################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 3436494 Genus_species: Moorella thermoacetica Taxid: 1525 Genome size: 1500 Libraries: ACOB, AAOS, AAOP, AGXN, AAOR ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 3436494 ------------------------------------------------------------------- ID=3436494 ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 2732159 # phrap: 2566037 # db: 0 2649098 +/- 83061 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length AAOP.5-48 197 98.56 668.86 AAOR.5-20 46 96.21 670.43 AAOS.5-20 32 98.50 748.81 ACOB.9-32 138 96.99 699.88 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s ACOB 138 69 96.56 693.36 69 97.42 706.39 AAOS 32 16 97.85 718.00 16 99.15 779.62 AAOP 197 99 98.67 672.56 98 98.45 665.13 AGXN 4 2 96.88 696.00 2 83.34 655.50 AAOR 46 23 95.82 667.26 23 96.59 673.61 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3436494_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 3436494_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3436494.out /home/copeland/scripts/librariesInfoTxt.sh 3436494 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3436494_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 3436494_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3436494.out /home/copeland/scripts/librariesInfoTxt.sh 3436494 phrap.out > librariesInfo.txt ################################################################### Library vector screening AAOP.000001.000100 screen.out.1 3436494_fasta.screen /tmp/pUC18.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta AAOP.000101.000200 screen.out.1 3436494_fasta.screen /tmp/pUC18.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta AAOR.000001.000100 screen.out.1 3436494_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta AAOS.000001.000100 screen.out.1 3436494_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta ACOB.000001.000100 screen.out.1 3436494_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta ACOB.000101.000200 screen.out.1 3436494_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta AAOP.000001.000100 screen.out.1 3436494_fasta.screen /tmp/pUC18.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta AAOP.000101.000200 screen.out.1 3436494_fasta.screen /tmp/pUC18.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta AAOR.000001.000100 screen.out.1 3436494_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta AAOS.000001.000100 screen.out.1 3436494_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta ACOB.000001.000100 screen.out.1 3436494_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta ACOB.000101.000200 screen.out.1 3436494_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3436494_fasta.screen /sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 3436494_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 54139 total values totalling 32981509.0000. <609.200558 +/- 166.474549> #Range: [ 22 - 954 ] #Most likely bin: [ 700 - 750 ] 11606 counts #Median bin: [ 650 - 700 ] 11413 counts | 0 - 50 : [ 142 0.00 0.00 ] |XX 50 - 100 : [ 717 0.01 0.02 ] |XXX 100 - 150 : [ 810 0.01 0.03 ] |XXX 150 - 200 : [ 890 0.02 0.05 ] |XXX 200 - 250 : [ 855 0.02 0.06 ] |XXX 250 - 300 : [ 969 0.02 0.08 ] |XXX 300 - 350 : [ 1011 0.02 0.10 ] |XXXX 350 - 400 : [ 1187 0.02 0.12 ] |XXXXX 400 - 450 : [ 1450 0.03 0.15 ] |XXXXXX 450 - 500 : [ 1805 0.03 0.18 ] |XXXXXXXXX 500 - 550 : [ 2606 0.05 0.23 ] |XXXXXXXXXXXXXXX 550 - 600 : [ 4309 0.08 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 7895 0.15 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 11413 0.21 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 11606 0.21 0.88 ] |XXXXXXXXXXXXXXXXXX 750 - 800 : [ 5218 0.10 0.98 ] |XXXX 800 - 850 : [ 1054 0.02 1.00 ] |X 850 - 900 : [ 176 0.00 1.00 ] | 900 - 950 : [ 25 0.00 1.00 ] | 950 - 1000 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for AAOP Command: /usr/xpg4/bin/grep AAOP 3436494_fasta.screen.screen.ids > reads.trim15.AAOP.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAOP.rl 2 50 #Found 20211 total values totalling 13443317.0000. <665.148533 +/- 106.665421> #Range: [ 22 - 954 ] #Most likely bin: [ 650 - 700 ] 6348 counts #Median bin: [ 650 - 700 ] 6348 counts |X 0 - 50 : [ 83 0.00 0.00 ] |X 50 - 100 : [ 88 0.00 0.01 ] | 100 - 150 : [ 63 0.00 0.01 ] | 150 - 200 : [ 71 0.00 0.02 ] | 200 - 250 : [ 65 0.00 0.02 ] | 250 - 300 : [ 79 0.00 0.02 ] |X 300 - 350 : [ 106 0.01 0.03 ] |X 350 - 400 : [ 140 0.01 0.03 ] |X 400 - 450 : [ 156 0.01 0.04 ] |X 450 - 500 : [ 163 0.01 0.05 ] |XX 500 - 550 : [ 324 0.02 0.07 ] |XXXXXXX 550 - 600 : [ 1060 0.05 0.12 ] |XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3313 0.16 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 6348 0.31 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6245 0.31 0.91 ] |XXXXXXXXXXX 750 - 800 : [ 1682 0.08 0.99 ] |X 800 - 850 : [ 140 0.01 1.00 ] | 850 - 900 : [ 70 0.00 1.00 ] | 900 - 950 : [ 14 0.00 1.00 ] | 950 - 1000 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for AAOR Command: /usr/xpg4/bin/grep AAOR 3436494_fasta.screen.screen.ids > reads.trim15.AAOR.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAOR.rl 2 50 #Found 10412 total values totalling 5757298.0000. <552.948329 +/- 156.261679> #Range: [ 22 - 944 ] #Most likely bin: [ 600 - 650 ] 2262 counts #Median bin: [ 600 - 650 ] 2262 counts |XX 0 - 50 : [ 109 0.01 0.01 ] |XX 50 - 100 : [ 121 0.01 0.02 ] |XX 100 - 150 : [ 116 0.01 0.03 ] |XXX 150 - 200 : [ 161 0.02 0.05 ] |XXX 200 - 250 : [ 187 0.02 0.07 ] |XXXX 250 - 300 : [ 254 0.02 0.09 ] |XXXXX 300 - 350 : [ 282 0.03 0.12 ] |XXXXXX 350 - 400 : [ 352 0.03 0.15 ] |XXXXXXXX 400 - 450 : [ 445 0.04 0.19 ] |XXXXXXXXXXX 450 - 500 : [ 634 0.06 0.26 ] |XXXXXXXXXXXXXXXXX 500 - 550 : [ 959 0.09 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1557 0.15 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2262 0.22 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1977 0.19 0.90 ] |XXXXXXXXXXXXXX 700 - 750 : [ 800 0.08 0.98 ] |XXX 750 - 800 : [ 159 0.02 1.00 ] | 800 - 850 : [ 25 0.00 1.00 ] | 850 - 900 : [ 10 0.00 1.00 ] | 900 - 950 : [ 2 0.00 1.00 ] JAZZ trim 15 readlength histogram for AAOS Command: /usr/xpg4/bin/grep AAOS 3436494_fasta.screen.screen.ids > reads.trim15.AAOS.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAOS.rl 2 50 #Found 3006 total values totalling 2245332.0000. <746.950100 +/- 106.989346> #Range: [ 24 - 901 ] #Most likely bin: [ 750 - 800 ] 1251 counts #Median bin: [ 750 - 800 ] 1251 counts | 0 - 50 : [ 13 0.00 0.00 ] | 50 - 100 : [ 6 0.00 0.01 ] | 100 - 150 : [ 2 0.00 0.01 ] | 150 - 200 : [ 4 0.00 0.01 ] | 200 - 250 : [ 12 0.00 0.01 ] | 250 - 300 : [ 15 0.00 0.02 ] | 300 - 350 : [ 15 0.00 0.02 ] | 350 - 400 : [ 11 0.00 0.03 ] |X 400 - 450 : [ 20 0.01 0.03 ] | 450 - 500 : [ 12 0.00 0.04 ] | 500 - 550 : [ 13 0.00 0.04 ] |X 550 - 600 : [ 31 0.01 0.05 ] |XX 600 - 650 : [ 67 0.02 0.07 ] |XXXXX 650 - 700 : [ 168 0.06 0.13 ] |XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 643 0.21 0.34 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1251 0.42 0.76 ] |XXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 665 0.22 0.98 ] |XX 850 - 900 : [ 57 0.02 1.00 ] | 900 - 950 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for ACOB Command: /usr/xpg4/bin/grep ACOB 3436494_fasta.screen.screen.ids > reads.trim15.ACOB.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACOB.rl 2 50 #Found 21733 total values totalling 11746712.0000. <540.501173 +/- 218.109430> #Range: [ 22 - 928 ] #Most likely bin: [ 700 - 750 ] 3975 counts #Median bin: [ 600 - 650 ] 2281 counts |XXXXXX 0 - 50 : [ 554 0.03 0.03 ] |XXXXXXXX 50 - 100 : [ 775 0.04 0.06 ] |XXXXXXX 100 - 150 : [ 677 0.03 0.09 ] |XXXXXXX 150 - 200 : [ 672 0.03 0.12 ] |XXXXXX 200 - 250 : [ 599 0.03 0.15 ] |XXXXXX 250 - 300 : [ 638 0.03 0.18 ] |XXXXXX 300 - 350 : [ 619 0.03 0.21 ] |XXXXXXX 350 - 400 : [ 693 0.03 0.24 ] |XXXXXXXX 400 - 450 : [ 837 0.04 0.28 ] |XXXXXXXXXX 450 - 500 : [ 1004 0.05 0.33 ] |XXXXXXXXXXXXX 500 - 550 : [ 1327 0.06 0.39 ] |XXXXXXXXXXXXXXXXX 550 - 600 : [ 1672 0.08 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2281 0.10 0.57 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2949 0.14 0.70 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3975 0.18 0.89 ] |XXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2180 0.10 0.99 ] |XX 800 - 850 : [ 234 0.01 1.00 ] | 850 - 900 : [ 39 0.00 1.00 ] | 900 - 950 : [ 8 0.00 1.00 ] JAZZ trim 15 readlength histogram for AGXN ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.3436494_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.3436494_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 54009 total values totalling 29895.5387. <0.553529 +/- 0.071250> #Range: [ 0 - 0.9656 ] #Most likely bin: [ 0.58 - 0.585 ] 1900 counts #Median bin: [ 0.56 - 0.565 ] 1702 counts | 0 - 0.005 : [ 1 0.00 0.00 ] #... | 0.2 - 0.205 : [ 1 0.00 0.00 ] | 0.205 - 0.21 : [ 2 0.00 0.00 ] | 0.21 - 0.215 : [ 1 0.00 0.00 ] | 0.215 - 0.22 : [ 4 0.00 0.00 ] | 0.22 - 0.225 : [ 3 0.00 0.00 ] | 0.225 - 0.23 : [ 3 0.00 0.00 ] | 0.23 - 0.235 : [ 2 0.00 0.00 ] | 0.235 - 0.24 : [ 3 0.00 0.00 ] | 0.24 - 0.245 : [ 5 0.00 0.00 ] | 0.245 - 0.25 : [ 2 0.00 0.00 ] | 0.25 - 0.255 : [ 9 0.00 0.00 ] | 0.255 - 0.26 : [ 6 0.00 0.00 ] | 0.26 - 0.265 : [ 3 0.00 0.00 ] | 0.265 - 0.27 : [ 14 0.00 0.00 ] | 0.27 - 0.275 : [ 12 0.00 0.00 ] | 0.275 - 0.28 : [ 11 0.00 0.00 ] | 0.28 - 0.285 : [ 11 0.00 0.00 ] | 0.285 - 0.29 : [ 15 0.00 0.00 ] |X 0.29 - 0.295 : [ 26 0.00 0.00 ] | 0.295 - 0.3 : [ 22 0.00 0.00 ] | 0.3 - 0.305 : [ 19 0.00 0.00 ] |X 0.305 - 0.31 : [ 43 0.00 0.00 ] |X 0.31 - 0.315 : [ 40 0.00 0.00 ] |X 0.315 - 0.32 : [ 38 0.00 0.01 ] |X 0.32 - 0.325 : [ 63 0.00 0.01 ] |X 0.325 - 0.33 : [ 70 0.00 0.01 ] |X 0.33 - 0.335 : [ 56 0.00 0.01 ] |XX 0.335 - 0.34 : [ 87 0.00 0.01 ] |XX 0.34 - 0.345 : [ 103 0.00 0.01 ] |XX 0.345 - 0.35 : [ 104 0.00 0.01 ] |XX 0.35 - 0.355 : [ 97 0.00 0.02 ] |XX 0.355 - 0.36 : [ 101 0.00 0.02 ] |XX 0.36 - 0.365 : [ 103 0.00 0.02 ] |XX 0.365 - 0.37 : [ 107 0.00 0.02 ] |XX 0.37 - 0.375 : [ 98 0.00 0.02 ] |XX 0.375 - 0.38 : [ 107 0.00 0.03 ] |XX 0.38 - 0.385 : [ 118 0.00 0.03 ] |XXX 0.385 - 0.39 : [ 132 0.00 0.03 ] |XXX 0.39 - 0.395 : [ 135 0.00 0.03 ] |XXX 0.395 - 0.4 : [ 152 0.00 0.04 ] |XXXX 0.4 - 0.405 : [ 185 0.00 0.04 ] |XXXX 0.405 - 0.41 : [ 202 0.00 0.04 ] |XXXXX 0.41 - 0.415 : [ 214 0.00 0.05 ] |XXXXX 0.415 - 0.42 : [ 237 0.00 0.05 ] |XXXXXX 0.42 - 0.425 : [ 265 0.00 0.06 ] |XXXXXX 0.425 - 0.43 : [ 275 0.01 0.06 ] |XXXXXX 0.43 - 0.435 : [ 300 0.01 0.07 ] |XXXXXX 0.435 - 0.44 : [ 288 0.01 0.07 ] |XXXXXXX 0.44 - 0.445 : [ 339 0.01 0.08 ] |XXXXXXXX 0.445 - 0.45 : [ 388 0.01 0.09 ] |XXXXXXX 0.45 - 0.455 : [ 351 0.01 0.09 ] |XXXXXXXXX 0.455 - 0.46 : [ 419 0.01 0.10 ] |XXXXXXXXXXX 0.46 - 0.465 : [ 517 0.01 0.11 ] |XXXXXXXXXXX 0.465 - 0.47 : [ 526 0.01 0.12 ] |XXXXXXXXXXXX 0.47 - 0.475 : [ 580 0.01 0.13 ] |XXXXXXXXXXXXX 0.475 - 0.48 : [ 631 0.01 0.14 ] |XXXXXXXXXXXXXXX 0.48 - 0.485 : [ 690 0.01 0.15 ] |XXXXXXXXXXXXXXX 0.485 - 0.49 : [ 707 0.01 0.17 ] |XXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 814 0.02 0.18 ] |XXXXXXXXXXXXXXX 0.495 - 0.5 : [ 713 0.01 0.20 ] |XXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1053 0.02 0.22 ] |XXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 866 0.02 0.23 ] |XXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 941 0.02 0.25 ] |XXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1010 0.02 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1153 0.02 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1181 0.02 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1316 0.02 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1353 0.03 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1372 0.03 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1397 0.03 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1509 0.03 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1663 0.03 0.47 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1702 0.03 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1801 0.03 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1861 0.03 0.57 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1828 0.03 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1900 0.04 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1840 0.03 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 1763 0.03 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 1683 0.03 0.74 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1736 0.03 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1527 0.03 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1427 0.03 0.82 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1301 0.02 0.85 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1192 0.02 0.87 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 1145 0.02 0.89 ] |XXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 958 0.02 0.91 ] |XXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 866 0.02 0.92 ] |XXXXXXXXXXXXXXX 0.64 - 0.645 : [ 731 0.01 0.94 ] |XXXXXXXXXXXXX 0.645 - 0.65 : [ 616 0.01 0.95 ] |XXXXXXXXXXX 0.65 - 0.655 : [ 520 0.01 0.96 ] |XXXXXXXXX 0.655 - 0.66 : [ 424 0.01 0.97 ] |XXXXXXXX 0.66 - 0.665 : [ 357 0.01 0.97 ] |XXXXXXX 0.665 - 0.67 : [ 330 0.01 0.98 ] |XXXXX 0.67 - 0.675 : [ 228 0.00 0.98 ] |XXXX 0.675 - 0.68 : [ 206 0.00 0.99 ] |XXX 0.68 - 0.685 : [ 136 0.00 0.99 ] |XX 0.685 - 0.69 : [ 113 0.00 0.99 ] |XX 0.69 - 0.695 : [ 94 0.00 0.99 ] |XX 0.695 - 0.7 : [ 75 0.00 1.00 ] |X 0.7 - 0.705 : [ 70 0.00 1.00 ] |X 0.705 - 0.71 : [ 45 0.00 1.00 ] |X 0.71 - 0.715 : [ 35 0.00 1.00 ] | 0.715 - 0.72 : [ 19 0.00 1.00 ] | 0.72 - 0.725 : [ 20 0.00 1.00 ] | 0.725 - 0.73 : [ 14 0.00 1.00 ] | 0.73 - 0.735 : [ 12 0.00 1.00 ] | 0.735 - 0.74 : [ 6 0.00 1.00 ] | 0.74 - 0.745 : [ 5 0.00 1.00 ] | 0.745 - 0.75 : [ 4 0.00 1.00 ] | 0.75 - 0.755 : [ 9 0.00 1.00 ] | 0.755 - 0.76 : [ 2 0.00 1.00 ] | 0.76 - 0.765 : [ 3 0.00 1.00 ] | 0.765 - 0.77 : [ 5 0.00 1.00 ] | 0.77 - 0.775 : [ 3 0.00 1.00 ] | 0.775 - 0.78 : [ 2 0.00 1.00 ] | 0.78 - 0.785 : [ 2 0.00 1.00 ] #... | 0.795 - 0.8 : [ 1 0.00 1.00 ] | 0.8 - 0.805 : [ 2 0.00 1.00 ] #... | 0.815 - 0.82 : [ 1 0.00 1.00 ] | 0.82 - 0.825 : [ 1 0.00 1.00 ] #... | 0.83 - 0.835 : [ 2 0.00 1.00 ] #... | 0.845 - 0.85 : [ 1 0.00 1.00 ] #... | 0.965 - 0.97 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones N/plate avg% LIBRARY @ 68 10245 5282 77.68 80.91 AAOR @ 16 2990 1517 94.81 98.76 AAOS @ 124 20818 10355 83.51 86.99 ACOB @ 108 20127 10176 94.22 98.15 AAOP @ ] 54180 27330 86.49 cumulative total@@ LIBRARY PLATE ID COUNT [ AAOR 68 AAOS 16 ACOB 124 AAOP 108 ] for 316 total 96 well plate ids. 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 = 1414 HQ Discrepant reads = 31 Chimeric reads = 207 Suspect alignments = 3915 ################################################################### C O N T I G I N F O R M A T I O N Thu Aug 12 19:51:58 2004 File: /psf/project/microbe2/3436494/edit_dir.08Jun04.QD/phrap.out Contig 92. 271 reads; 9933 bp (untrimmed), 9859 (trimmed). Contig 93. 282 reads; 19965 bp (untrimmed), 19963 (trimmed). Contig 94. 358 reads; 16829 bp (untrimmed), 16829 (trimmed). Contig 95. 515 reads; 31712 bp (untrimmed), 31712 (trimmed). Contig 96. 581 reads; 36050 bp (untrimmed), 36050 (trimmed). Contig 97. 745 reads; 42060 bp (untrimmed), 41026 (trimmed). Contig 98. 747 reads; 34307 bp (untrimmed), 34307 (trimmed). Contig 99. 868 reads; 41450 bp (untrimmed), 41450 (trimmed). Contig 100. 943 reads; 41956 bp (untrimmed), 41956 (trimmed). Contig 101. 1127 reads; 65478 bp (untrimmed), 65478 (trimmed). Contig 102. 1301 reads; 66343 bp (untrimmed), 66037 (trimmed). Contig 103. 1398 reads; 71512 bp (untrimmed), 71512 (trimmed). Contig 104. 1499 reads; 68398 bp (untrimmed), 68393 (trimmed). Contig 105. 1749 reads; 89267 bp (untrimmed), 89267 (trimmed). Contig 106. 1806 reads; 88008 bp (untrimmed), 88004 (trimmed). Contig 107. 1890 reads; 91256 bp (untrimmed), 91237 (trimmed). Contig 108. 2041 reads; 96149 bp (untrimmed), 95874 (trimmed). Contig 109. 2119 reads; 95780 bp (untrimmed), 95779 (trimmed). Contig 110. 2505 reads; 110124 bp (untrimmed), 110124 (trimmed). Contig 111. 2601 reads; 149568 bp (untrimmed), 149103 (trimmed). Contig 112. 2894 reads; 133726 bp (untrimmed), 133726 (trimmed). Contig 113. 3249 reads; 168298 bp (untrimmed), 168232 (trimmed). Contig 114. 3485 reads; 149988 bp (untrimmed), 149649 (trimmed). Contig 115. 3504 reads; 146641 bp (untrimmed), 146632 (trimmed). Contig 116. 3764 reads; 166343 bp (untrimmed), 166343 (trimmed). Contig 117. 4810 reads; 232403 bp (untrimmed), 232323 (trimmed). Contig 118. 5167 reads; 280156 bp (untrimmed), 280156 (trimmed). -------------------------------------------------------------- Totals 53588 reads; 2753507 bp (untrimmed), 2732159 (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 36 total values totalling 2628367.0000. <73010.194444 +/- 67507.533194> #Range: [ 4346 - 280156 ] #Most likely bin: [ 4000 - 6000 ] 5 counts #Median bin: [ 40000 - 42000 ] 3 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 6000 : [ 5 0.14 0.14 ] #... |XXXXXXXX 8000 - 10000 : [ 1 0.03 0.17 ] #... |XXXXXXXXXXXXXXXX 12000 - 14000 : [ 2 0.06 0.22 ] #... |XXXXXXXXXXXXXXXX 16000 - 18000 : [ 2 0.06 0.28 ] |XXXXXXXXXXXXXXXX 18000 - 20000 : [ 2 0.06 0.33 ] #... |XXXXXXXX 30000 - 32000 : [ 1 0.03 0.36 ] #... |XXXXXXXX 34000 - 36000 : [ 1 0.03 0.39 ] |XXXXXXXX 36000 - 38000 : [ 1 0.03 0.42 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 40000 - 42000 : [ 3 0.08 0.50 ] #... |XXXXXXXX 64000 - 66000 : [ 1 0.03 0.53 ] |XXXXXXXX 66000 - 68000 : [ 1 0.03 0.56 ] |XXXXXXXX 68000 - 70000 : [ 1 0.03 0.58 ] |XXXXXXXX 70000 - 72000 : [ 1 0.03 0.61 ] #... |XXXXXXXXXXXXXXXX 88000 - 90000 : [ 2 0.06 0.67 ] |XXXXXXXX 90000 - 92000 : [ 1 0.03 0.69 ] #... |XXXXXXXXXXXXXXXX 94000 - 96000 : [ 2 0.06 0.75 ] #... |XXXXXXXX 110000 - 112000 : [ 1 0.03 0.78 ] #... |XXXXXXXX 132000 - 134000 : [ 1 0.03 0.81 ] #... |XXXXXXXX 146000 - 148000 : [ 1 0.03 0.83 ] |XXXXXXXXXXXXXXXX 148000 - 150000 : [ 2 0.06 0.89 ] #... |XXXXXXXX 166000 - 168000 : [ 1 0.03 0.92 ] |XXXXXXXX 168000 - 170000 : [ 1 0.03 0.94 ] #... |XXXXXXXX 232000 - 234000 : [ 1 0.03 0.97 ] #... |XXXXXXXX 280000 - 282000 : [ 1 0.03 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 11319778 C = 13782448 G = 13893211 T = 10988287 N = 274922 X = 2882617 GC fraction = 0.52 Total = 53141263 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 3436494_fasta.screen.contigs A 617405 C 761094 G 754022 N 1530 T 619456 fraction GC = 0.55 total bases = 2753507 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 2904341 bases = 15.54 +- 9.01 = 0.39 +- 6.93 m1 = 5.23 m2 = 8.31 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 240 total values totalling 959.0600. <3.996083 +/- 5.101181> #Range: [ 1.04 - 22.38 ] #Most likely bin: [ 1.5 - 2 ] 74 counts #Median bin: [ 1.5 - 2 ] 74 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 69 0.29 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 74 0.31 0.60 ] |XXXXXXXXXXXX 2 - 2.5 : [ 22 0.09 0.69 ] |XXXXXXXXXXXX 2.5 - 3 : [ 22 0.09 0.78 ] |XXX 3 - 3.5 : [ 6 0.03 0.80 ] |X 3.5 - 4 : [ 2 0.01 0.81 ] |X 4 - 4.5 : [ 1 0.00 0.82 ] |X 4.5 - 5 : [ 1 0.00 0.82 ] |X 5 - 5.5 : [ 2 0.01 0.83 ] #... |XX 6.5 - 7 : [ 3 0.01 0.84 ] |X 7 - 7.5 : [ 2 0.01 0.85 ] |XX 7.5 - 8 : [ 3 0.01 0.86 ] #... |X 9 - 9.5 : [ 1 0.00 0.87 ] #... |X 11 - 11.5 : [ 1 0.00 0.87 ] |XX 11.5 - 12 : [ 3 0.01 0.88 ] #... |XX 13 - 13.5 : [ 3 0.01 0.90 ] #... |XX 14.5 - 15 : [ 3 0.01 0.91 ] |X 15 - 15.5 : [ 2 0.01 0.92 ] #... |XX 16 - 16.5 : [ 3 0.01 0.93 ] |X 16.5 - 17 : [ 1 0.00 0.93 ] |XXX 17 - 17.5 : [ 5 0.02 0.95 ] |X 17.5 - 18 : [ 1 0.00 0.96 ] |XX 18 - 18.5 : [ 3 0.01 0.97 ] |XX 18.5 - 19 : [ 3 0.01 0.98 ] |X 19 - 19.5 : [ 2 0.01 0.99 ] #... |X 20 - 20.5 : [ 1 0.00 1.00 ] #... |X 22 - 22.5 : [ 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 36 total values totalling 539.7500. <14.993056 +/- 4.377870> #Range: [ 5.13 - 22.38 ] #Most likely bin: [ 17 - 17.5 ] 5 counts #Median bin: [ 16 - 16.5 ] 3 counts |XXXXXXXXXXXXXXXX 5 - 5.5 : [ 2 0.06 0.06 ] #... |XXXXXXXX 6.5 - 7 : [ 1 0.03 0.08 ] |XXXXXXXX 7 - 7.5 : [ 1 0.03 0.11 ] |XXXXXXXXXXXXXXXX 7.5 - 8 : [ 2 0.06 0.17 ] #... |XXXXXXXX 11 - 11.5 : [ 1 0.03 0.19 ] |XXXXXXXX 11.5 - 12 : [ 1 0.03 0.22 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 3 0.08 0.31 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 14.5 - 15 : [ 3 0.08 0.39 ] |XXXXXXXXXXXXXXXX 15 - 15.5 : [ 2 0.06 0.44 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 16 - 16.5 : [ 3 0.08 0.53 ] |XXXXXXXX 16.5 - 17 : [ 1 0.03 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 17 - 17.5 : [ 5 0.14 0.69 ] |XXXXXXXX 17.5 - 18 : [ 1 0.03 0.72 ] |XXXXXXXXXXXXXXXXXXXXXXXX 18 - 18.5 : [ 3 0.08 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXXX 18.5 - 19 : [ 3 0.08 0.89 ] |XXXXXXXXXXXXXXXX 19 - 19.5 : [ 2 0.06 0.94 ] #... |XXXXXXXX 20 - 20.5 : [ 1 0.03 0.97 ] #... |XXXXXXXX 22 - 22.5 : [ 1 0.03 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 72 2 reads 1834 bases = 1.04 +- 0.20 = 1.04 +- 0.20 m1 = 0.04 m2 = 0.00 Contig 125 2 reads 1771 bases = 1.06 +- 0.23 = 0.19 +- 0.95 m1 = 0.05 m2 = -0.21 Contig 129 2 reads 1543 bases = 1.06 +- 0.23 = 1.06 +- 0.23 m1 = 0.05 m2 = 0.00 Contig 99 2 reads 2226 bases = 1.11 +- 0.32 = 0.17 +- 0.93 m1 = 0.09 m2 = -0.19 Contig 164 2 reads 1840 bases = 1.12 +- 0.32 = 0.01 +- 0.94 m1 = 0.09 m2 = -0.19 Contig 117 2 reads 1492 bases = 1.14 +- 0.35 = 1.14 +- 0.35 m1 = 0.11 m2 = 0.00 Contig 123 2 reads 1500 bases = 1.16 +- 0.36 = 0.03 +- 0.92 m1 = 0.11 m2 = -0.18 Contig 135 2 reads 1770 bases = 1.16 +- 0.37 = 1.16 +- 0.37 m1 = 0.12 m2 = 0.00 Contig 18 2 reads 1439 bases = 1.18 +- 0.39 = 1.18 +- 0.39 m1 = 0.13 m2 = 0.00 Contig 66 2 reads 1298 bases = 1.18 +- 0.38 = -0.43 +- 0.80 m1 = 0.12 m2 = -0.12 Contig 85 2 reads 1785 bases = 1.19 +- 0.39 = 1.19 +- 0.39 m1 = 0.13 m2 = 0.00 Contig 201 3 reads 744 bases = 1.20 +- 0.61 = 1.00 +- 0.00 m1 = 0.30 m2 = 0.09 Contig 53 2 reads 1533 bases = 1.20 +- 0.40 = 1.20 +- 0.40 m1 = 0.14 m2 = 0.00 Contig 146 2 reads 1539 bases = 1.21 +- 0.41 = -0.20 +- 0.86 m1 = 0.14 m2 = -0.14 Contig 90 2 reads 1218 bases = 1.21 +- 0.40 = -0.45 +- 0.77 m1 = 0.14 m2 = -0.11 Contig 161 2 reads 1289 bases = 1.22 +- 0.41 = 1.22 +- 0.41 m1 = 0.14 m2 = 0.00 Contig 26 2 reads 900 bases = 1.22 +- 0.41 = 1.22 +- 0.41 m1 = 0.14 m2 = 0.00 Contig 121 2 reads 1577 bases = 1.23 +- 0.42 = 1.23 +- 0.42 m1 = 0.14 m2 = 0.00 Contig 152 2 reads 1574 bases = 1.23 +- 0.42 = 1.23 +- 0.42 m1 = 0.14 m2 = 0.00 Contig 174 2 reads 1696 bases = 1.23 +- 0.42 = -0.03 +- 0.88 m1 = 0.14 m2 = -0.15 Contig 282 1420 reads 71512 bases = 16.00 +- 6.92 = 0.24 +- 8.04 m1 = 2.99 m2 = -4.20 Contig 292 3299 reads 168298 bases = 16.25 +- 7.56 = 0.42 +- 7.45 m1 = 3.51 m2 = 0.39 Contig 284 1774 reads 89267 bases = 16.35 +- 8.08 = 0.09 +- 7.76 m1 = 3.99 m2 = 1.26 Contig 281 1320 reads 66343 bases = 16.54 +- 8.24 = 0.18 +- 7.08 m1 = 4.11 m2 = 4.44 Contig 285 1827 reads 88008 bases = 17.18 +- 7.35 = 0.70 +- 7.72 m1 = 3.14 m2 = -1.40 Contig 286 1905 reads 91256 bases = 17.43 +- 7.40 = 0.69 +- 8.17 m1 = 3.14 m2 = -2.98 Contig 278 880 reads 41450 bases = 17.46 +- 7.89 = 0.19 +- 8.20 m1 = 3.56 m2 = -1.28 Contig 296 4884 reads 232406 bases = 17.47 +- 8.70 = -0.11 +- 6.42 m1 = 4.33 m2 = 8.60 Contig 273 366 reads 16829 bases = 17.48 +- 6.46 = 3.47 +- 5.86 m1 = 2.38 m2 = 1.85 Contig 287 2082 reads 96149 bases = 17.99 +- 6.80 = 0.27 +- 7.36 m1 = 2.57 m2 = -1.99 Contig 277 761 reads 34307 bases = 18.19 +- 6.90 = 1.24 +- 6.75 m1 = 2.62 m2 = 0.52 Contig 291 2933 reads 133726 bases = 18.22 +- 8.72 = 0.08 +- 6.89 m1 = 4.17 m2 = 7.14 Contig 283 1517 reads 68398 bases = 18.23 +- 7.74 = 0.00 +- 6.67 m1 = 3.28 m2 = 3.83 Contig 288 2151 reads 95780 bases = 18.63 +- 9.31 = 0.03 +- 6.57 m1 = 4.65 m2 = 10.84 Contig 279 962 reads 41956 bases = 18.79 +- 8.62 = 1.04 +- 6.60 m1 = 3.96 m2 = 7.71 Contig 295 3820 reads 166343 bases = 18.90 +- 7.96 = 0.01 +- 7.69 m1 = 3.35 m2 = 1.05 Contig 289 2540 reads 110124 bases = 19.03 +- 7.83 = 0.14 +- 7.06 m1 = 3.22 m2 = 2.86 Contig 293 3544 reads 149988 bases = 19.44 +- 8.26 = 0.14 +- 7.14 m1 = 3.51 m2 = 4.30 Contig 294 3555 reads 146641 bases = 20.13 +- 8.23 = 0.31 +- 8.02 m1 = 3.37 m2 = 0.88 Contig 271 273 reads 9933 bases = 22.38 +- 9.89 = 8.41 +- 5.20 m1 = 4.37 m2 = 17.69 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 118 total values totalling 53588.0000. <454.135593 +/- 1031.613841> #Range: [ 1 - 5167 ] #Most likely bin: [ 3 - 4 ] 45 counts #Median bin: [ 4 - 5 ] 11 counts |XX 1 - 2 : [ 2 0.02 0.02 ] |X 2 - 3 : [ 1 0.01 0.03 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 4 : [ 45 0.38 0.41 ] |XXXXXXXXXX 4 - 5 : [ 11 0.09 0.50 ] |XXXXX 5 - 6 : [ 6 0.05 0.55 ] |XXXXX 6 - 7 : [ 6 0.05 0.60 ] |XX 7 - 8 : [ 2 0.02 0.62 ] |X 8 - 9 : [ 1 0.01 0.63 ] |X 9 - 10 : [ 1 0.01 0.64 ] #... |X 12 - 13 : [ 1 0.01 0.64 ] #... |X 14 - 15 : [ 1 0.01 0.65 ] #... |X 16 - 17 : [ 1 0.01 0.66 ] |XX 17 - 18 : [ 2 0.02 0.68 ] |X 18 - 19 : [ 1 0.01 0.69 ] #... |X 21 - 22 : [ 1 0.01 0.69 ] #... |X 25 - 26 : [ 1 0.01 0.70 ] #... |X 38 - 39 : [ 1 0.01 0.71 ] |X 39 - 40 : [ 1 0.01 0.72 ] #... |X 41 - 42 : [ 1 0.01 0.73 ] #... |X 89 - 90 : [ 1 0.01 0.74 ] #... |X 120 - 121 : [ 1 0.01 0.75 ] #... |X 141 - 142 : [ 1 0.01 0.75 ] #... |X 239 - 240 : [ 1 0.01 0.76 ] #... |X 242 - 243 : [ 1 0.01 0.77 ] #... |X 271 - 272 : [ 1 0.01 0.78 ] #... |X 282 - 283 : [ 1 0.01 0.79 ] #... |X 358 - 359 : [ 1 0.01 0.80 ] #... |X 515 - 516 : [ 1 0.01 0.81 ] #... |X 581 - 582 : [ 1 0.01 0.81 ] #... |X 745 - 746 : [ 1 0.01 0.82 ] #... |X 747 - 748 : [ 1 0.01 0.83 ] #... |X 868 - 869 : [ 1 0.01 0.84 ] #... |X 943 - 944 : [ 1 0.01 0.85 ] #... |X 1127 - 1128 : [ 1 0.01 0.86 ] #... |X 1301 - 1302 : [ 1 0.01 0.86 ] #... |X 1398 - 1399 : [ 1 0.01 0.87 ] #... |X 1499 - 1500 : [ 1 0.01 0.88 ] #... |X 1749 - 1750 : [ 1 0.01 0.89 ] #... |X 1806 - 1807 : [ 1 0.01 0.90 ] #... |X 1890 - 1891 : [ 1 0.01 0.91 ] #... |X 2041 - 2042 : [ 1 0.01 0.92 ] #... |X 2119 - 2120 : [ 1 0.01 0.92 ] #... |X 2505 - 2506 : [ 1 0.01 0.93 ] #... |X 2601 - 2602 : [ 1 0.01 0.94 ] #... |X 2894 - 2895 : [ 1 0.01 0.95 ] #... |X 3249 - 3250 : [ 1 0.01 0.96 ] #... |X 3485 - 3486 : [ 1 0.01 0.97 ] #... |X 3504 - 3505 : [ 1 0.01 0.97 ] #... |X 3764 - 3765 : [ 1 0.01 0.98 ] #... |X 4810 - 4811 : [ 1 0.01 0.99 ] #... |X 5167 - 5168 : [ 1 0.01 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 118 total values totalling 2753507.0000. <23334.805085 +/- 49779.787216> #Range: [ 108 - 280156 ] #Most likely bin: [ 1000 - 2000 ] 57 counts #Median bin: [ 1000 - 2000 ] 57 counts |XXXXXXXXXXX 0 - 1000 : [ 15 0.13 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 57 0.48 0.61 ] |XXXXXX 2000 - 3000 : [ 9 0.08 0.69 ] |X 3000 - 4000 : [ 1 0.01 0.69 ] |XX 4000 - 5000 : [ 3 0.03 0.72 ] |X 5000 - 6000 : [ 1 0.01 0.73 ] |X 6000 - 7000 : [ 1 0.01 0.74 ] #... |X 9000 - 10000 : [ 1 0.01 0.75 ] #... |X 13000 - 14000 : [ 2 0.02 0.76 ] #... |X 16000 - 17000 : [ 1 0.01 0.77 ] |X 17000 - 18000 : [ 1 0.01 0.78 ] |X 18000 - 19000 : [ 1 0.01 0.79 ] |X 19000 - 20000 : [ 1 0.01 0.80 ] #... |X 31000 - 32000 : [ 1 0.01 0.81 ] #... |X 34000 - 35000 : [ 1 0.01 0.81 ] #... |X 36000 - 37000 : [ 1 0.01 0.82 ] #... |X 41000 - 42000 : [ 2 0.02 0.84 ] |X 42000 - 43000 : [ 1 0.01 0.85 ] #... |X 65000 - 66000 : [ 1 0.01 0.86 ] |X 66000 - 67000 : [ 1 0.01 0.86 ] #... |X 68000 - 69000 : [ 1 0.01 0.87 ] #... |X 71000 - 72000 : [ 1 0.01 0.88 ] #... |X 88000 - 89000 : [ 1 0.01 0.89 ] |X 89000 - 90000 : [ 1 0.01 0.90 ] #... |X 91000 - 92000 : [ 1 0.01 0.91 ] #... |X 95000 - 96000 : [ 1 0.01 0.92 ] |X 96000 - 97000 : [ 1 0.01 0.92 ] #... |X 110000 - 111000 : [ 1 0.01 0.93 ] #... |X 133000 - 134000 : [ 1 0.01 0.94 ] #... |X 146000 - 147000 : [ 1 0.01 0.95 ] #... |X 149000 - 150000 : [ 2 0.02 0.97 ] #... |X 166000 - 167000 : [ 1 0.01 0.97 ] #... |X 168000 - 169000 : [ 1 0.01 0.98 ] #... |X 232000 - 233000 : [ 1 0.01 0.99 ] #... |X 280000 - 281000 : [ 1 0.01 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 AAOP reads.list > grep.reads.list.AAOP Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAOP 4 500 #Found 8826 total values totalling 30633230.0000. <3470.794244 +/- 1747.501521> #Range: [ - 35028 ] #Most likely bin: [ 3000 - 3500 ] 2568 counts #Median bin: [ 3000 - 3500 ] 2568 counts | 0 - 500 : [ 2 0.00 0.00 ] |X 500 - 1000 : [ 33 0.00 0.00 ] |XX 1000 - 1500 : [ 136 0.02 0.02 ] |XX 1500 - 2000 : [ 120 0.01 0.03 ] |XXXX 2000 - 2500 : [ 255 0.03 0.06 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2159 0.24 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2568 0.29 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1858 0.21 0.81 ] |XXXXXXXXXXXXXXXX 4000 - 4500 : [ 1050 0.12 0.93 ] |XXXXXXXX 4500 - 5000 : [ 506 0.06 0.98 ] |XX 5000 - 5500 : [ 103 0.01 1.00 ] | 5500 - 6000 : [ 1 0.00 1.00 ] #... | 10000 - 10500 : [ 1 0.00 1.00 ] #... | 11000 - 11500 : [ 1 0.00 1.00 ] #... | 21000 - 21500 : [ 1 0.00 1.00 ] #... | 24000 - 24500 : [ 3 0.00 1.00 ] | 24500 - 25000 : [ 2 0.00 1.00 ] | 25000 - 25500 : [ 5 0.00 1.00 ] | 25500 - 26000 : [ 6 0.00 1.00 ] #... | 32000 - 32500 : [ 1 0.00 1.00 ] | 32500 - 33000 : [ 6 0.00 1.00 ] | 33000 - 33500 : [ 4 0.00 1.00 ] #... | 34000 - 34500 : [ 2 0.00 1.00 ] | 34500 - 35000 : [ 2 0.00 1.00 ] | 35000 - 35500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AAOR reads.list > grep.reads.list.AAOR Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAOR 4 500 #Found 4525 total values totalling 29624815.0000. <6546.920442 +/- 3152.395051> #Range: [ - 40420 ] #Most likely bin: [ 7500 - 8000 ] 479 counts #Median bin: [ 6500 - 7000 ] 274 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 3 0.00 0.00 ] |XXXXXXXX 1000 - 1500 : [ 99 0.02 0.02 ] |XXXXXXXXXXXX 1500 - 2000 : [ 149 0.03 0.06 ] |XXXXXXXXXXXXX 2000 - 2500 : [ 157 0.03 0.09 ] |XXXXXXXXXXXXXX 2500 - 3000 : [ 171 0.04 0.13 ] |XXXXXXXXXXXX 3000 - 3500 : [ 145 0.03 0.16 ] |XXXXXXXXXXXXXXX 3500 - 4000 : [ 176 0.04 0.20 ] |XXXXXXXXXXXXXX 4000 - 4500 : [ 173 0.04 0.24 ] |XXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 210 0.05 0.28 ] |XXXXXXXXXXXXXXXXXX 5000 - 5500 : [ 218 0.05 0.33 ] |XXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 240 0.05 0.38 ] |XXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 254 0.06 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 274 0.06 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 396 0.09 0.59 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 479 0.11 0.70 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 432 0.10 0.79 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 355 0.08 0.87 ] |XXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 271 0.06 0.93 ] |XXXXXXXXXXXXX 9500 - 10000 : [ 151 0.03 0.96 ] |XXXXXXX 10000 - 10500 : [ 86 0.02 0.98 ] |XXX 10500 - 11000 : [ 38 0.01 0.99 ] |X 11000 - 11500 : [ 16 0.00 0.99 ] |X 11500 - 12000 : [ 7 0.00 0.99 ] | 12000 - 12500 : [ 1 0.00 0.99 ] #... | 13000 - 13500 : [ 1 0.00 1.00 ] #... | 24500 - 25000 : [ 1 0.00 1.00 ] #... | 29000 - 29500 : [ 2 0.00 1.00 ] | 29500 - 30000 : [ 1 0.00 1.00 ] | 30000 - 30500 : [ 1 0.00 1.00 ] #... | 31000 - 31500 : [ 1 0.00 1.00 ] #... | 32500 - 33000 : [ 1 0.00 1.00 ] #... | 36000 - 36500 : [ 2 0.00 1.00 ] | 36500 - 37000 : [ 1 0.00 1.00 ] |X 37000 - 37500 : [ 6 0.00 1.00 ] | 37500 - 38000 : [ 1 0.00 1.00 ] | 38000 - 38500 : [ 2 0.00 1.00 ] | 38500 - 39000 : [ 1 0.00 1.00 ] | 39000 - 39500 : [ 1 0.00 1.00 ] #... | 40000 - 40500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AAOS reads.list > grep.reads.list.AAOS Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAOS 4 500 #Found 936 total values totalling 35526101.0000. <37955.236111 +/- 5677.756813> #Range: [ - 74429 ] #Most likely bin: [ 35500 - 36000 ] 66 counts #Median bin: [ 37000 - 37500 ] 53 counts |X 0 - 500 : [ 1 0.00 0.00 ] #... |X 25500 - 26000 : [ 2 0.00 0.00 ] #... |X 26500 - 27000 : [ 1 0.00 0.00 ] |X 27000 - 27500 : [ 1 0.00 0.01 ] #... |XX 28000 - 28500 : [ 3 0.00 0.01 ] |X 28500 - 29000 : [ 2 0.00 0.01 ] |XXX 29000 - 29500 : [ 5 0.01 0.02 ] |XX 29500 - 30000 : [ 3 0.00 0.02 ] |XXX 30000 - 30500 : [ 5 0.01 0.02 ] |XXXX 30500 - 31000 : [ 6 0.01 0.03 ] |XXXX 31000 - 31500 : [ 6 0.01 0.04 ] |XXXXXX 31500 - 32000 : [ 10 0.01 0.05 ] |XXXXXXXX 32000 - 32500 : [ 13 0.01 0.06 ] |XXXXXXXXXX 32500 - 33000 : [ 17 0.02 0.08 ] |XXXXXXXXXXXXX 33000 - 33500 : [ 22 0.02 0.10 ] |XXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 31 0.03 0.14 ] |XXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 38 0.04 0.18 ] |XXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 36 0.04 0.22 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 55 0.06 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 66 0.07 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 65 0.07 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 52 0.06 0.47 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 53 0.06 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 57 0.06 0.59 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 56 0.06 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 54 0.06 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 48 0.05 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 42 0.04 0.80 ] |XXXXXXXXXXXXXXXX 40000 - 40500 : [ 26 0.03 0.83 ] |XXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 34 0.04 0.87 ] |XXXXXXXXXXXXXXXX 41000 - 41500 : [ 27 0.03 0.89 ] |XXXXXXXXXXXXX 41500 - 42000 : [ 21 0.02 0.92 ] |XXXXXXXX 42000 - 42500 : [ 13 0.01 0.93 ] |XXXX 42500 - 43000 : [ 6 0.01 0.94 ] |XXXX 43000 - 43500 : [ 7 0.01 0.94 ] |XXXX 43500 - 44000 : [ 6 0.01 0.95 ] |XX 44000 - 44500 : [ 3 0.00 0.95 ] |X 44500 - 45000 : [ 1 0.00 0.96 ] |XX 45000 - 45500 : [ 4 0.00 0.96 ] #... |X 51500 - 52000 : [ 1 0.00 0.96 ] |X 52000 - 52500 : [ 2 0.00 0.96 ] |X 52500 - 53000 : [ 2 0.00 0.96 ] |XX 53000 - 53500 : [ 4 0.00 0.97 ] |X 53500 - 54000 : [ 2 0.00 0.97 ] |X 54000 - 54500 : [ 2 0.00 0.97 ] |X 54500 - 55000 : [ 1 0.00 0.97 ] |X 55000 - 55500 : [ 2 0.00 0.98 ] |X 55500 - 56000 : [ 1 0.00 0.98 ] #... |X 56500 - 57000 : [ 2 0.00 0.98 ] #... |X 57500 - 58000 : [ 2 0.00 0.98 ] |X 58000 - 58500 : [ 2 0.00 0.98 ] |X 58500 - 59000 : [ 1 0.00 0.99 ] #... |X 59500 - 60000 : [ 1 0.00 0.99 ] #... |X 61500 - 62000 : [ 1 0.00 0.99 ] #... |X 64500 - 65000 : [ 1 0.00 0.99 ] |X 65000 - 65500 : [ 1 0.00 0.99 ] |X 65500 - 66000 : [ 1 0.00 0.99 ] #... |X 66500 - 67000 : [ 1 0.00 0.99 ] #... |X 68500 - 69000 : [ 2 0.00 0.99 ] |X 69000 - 69500 : [ 2 0.00 1.00 ] #... |X 71000 - 71500 : [ 2 0.00 1.00 ] |X 71500 - 72000 : [ 1 0.00 1.00 ] #... |X 74000 - 74500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep ACOB reads.list > grep.reads.list.ACOB Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACOB 4 500 #Found 8513 total values totalling 62325106.0000. <7321.168331 +/- 2426.927057> #Range: [ - 51734 ] #Most likely bin: [ 6500 - 7000 ] 1562 counts #Median bin: [ 7000 - 7500 ] 1466 counts | 0 - 500 : [ 3 0.00 0.00 ] | 500 - 1000 : [ 7 0.00 0.00 ] |X 1000 - 1500 : [ 39 0.00 0.01 ] |X 1500 - 2000 : [ 38 0.00 0.01 ] |X 2000 - 2500 : [ 36 0.00 0.01 ] |X 2500 - 3000 : [ 37 0.00 0.02 ] |X 3000 - 3500 : [ 52 0.01 0.02 ] |X 3500 - 4000 : [ 29 0.00 0.03 ] |X 4000 - 4500 : [ 45 0.01 0.03 ] |XX 4500 - 5000 : [ 87 0.01 0.04 ] |XXXXX 5000 - 5500 : [ 197 0.02 0.07 ] |XXXXXXXXXXXXX 5500 - 6000 : [ 512 0.06 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1035 0.12 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1562 0.18 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1466 0.17 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1227 0.14 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 902 0.11 0.85 ] |XXXXXXXXXXXXXXX 8500 - 9000 : [ 593 0.07 0.92 ] |XXXXXXXXX 9000 - 9500 : [ 361 0.04 0.97 ] |XXXX 9500 - 10000 : [ 171 0.02 0.99 ] |X 10000 - 10500 : [ 48 0.01 0.99 ] | 10500 - 11000 : [ 5 0.00 0.99 ] #... | 23000 - 23500 : [ 1 0.00 0.99 ] | 23500 - 24000 : [ 3 0.00 0.99 ] | 24000 - 24500 : [ 6 0.00 0.99 ] | 24500 - 25000 : [ 5 0.00 0.99 ] | 25000 - 25500 : [ 12 0.00 1.00 ] | 25500 - 26000 : [ 3 0.00 1.00 ] | 26000 - 26500 : [ 6 0.00 1.00 ] #... | 35500 - 36000 : [ 4 0.00 1.00 ] | 36000 - 36500 : [ 5 0.00 1.00 ] | 36500 - 37000 : [ 4 0.00 1.00 ] | 37000 - 37500 : [ 2 0.00 1.00 ] | 37500 - 38000 : [ 4 0.00 1.00 ] | 38000 - 38500 : [ 3 0.00 1.00 ] | 38500 - 39000 : [ 1 0.00 1.00 ] | 39000 - 39500 : [ 1 0.00 1.00 ] #... | 51500 - 52000 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # AAOS 37183 +- 3095 (n=445) # ACOB 7092 +- 2594 (n=4184) # AAOP 3326 +- 1474 (n=4537) # AAOR 6146 +- 3153 (n=2274) ################################################################### 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 609.200558 bp, 53588 reads, genome size 2649098 bp Command: idealAssembly 2649098 53588 609.200558 ------------------------------------------------------------------- Genome = 2649098 bases Nreads = 53588 readLength = 609.200558 Depth = 12.32 N_contigs = N_gaps = 0 mean gap size = 48 bases mean contig size = 224893 reads (~ 11117474 bases) %cover = 100.00 %singlet = 0.00 assembly size = 2649086 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 0 contigs containing at least 377370 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: 3436494 Command line options used were: -c -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 40942 Number of reads with percent X's >= 20%: 522 = 1.0% Number of reads with percent X's >= 50%: 224 = 0.4% Number of reads with percent X's >= 80%: 23 = 0.0% Total nr of reads in project is: 54180 Total nr of X's: 2882617 Total nr not found in screened files: 0 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with L09136-pUC18 9235 158 55 4 Nr with pCC1Fos 1451 0 0 0 Nr with pMCL200 30256 364 169 19 Nr with P53 27 2 0 0 ################################################################### Contam Summary with *.singlets: Command: contam_summary -c -s -g ------------------------------------------------------------------- Contamination Summary for JGI id: 3436494 Command line options used were: -c -g -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 514 Number of reads with percent X's >= 20%: 4 = 0.7% Number of reads with percent X's >= 50%: 4 = 0.7% Number of reads with percent X's >= 80%: 2 = 0.3% Total nr of reads in project is: 592 Total nr of X's: 39444 Total nr not found in screened files: 0 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with L09136-pUC18 8 2 2 2 Nr with pCC1Fos 11 0 0 0 Nr with pMCL200 495 2 2 0 ################################################################### Bad M1 Contigs ------------------------------------------------------------------- ################################################################### Bad M2 Contigs ------------------------------------------------------------------- ################################################################### Ran Plates2contigs: Output Location: Ran in.dir: Output Location: Viewed Contigs with Phrapview: ################################################################### Conclusions: