################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 2351477 Genus_species: Burkholderia fungorum Taxid: 134537 Genome size: 8100 Libraries: AGXI, TAG, WTB, KPT, TDE ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 2351477 ------------------------------------------------------------------- ID=2351477 Lineage for 'Burkholderia fungorum': Burkholderia fungorum species Burkholderia genus Burkholderiaceae family Burkholderiales order Betaproteobacteria class Proteobacteria phylum Bacteria superkingdom cellular organisms no rank root no rank ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 10069399 # phrap: 9476800 # db: 8100000 9215399 +/- 824977 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s AGXI 0 0 0.00 0.00 0 0.00 0.00 TAG 120 60 91.48 629.80 60 94.67 684.50 WTB 763 382 98.31 649.82 381 98.41 646.25 KPT 1 0 0.00 0.00 1 62.50 248.00 TDE 598 299 98.26 676.47 299 98.35 672.38 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 2351477_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 2351477_fasta.screen.contigs /sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out /home/copeland/scripts/asseminfo phrap.out > asseminfo.2351477.out ################################################################### Library vector screening KPT.000001.000100 screen.out.1 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000101.000200 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000201.000300 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000301.000400 screen.out.1 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000401.000500 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000501.000600 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000601.000700 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000701.000800 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000801.000900 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000901.001000 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.001001.001100 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta TAG.000001.000100 screen.out.1 2351477_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta TDE.000001.000100 screen.out 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta TDE.000101.000200 screen.out 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta TDE.000201.000300 screen.out 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta TDE.000301.000400 screen.out 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta WTB.000001.000100 screen.out 2351477_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta WTB.000101.000200 screen.out 2351477_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta WTB.000201.000300 screen.out 2351477_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta WTB.000301.000400 screen.out.1 2351477_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta WTB.000401.000500 screen.out.1 2351477_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000001.000100 screen.out.1 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000101.000200 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000201.000300 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000301.000400 screen.out.1 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000401.000500 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000501.000600 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000601.000700 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000701.000800 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000801.000900 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.000901.001000 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta KPT.001001.001100 screen.out.1 2351477_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta TAG.000001.000100 screen.out.1 2351477_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 2351477_fasta.screen /sequences/LRS.fasta TDE.000001.000100 screen.out 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta TDE.000101.000200 screen.out 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta TDE.000201.000300 screen.out 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta TDE.000301.000400 screen.out 2351477_fasta.screen /sequences/pUC.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta WTB.000001.000100 screen.out 2351477_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta WTB.000101.000200 screen.out 2351477_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta WTB.000201.000300 screen.out 2351477_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta WTB.000301.000400 screen.out.1 2351477_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta WTB.000401.000500 screen.out.1 2351477_fasta.screen /sequences/pMCL200.fasta screen.out.std 2351477_fasta.screen /sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 2351477_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 270908 total values totalling 154676155.0000. <570.954549 +/- 181.580582> #Range: [ 23 - 906 ] #Most likely bin: [ 650 - 700 ] 69441 counts #Median bin: [ 600 - 650 ] 46481 counts |X 0 - 50 : [ 908 0.00 0.00 ] |XXX 50 - 100 : [ 5168 0.02 0.02 ] |XXXX 100 - 150 : [ 7717 0.03 0.05 ] |XXXXX 150 - 200 : [ 8553 0.03 0.08 ] |XXX 200 - 250 : [ 5973 0.02 0.10 ] |XXX 250 - 300 : [ 5648 0.02 0.13 ] |XXX 300 - 350 : [ 5787 0.02 0.15 ] |XXXX 350 - 400 : [ 6484 0.02 0.17 ] |XXXX 400 - 450 : [ 7306 0.03 0.20 ] |XXXXXX 450 - 500 : [ 9559 0.04 0.23 ] |XXXXXXXX 500 - 550 : [ 14300 0.05 0.29 ] |XXXXXXXXXXXXXX 550 - 600 : [ 23641 0.09 0.37 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 46481 0.17 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 69441 0.26 0.80 ] |XXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 37939 0.14 0.94 ] |XXXXXXXX 750 - 800 : [ 13687 0.05 0.99 ] |X 800 - 850 : [ 2138 0.01 1.00 ] | 850 - 900 : [ 177 0.00 1.00 ] | 900 - 950 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for KPT Command: /usr/xpg4/bin/grep KPT 2351477_fasta.screen.screen.ids > reads.trim15.KPT.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.KPT.rl 2 50 #Found 127726 total values totalling 64037953.0000. <501.369752 +/- 200.735717> #Range: [ 23 - 788 ] #Most likely bin: [ 650 - 700 ] 31364 counts #Median bin: [ 550 - 600 ] 10504 counts |X 0 - 50 : [ 628 0.00 0.00 ] |XXXXX 50 - 100 : [ 4129 0.03 0.04 ] |XXXXXXXX 100 - 150 : [ 6407 0.05 0.09 ] |XXXXXXXXX 150 - 200 : [ 7228 0.06 0.14 ] |XXXXXX 200 - 250 : [ 4747 0.04 0.18 ] |XXXXXX 250 - 300 : [ 4352 0.03 0.22 ] |XXXXXX 300 - 350 : [ 4417 0.03 0.25 ] |XXXXXX 350 - 400 : [ 4773 0.04 0.29 ] |XXXXXX 400 - 450 : [ 5057 0.04 0.33 ] |XXXXXXXX 450 - 500 : [ 5948 0.05 0.37 ] |XXXXXXXXXX 500 - 550 : [ 7535 0.06 0.43 ] |XXXXXXXXXXXXX 550 - 600 : [ 10504 0.08 0.51 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 21703 0.17 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 31364 0.25 0.93 ] |XXXXXXXXXXX 700 - 750 : [ 8737 0.07 1.00 ] | 750 - 800 : [ 197 0.00 1.00 ] JAZZ trim 15 readlength histogram for TDE Command: /usr/xpg4/bin/grep TDE 2351477_fasta.screen.screen.ids > reads.trim15.TDE.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.TDE.rl 2 50 #Found 60118 total values totalling 39855242.0000. <662.950231 +/- 118.173654> #Range: [ 27 - 852 ] #Most likely bin: [ 700 - 750 ] 18362 counts #Median bin: [ 650 - 700 ] 15689 counts | 0 - 50 : [ 60 0.00 0.00 ] |X 50 - 100 : [ 289 0.00 0.01 ] |X 100 - 150 : [ 318 0.01 0.01 ] |X 150 - 200 : [ 340 0.01 0.02 ] |X 200 - 250 : [ 314 0.01 0.02 ] |X 250 - 300 : [ 400 0.01 0.03 ] |X 300 - 350 : [ 443 0.01 0.04 ] |X 350 - 400 : [ 556 0.01 0.05 ] |XX 400 - 450 : [ 759 0.01 0.06 ] |XX 450 - 500 : [ 1022 0.02 0.07 ] |XXX 500 - 550 : [ 1589 0.03 0.10 ] |XXXXXXX 550 - 600 : [ 3196 0.05 0.15 ] |XXXXXXXXXXXXXXXXX 600 - 650 : [ 7870 0.13 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 15689 0.26 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 18362 0.31 0.85 ] |XXXXXXXXXXXXXXXXXX 750 - 800 : [ 8385 0.14 0.99 ] |X 800 - 850 : [ 525 0.01 1.00 ] | 850 - 900 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for WTB Command: /usr/xpg4/bin/grep WTB 2351477_fasta.screen.screen.ids > reads.trim15.WTB.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.WTB.rl 2 50 #Found 72504 total values totalling 43395859.0000. <598.530550 +/- 135.995573> #Range: [ 23 - 827 ] #Most likely bin: [ 650 - 700 ] 21284 counts #Median bin: [ 600 - 650 ] 16393 counts | 0 - 50 : [ 184 0.00 0.00 ] |X 50 - 100 : [ 664 0.01 0.01 ] |XX 100 - 150 : [ 899 0.01 0.02 ] |XX 150 - 200 : [ 890 0.01 0.04 ] |XX 200 - 250 : [ 833 0.01 0.05 ] |XX 250 - 300 : [ 820 0.01 0.06 ] |XX 300 - 350 : [ 805 0.01 0.07 ] |XX 350 - 400 : [ 1027 0.01 0.08 ] |XXX 400 - 450 : [ 1378 0.02 0.10 ] |XXXXX 450 - 500 : [ 2466 0.03 0.14 ] |XXXXXXXXX 500 - 550 : [ 4959 0.07 0.21 ] |XXXXXXXXXXXXXXXXXX 550 - 600 : [ 9622 0.13 0.34 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 16393 0.23 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 21284 0.29 0.86 ] |XXXXXXXXXXXXXXXX 700 - 750 : [ 8534 0.12 0.98 ] |XXX 750 - 800 : [ 1704 0.02 1.00 ] | 800 - 850 : [ 42 0.00 1.00 ] JAZZ trim 15 readlength histogram for TAG Command: /usr/xpg4/bin/grep TAG 2351477_fasta.screen.screen.ids > reads.trim15.TAG.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.TAG.rl 2 50 #Found 10560 total values totalling 7387101.0000. <699.536080 +/- 153.272853> #Range: [ 24 - 906 ] #Most likely bin: [ 750 - 800 ] 3401 counts #Median bin: [ 700 - 750 ] 2306 counts | 0 - 50 : [ 36 0.00 0.00 ] |X 50 - 100 : [ 86 0.01 0.01 ] |X 100 - 150 : [ 93 0.01 0.02 ] |X 150 - 200 : [ 95 0.01 0.03 ] |X 200 - 250 : [ 79 0.01 0.04 ] |X 250 - 300 : [ 76 0.01 0.04 ] |X 300 - 350 : [ 122 0.01 0.06 ] |XX 350 - 400 : [ 128 0.01 0.07 ] |X 400 - 450 : [ 112 0.01 0.08 ] |X 450 - 500 : [ 123 0.01 0.09 ] |XXX 500 - 550 : [ 217 0.02 0.11 ] |XXXX 550 - 600 : [ 319 0.03 0.14 ] |XXXXXX 600 - 650 : [ 515 0.05 0.19 ] |XXXXXXXXXXXXX 650 - 700 : [ 1104 0.10 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2306 0.22 0.51 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3401 0.32 0.83 ] |XXXXXXXXXXXXXXXXXX 800 - 850 : [ 1571 0.15 0.98 ] |XX 850 - 900 : [ 176 0.02 1.00 ] | 900 - 950 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for AGXI ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.2351477_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.2351477_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 270080 total values totalling 168948.1343. <0.625548 +/- 0.048058> #Range: [ 0 - 0.9714 ] #Most likely bin: [ 0.635 - 0.64 ] 13883 counts #Median bin: [ 0.63 - 0.635 ] 13779 counts | 0 - 0.005 : [ 1 0.00 0.00 ] #... | 0.15 - 0.155 : [ 1 0.00 0.00 ] #... | 0.17 - 0.175 : [ 1 0.00 0.00 ] | 0.175 - 0.18 : [ 1 0.00 0.00 ] | 0.18 - 0.185 : [ 1 0.00 0.00 ] | 0.185 - 0.19 : [ 2 0.00 0.00 ] | 0.19 - 0.195 : [ 1 0.00 0.00 ] #... | 0.2 - 0.205 : [ 2 0.00 0.00 ] #... | 0.21 - 0.215 : [ 1 0.00 0.00 ] | 0.215 - 0.22 : [ 1 0.00 0.00 ] | 0.22 - 0.225 : [ 2 0.00 0.00 ] #... | 0.23 - 0.235 : [ 4 0.00 0.00 ] | 0.235 - 0.24 : [ 2 0.00 0.00 ] | 0.24 - 0.245 : [ 4 0.00 0.00 ] | 0.245 - 0.25 : [ 3 0.00 0.00 ] | 0.25 - 0.255 : [ 3 0.00 0.00 ] | 0.255 - 0.26 : [ 5 0.00 0.00 ] | 0.26 - 0.265 : [ 3 0.00 0.00 ] | 0.265 - 0.27 : [ 6 0.00 0.00 ] | 0.27 - 0.275 : [ 6 0.00 0.00 ] | 0.275 - 0.28 : [ 6 0.00 0.00 ] | 0.28 - 0.285 : [ 5 0.00 0.00 ] | 0.285 - 0.29 : [ 9 0.00 0.00 ] | 0.29 - 0.295 : [ 9 0.00 0.00 ] | 0.295 - 0.3 : [ 15 0.00 0.00 ] | 0.3 - 0.305 : [ 21 0.00 0.00 ] | 0.305 - 0.31 : [ 17 0.00 0.00 ] | 0.31 - 0.315 : [ 15 0.00 0.00 ] | 0.315 - 0.32 : [ 29 0.00 0.00 ] | 0.32 - 0.325 : [ 27 0.00 0.00 ] | 0.325 - 0.33 : [ 47 0.00 0.00 ] | 0.33 - 0.335 : [ 35 0.00 0.00 ] | 0.335 - 0.34 : [ 38 0.00 0.00 ] | 0.34 - 0.345 : [ 41 0.00 0.00 ] | 0.345 - 0.35 : [ 46 0.00 0.00 ] | 0.35 - 0.355 : [ 51 0.00 0.00 ] | 0.355 - 0.36 : [ 53 0.00 0.00 ] | 0.36 - 0.365 : [ 45 0.00 0.00 ] | 0.365 - 0.37 : [ 48 0.00 0.00 ] | 0.37 - 0.375 : [ 58 0.00 0.00 ] | 0.375 - 0.38 : [ 46 0.00 0.00 ] | 0.38 - 0.385 : [ 46 0.00 0.00 ] | 0.385 - 0.39 : [ 48 0.00 0.00 ] | 0.39 - 0.395 : [ 57 0.00 0.00 ] | 0.395 - 0.4 : [ 50 0.00 0.00 ] | 0.4 - 0.405 : [ 45 0.00 0.00 ] | 0.405 - 0.41 : [ 41 0.00 0.00 ] | 0.41 - 0.415 : [ 39 0.00 0.00 ] | 0.415 - 0.42 : [ 56 0.00 0.00 ] | 0.42 - 0.425 : [ 47 0.00 0.00 ] | 0.425 - 0.43 : [ 59 0.00 0.00 ] | 0.43 - 0.435 : [ 72 0.00 0.00 ] | 0.435 - 0.44 : [ 56 0.00 0.00 ] | 0.44 - 0.445 : [ 70 0.00 0.01 ] | 0.445 - 0.45 : [ 80 0.00 0.01 ] | 0.45 - 0.455 : [ 87 0.00 0.01 ] | 0.455 - 0.46 : [ 93 0.00 0.01 ] | 0.46 - 0.465 : [ 103 0.00 0.01 ] | 0.465 - 0.47 : [ 122 0.00 0.01 ] | 0.47 - 0.475 : [ 134 0.00 0.01 ] | 0.475 - 0.48 : [ 155 0.00 0.01 ] |X 0.48 - 0.485 : [ 257 0.00 0.01 ] |X 0.485 - 0.49 : [ 267 0.00 0.01 ] |X 0.49 - 0.495 : [ 310 0.00 0.01 ] |X 0.495 - 0.5 : [ 294 0.00 0.01 ] |XX 0.5 - 0.505 : [ 676 0.00 0.01 ] |XX 0.505 - 0.51 : [ 558 0.00 0.02 ] |XX 0.51 - 0.515 : [ 706 0.00 0.02 ] |XX 0.515 - 0.52 : [ 785 0.00 0.02 ] |XXX 0.52 - 0.525 : [ 975 0.00 0.03 ] |XXX 0.525 - 0.53 : [ 1167 0.00 0.03 ] |XXXX 0.53 - 0.535 : [ 1411 0.01 0.04 ] |XXXXX 0.535 - 0.54 : [ 1784 0.01 0.04 ] |XXXXXX 0.54 - 0.545 : [ 1953 0.01 0.05 ] |XXXXXXX 0.545 - 0.55 : [ 2298 0.01 0.06 ] |XXXXXXXXX 0.55 - 0.555 : [ 2969 0.01 0.07 ] |XXXXXXXXXXXX 0.555 - 0.56 : [ 4242 0.02 0.08 ] |XXXXXXXXXXX 0.56 - 0.565 : [ 3654 0.01 0.10 ] |XXXXXXXXXXX 0.565 - 0.57 : [ 3986 0.01 0.11 ] |XXXXXXXXXXXXX 0.57 - 0.575 : [ 4353 0.02 0.13 ] |XXXXXXXXXXXXXX 0.575 - 0.58 : [ 4974 0.02 0.15 ] |XXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 5401 0.02 0.17 ] |XXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 6453 0.02 0.19 ] |XXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 7129 0.03 0.22 ] |XXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 7670 0.03 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 9264 0.03 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 9850 0.04 0.32 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 10944 0.04 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 11430 0.04 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 12268 0.05 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 13427 0.05 0.49 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 13779 0.05 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 13883 0.05 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 13529 0.05 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 12931 0.05 0.70 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 12257 0.05 0.74 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 11165 0.04 0.78 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 10059 0.04 0.82 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 9251 0.03 0.85 ] |XXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 7781 0.03 0.88 ] |XXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 6584 0.02 0.91 ] |XXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 5566 0.02 0.93 ] |XXXXXXXXXXXXX 0.685 - 0.69 : [ 4421 0.02 0.94 ] |XXXXXXXXXX 0.69 - 0.695 : [ 3578 0.01 0.96 ] |XXXXXXXX 0.695 - 0.7 : [ 2636 0.01 0.97 ] |XXXXXX 0.7 - 0.705 : [ 2246 0.01 0.97 ] |XXXXX 0.705 - 0.71 : [ 1625 0.01 0.98 ] |XXX 0.71 - 0.715 : [ 1180 0.00 0.99 ] |XX 0.715 - 0.72 : [ 813 0.00 0.99 ] |XX 0.72 - 0.725 : [ 689 0.00 0.99 ] |X 0.725 - 0.73 : [ 506 0.00 0.99 ] |X 0.73 - 0.735 : [ 398 0.00 0.99 ] |X 0.735 - 0.74 : [ 295 0.00 1.00 ] |X 0.74 - 0.745 : [ 240 0.00 1.00 ] | 0.745 - 0.75 : [ 144 0.00 1.00 ] |X 0.75 - 0.755 : [ 195 0.00 1.00 ] | 0.755 - 0.76 : [ 122 0.00 1.00 ] | 0.76 - 0.765 : [ 83 0.00 1.00 ] | 0.765 - 0.77 : [ 81 0.00 1.00 ] | 0.77 - 0.775 : [ 74 0.00 1.00 ] | 0.775 - 0.78 : [ 62 0.00 1.00 ] | 0.78 - 0.785 : [ 45 0.00 1.00 ] | 0.785 - 0.79 : [ 44 0.00 1.00 ] | 0.79 - 0.795 : [ 27 0.00 1.00 ] | 0.795 - 0.8 : [ 10 0.00 1.00 ] | 0.8 - 0.805 : [ 42 0.00 1.00 ] | 0.805 - 0.81 : [ 14 0.00 1.00 ] | 0.81 - 0.815 : [ 17 0.00 1.00 ] | 0.815 - 0.82 : [ 9 0.00 1.00 ] | 0.82 - 0.825 : [ 12 0.00 1.00 ] | 0.825 - 0.83 : [ 12 0.00 1.00 ] | 0.83 - 0.835 : [ 6 0.00 1.00 ] | 0.835 - 0.84 : [ 3 0.00 1.00 ] | 0.84 - 0.845 : [ 3 0.00 1.00 ] | 0.845 - 0.85 : [ 4 0.00 1.00 ] | 0.85 - 0.855 : [ 4 0.00 1.00 ] | 0.855 - 0.86 : [ 3 0.00 1.00 ] | 0.86 - 0.865 : [ 3 0.00 1.00 ] | 0.865 - 0.87 : [ 4 0.00 1.00 ] | 0.87 - 0.875 : [ 4 0.00 1.00 ] | 0.875 - 0.88 : [ 3 0.00 1.00 ] | 0.88 - 0.885 : [ 7 0.00 1.00 ] #... | 0.89 - 0.895 : [ 2 0.00 1.00 ] #... | 0.905 - 0.91 : [ 1 0.00 1.00 ] | 0.91 - 0.915 : [ 1 0.00 1.00 ] #... | 0.97 - 0.975 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones LIBRARY @ ] 270915 146152 83.80 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 = 6904 HQ Discrepant reads = 84 Chimeric reads = 3834 Suspect alignments = 20217 ################################################################### C O N T I G I N F O R M A T I O N Thu Aug 12 05:40:39 2004 File: /psf/project/microbe2/2351477/edit_dir.16Nov03.QD/phrap.out Contig 689. 1588 reads; 56705 bp (untrimmed), 56482 (trimmed). Contig 690. 1772 reads; 76425 bp (untrimmed), 76069 (trimmed). Contig 691. 1786 reads; 56400 bp (untrimmed), 56359 (trimmed). Contig 692. 2113 reads; 87133 bp (untrimmed), 87133 (trimmed). Contig 693. 2130 reads; 79376 bp (untrimmed), 79013 (trimmed). Contig 694. 2234 reads; 91677 bp (untrimmed), 91581 (trimmed). Contig 695. 2506 reads; 2623 bp (untrimmed), 2617 (trimmed). Contig 696. 2632 reads; 103643 bp (untrimmed), 103643 (trimmed). Contig 697. 3357 reads; 110729 bp (untrimmed), 110729 (trimmed). Contig 698. 4280 reads; 156886 bp (untrimmed), 156882 (trimmed). Contig 699. 4606 reads; 163992 bp (untrimmed), 163893 (trimmed). Contig 700. 4823 reads; 172828 bp (untrimmed), 172828 (trimmed). Contig 701. 5122 reads; 178936 bp (untrimmed), 178925 (trimmed). Contig 702. 5906 reads; 214710 bp (untrimmed), 214710 (trimmed). Contig 703. 6256 reads; 218181 bp (untrimmed), 217997 (trimmed). Contig 704. 7284 reads; 287011 bp (untrimmed), 286964 (trimmed). Contig 705. 8232 reads; 252382 bp (untrimmed), 252347 (trimmed). Contig 706. 9258 reads; 342903 bp (untrimmed), 342866 (trimmed). Contig 707. 11973 reads; 493548 bp (untrimmed), 493509 (trimmed). Contig 708. 13889 reads; 460921 bp (untrimmed), 460883 (trimmed). Contig 709. 13946 reads; 512032 bp (untrimmed), 512008 (trimmed). Contig 710. 14054 reads; 537163 bp (untrimmed), 536896 (trimmed). Contig 711. 16212 reads; 546443 bp (untrimmed), 546439 (trimmed). Contig 712. 17455 reads; 613496 bp (untrimmed), 613494 (trimmed). Contig 713. 17473 reads; 642151 bp (untrimmed), 642151 (trimmed). Contig 714. 20860 reads; 676811 bp (untrimmed), 676785 (trimmed). Contig 715. 51966 reads; 1927566 bp (untrimmed), 1927480 (trimmed). -------------------------------------------------------------- Totals 270070 reads; 10130405 bp (untrimmed), 10069399 (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 50 total values totalling 9656114.0000. <193122.280000 +/- 314653.121225> #Range: [ 2617 - 1927480 ] #Most likely bin: [ 32000 - 34000 ] 3 counts #Median bin: [ 56000 - 58000 ] 3 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 3 0.06 0.06 ] #... |XXXXXXXXXXXXX 6000 - 8000 : [ 1 0.02 0.08 ] |XXXXXXXXXXXXX 8000 - 10000 : [ 1 0.02 0.10 ] |XXXXXXXXXXXXX 10000 - 12000 : [ 1 0.02 0.12 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 12000 - 14000 : [ 2 0.04 0.16 ] #... |XXXXXXXXXXXXX 18000 - 20000 : [ 1 0.02 0.18 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 20000 - 22000 : [ 2 0.04 0.22 ] #... |XXXXXXXXXXXXX 24000 - 26000 : [ 1 0.02 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 26000 - 28000 : [ 2 0.04 0.28 ] |XXXXXXXXXXXXX 28000 - 30000 : [ 1 0.02 0.30 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 32000 - 34000 : [ 3 0.06 0.36 ] |XXXXXXXXXXXXX 34000 - 36000 : [ 1 0.02 0.38 ] #... |XXXXXXXXXXXXX 38000 - 40000 : [ 1 0.02 0.40 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 44000 - 46000 : [ 3 0.06 0.46 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 56000 - 58000 : [ 3 0.06 0.52 ] #... |XXXXXXXXXXXXX 76000 - 78000 : [ 1 0.02 0.54 ] |XXXXXXXXXXXXX 78000 - 80000 : [ 1 0.02 0.56 ] #... |XXXXXXXXXXXXX 86000 - 88000 : [ 1 0.02 0.58 ] #... |XXXXXXXXXXXXX 90000 - 92000 : [ 1 0.02 0.60 ] #... |XXXXXXXXXXXXX 102000 - 104000 : [ 1 0.02 0.62 ] #... |XXXXXXXXXXXXX 110000 - 112000 : [ 1 0.02 0.64 ] #... |XXXXXXXXXXXXX 156000 - 158000 : [ 1 0.02 0.66 ] #... |XXXXXXXXXXXXX 162000 - 164000 : [ 1 0.02 0.68 ] #... |XXXXXXXXXXXXX 172000 - 174000 : [ 1 0.02 0.70 ] #... |XXXXXXXXXXXXX 178000 - 180000 : [ 1 0.02 0.72 ] #... |XXXXXXXXXXXXX 214000 - 216000 : [ 1 0.02 0.74 ] |XXXXXXXXXXXXX 216000 - 218000 : [ 1 0.02 0.76 ] #... |XXXXXXXXXXXXX 252000 - 254000 : [ 1 0.02 0.78 ] #... |XXXXXXXXXXXXX 286000 - 288000 : [ 1 0.02 0.80 ] #... |XXXXXXXXXXXXX 342000 - 344000 : [ 1 0.02 0.82 ] #... |XXXXXXXXXXXXX 460000 - 462000 : [ 1 0.02 0.84 ] #... |XXXXXXXXXXXXX 492000 - 494000 : [ 1 0.02 0.86 ] #... |XXXXXXXXXXXXX 512000 - 514000 : [ 1 0.02 0.88 ] #... |XXXXXXXXXXXXX 536000 - 538000 : [ 1 0.02 0.90 ] #... |XXXXXXXXXXXXX 546000 - 548000 : [ 1 0.02 0.92 ] #... |XXXXXXXXXXXXX 612000 - 614000 : [ 1 0.02 0.94 ] #... |XXXXXXXXXXXXX 642000 - 644000 : [ 1 0.02 0.96 ] #... |XXXXXXXXXXXXX 676000 - 678000 : [ 1 0.02 0.98 ] #... |XXXXXXXXXXXXX 1926000 - 1928000 : [ 1 0.02 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 40786358 C = 65201229 G = 65723286 T = 39406612 N = 1234973 X = 8576742 GC fraction = 0.59 Total = 220929200 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 2351477_fasta.screen.contigs A 1939373 C 3144632 G 3112094 N 2422 T 1928446 X 3438 fraction GC = 0.62 total bases = 10130405 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 9660475 bases = 19.88 +- 15.02 = 0.12 +- 6.11 m1 = 11.34 m2 = 47.04 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 50 total values totalling 1340.6300. <26.812600 +/- 60.993286> #Range: [ 1.53 - 452.69 ] #Most likely bin: [ 19.5 - 20 ] 6 counts #Median bin: [ 19 - 19.5 ] 6 counts |XXXXXXX 1.5 - 2 : [ 1 0.02 0.02 ] #... |XXXXXXX 3.5 - 4 : [ 1 0.02 0.04 ] #... |XXXXXXX 5.5 - 6 : [ 1 0.02 0.06 ] #... |XXXXXXX 10 - 10.5 : [ 1 0.02 0.08 ] #... |XXXXXXX 13.5 - 14 : [ 1 0.02 0.10 ] #... |XXXXXXX 15 - 15.5 : [ 1 0.02 0.12 ] #... |XXXXXXXXXXXXXXXXXXXX 16.5 - 17 : [ 3 0.06 0.18 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 17 - 17.5 : [ 4 0.08 0.26 ] |XXXXXXXXXXXXXXXXXXXX 17.5 - 18 : [ 3 0.06 0.32 ] |XXXXXXXXXXXXXXXXXXXX 18 - 18.5 : [ 3 0.06 0.38 ] |XXXXXXXXXXXXXXXXXXXX 18.5 - 19 : [ 3 0.06 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 19 - 19.5 : [ 6 0.12 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 19.5 - 20 : [ 6 0.12 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 20 - 20.5 : [ 6 0.12 0.80 ] |XXXXXXX 20.5 - 21 : [ 1 0.02 0.82 ] |XXXXXXXXXXXXX 21 - 21.5 : [ 2 0.04 0.86 ] |XXXXXXXXXXXXX 21.5 - 22 : [ 2 0.04 0.90 ] |XXXXXXX 22 - 22.5 : [ 1 0.02 0.92 ] |XXXXXXX 22.5 - 23 : [ 1 0.02 0.94 ] |XXXXXXX 23 - 23.5 : [ 1 0.02 0.96 ] |XXXXXXX 23.5 - 24 : [ 1 0.02 0.98 ] #... |XXXXXXX 452.5 - 453 : [ 1 0.02 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 50 total values totalling 1340.6300. <26.812600 +/- 60.993286> #Range: [ 1.53 - 452.69 ] #Most likely bin: [ 19.5 - 20 ] 6 counts #Median bin: [ 19 - 19.5 ] 6 counts |XXXXXXX 1.5 - 2 : [ 1 0.02 0.02 ] #... |XXXXXXX 3.5 - 4 : [ 1 0.02 0.04 ] #... |XXXXXXX 5.5 - 6 : [ 1 0.02 0.06 ] #... |XXXXXXX 10 - 10.5 : [ 1 0.02 0.08 ] #... |XXXXXXX 13.5 - 14 : [ 1 0.02 0.10 ] #... |XXXXXXX 15 - 15.5 : [ 1 0.02 0.12 ] #... |XXXXXXXXXXXXXXXXXXXX 16.5 - 17 : [ 3 0.06 0.18 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 17 - 17.5 : [ 4 0.08 0.26 ] |XXXXXXXXXXXXXXXXXXXX 17.5 - 18 : [ 3 0.06 0.32 ] |XXXXXXXXXXXXXXXXXXXX 18 - 18.5 : [ 3 0.06 0.38 ] |XXXXXXXXXXXXXXXXXXXX 18.5 - 19 : [ 3 0.06 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 19 - 19.5 : [ 6 0.12 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 19.5 - 20 : [ 6 0.12 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 20 - 20.5 : [ 6 0.12 0.80 ] |XXXXXXX 20.5 - 21 : [ 1 0.02 0.82 ] |XXXXXXXXXXXXX 21 - 21.5 : [ 2 0.04 0.86 ] |XXXXXXXXXXXXX 21.5 - 22 : [ 2 0.04 0.90 ] |XXXXXXX 22 - 22.5 : [ 1 0.02 0.92 ] |XXXXXXX 22.5 - 23 : [ 1 0.02 0.94 ] |XXXXXXX 23 - 23.5 : [ 1 0.02 0.96 ] |XXXXXXX 23.5 - 24 : [ 1 0.02 0.98 ] #... |XXXXXXX 452.5 - 453 : [ 1 0.02 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 660 10 reads 3340 bases = 1.53 +- 0.81 = 0.49 +- 0.92 m1 = 0.43 m2 = -0.05 Contig 662 18 reads 3860 bases = 3.70 +- 2.69 = 0.55 +- 1.05 m1 = 1.96 m2 = 1.54 Contig 667 59 reads 7225 bases = 5.67 +- 2.30 = 0.60 +- 3.02 m1 = 0.93 m2 = -0.96 Contig 669 131 reads 9217 bases = 10.48 +- 5.47 = 2.78 +- 4.19 m1 = 2.85 m2 = 3.09 Contig 673 359 reads 19281 bases = 13.53 +- 4.62 = 0.63 +- 5.02 m1 = 1.58 m2 = -0.96 Contig 676 612 reads 29366 bases = 15.12 +- 5.49 = 0.24 +- 4.24 m1 = 1.99 m2 = 3.05 Contig 688 1306 reads 56220 bases = 16.72 +- 5.52 = 0.25 +- 5.61 m1 = 1.82 m2 = -0.26 Contig 690 1772 reads 76425 bases = 16.74 +- 5.31 = 0.05 +- 5.30 m1 = 1.68 m2 = 0.02 Contig 685 1084 reads 46006 bases = 16.84 +- 6.80 = 0.91 +- 5.83 m1 = 2.75 m2 = 3.07 Contig 707 11973 reads 493548 bases = 17.31 +- 5.45 = 0.02 +- 4.92 m1 = 1.72 m2 = 1.38 Contig 692 2113 reads 87133 bases = 17.33 +- 5.63 = 0.33 +- 4.75 m1 = 1.83 m2 = 2.27 Contig 674 520 reads 21399 bases = 17.37 +- 6.28 = 0.65 +- 4.83 m1 = 2.27 m2 = 4.01 Contig 694 2234 reads 91677 bases = 17.48 +- 4.75 = 0.17 +- 4.69 m1 = 1.29 m2 = 0.15 Contig 670 267 reads 10638 bases = 17.63 +- 4.75 = 0.73 +- 4.23 m1 = 1.28 m2 = 1.16 Contig 671 315 reads 12660 bases = 17.79 +- 6.21 = 0.08 +- 5.55 m1 = 2.17 m2 = 1.96 Contig 677 665 reads 26193 bases = 17.98 +- 5.14 = 1.23 +- 4.88 m1 = 1.47 m2 = 0.65 Contig 704 7284 reads 287011 bases = 18.00 +- 5.58 = 0.09 +- 5.11 m1 = 1.73 m2 = 1.27 Contig 680 859 reads 32993 bases = 18.03 +- 5.15 = 0.13 +- 4.70 m1 = 1.47 m2 = 1.09 Contig 696 2632 reads 103643 bases = 18.40 +- 5.75 = 0.52 +- 5.11 m1 = 1.80 m2 = 1.74 Contig 710 14054 reads 537163 bases = 18.65 +- 5.24 = 0.10 +- 5.31 m1 = 1.47 m2 = -0.18 Contig 706 9258 reads 342903 bases = 19.66 +- 6.19 = 0.05 +- 5.39 m1 = 1.95 m2 = 2.33 Contig 702 5906 reads 214710 bases = 19.73 +- 5.28 = 0.09 +- 5.10 m1 = 1.41 m2 = 0.48 Contig 687 1265 reads 45924 bases = 19.90 +- 5.72 = 0.15 +- 4.98 m1 = 1.65 m2 = 1.98 Contig 682 935 reads 33478 bases = 19.91 +- 7.43 = 0.54 +- 4.93 m1 = 2.77 m2 = 7.70 Contig 699 4606 reads 163992 bases = 20.12 +- 4.95 = -0.01 +- 4.98 m1 = 1.22 m2 = -0.08 Contig 700 4823 reads 172828 bases = 20.21 +- 6.02 = 0.44 +- 5.05 m1 = 1.79 m2 = 2.69 Contig 712 17455 reads 613496 bases = 20.32 +- 5.37 = 0.03 +- 5.22 m1 = 1.42 m2 = 0.40 Contig 683 1009 reads 35296 bases = 20.35 +- 4.66 = 0.58 +- 5.57 m1 = 1.07 m2 = -2.31 Contig 689 1588 reads 56705 bases = 20.35 +- 5.96 = 0.56 +- 6.29 m1 = 1.74 m2 = -1.03 Contig 703 6256 reads 218181 bases = 20.44 +- 6.63 = 0.22 +- 5.62 m1 = 2.15 m2 = 3.11 Contig 701 5122 reads 178936 bases = 20.55 +- 5.62 = 0.36 +- 4.97 m1 = 1.54 m2 = 1.73 Contig 679 826 reads 27946 bases = 21.21 +- 6.66 = -0.30 +- 5.23 m1 = 2.09 m2 = 4.25 Contig 711 16212 reads 546443 bases = 21.32 +- 9.66 = 0.14 +- 5.50 m1 = 4.38 m2 = 15.76 Contig 708 13889 reads 460921 bases = 21.56 +- 6.10 = -0.00 +- 5.24 m1 = 1.73 m2 = 2.45 Contig 697 3357 reads 110729 bases = 21.78 +- 7.47 = 0.47 +- 5.39 m1 = 2.56 m2 = 6.68 Contig 714 20860 reads 676811 bases = 22.18 +- 5.74 = 0.07 +- 5.50 m1 = 1.48 m2 = 0.67 Contig 691 1786 reads 56400 bases = 22.93 +- 6.00 = 1.07 +- 5.05 m1 = 1.57 m2 = 2.64 Contig 678 815 reads 25115 bases = 23.18 +- 6.07 = 0.36 +- 4.88 m1 = 1.59 m2 = 3.25 Contig 705 8232 reads 252382 bases = 23.79 +- 5.94 = 0.02 +- 6.01 m1 = 1.48 m2 = -0.21 Contig 695 2506 reads 2623 bases = 452.69 +- 690.97 = -88.69 +- 161.85 m1 = 1054.66 m2 = 112809.41 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 715 total values totalling 270070.0000. <377.720280 +/- 2661.613497> #Range: [ 1 - 51966 ] #Most likely bin: [ 1 - 2 ] 319 counts #Median bin: [ 2 - 3 ] 299 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 2 : [ 319 0.45 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 3 : [ 299 0.42 0.86 ] |XXX 3 - 4 : [ 21 0.03 0.89 ] |X 4 - 5 : [ 10 0.01 0.91 ] | 5 - 6 : [ 3 0.00 0.91 ] | 6 - 7 : [ 1 0.00 0.91 ] |X 7 - 8 : [ 5 0.01 0.92 ] | 8 - 9 : [ 1 0.00 0.92 ] #... | 10 - 11 : [ 1 0.00 0.92 ] | 11 - 12 : [ 1 0.00 0.92 ] #... | 18 - 19 : [ 1 0.00 0.93 ] | 19 - 20 : [ 1 0.00 0.93 ] #... | 21 - 22 : [ 1 0.00 0.93 ] #... | 24 - 25 : [ 1 0.00 0.93 ] #... | 33 - 34 : [ 1 0.00 0.93 ] #... | 59 - 60 : [ 1 0.00 0.93 ] #... | 73 - 74 : [ 1 0.00 0.93 ] #... | 131 - 132 : [ 1 0.00 0.94 ] #... | 267 - 268 : [ 1 0.00 0.94 ] #... | 315 - 316 : [ 1 0.00 0.94 ] #... | 357 - 358 : [ 1 0.00 0.94 ] #... | 359 - 360 : [ 1 0.00 0.94 ] #... | 520 - 521 : [ 1 0.00 0.94 ] #... | 551 - 552 : [ 1 0.00 0.94 ] #... | 612 - 613 : [ 1 0.00 0.95 ] #... | 665 - 666 : [ 1 0.00 0.95 ] #... | 815 - 816 : [ 1 0.00 0.95 ] #... | 826 - 827 : [ 1 0.00 0.95 ] #... | 859 - 860 : [ 1 0.00 0.95 ] #... | 887 - 888 : [ 1 0.00 0.95 ] #... | 935 - 936 : [ 1 0.00 0.95 ] #... | 1009 - 1010 : [ 1 0.00 0.96 ] #... | 1031 - 1032 : [ 1 0.00 0.96 ] #... | 1084 - 1085 : [ 1 0.00 0.96 ] #... | 1211 - 1212 : [ 1 0.00 0.96 ] #... | 1265 - 1266 : [ 1 0.00 0.96 ] #... | 1306 - 1307 : [ 1 0.00 0.96 ] #... | 1588 - 1589 : [ 1 0.00 0.96 ] #... | 1772 - 1773 : [ 1 0.00 0.97 ] #... | 1786 - 1787 : [ 1 0.00 0.97 ] #... | 2113 - 2114 : [ 1 0.00 0.97 ] #... | 2130 - 2131 : [ 1 0.00 0.97 ] #... | 2234 - 2235 : [ 1 0.00 0.97 ] #... | 2506 - 2507 : [ 1 0.00 0.97 ] #... | 2632 - 2633 : [ 1 0.00 0.97 ] #... | 3357 - 3358 : [ 1 0.00 0.97 ] #... | 4280 - 4281 : [ 1 0.00 0.98 ] #... | 4606 - 4607 : [ 1 0.00 0.98 ] #... | 4823 - 4824 : [ 1 0.00 0.98 ] #... | 5122 - 5123 : [ 1 0.00 0.98 ] #... | 5906 - 5907 : [ 1 0.00 0.98 ] #... | 6256 - 6257 : [ 1 0.00 0.98 ] #... | 7284 - 7285 : [ 1 0.00 0.98 ] #... | 8232 - 8233 : [ 1 0.00 0.99 ] #... | 9258 - 9259 : [ 1 0.00 0.99 ] #... | 11973 - 11974 : [ 1 0.00 0.99 ] #... | 13889 - 13890 : [ 1 0.00 0.99 ] #... | 13946 - 13947 : [ 1 0.00 0.99 ] #... | 14054 - 14055 : [ 1 0.00 0.99 ] #... | 16212 - 16213 : [ 1 0.00 0.99 ] #... | 17455 - 17456 : [ 1 0.00 1.00 ] #... | 17473 - 17474 : [ 1 0.00 1.00 ] #... | 20860 - 20861 : [ 1 0.00 1.00 ] #... | 51966 - 51967 : [ 1 0.00 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 715 total values totalling 10130405.0000. <14168.398601 +/- 96608.565034> #Range: [ 100 - 1927566 ] #Most likely bin: [ 0 - 1000 ] 576 counts #Median bin: [ 0 - 1000 ] 576 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 1000 : [ 576 0.81 0.81 ] |XXXXXX 1000 - 2000 : [ 81 0.11 0.92 ] |X 2000 - 3000 : [ 8 0.01 0.93 ] | 3000 - 4000 : [ 3 0.00 0.93 ] #... | 7000 - 8000 : [ 1 0.00 0.94 ] #... | 9000 - 10000 : [ 1 0.00 0.94 ] | 10000 - 11000 : [ 1 0.00 0.94 ] #... | 12000 - 13000 : [ 1 0.00 0.94 ] | 13000 - 14000 : [ 1 0.00 0.94 ] #... | 19000 - 20000 : [ 1 0.00 0.94 ] | 20000 - 21000 : [ 1 0.00 0.94 ] | 21000 - 22000 : [ 1 0.00 0.95 ] #... | 25000 - 26000 : [ 1 0.00 0.95 ] | 26000 - 27000 : [ 1 0.00 0.95 ] | 27000 - 28000 : [ 1 0.00 0.95 ] #... | 29000 - 30000 : [ 1 0.00 0.95 ] #... | 32000 - 33000 : [ 1 0.00 0.95 ] | 33000 - 34000 : [ 2 0.00 0.96 ] #... | 35000 - 36000 : [ 1 0.00 0.96 ] #... | 38000 - 39000 : [ 1 0.00 0.96 ] #... | 45000 - 46000 : [ 2 0.00 0.96 ] | 46000 - 47000 : [ 1 0.00 0.96 ] #... | 56000 - 57000 : [ 3 0.00 0.97 ] #... | 76000 - 77000 : [ 1 0.00 0.97 ] #... | 79000 - 80000 : [ 1 0.00 0.97 ] #... | 87000 - 88000 : [ 1 0.00 0.97 ] #... | 91000 - 92000 : [ 1 0.00 0.97 ] #... | 103000 - 104000 : [ 1 0.00 0.97 ] #... | 110000 - 111000 : [ 1 0.00 0.97 ] #... | 156000 - 157000 : [ 1 0.00 0.98 ] #... | 163000 - 164000 : [ 1 0.00 0.98 ] #... | 172000 - 173000 : [ 1 0.00 0.98 ] #... | 178000 - 179000 : [ 1 0.00 0.98 ] #... | 214000 - 215000 : [ 1 0.00 0.98 ] #... | 218000 - 219000 : [ 1 0.00 0.98 ] #... | 252000 - 253000 : [ 1 0.00 0.98 ] #... | 287000 - 288000 : [ 1 0.00 0.99 ] #... | 342000 - 343000 : [ 1 0.00 0.99 ] #... | 460000 - 461000 : [ 1 0.00 0.99 ] #... | 493000 - 494000 : [ 1 0.00 0.99 ] #... | 512000 - 513000 : [ 1 0.00 0.99 ] #... | 537000 - 538000 : [ 1 0.00 0.99 ] #... | 546000 - 547000 : [ 1 0.00 0.99 ] #... | 613000 - 614000 : [ 1 0.00 1.00 ] #... | 642000 - 643000 : [ 1 0.00 1.00 ] #... | 676000 - 677000 : [ 1 0.00 1.00 ] #... | 1927000 - 1928000 : [ 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 KPT reads.list > grep.reads.list.KPT Command: /home/copeland/scripts/histogram2.pl grep.reads.list.KPT 4 500 #Found 51395 total values totalling 187604255.0000. <3650.243312 +/- 15313.479980> #Range: [ - 1625411 ] #Most likely bin: [ 3000 - 3500 ] 20449 counts #Median bin: [ 3000 - 3500 ] 20449 counts | 0 - 500 : [ 23 0.00 0.00 ] |XX 500 - 1000 : [ 1140 0.02 0.02 ] |XXX 1000 - 1500 : [ 1480 0.03 0.05 ] |XX 1500 - 2000 : [ 1200 0.02 0.07 ] |XX 2000 - 2500 : [ 1037 0.02 0.09 ] |XXXXXXX 2500 - 3000 : [ 3337 0.06 0.16 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 20449 0.40 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 12977 0.25 0.81 ] |XXXXXXXXXXXXX 4000 - 4500 : [ 6576 0.13 0.94 ] |XXXXX 4500 - 5000 : [ 2447 0.05 0.99 ] |X 5000 - 5500 : [ 603 0.01 1.00 ] | 5500 - 6000 : [ 96 0.00 1.00 ] | 6000 - 6500 : [ 3 0.00 1.00 ] #... | 8500 - 9000 : [ 1 0.00 1.00 ] #... | 13500 - 14000 : [ 1 0.00 1.00 ] | 14000 - 14500 : [ 2 0.00 1.00 ] #... | 23500 - 24000 : [ 1 0.00 1.00 ] #... | 24500 - 25000 : [ 1 0.00 1.00 ] #... | 93000 - 93500 : [ 1 0.00 1.00 ] | 93500 - 94000 : [ 1 0.00 1.00 ] #... | 124500 - 125000 : [ 1 0.00 1.00 ] #... | 202000 - 202500 : [ 1 0.00 1.00 ] #... | 214500 - 215000 : [ 1 0.00 1.00 ] #... | 311000 - 311500 : [ 1 0.00 1.00 ] #... | 481500 - 482000 : [ 1 0.00 1.00 ] #... | 566000 - 566500 : [ 2 0.00 1.00 ] | 566500 - 567000 : [ 5 0.00 1.00 ] #... | 659000 - 659500 : [ 1 0.00 1.00 ] #... | 679000 - 679500 : [ 1 0.00 1.00 ] #... | 714000 - 714500 : [ 1 0.00 1.00 ] #... | 892500 - 893000 : [ 1 0.00 1.00 ] #... | 1497000 - 1497500 : [ 1 0.00 1.00 ] #... | 1524500 - 1525000 : [ 1 0.00 1.00 ] #... | 1625000 - 1625500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep TDE reads.list > grep.reads.list.TDE Command: /home/copeland/scripts/histogram2.pl grep.reads.list.TDE 4 500 #Found 26698 total values totalling 113856137.0000. <4264.594239 +/- 17562.957374> #Range: [ - 1436159 ] #Most likely bin: [ 3000 - 3500 ] 6211 counts #Median bin: [ 3500 - 4000 ] 6208 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 8 0.00 0.00 ] | 1000 - 1500 : [ 45 0.00 0.00 ] | 1500 - 2000 : [ 55 0.00 0.00 ] |XX 2000 - 2500 : [ 306 0.01 0.02 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 3969 0.15 0.16 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 6211 0.23 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 6208 0.23 0.63 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 4662 0.17 0.80 ] |XXXXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 3301 0.12 0.93 ] |XXXXXXXXXX 5000 - 5500 : [ 1504 0.06 0.98 ] |XX 5500 - 6000 : [ 357 0.01 1.00 ] | 6000 - 6500 : [ 28 0.00 1.00 ] | 6500 - 7000 : [ 1 0.00 1.00 ] #... | 9000 - 9500 : [ 1 0.00 1.00 ] #... | 13500 - 14000 : [ 2 0.00 1.00 ] | 14000 - 14500 : [ 3 0.00 1.00 ] #... | 21000 - 21500 : [ 1 0.00 1.00 ] #... | 23000 - 23500 : [ 1 0.00 1.00 ] #... | 38500 - 39000 : [ 1 0.00 1.00 ] #... | 41500 - 42000 : [ 1 0.00 1.00 ] #... | 49000 - 49500 : [ 1 0.00 1.00 ] #... | 83500 - 84000 : [ 1 0.00 1.00 ] #... | 88000 - 88500 : [ 1 0.00 1.00 ] #... | 90500 - 91000 : [ 1 0.00 1.00 ] #... | 96500 - 97000 : [ 1 0.00 1.00 ] #... | 99000 - 99500 : [ 1 0.00 1.00 ] #... | 132000 - 132500 : [ 1 0.00 1.00 ] #... | 139500 - 140000 : [ 1 0.00 1.00 ] #... | 149500 - 150000 : [ 1 0.00 1.00 ] #... | 159000 - 159500 : [ 1 0.00 1.00 ] #... | 188000 - 188500 : [ 1 0.00 1.00 ] #... | 222500 - 223000 : [ 1 0.00 1.00 ] #... | 246000 - 246500 : [ 1 0.00 1.00 ] #... | 255500 - 256000 : [ 1 0.00 1.00 ] #... | 292000 - 292500 : [ 1 0.00 1.00 ] #... | 298500 - 299000 : [ 1 0.00 1.00 ] #... | 344500 - 345000 : [ 1 0.00 1.00 ] #... | 480500 - 481000 : [ 1 0.00 1.00 ] #... | 489000 - 489500 : [ 1 0.00 1.00 ] #... | 550500 - 551000 : [ 1 0.00 1.00 ] #... | 566000 - 566500 : [ 2 0.00 1.00 ] | 566500 - 567000 : [ 4 0.00 1.00 ] | 567000 - 567500 : [ 1 0.00 1.00 ] | 567500 - 568000 : [ 2 0.00 1.00 ] | 568000 - 568500 : [ 1 0.00 1.00 ] #... | 1278000 - 1278500 : [ 1 0.00 1.00 ] #... | 1436000 - 1436500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep WTB reads.list > grep.reads.list.WTB Command: /home/copeland/scripts/histogram2.pl grep.reads.list.WTB 4 500 #Found 28846 total values totalling 264166675.0000. <9157.826908 +/- 29758.517238> #Range: [ - 1762429 ] #Most likely bin: [ 8000 - 8500 ] 4049 counts #Median bin: [ 8000 - 8500 ] 4049 counts | 0 - 500 : [ 1 0.00 0.00 ] |X 500 - 1000 : [ 54 0.00 0.00 ] |XX 1000 - 1500 : [ 180 0.01 0.01 ] |XX 1500 - 2000 : [ 252 0.01 0.02 ] |XXX 2000 - 2500 : [ 318 0.01 0.03 ] |XXX 2500 - 3000 : [ 310 0.01 0.04 ] |XXX 3000 - 3500 : [ 346 0.01 0.05 ] |XXXX 3500 - 4000 : [ 367 0.01 0.06 ] |XXXX 4000 - 4500 : [ 398 0.01 0.08 ] |XXXXX 4500 - 5000 : [ 543 0.02 0.10 ] |XXXXXXX 5000 - 5500 : [ 671 0.02 0.12 ] |XXXXXXXX 5500 - 6000 : [ 846 0.03 0.15 ] |XXXXXXXXXX 6000 - 6500 : [ 1021 0.04 0.18 ] |XXXXXXXXXXXX 6500 - 7000 : [ 1215 0.04 0.23 ] |XXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1724 0.06 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 2877 0.10 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 4049 0.14 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 4034 0.14 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 3155 0.11 0.78 ] |XXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 2317 0.08 0.86 ] |XXXXXXXXXXXXXXX 10000 - 10500 : [ 1541 0.05 0.91 ] |XXXXXXXXXX 10500 - 11000 : [ 1037 0.04 0.94 ] |XXXXXXX 11000 - 11500 : [ 675 0.02 0.97 ] |XXX 11500 - 12000 : [ 347 0.01 0.98 ] |XX 12000 - 12500 : [ 246 0.01 0.99 ] |X 12500 - 13000 : [ 137 0.00 0.99 ] |X 13000 - 13500 : [ 62 0.00 1.00 ] | 13500 - 14000 : [ 30 0.00 1.00 ] | 14000 - 14500 : [ 10 0.00 1.00 ] | 14500 - 15000 : [ 5 0.00 1.00 ] | 15000 - 15500 : [ 2 0.00 1.00 ] #... | 24500 - 25000 : [ 2 0.00 1.00 ] #... | 52000 - 52500 : [ 1 0.00 1.00 ] #... | 57500 - 58000 : [ 1 0.00 1.00 ] #... | 59000 - 59500 : [ 1 0.00 1.00 ] | 59500 - 60000 : [ 1 0.00 1.00 ] | 60000 - 60500 : [ 1 0.00 1.00 ] #... | 61000 - 61500 : [ 1 0.00 1.00 ] | 61500 - 62000 : [ 6 0.00 1.00 ] | 62000 - 62500 : [ 1 0.00 1.00 ] | 62500 - 63000 : [ 2 0.00 1.00 ] | 63000 - 63500 : [ 1 0.00 1.00 ] | 63500 - 64000 : [ 2 0.00 1.00 ] | 64000 - 64500 : [ 2 0.00 1.00 ] #... | 68500 - 69000 : [ 1 0.00 1.00 ] #... | 72500 - 73000 : [ 1 0.00 1.00 ] #... | 78000 - 78500 : [ 1 0.00 1.00 ] #... | 89500 - 90000 : [ 1 0.00 1.00 ] #... | 101500 - 102000 : [ 1 0.00 1.00 ] #... | 118000 - 118500 : [ 1 0.00 1.00 ] #... | 137500 - 138000 : [ 1 0.00 1.00 ] #... | 169000 - 169500 : [ 1 0.00 1.00 ] #... | 194500 - 195000 : [ 1 0.00 1.00 ] #... | 213500 - 214000 : [ 1 0.00 1.00 ] #... | 216500 - 217000 : [ 1 0.00 1.00 ] #... | 245000 - 245500 : [ 1 0.00 1.00 ] #... | 250500 - 251000 : [ 1 0.00 1.00 ] #... | 254500 - 255000 : [ 1 0.00 1.00 ] #... | 259000 - 259500 : [ 1 0.00 1.00 ] #... | 280000 - 280500 : [ 1 0.00 1.00 ] #... | 325000 - 325500 : [ 1 0.00 1.00 ] #... | 342000 - 342500 : [ 1 0.00 1.00 ] #... | 348500 - 349000 : [ 1 0.00 1.00 ] #... | 352000 - 352500 : [ 1 0.00 1.00 ] #... | 382000 - 382500 : [ 1 0.00 1.00 ] #... | 410000 - 410500 : [ 1 0.00 1.00 ] #... | 458500 - 459000 : [ 1 0.00 1.00 ] #... | 491500 - 492000 : [ 1 0.00 1.00 ] #... | 525500 - 526000 : [ 1 0.00 1.00 ] #... | 567000 - 567500 : [ 1 0.00 1.00 ] #... | 569500 - 570000 : [ 1 0.00 1.00 ] #... | 570500 - 571000 : [ 1 0.00 1.00 ] | 571000 - 571500 : [ 1 0.00 1.00 ] | 571500 - 572000 : [ 3 0.00 1.00 ] | 572000 - 572500 : [ 1 0.00 1.00 ] | 572500 - 573000 : [ 1 0.00 1.00 ] | 573000 - 573500 : [ 1 0.00 1.00 ] #... | 574000 - 574500 : [ 1 0.00 1.00 ] | 574500 - 575000 : [ 1 0.00 1.00 ] #... | 599000 - 599500 : [ 1 0.00 1.00 ] #... | 636000 - 636500 : [ 1 0.00 1.00 ] #... | 666000 - 666500 : [ 1 0.00 1.00 ] #... | 690500 - 691000 : [ 1 0.00 1.00 ] #... | 746000 - 746500 : [ 1 0.00 1.00 ] #... | 844000 - 844500 : [ 1 0.00 1.00 ] #... | 911000 - 911500 : [ 1 0.00 1.00 ] #... | 914000 - 914500 : [ 1 0.00 1.00 ] #... | 969000 - 969500 : [ 1 0.00 1.00 ] #... | 1015500 - 1016000 : [ 1 0.00 1.00 ] #... | 1106500 - 1107000 : [ 1 0.00 1.00 ] #... | 1206500 - 1207000 : [ 1 0.00 1.00 ] #... | 1231500 - 1232000 : [ 1 0.00 1.00 ] #... | 1251000 - 1251500 : [ 1 0.00 1.00 ] #... | 1472500 - 1473000 : [ 1 0.00 1.00 ] #... | 1500500 - 1501000 : [ 1 0.00 1.00 ] #... | 1762000 - 1762500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep TAG reads.list > grep.reads.list.TAG Command: /home/copeland/scripts/histogram2.pl grep.reads.list.TAG 4 500 #Found 4021 total values totalling 158559133.0000. <39432.761253 +/- 13745.100613> #Range: [ - 603317 ] #Most likely bin: [ 37500 - 38000 ] 270 counts #Median bin: [ 38500 - 39000 ] 238 counts | 0 - 500 : [ 1 0.00 0.00 ] #... | 15500 - 16000 : [ 1 0.00 0.00 ] #... | 17500 - 18000 : [ 1 0.00 0.00 ] #... | 19500 - 20000 : [ 1 0.00 0.00 ] #... | 20500 - 21000 : [ 1 0.00 0.00 ] #... | 26000 - 26500 : [ 1 0.00 0.00 ] #... | 27000 - 27500 : [ 1 0.00 0.00 ] | 27500 - 28000 : [ 1 0.00 0.00 ] #... | 29000 - 29500 : [ 1 0.00 0.00 ] | 29500 - 30000 : [ 2 0.00 0.00 ] |X 30000 - 30500 : [ 5 0.00 0.00 ] | 30500 - 31000 : [ 3 0.00 0.00 ] |X 31000 - 31500 : [ 6 0.00 0.01 ] |XX 31500 - 32000 : [ 12 0.00 0.01 ] |XXX 32000 - 32500 : [ 18 0.00 0.01 ] |XX 32500 - 33000 : [ 16 0.00 0.02 ] |XXXXXXX 33000 - 33500 : [ 46 0.01 0.03 ] |XXXXXXXXXX 33500 - 34000 : [ 70 0.02 0.05 ] |XXXXXXXXXXXXX 34000 - 34500 : [ 91 0.02 0.07 ] |XXXXXXXXXXXXXXXXX 34500 - 35000 : [ 114 0.03 0.10 ] |XXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 142 0.04 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 177 0.04 0.18 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 178 0.04 0.22 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 217 0.05 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 225 0.06 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 270 0.07 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 254 0.06 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 238 0.06 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 227 0.06 0.58 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 192 0.05 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 204 0.05 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 198 0.05 0.72 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 197 0.05 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 177 0.04 0.82 ] |XXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 159 0.04 0.86 ] |XXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 158 0.04 0.90 ] |XXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 129 0.03 0.93 ] |XXXXXXXXXXXXXX 43500 - 44000 : [ 95 0.02 0.95 ] |XXXXXXXXXXX 44000 - 44500 : [ 77 0.02 0.97 ] |XXXXXX 44500 - 45000 : [ 41 0.01 0.98 ] |XXXX 45000 - 45500 : [ 29 0.01 0.99 ] |XXX 45500 - 46000 : [ 19 0.00 0.99 ] |X 46000 - 46500 : [ 5 0.00 0.99 ] |X 46500 - 47000 : [ 4 0.00 1.00 ] #... | 87000 - 87500 : [ 1 0.00 1.00 ] #... | 89500 - 90000 : [ 1 0.00 1.00 ] #... | 92000 - 92500 : [ 2 0.00 1.00 ] | 92500 - 93000 : [ 1 0.00 1.00 ] |X 93000 - 93500 : [ 4 0.00 1.00 ] | 93500 - 94000 : [ 1 0.00 1.00 ] #... | 96000 - 96500 : [ 1 0.00 1.00 ] | 96500 - 97000 : [ 1 0.00 1.00 ] | 97000 - 97500 : [ 1 0.00 1.00 ] #... | 98000 - 98500 : [ 1 0.00 1.00 ] #... | 263500 - 264000 : [ 1 0.00 1.00 ] #... | 595500 - 596000 : [ 1 0.00 1.00 ] #... | 603000 - 603500 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # TAG 38841 +- 3023 (n=2006) # WTB 7820 +- 2301 (n=14736) # KPT 3224 +- 997 (n=26855) # TDE 3696 +- 1003 (n=13373) ################################################################### 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 570.954549 bp, 270070 reads, genome size 9215399 bp Command: idealAssembly 9215399 270070 570.954549 ------------------------------------------------------------------- Genome = 9215399 bases Nreads = 270070 readLength = 570.954549 Depth = 16.73 N_contigs = N_gaps = 0 mean gap size = 33 bases mean contig size = 18487621 reads (~ 630839413 bases) %cover = 100.00 %singlet = 0.00 assembly size = 9215399 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 0 contigs containing at least 31022227 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. ################################################################### Bad M1 Contigs------------------------------------------------------------------- ################################################################### Bad M2 Contigs ------------------------------------------------------------------- ################################################################### Ran Plates2contigs: Output Location: Ran in.dir: Output Location: Viewed Contigs with Phrapview: ################################################################### Conclusions: