0.02 0.87 ] |XXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 2571 0.02 0.88 ] |XXXXXXXXXXXXXX 0.55 - 0.555 : [ 2146 0.01 0.90 ] |XXXXXXXXXXXX 0.555 - 0.56 : [ 1794 0.01 0.91 ] |XXXXXXXXXX 0.56 - 0.565 : [ 1583 0.01 0.92 ] |XXXXXXXX 0.565 - 0.57 : [ 1230 0.01 0.93 ] |XXXXXX 0.57 - 0.575 : [ 962 0.01 0.94 ] |XXXXX 0.575 - 0.58 : [ 725 0.00 0.94 ] |XXXX 0.58 - 0.585 : [ 615 0.00 0.94 ] |XXX 0.585 - 0.59 : [ 470 0.00 0.95 ] |XX 0.59 - 0.595 : [ 338 0.00 0.95 ] |XX 0.595 - 0.6 : [ 290 0.00 0.95 ] |XX 0.6 - 0.605 : [ 274 0.00 0.95 ] |XX 0.605 - 0.61 : [ 234 0.00 0.96 ] |X 0.61 - 0.615 : [ 190 0.00 0.96 ] |X 0.615 - 0.62 : [ 186 0.00 0.96 ] |X 0.62 - 0.625 : [ 164 0.00 0.96 ] |X 0.625 - 0.63 : [ 199 0.00 0.96 ] |X 0.63 - 0.635 : [ 172 0.00 0.96 ] |X 0.635 - 0.64 : [ 202 0.00 0.96 ] |X 0.64 - 0.645 : [ 205 0.00 0.96 ] |X 0.645 - 0.65 : [ 183 0.00 0.97 ] |X 0.65 - 0.655 : [ 195 0.00 0.97 ] |XX 0.655 - 0.66 : [ 240 0.00 0.97 ] |XX 0.66 - 0.665 : [ 257 0.00 0.97 ] |XX 0.665 - 0.67 : [ 266 0.00 0.97 ] |XX 0.67 - 0.675 : [ 268 0.00 0.97 ] |XX 0.675 - 0.68 : [ 236 0.00 0.97 ] |XX 0.68 - 0.685 : [ 292 0.00 0.98 ] |XX 0.685 - 0.69 : [ 270 0.00 0.98 ] |XX 0.69 - 0.695 : [ 297 0.00 0.98 ] |XX 0.695 - 0.7 : [ 306 0.00 0.98 ] |XX 0.7 - 0.705 : [ 325 0.00 0.98 ] |XX 0.705 - 0.71 : [ 317 0.00 0.99 ] |XX 0.71 - 0.715 : [ 291 0.00 0.99 ] |XX 0.715 - 0.72 : [ 261 0.00 0.99 ] |X 0.72 - 0.725 : [ 231 0.00 0.99 ] |X 0.725 - 0.73 : [ 213 0.00 0.99 ] |X 0.73 - 0.735 : [ 184 0.00 0.99 ] |X 0.735 - 0.74 : [ 154 0.00 1.00 ] |X 0.74 - 0.745 : [ 124 0.00 1.00 ] |X 0.745 - 0.75 : [ 100 0.00 1.00 ] |X 0.75 - 0.755 : [ 106 0.00 1.00 ] | 0.755 - 0.76 : [ 61 0.00 1.00 ] | 0.76 - 0.765 : [ 56 0.00 1.00 ] | 0.765 - 0.77 : [ 38 0.00 1.00 ] | 0.77 - 0.775 : [ 28 0.00 1.00 ] | 0.775 - 0.78 : [ 27 0.00 1.00 ] | 0.78 - 0.785 : [ 22 0.00 1.00 ] | 0.785 - 0.79 : [ 18 0.00 1.00 ] | 0.79 - 0.795 : [ 15 0.00 1.00 ] | 0.795 - 0.8 : [ 4 0.00 1.00 ] | 0.8 - 0.805 : [ 8 0.00 1.00 ] | 0.805 - 0.81 : [ 5 0.00 1.00 ] | 0.81 - 0.815 : [ 10 0.00 1.00 ] | 0.815 - 0.82 : [ 5 0.00 1.00 ] | 0.82 - 0.825 : [ 6 0.00 1.00 ] | 0.825 - 0.83 : [ 2 0.00 1.00 ] | 0.83 - 0.835 : [ 3 0.00 1.00 ] | 0.835 - 0.84 : [ 2 0.00 1.00 ] #... | 0.845 - 0.85 : [ 1 0.00 1.00 ] #... | 0.855 - 0.86 : [ 1 0.00 1.00 ] | 0.86 - 0.865 : [ 2 0.00 1.00 ] | 0.865 - 0.87 : [ 1 0.00 1.00 ] | 0.87 - 0.875 : [ 1 0.00 1.00 ] #... | 0.885 - 0.89 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones LIBRARY @ ] 150706 81692 74.13 cumulative total @@ Only indicates plates present in input file. Make no assumption regarding plates (not) present in project that do not appear above. ################################################################### Reads in assembly summary Small Inserts = 7994 HQ Discrepant reads = 224 Chimeric reads = 1421 Suspect alignments = 20163 ################################################################### C O N T I G I N F O R M A T I O N Sun Sep 5 10:38:50 2004 File: /psf/project/microbe3/2351519/edit_dir.22Mar04.QD/phrap.out Contig 1142. 1669 reads; 66181 bp (untrimmed), 66154 (trimmed). Contig 1143. 1704 reads; 75976 bp (untrimmed), 75788 (trimmed). Contig 1144. 1896 reads; 84606 bp (untrimmed), 84555 (trimmed). Contig 1145. 1978 reads; 75768 bp (untrimmed), 75742 (trimmed). Contig 1146. 2008 reads; 72908 bp (untrimmed), 72819 (trimmed). Contig 1147. 2012 reads; 80519 bp (untrimmed), 80352 (trimmed). Contig 1148. 2031 reads; 83248 bp (untrimmed), 83231 (trimmed). Contig 1149. 2031 reads; 70028 bp (untrimmed), 70025 (trimmed). Contig 1150. 2199 reads; 78536 bp (untrimmed), 78536 (trimmed). Contig 1151. 2270 reads; 77960 bp (untrimmed), 77694 (trimmed). Contig 1152. 2317 reads; 90606 bp (untrimmed), 90471 (trimmed). Contig 1153. 2401 reads; 74677 bp (untrimmed), 74640 (trimmed). Contig 1154. 2530 reads; 109256 bp (untrimmed), 109218 (trimmed). Contig 1155. 2538 reads; 94851 bp (untrimmed), 94851 (trimmed). Contig 1156. 2663 reads; 94190 bp (untrimmed), 93960 (trimmed). Contig 1157. 2829 reads; 64562 bp (untrimmed), 64543 (trimmed). Contig 1158. 2879 reads; 82327 bp (untrimmed), 82305 (trimmed). Contig 1159. 2888 reads; 86189 bp (untrimmed), 86168 (trimmed). Contig 1160. 2976 reads; 122382 bp (untrimmed), 122192 (trimmed). Contig 1161. 3774 reads; 126153 bp (untrimmed), 125875 (trimmed). Contig 1162. 3779 reads; 125858 bp (untrimmed), 125711 (trimmed). Contig 1163. 5291 reads; 173934 bp (untrimmed), 173877 (trimmed). Contig 1164. 5687 reads; 191520 bp (untrimmed), 191520 (trimmed). Contig 1165. 6041 reads; 171891 bp (untrimmed), 171814 (trimmed). Contig 1166. 7101 reads; 204065 bp (untrimmed), 204045 (trimmed). Contig 1167. 7192 reads; 187758 bp (untrimmed), 187713 (trimmed). Contig 1168. 13532 reads; 383365 bp (untrimmed), 383328 (trimmed). -------------------------------------------------------------- Totals 147175 reads; 6553765 bp (untrimmed), 6372309 (trimmed). ################################################################### Histogram of Good Contig Trimmed Length (>=2000 bp & >=10 reads) ------------------------------------------------------------------- Command: contig | grep '^Contig' | hist - 8 2000 3 10 10000000 8 2000 10000000 Total Good Ctgs: Total Size Good Ctgs: #Found 136 total values totalling 5192848.0000. <38182.705882 +/- 51070.070795> #Range: [ 2008 - 383328 ] #Most likely bin: [ 2000 - 4000 ] 19 counts #Median bin: [ 20000 - 22000 ] 4 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 19 0.14 0.14 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 6000 : [ 15 0.11 0.25 ] |XXXXXXXX 6000 - 8000 : [ 4 0.03 0.28 ] |XXXXXXXXXXXXX 8000 - 10000 : [ 6 0.04 0.32 ] |XXXXXXXXXXXXXXXXX 10000 - 12000 : [ 8 0.06 0.38 ] |XXXXXXXXXXX 12000 - 14000 : [ 5 0.04 0.42 ] |XX 14000 - 16000 : [ 1 0.01 0.43 ] |XXXXXXXX 16000 - 18000 : [ 4 0.03 0.46 ] |XXXXXXXXXXX 18000 - 20000 : [ 5 0.04 0.49 ] |XXXXXXXX 20000 - 22000 : [ 4 0.03 0.52 ] |XXXXXX 22000 - 24000 : [ 3 0.02 0.54 ] |XXXX 24000 - 26000 : [ 2 0.01 0.56 ] |XXXXXXXX 26000 - 28000 : [ 4 0.03 0.59 ] |XXXXXXXX 28000 - 30000 : [ 4 0.03 0.62 ] |XX 30000 - 32000 : [ 1 0.01 0.62 ] |XXXX 32000 - 34000 : [ 2 0.01 0.64 ] |XXXX 34000 - 36000 : [ 2 0.01 0.65 ] |XXXXXXXX 36000 - 38000 : [ 4 0.03 0.68 ] |XX 38000 - 40000 : [ 1 0.01 0.69 ] |XXXXXX 40000 - 42000 : [ 3 0.02 0.71 ] |XXXX 42000 - 44000 : [ 2 0.01 0.73 ] |XXXX 44000 - 46000 : [ 2 0.01 0.74 ] |XXXX 46000 - 48000 : [ 2 0.01 0.76 ] |XXXX 48000 - 50000 : [ 2 0.01 0.77 ] |XX 50000 - 52000 : [ 1 0.01 0.78 ] |XX 52000 - 54000 : [ 1 0.01 0.79 ] #... |XX 56000 - 58000 : [ 1 0.01 0.79 ] #... |XX 64000 - 66000 : [ 1 0.01 0.80 ] |XX 66000 - 68000 : [ 1 0.01 0.81 ] #... |XX 70000 - 72000 : [ 1 0.01 0.82 ] |XXXX 72000 - 74000 : [ 2 0.01 0.83 ] |XXXXXX 74000 - 76000 : [ 3 0.02 0.85 ] |XX 76000 - 78000 : [ 1 0.01 0.86 ] |XX 78000 - 80000 : [ 1 0.01 0.87 ] |XX 80000 - 82000 : [ 1 0.01 0.88 ] |XXXX 82000 - 84000 : [ 2 0.01 0.89 ] |XX 84000 - 86000 : [ 1 0.01 0.90 ] |XX 86000 - 88000 : [ 1 0.01 0.90 ] #... |XX 90000 - 92000 : [ 1 0.01 0.91 ] |XX 92000 - 94000 : [ 1 0.01 0.92 ] |XX 94000 - 96000 : [ 1 0.01 0.93 ] #... |XX 108000 - 110000 : [ 1 0.01 0.93 ] #... |XX 122000 - 124000 : [ 1 0.01 0.94 ] |XXXX 124000 - 126000 : [ 2 0.01 0.96 ] #... |XX 170000 - 172000 : [ 1 0.01 0.96 ] |XX 172000 - 174000 : [ 1 0.01 0.97 ] #... |XX 186000 - 188000 : [ 1 0.01 0.98 ] #... |XX 190000 - 192000 : [ 1 0.01 0.99 ] #... |XX 204000 - 206000 : [ 1 0.01 0.99 ] #... |XX 382000 - 384000 : [ 1 0.01 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 33433852 C = 31382746 G = 31557568 T = 32309543 N = 610555 X = 3499111 GC fraction = 0.47 Total = 132793375 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 2351519_fasta.screen.contigs A 1582972 C 1711148 G 1669753 N 1297 T 1588225 X 370 fraction GC = 0.52 total bases = 6553765 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 6522445 bases = 17.69 +- 13.35 = 0.51 +- 8.28 m1 = 10.08 m2 = 27.40 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 1085 total values totalling 4016.8700. <3.702184 +/- 5.632227> #Range: [ 1.04 - 44.69 ] #Most likely bin: [ 1.5 - 2 ] 393 counts #Median bin: [ 1.5 - 2 ] 393 counts |XXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 252 0.23 0.23 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 393 0.36 0.59 ] |XXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 207 0.19 0.79 ] |XXXXXXX 2.5 - 3 : [ 66 0.06 0.85 ] |XX 3 - 3.5 : [ 19 0.02 0.86 ] |X 3.5 - 4 : [ 8 0.01 0.87 ] |X 4 - 4.5 : [ 7 0.01 0.88 ] |X 4.5 - 5 : [ 6 0.01 0.88 ] |X 5 - 5.5 : [ 5 0.00 0.89 ] | 5.5 - 6 : [ 2 0.00 0.89 ] |X 6 - 6.5 : [ 5 0.00 0.89 ] | 6.5 - 7 : [ 2 0.00 0.90 ] | 7 - 7.5 : [ 2 0.00 0.90 ] | 7.5 - 8 : [ 1 0.00 0.90 ] | 8 - 8.5 : [ 2 0.00 0.90 ] | 8.5 - 9 : [ 1 0.00 0.90 ] #... | 10 - 10.5 : [ 1 0.00 0.90 ] | 10.5 - 11 : [ 2 0.00 0.90 ] | 11 - 11.5 : [ 3 0.00 0.91 ] | 11.5 - 12 : [ 2 0.00 0.91 ] |X 12 - 12.5 : [ 5 0.00 0.91 ] | 12.5 - 13 : [ 4 0.00 0.92 ] | 13 - 13.5 : [ 1 0.00 0.92 ] | 13.5 - 14 : [ 2 0.00 0.92 ] | 14 - 14.5 : [ 4 0.00 0.92 ] #... |X 15 - 15.5 : [ 5 0.00 0.93 ] | 15.5 - 16 : [ 2 0.00 0.93 ] | 16 - 16.5 : [ 1 0.00 0.93 ] | 16.5 - 17 : [ 1 0.00 0.93 ] |X 17 - 17.5 : [ 6 0.01 0.94 ] |X 17.5 - 18 : [ 6 0.01 0.94 ] | 18 - 18.5 : [ 3 0.00 0.95 ] | 18.5 - 19 : [ 4 0.00 0.95 ] | 19 - 19.5 : [ 3 0.00 0.95 ] | 19.5 - 20 : [ 4 0.00 0.96 ] |X 20 - 20.5 : [ 7 0.01 0.96 ] | 20.5 - 21 : [ 3 0.00 0.96 ] |X 21 - 21.5 : [ 5 0.00 0.97 ] | 21.5 - 22 : [ 3 0.00 0.97 ] #... |X 22.5 - 23 : [ 5 0.00 0.98 ] |X 23 - 23.5 : [ 5 0.00 0.98 ] | 23.5 - 24 : [ 3 0.00 0.98 ] #... | 24.5 - 25 : [ 2 0.00 0.99 ] | 25 - 25.5 : [ 1 0.00 0.99 ] #... | 26.5 - 27 : [ 2 0.00 0.99 ] | 27 - 27.5 : [ 4 0.00 0.99 ] | 27.5 - 28 : [ 1 0.00 0.99 ] #... | 30 - 30.5 : [ 1 0.00 0.99 ] | 30.5 - 31 : [ 1 0.00 1.00 ] | 31 - 31.5 : [ 1 0.00 1.00 ] | 31.5 - 32 : [ 1 0.00 1.00 ] #... | 34 - 34.5 : [ 1 0.00 1.00 ] | 34.5 - 35 : [ 1 0.00 1.00 ] #... | 44.5 - 45 : [ 1 0.00 1.00 ] Histogram of Major Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000 #Found 138 total values totalling 2189.2900. <15.864420 +/- 8.320306> #Range: [ 2.02 - 44.69 ] #Most likely bin: [ 20 - 20.5 ] 7 counts #Median bin: [ 17 - 17.5 ] 6 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 6 0.04 0.04 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 6 0.04 0.09 ] |XXXXXXXXXXXXXXXXX 3 - 3.5 : [ 3 0.02 0.11 ] |XXXXXX 3.5 - 4 : [ 1 0.01 0.12 ] |XXXXXXXXXXX 4 - 4.5 : [ 2 0.01 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 4 0.03 0.16 ] |XXXXXXXXXXXXXXXXX 5 - 5.5 : [ 3 0.02 0.18 ] |XXXXXX 5.5 - 6 : [ 1 0.01 0.19 ] |XXXXXXXXXXXXXXXXX 6 - 6.5 : [ 3 0.02 0.21 ] |XXXXXX 6.5 - 7 : [ 1 0.01 0.22 ] |XXXXXX 7 - 7.5 : [ 1 0.01 0.22 ] |XXXXXX 7.5 - 8 : [ 1 0.01 0.23 ] #... |XXXXXX 8.5 - 9 : [ 1 0.01 0.24 ] #... |XXXXXX 10 - 10.5 : [ 1 0.01 0.25 ] |XXXXXXXXXXX 10.5 - 11 : [ 2 0.01 0.26 ] |XXXXXXXXXXXXXXXXX 11 - 11.5 : [ 3 0.02 0.28 ] |XXXXXXXXXXX 11.5 - 12 : [ 2 0.01 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 5 0.04 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.03 0.36 ] |XXXXXX 13 - 13.5 : [ 1 0.01 0.37 ] |XXXXXX 13.5 - 14 : [ 1 0.01 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 4 0.03 0.41 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15 - 15.5 : [ 5 0.04 0.44 ] |XXXXXXXXXXX 15.5 - 16 : [ 2 0.01 0.46 ] |XXXXXX 16 - 16.5 : [ 1 0.01 0.46 ] |XXXXXX 16.5 - 17 : [ 1 0.01 0.47 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 17 - 17.5 : [ 6 0.04 0.51 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 17.5 - 18 : [ 6 0.04 0.56 ] |XXXXXXXXXXXXXXXXX 18 - 18.5 : [ 3 0.02 0.58 ] |XXXXXXXXXXXXXXXXXXXXXXX 18.5 - 19 : [ 4 0.03 0.61 ] |XXXXXXXXXXXXXXXXX 19 - 19.5 : [ 3 0.02 0.63 ] |XXXXXXXXXXXXXXXXXXXXXXX 19.5 - 20 : [ 4 0.03 0.66 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 20 - 20.5 : [ 7 0.05 0.71 ] |XXXXXXXXXXXXXXXXX 20.5 - 21 : [ 3 0.02 0.73 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 21 - 21.5 : [ 5 0.04 0.77 ] |XXXXXXXXXXXXXXXXX 21.5 - 22 : [ 3 0.02 0.79 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 22.5 - 23 : [ 5 0.04 0.83 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 23 - 23.5 : [ 5 0.04 0.86 ] |XXXXXXXXXXXXXXXXX 23.5 - 24 : [ 3 0.02 0.88 ] #... |XXXXXXXXXXX 24.5 - 25 : [ 2 0.01 0.90 ] |XXXXXX 25 - 25.5 : [ 1 0.01 0.91 ] #... |XXXXXXXXXXX 26.5 - 27 : [ 2 0.01 0.92 ] |XXXXXXXXXXXXXXXXXXXXXXX 27 - 27.5 : [ 4 0.03 0.95 ] |XXXXXX 27.5 - 28 : [ 1 0.01 0.96 ] #... |XXXXXX 30 - 30.5 : [ 1 0.01 0.96 ] |XXXXXX 30.5 - 31 : [ 1 0.01 0.97 ] #... |XXXXXX 31.5 - 32 : [ 1 0.01 0.98 ] #... |XXXXXX 34 - 34.5 : [ 1 0.01 0.99 ] |XXXXXX 34.5 - 35 : [ 1 0.01 0.99 ] #... |XXXXXX 44.5 - 45 : [ 1 0.01 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 63 2 reads 1825 bases = 1.04 +- 0.21 = 0.05 +- 0.98 m1 = 0.04 m2 = -0.23 Contig 20 2 reads 1306 bases = 1.05 +- 0.23 = 1.05 +- 0.23 m1 = 0.05 m2 = 0.00 Contig 161 2 reads 1836 bases = 1.06 +- 0.24 = -0.02 +- 0.97 m1 = 0.05 m2 = -0.22 Contig 178 2 reads 1764 bases = 1.06 +- 0.23 = -0.02 +- 0.97 m1 = 0.05 m2 = -0.22 Contig 181 2 reads 1471 bases = 1.06 +- 0.23 = -0.35 +- 0.91 m1 = 0.05 m2 = -0.19 Contig 105 2 reads 1215 bases = 1.08 +- 0.27 = 0.55 +- 0.79 m1 = 0.07 m2 = -0.14 Contig 184 2 reads 1150 bases = 1.09 +- 0.29 = -0.32 +- 0.90 m1 = 0.08 m2 = -0.18 Contig 188 2 reads 1718 bases = 1.09 +- 0.29 = 0.04 +- 0.95 m1 = 0.08 m2 = -0.21 Contig 201 2 reads 1453 bases = 1.09 +- 0.28 = 1.09 +- 0.28 m1 = 0.07 m2 = 0.00 Contig 29 2 reads 1949 bases = 1.09 +- 0.28 = 0.11 +- 0.95 m1 = 0.07 m2 = -0.21 Contig 132 2 reads 1582 bases = 1.10 +- 0.29 = 1.10 +- 0.29 m1 = 0.08 m2 = 0.00 Contig 195 2 reads 1201 bases = 1.10 +- 0.30 = 1.10 +- 0.30 m1 = 0.08 m2 = 0.00 Contig 247 2 reads 1592 bases = 1.11 +- 0.31 = 0.18 +- 0.93 m1 = 0.09 m2 = -0.19 Contig 96 2 reads 1175 bases = 1.11 +- 0.31 = 1.11 +- 0.31 m1 = 0.09 m2 = 0.00 Contig 199 2 reads 1631 bases = 1.12 +- 0.32 = 1.12 +- 0.32 m1 = 0.09 m2 = 0.00 Contig 171 2 reads 1595 bases = 1.13 +- 0.34 = 0.13 +- 0.92 m1 = 0.10 m2 = -0.19 Contig 209 2 reads 1568 bases = 1.13 +- 0.34 = 1.13 +- 0.34 m1 = 0.10 m2 = 0.00 Contig 42 2 reads 1092 bases = 1.13 +- 0.34 = 1.13 +- 0.34 m1 = 0.10 m2 = 0.00 Contig 61 2 reads 945 bases = 1.13 +- 0.33 = -0.10 +- 0.93 m1 = 0.10 m2 = -0.19 Contig 133 2 reads 1538 bases = 1.14 +- 0.35 = -0.05 +- 0.92 m1 = 0.11 m2 = -0.18 Contig 1161 3774 reads 126153 bases = 23.57 +- 12.28 = 0.31 +- 8.96 m1 = 6.40 m2 = 17.64 Contig 1162 3779 reads 125858 bases = 23.78 +- 10.37 = 0.36 +- 9.49 m1 = 4.52 m2 = 4.38 Contig 1163 5291 reads 173934 bases = 23.89 +- 11.50 = 0.28 +- 9.45 m1 = 5.53 m2 = 10.73 Contig 1111 592 reads 18564 bases = 24.84 +- 9.77 = -0.16 +- 10.36 m1 = 3.84 m2 = -2.95 Contig 1153 2401 reads 74677 bases = 24.93 +- 10.51 = 0.55 +- 11.48 m1 = 4.43 m2 = -5.33 Contig 1131 1186 reads 37269 bases = 25.01 +- 12.71 = 0.59 +- 9.75 m1 = 6.46 m2 = 16.65 Contig 1159 2888 reads 86189 bases = 26.50 +- 17.12 = 0.23 +- 10.22 m1 = 11.07 m2 = 47.18 Contig 1130 1160 reads 34591 bases = 26.73 +- 16.17 = 1.21 +- 7.72 m1 = 9.78 m2 = 50.44 Contig 1139 1550 reads 45198 bases = 27.28 +- 9.83 = 0.70 +- 9.69 m1 = 3.54 m2 = 0.70 Contig 1165 6041 reads 171891 bases = 27.33 +- 9.64 = 0.43 +- 9.88 m1 = 3.40 m2 = -1.16 Contig 1166 7101 reads 204065 bases = 27.36 +- 12.10 = 0.15 +- 8.68 m1 = 5.36 m2 = 17.81 Contig 1158 2879 reads 82327 bases = 27.38 +- 12.27 = -0.10 +- 10.04 m1 = 5.50 m2 = 12.43 Contig 1168 13532 reads 383365 bases = 27.62 +- 11.73 = 0.19 +- 9.13 m1 = 4.98 m2 = 13.59 Contig 1167 7192 reads 187758 bases = 30.04 +- 11.79 = 0.04 +- 9.69 m1 = 4.63 m2 = 11.27 Contig 1136 1457 reads 37182 bases = 30.79 +- 15.67 = 0.00 +- 17.51 m1 = 7.97 m2 = -15.29 Contig 1060 45 reads 886 bases = 31.16 +- 7.87 = 16.02 +- 11.90 m1 = 1.99 m2 = -19.89 Contig 1141 1662 reads 40969 bases = 31.75 +- 13.12 = 0.70 +- 8.95 m1 = 5.42 m2 = 22.99 Contig 1157 2829 reads 64562 bases = 34.37 +- 15.43 = 1.02 +- 13.72 m1 = 6.92 m2 = 12.44 Contig 1106 523 reads 11515 bases = 34.50 +- 12.70 = 3.73 +- 9.82 m1 = 4.67 m2 = 16.21 Contig 1093 338 reads 2029 bases = 44.69 +- 44.89 = 10.57 +- 19.23 m1 = 45.09 m2 = 411.41 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 1168 total values totalling 147175.0000. <126.005993 +/- 679.067881> #Range: [ 1 - 13532 ] #Most likely bin: [ 3 - 4 ] 345 counts #Median bin: [ 3 - 4 ] 345 counts |XX 1 - 2 : [ 17 0.01 0.01 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 3 : [ 264 0.23 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 4 : [ 345 0.30 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXX 4 - 5 : [ 202 0.17 0.71 ] |XXXXXXXXXX 5 - 6 : [ 86 0.07 0.78 ] |XXXXX 6 - 7 : [ 47 0.04 0.82 ] |XXX 7 - 8 : [ 28 0.02 0.85 ] |XX 8 - 9 : [ 19 0.02 0.86 ] |X 9 - 10 : [ 10 0.01 0.87 ] |X 10 - 11 : [ 9 0.01 0.88 ] | 11 - 12 : [ 4 0.00 0.88 ] | 12 - 13 : [ 1 0.00 0.88 ] | 13 - 14 : [ 1 0.00 0.88 ] | 14 - 15 : [ 2 0.00 0.89 ] | 15 - 16 : [ 3 0.00 0.89 ] #... | 17 - 18 : [ 4 0.00 0.89 ] | 18 - 19 : [ 4 0.00 0.90 ] | 19 - 20 : [ 3 0.00 0.90 ] #... | 21 - 22 : [ 1 0.00 0.90 ] #... | 24 - 25 : [ 1 0.00 0.90 ] | 25 - 26 : [ 1 0.00 0.90 ] #... | 29 - 30 : [ 1 0.00 0.90 ] | 30 - 31 : [ 2 0.00 0.90 ] #... | 32 - 33 : [ 1 0.00 0.90 ] #... | 36 - 37 : [ 1 0.00 0.90 ] #... | 40 - 41 : [ 2 0.00 0.91 ] #... | 45 - 46 : [ 1 0.00 0.91 ] | 46 - 47 : [ 1 0.00 0.91 ] #... | 49 - 50 : [ 1 0.00 0.91 ] #... | 52 - 53 : [ 1 0.00 0.91 ] #... | 55 - 56 : [ 1 0.00 0.91 ] #... | 68 - 69 : [ 1 0.00 0.91 ] #... | 84 - 85 : [ 1 0.00 0.91 ] #... | 107 - 108 : [ 1 0.00 0.91 ] #... | 131 - 132 : [ 1 0.00 0.91 ] #... | 134 - 135 : [ 1 0.00 0.92 ] #... | 136 - 137 : [ 1 0.00 0.92 ] #... | 150 - 151 : [ 1 0.00 0.92 ] #... | 162 - 163 : [ 1 0.00 0.92 ] #... | 173 - 174 : [ 2 0.00 0.92 ] #... | 180 - 181 : [ 1 0.00 0.92 ] #... | 183 - 184 : [ 1 0.00 0.92 ] #... | 186 - 187 : [ 1 0.00 0.92 ] #... | 192 - 193 : [ 1 0.00 0.92 ] #... | 195 - 196 : [ 1 0.00 0.92 ] #... | 205 - 206 : [ 1 0.00 0.92 ] #... | 228 - 229 : [ 1 0.00 0.93 ] #... | 232 - 233 : [ 2 0.00 0.93 ] #... | 245 - 246 : [ 1 0.00 0.93 ] #... | 255 - 256 : [ 1 0.00 0.93 ] #... | 257 - 258 : [ 1 0.00 0.93 ] #... | 264 - 265 : [ 1 0.00 0.93 ] #... | 289 - 290 : [ 1 0.00 0.93 ] #... | 313 - 314 : [ 1 0.00 0.93 ] #... | 316 - 317 : [ 1 0.00 0.93 ] #... | 324 - 325 : [ 1 0.00 0.93 ] #... | 337 - 338 : [ 1 0.00 0.93 ] | 338 - 339 : [ 1 0.00 0.94 ] #... | 349 - 350 : [ 1 0.00 0.94 ] #... | 353 - 354 : [ 1 0.00 0.94 ] #... | 362 - 363 : [ 1 0.00 0.94 ] #... | 373 - 374 : [ 1 0.00 0.94 ] #... | 399 - 400 : [ 1 0.00 0.94 ] #... | 402 - 403 : [ 1 0.00 0.94 ] #... | 438 - 439 : [ 1 0.00 0.94 ] #... | 457 - 458 : [ 1 0.00 0.94 ] #... | 477 - 478 : [ 1 0.00 0.94 ] #... | 485 - 486 : [ 1 0.00 0.94 ] #... | 490 - 491 : [ 1 0.00 0.95 ] #... | 509 - 510 : [ 1 0.00 0.95 ] #... | 523 - 524 : [ 1 0.00 0.95 ] | 524 - 525 : [ 1 0.00 0.95 ] #... | 545 - 546 : [ 1 0.00 0.95 ] #... | 552 - 553 : [ 1 0.00 0.95 ] #... | 570 - 571 : [ 1 0.00 0.95 ] #... | 592 - 593 : [ 2 0.00 0.95 ] #... | 603 - 604 : [ 1 0.00 0.95 ] #... | 660 - 661 : [ 1 0.00 0.95 ] #... | 740 - 741 : [ 1 0.00 0.95 ] #... | 745 - 746 : [ 1 0.00 0.96 ] #... | 775 - 776 : [ 1 0.00 0.96 ] #... | 783 - 784 : [ 1 0.00 0.96 ] #... | 791 - 792 : [ 1 0.00 0.96 ] #... | 812 - 813 : [ 1 0.00 0.96 ] #... | 845 - 846 : [ 1 0.00 0.96 ] | 846 - 847 : [ 1 0.00 0.96 ] #... | 888 - 889 : [ 1 0.00 0.96 ] #... | 912 - 913 : [ 1 0.00 0.96 ] #... | 936 - 937 : [ 1 0.00 0.96 ] #... | 978 - 979 : [ 1 0.00 0.96 ] #... | 1060 - 1061 : [ 1 0.00 0.96 ] #... | 1078 - 1079 : [ 1 0.00 0.97 ] #... | 1143 - 1144 : [ 1 0.00 0.97 ] #... | 1160 - 1161 : [ 1 0.00 0.97 ] #... | 1186 - 1187 : [ 1 0.00 0.97 ] #... | 1245 - 1246 : [ 1 0.00 0.97 ] | 1246 - 1247 : [ 1 0.00 0.97 ] #... | 1278 - 1279 : [ 1 0.00 0.97 ] #... | 1415 - 1416 : [ 1 0.00 0.97 ] #... | 1457 - 1458 : [ 1 0.00 0.97 ] #... | 1481 - 1482 : [ 1 0.00 0.97 ] | 1482 - 1483 : [ 1 0.00 0.97 ] #... | 1550 - 1551 : [ 1 0.00 0.98 ] #... | 1600 - 1601 : [ 1 0.00 0.98 ] #... | 1662 - 1663 : [ 1 0.00 0.98 ] #... | 1669 - 1670 : [ 1 0.00 0.98 ] #... | 1704 - 1705 : [ 1 0.00 0.98 ] #... | 1896 - 1897 : [ 1 0.00 0.98 ] #... | 1978 - 1979 : [ 1 0.00 0.98 ] #... | 2008 - 2009 : [ 1 0.00 0.98 ] #... | 2012 - 2013 : [ 1 0.00 0.98 ] #... | 2031 - 2032 : [ 2 0.00 0.98 ] #... | 2199 - 2200 : [ 1 0.00 0.98 ] #... | 2270 - 2271 : [ 1 0.00 0.99 ] #... | 2317 - 2318 : [ 1 0.00 0.99 ] #... | 2401 - 2402 : [ 1 0.00 0.99 ] #... | 2530 - 2531 : [ 1 0.00 0.99 ] #... | 2538 - 2539 : [ 1 0.00 0.99 ] #... | 2663 - 2664 : [ 1 0.00 0.99 ] #... | 2829 - 2830 : [ 1 0.00 0.99 ] #... | 2879 - 2880 : [ 1 0.00 0.99 ] #... | 2888 - 2889 : [ 1 0.00 0.99 ] #... | 2976 - 2977 : [ 1 0.00 0.99 ] #... | 3774 - 3775 : [ 1 0.00 0.99 ] #... | 3779 - 3780 : [ 1 0.00 0.99 ] #... | 5291 - 5292 : [ 1 0.00 1.00 ] #... | 5687 - 5688 : [ 1 0.00 1.00 ] #... | 6041 - 6042 : [ 1 0.00 1.00 ] #... | 7101 - 7102 : [ 1 0.00 1.00 ] #... | 7192 - 7193 : [ 1 0.00 1.00 ] #... | 13532 - 13533 : [ 1 0.00 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 1168 total values totalling 6553765.0000. <5611.100171 +/- 21082.648059> #Range: [ 121 - 383365 ] #Most likely bin: [ 1000 - 2000 ] 637 counts #Median bin: [ 1000 - 2000 ] 637 counts |XXXXXXXXXXXXXXXXXX 0 - 1000 : [ 286 0.24 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 637 0.55 0.79 ] |XXXXXXX 2000 - 3000 : [ 113 0.10 0.89 ] |X 3000 - 4000 : [ 14 0.01 0.90 ] |X 4000 - 5000 : [ 10 0.01 0.91 ] | 5000 - 6000 : [ 5 0.00 0.91 ] | 6000 - 7000 : [ 3 0.00 0.91 ] | 7000 - 8000 : [ 2 0.00 0.92 ] | 8000 - 9000 : [ 3 0.00 0.92 ] | 9000 - 10000 : [ 2 0.00 0.92 ] | 10000 - 11000 : [ 4 0.00 0.92 ] | 11000 - 12000 : [ 5 0.00 0.93 ] | 12000 - 13000 : [ 3 0.00 0.93 ] | 13000 - 14000 : [ 2 0.00 0.93 ] | 14000 - 15000 : [ 1 0.00 0.93 ] #... | 16000 - 17000 : [ 1 0.00 0.93 ] | 17000 - 18000 : [ 2 0.00 0.94 ] | 18000 - 19000 : [ 5 0.00 0.94 ] | 19000 - 20000 : [ 1 0.00 0.94 ] | 20000 - 21000 : [ 3 0.00 0.94 ] | 21000 - 22000 : [ 1 0.00 0.94 ] | 22000 - 23000 : [ 1 0.00 0.95 ] | 23000 - 24000 : [ 2 0.00 0.95 ] | 24000 - 25000 : [ 1 0.00 0.95 ] | 25000 - 26000 : [ 1 0.00 0.95 ] #... | 27000 - 28000 : [ 4 0.00 0.95 ] | 28000 - 29000 : [ 2 0.00 0.95 ] | 29000 - 30000 : [ 1 0.00 0.95 ] | 30000 - 31000 : [ 1 0.00 0.96 ] | 31000 - 32000 : [ 1 0.00 0.96 ] | 32000 - 33000 : [ 1 0.00 0.96 ] | 33000 - 34000 : [ 1 0.00 0.96 ] | 34000 - 35000 : [ 2 0.00 0.96 ] #... | 36000 - 37000 : [ 1 0.00 0.96 ] | 37000 - 38000 : [ 3 0.00 0.96 ] | 38000 - 39000 : [ 1 0.00 0.96 ] #... | 40000 - 41000 : [ 1 0.00 0.96 ] | 41000 - 42000 : [ 2 0.00 0.97 ] | 42000 - 43000 : [ 2 0.00 0.97 ] #... | 44000 - 45000 : [ 1 0.00 0.97 ] | 45000 - 46000 : [ 1 0.00 0.97 ] #... | 47000 - 48000 : [ 1 0.00 0.97 ] | 48000 - 49000 : [ 3 0.00 0.97 ] #... | 50000 - 51000 : [ 1 0.00 0.97 ] #... | 52000 - 53000 : [ 1 0.00 0.98 ] #... | 56000 - 57000 : [ 1 0.00 0.98 ] #... | 64000 - 65000 : [ 1 0.00 0.98 ] #... | 66000 - 67000 : [ 1 0.00 0.98 ] #... | 70000 - 71000 : [ 1 0.00 0.98 ] #... | 72000 - 73000 : [ 1 0.00 0.98 ] | 73000 - 74000 : [ 1 0.00 0.98 ] | 74000 - 75000 : [ 1 0.00 0.98 ] | 75000 - 76000 : [ 2 0.00 0.98 ] #... | 77000 - 78000 : [ 1 0.00 0.98 ] | 78000 - 79000 : [ 1 0.00 0.98 ] #... | 80000 - 81000 : [ 1 0.00 0.99 ] #... | 82000 - 83000 : [ 1 0.00 0.99 ] | 83000 - 84000 : [ 1 0.00 0.99 ] | 84000 - 85000 : [ 1 0.00 0.99 ] #... | 86000 - 87000 : [ 1 0.00 0.99 ] #... | 90000 - 91000 : [ 1 0.00 0.99 ] #... | 94000 - 95000 : [ 2 0.00 0.99 ] #... | 109000 - 110000 : [ 1 0.00 0.99 ] #... | 122000 - 123000 : [ 1 0.00 0.99 ] #... | 125000 - 126000 : [ 1 0.00 0.99 ] | 126000 - 127000 : [ 1 0.00 0.99 ] #... | 171000 - 172000 : [ 1 0.00 1.00 ] #... | 173000 - 174000 : [ 1 0.00 1.00 ] #... | 187000 - 188000 : [ 1 0.00 1.00 ] #... | 191000 - 192000 : [ 1 0.00 1.00 ] #... | 204000 - 205000 : [ 1 0.00 1.00 ] #... | 383000 - 384000 : [ 1 0.00 1.00 ] ################################################################### Histogram of Assembled Average Insert Sizes Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list ------------------------------------------------------------------- Command: /usr/xpg4/bin/grep AAZH reads.list > grep.reads.list.AAZH Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAZH 4 500 #Found 7783 total values totalling 50675637.0000. <6511.067326 +/- 1682.107513> #Range: [ - 91450 ] #Most likely bin: [ 5500 - 6000 ] 1509 counts #Median bin: [ 6000 - 6500 ] 1369 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 4 0.00 0.00 ] |X 1000 - 1500 : [ 31 0.00 0.00 ] |X 1500 - 2000 : [ 22 0.00 0.01 ] |X 2000 - 2500 : [ 41 0.01 0.01 ] |X 2500 - 3000 : [ 40 0.01 0.02 ] |X 3000 - 3500 : [ 35 0.00 0.02 ] |XX 3500 - 4000 : [ 70 0.01 0.03 ] |XXX 4000 - 4500 : [ 99 0.01 0.04 ] |XXXXX 4500 - 5000 : [ 203 0.03 0.07 ] |XXXXXXXXXXXXXXXXXXXXX 5000 - 5500 : [ 798 0.10 0.17 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1509 0.19 0.37 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1369 0.18 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1102 0.14 0.68 ] |XXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 825 0.11 0.79 ] |XXXXXXXXXXXXXXXXX 7500 - 8000 : [ 633 0.08 0.87 ] |XXXXXXXXXXXX 8000 - 8500 : [ 463 0.06 0.93 ] |XXXXXXX 8500 - 9000 : [ 255 0.03 0.96 ] |XXXX 9000 - 9500 : [ 140 0.02 0.98 ] |XX 9500 - 10000 : [ 81 0.01 0.99 ] |X 10000 - 10500 : [ 40 0.01 1.00 ] | 10500 - 11000 : [ 16 0.00 1.00 ] | 11000 - 11500 : [ 4 0.00 1.00 ] #... | 35000 - 35500 : [ 1 0.00 1.00 ] #... | 91000 - 91500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep KVE reads.list > grep.reads.list.KVE Command: /home/copeland/scripts/histogram2.pl grep.reads.list.KVE 4 500 #Found 4955 total values totalling 18101707.0000. <3653.220383 +/- 833.982555> #Range: [ - 24442 ] #Most likely bin: [ 3500 - 4000 ] 1954 counts #Median bin: [ 3500 - 4000 ] 1954 counts | 0 - 500 : [ 1 0.00 0.00 ] |X 500 - 1000 : [ 26 0.01 0.01 ] |XXX 1000 - 1500 : [ 139 0.03 0.03 ] |XX 1500 - 2000 : [ 121 0.02 0.06 ] |XXX 2000 - 2500 : [ 132 0.03 0.08 ] |XX 2500 - 3000 : [ 121 0.02 0.11 ] |XXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1061 0.21 0.32 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1954 0.39 0.72 ] |XXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 943 0.19 0.91 ] |XXXXXXX 4500 - 5000 : [ 338 0.07 0.98 ] |XX 5000 - 5500 : [ 97 0.02 1.00 ] | 5500 - 6000 : [ 20 0.00 1.00 ] | 6000 - 6500 : [ 1 0.00 1.00 ] #... | 24000 - 24500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep KYR reads.list > grep.reads.list.KYR Command: /home/copeland/scripts/histogram2.pl grep.reads.list.KYR 4 500 #Found 16052 total values totalling 58819879.0000. <3664.333354 +/- 1240.811830> #Range: [ - 88464 ] #Most likely bin: [ 3500 - 4000 ] 6360 counts #Median bin: [ 3500 - 4000 ] 6360 counts | 0 - 500 : [ 1 0.00 0.00 ] |X 500 - 1000 : [ 122 0.01 0.01 ] |XXX 1000 - 1500 : [ 438 0.03 0.03 ] |XXX 1500 - 2000 : [ 469 0.03 0.06 ] |XX 2000 - 2500 : [ 393 0.02 0.09 ] |XXX 2500 - 3000 : [ 445 0.03 0.12 ] |XXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3153 0.20 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 6360 0.40 0.71 ] |XXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 3054 0.19 0.90 ] |XXXXXXX 4500 - 5000 : [ 1135 0.07 0.97 ] |XX 5000 - 5500 : [ 385 0.02 0.99 ] |X 5500 - 6000 : [ 88 0.01 1.00 ] | 6000 - 6500 : [ 6 0.00 1.00 ] #... | 12000 - 12500 : [ 1 0.00 1.00 ] #... | 86500 - 87000 : [ 1 0.00 1.00 ] #... | 88000 - 88500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep WTA reads.list > grep.reads.list.WTA Command: /home/copeland/scripts/histogram2.pl grep.reads.list.WTA 4 500 #Found 10124 total values totalling 64553896.0000. <6376.323192 +/- 1427.006232> #Range: [ - 66050 ] #Most likely bin: [ 5500 - 6000 ] 2075 counts #Median bin: [ 6000 - 6500 ] 1753 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 1 0.00 0.00 ] | 1000 - 1500 : [ 11 0.00 0.00 ] | 1500 - 2000 : [ 16 0.00 0.00 ] | 2000 - 2500 : [ 22 0.00 0.01 ] |X 2500 - 3000 : [ 30 0.00 0.01 ] |X 3000 - 3500 : [ 53 0.01 0.01 ] |XX 3500 - 4000 : [ 80 0.01 0.02 ] |XXX 4000 - 4500 : [ 133 0.01 0.03 ] |XXXXXXXX 4500 - 5000 : [ 412 0.04 0.07 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5000 - 5500 : [ 1497 0.15 0.22 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 2075 0.20 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1753 0.17 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1319 0.13 0.73 ] |XXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 984 0.10 0.83 ] |XXXXXXXXXXXXX 7500 - 8000 : [ 683 0.07 0.90 ] |XXXXXXXXX 8000 - 8500 : [ 464 0.05 0.94 ] |XXXXXX 8500 - 9000 : [ 299 0.03 0.97 ] |XXX 9000 - 9500 : [ 160 0.02 0.99 ] |X 9500 - 10000 : [ 76 0.01 0.99 ] |X 10000 - 10500 : [ 38 0.00 1.00 ] | 10500 - 11000 : [ 11 0.00 1.00 ] | 11000 - 11500 : [ 3 0.00 1.00 ] | 11500 - 12000 : [ 1 0.00 1.00 ] #... | 47000 - 47500 : [ 1 0.00 1.00 ] #... | 66000 - 66500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep TAN reads.list > grep.reads.list.TAN Command: /home/copeland/scripts/histogram2.pl grep.reads.list.TAN 4 500 #Found 2036 total values totalling 73748355.0000. <36222.178291 +/- 3085.805900> #Range: [ - 48182 ] #Most likely bin: [ 34500 - 35000 ] 150 counts #Median bin: [ 36000 - 36500 ] 131 counts | 0 - 500 : [ 1 0.00 0.00 ] #... | 22500 - 23000 : [ 1 0.00 0.00 ] #... | 23500 - 24000 : [ 1 0.00 0.00 ] #... | 25000 - 25500 : [ 1 0.00 0.00 ] |X 25500 - 26000 : [ 2 0.00 0.00 ] |X 26000 - 26500 : [ 3 0.00 0.00 ] | 26500 - 27000 : [ 1 0.00 0.00 ] |X 27000 - 27500 : [ 4 0.00 0.01 ] |X 27500 - 28000 : [ 3 0.00 0.01 ] |X 28000 - 28500 : [ 4 0.00 0.01 ] | 28500 - 29000 : [ 1 0.00 0.01 ] |X 29000 - 29500 : [ 5 0.00 0.01 ] |XXX 29500 - 30000 : [ 10 0.00 0.02 ] |XX 30000 - 30500 : [ 8 0.00 0.02 ] |XXXXX 30500 - 31000 : [ 20 0.01 0.03 ] |XXXXXXX 31000 - 31500 : [ 25 0.01 0.04 ] |XXXXXXXX 31500 - 32000 : [ 30 0.01 0.06 ] |XXXXXXXXXXXXX 32000 - 32500 : [ 48 0.02 0.08 ] |XXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 69 0.03 0.12 ] |XXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 75 0.04 0.15 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 118 0.06 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 133 0.07 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 150 0.07 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 149 0.07 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 133 0.07 0.49 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 131 0.06 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 143 0.07 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 127 0.06 0.69 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 104 0.05 0.74 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 103 0.05 0.79 ] |XXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 84 0.04 0.83 ] |XXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 69 0.03 0.86 ] |XXXXXXXXXXXXXXXX 39500 - 40000 : [ 59 0.03 0.89 ] |XXXXXXXXXXXXX 40000 - 40500 : [ 50 0.02 0.92 ] |XXXXXXXXXXXX 40500 - 41000 : [ 46 0.02 0.94 ] |XXXXXX 41000 - 41500 : [ 24 0.01 0.95 ] |XXXXXXXXXX 41500 - 42000 : [ 36 0.02 0.97 ] |XXXXX 42000 - 42500 : [ 17 0.01 0.98 ] |XXXX 42500 - 43000 : [ 15 0.01 0.98 ] |XXXX 43000 - 43500 : [ 16 0.01 0.99 ] |X 43500 - 44000 : [ 2 0.00 0.99 ] |XX 44000 - 44500 : [ 9 0.00 1.00 ] |X 44500 - 45000 : [ 4 0.00 1.00 ] | 45000 - 45500 : [ 1 0.00 1.00 ] #... | 48000 - 48500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AIZS reads.list > grep.reads.list.AIZS Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIZS 4 500 #Found 19177 total values totalling 54761713.0000. <2855.593315 +/- 2579.191259> #Range: [ - 337501 ] #Most likely bin: [ 2500 - 3000 ] 10433 counts #Median bin: [ 2500 - 3000 ] 10433 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 13 0.00 0.00 ] |X 1000 - 1500 : [ 291 0.02 0.02 ] |XX 1500 - 2000 : [ 634 0.03 0.05 ] |XXXXX 2000 - 2500 : [ 1417 0.07 0.12 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 10433 0.54 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 6173 0.32 0.99 ] |X 3500 - 4000 : [ 212 0.01 1.00 ] #... | 33000 - 33500 : [ 1 0.00 1.00 ] #... | 110500 - 111000 : [ 1 0.00 1.00 ] #... | 337500 - 338000 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # KVE 3510 +- 1029 (n=2562) # KYR 3505 +- 963 (n=8367) # AAZH 6308 +- 1415 (n=3959) # TAN 36053 +- 2982 (n=1008) # AIZS 2712 +- 469 (n=9634) # WTA 6317 +- 1243 (n=5029) ################################################################### N50 Calculations: * N50 Contig Reads * Total Assemb Reads: 1/2 (Tot. Assemb Reads): Command: hist contig.grep 3 10 3 (10) (100) Result: Half the total assembled reads are in n of largest contigs containing at least n reads each. ------------------------------------------------------------------- ################################################################### Ideal Assembly with avg read len of 605.611213 bp, 147175 reads, genome size 5512594 bp Command: idealAssembly 5512594 147175 605.611213 ------------------------------------------------------------------- Genome = 5512594 bases Nreads = 147175 readLength = 605.611213 Depth = 16.17 N_contigs = N_gaps = 0 mean gap size = 36 bases mean contig size = 10517829 reads (~ 393956324 bases) %cover = 100.00 %singlet = 0.00 assembly size = 5512593 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 0 contigs containing at least 17648917 reads each * N50 Contig Sizes * Total Assemb Size: 1/2 (Tot.Assemb. Size): Command: hist contig.grep 5 1000 5 (2200) (15000) Result: Half of the total Assembled Size of the genome is contained in n of the largest contigs equaling n bps. ################################################################### Contam Summary with *.contigs: Command: contam_summary -c -s ------------------------------------------------------------------- Contamination Summary for JGI id: 2351519 Command line options used were: -c -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 60442 Number of reads with percent X's >= 20%: 2432 = 1.6% Number of reads with percent X's >= 50%: 1311 = 0.9% Number of reads with percent X's >= 80%: 69 = 0.0% Total nr of reads in project is: 150706 Total nr of X's: 3499111 Total nr not found in screened files: 0 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with p21 68 20 7 1 Nr with L09136-pUC18 46199 2317 1244 61 Nr with pMCL200 10649 94 60 7 Nr with pCC1FOS_vector 3526 1 0 0 ################################################################### Contam Summary with *.singlets: Command: contam_summary -c -s -g ------------------------------------------------------------------- Contamination Summary for JGI id: 2351519 Command line options used were: -c -g -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 1437 Number of reads with percent X's >= 20%: 43 = 1.3% Number of reads with percent X's >= 50%: 34 = 1.0% Number of reads with percent X's >= 80%: 3 = 0.1% Total nr of reads in project is: 3422 Total nr of X's: 70787 Total nr not found in screened files: 0 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with p21 1 1 1 0 Nr with L09136-pUC18 1204 37 28 3 Nr with pMCL200 86 5 5 0 Nr with pCC1FOS_vector 146 0 0 0 ################################################################### Bad M1 Contigs ------------------------------------------------------------------- ################################################################### Bad M2 Contigs ------------------------------------------------------------------- ################################################################### Ran Plates2contigs: Output Location: Ran in.dir: Output Location: Viewed Contigs with Phrapview: ################################################################### Conclusions: