################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 2351472 Genus_species: Clostridium thermocellum Taxid: 1515 Genome size: 5000 Libraries: LCL, PKV, AKBA, XUC, TQX, LAQ, WSV, LAO, KPP, AONA, KXP ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 2351472 ------------------------------------------------------------------- ID=2351472 Lineage for 'Clostridium thermocellum': Clostridium thermocellum species Clostridium genus Clostridiaceae family Clostridiales order Clostridia class Firmicutes phylum Bacteria superkingdom cellular organisms no rank root no rank ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 3843457 # phrap: 3712730 # db: 5000000 4185395 +/- 578479 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s PKV 641 323 91.73 556.54 318 89.22 522.09 LCL 0 0 0.00 0.00 0 0.00 0.00 XUC 60 28 56.99 247.00 32 33.56 125.97 TQX 13 5 74.58 507.00 8 86.33 639.88 AKBA 8 4 84.89 575.00 4 94.53 660.50 WSV 62 31 89.63 531.55 31 92.79 583.32 LAQ 0 0 0.00 0.00 0 0.00 0.00 LAO 0 0 0.00 0.00 0 0.00 0.00 KPP 0 0 0.00 0.00 0 0.00 0.00 KXP 0 0 0.00 0.00 0 0.00 0.00 AONA 0 0 0.00 0.00 0 0.00 0.00 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 2351472_fasta.screen -new_ace -view -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 2351472_fasta.screen.contigs /sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out /home/copeland/scripts/asseminfo phrap.out > asseminfo.2351472.out ################################################################### Library vector screening AKBA.000001.000100 screen.out.1 2351472_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 2351472_fasta.screen /usr/local/sequences/LRS.fasta KPP.000001.000100 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta KXP.000001.000100 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta LAO.000001.000100 screen.out 2351472_fasta /sequences/microbe_vector.seq PKV.000001.000100 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta PKV.000101.000200 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta PKV.000201.000300 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta PKV.000301.000400 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta PKV.000401.000500 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta TQX.000001.000100 screen.out 2351472_fasta /sequences/microbe_vector.seq WSV.000001.000100 screen.out 2351472_fasta /sequences/microbe_vector.seq WSV.000101.000200 screen.out 2351472_fasta /sequences/microbe_vector.seq XUC.000001.000100 screen.out.1 2351472_fasta.screen /tmp/pFOS1.fa.4 screen.out.std 2351472_fasta.screen /sequences/LRS.fasta AKBA.000001.000100 screen.out.1 2351472_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 2351472_fasta.screen /usr/local/sequences/LRS.fasta KPP.000001.000100 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta KXP.000001.000100 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta LAO.000001.000100 screen.out 2351472_fasta /sequences/microbe_vector.seq PKV.000001.000100 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta PKV.000101.000200 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta PKV.000201.000300 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta PKV.000301.000400 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta PKV.000401.000500 screen.out 2351472_fasta.screen /sequences/pUC.fasta screen.out.std 2351472_fasta.screen /sequences/LRS.fasta TQX.000001.000100 screen.out 2351472_fasta /sequences/microbe_vector.seq WSV.000001.000100 screen.out 2351472_fasta /sequences/microbe_vector.seq WSV.000101.000200 screen.out 2351472_fasta /sequences/microbe_vector.seq XUC.000001.000100 screen.out.1 2351472_fasta.screen /tmp/pFOS1.fa.4 screen.out.std 2351472_fasta.screen /sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 2351472_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 101246 total values totalling 51835303.0000. <511.973836 +/- 175.567032> #Range: [ 22 - 938 ] #Most likely bin: [ 600 - 650 ] 19821 counts #Median bin: [ 550 - 600 ] 13701 counts |X 0 - 50 : [ 601 0.01 0.01 ] |XXXXX 50 - 100 : [ 2362 0.02 0.03 ] |XXXXXX 100 - 150 : [ 2878 0.03 0.06 ] |XXXXXX 150 - 200 : [ 3094 0.03 0.09 ] |XXXXXX 200 - 250 : [ 3058 0.03 0.12 ] |XXXXXXX 250 - 300 : [ 3319 0.03 0.15 ] |XXXXXXXX 300 - 350 : [ 3765 0.04 0.19 ] |XXXXXXXXX 350 - 400 : [ 4586 0.05 0.23 ] |XXXXXXXXXXX 400 - 450 : [ 5456 0.05 0.29 ] |XXXXXXXXXXXXXX 450 - 500 : [ 6852 0.07 0.36 ] |XXXXXXXXXXXXXXXXXXX 500 - 550 : [ 9274 0.09 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 13701 0.14 0.58 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 19821 0.20 0.78 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 16738 0.17 0.94 ] |XXXXXXXXX 700 - 750 : [ 4654 0.05 0.99 ] |X 750 - 800 : [ 680 0.01 1.00 ] | 800 - 850 : [ 191 0.00 1.00 ] | 850 - 900 : [ 185 0.00 1.00 ] | 900 - 950 : [ 31 0.00 1.00 ] JAZZ trim 15 readlength histogram for LAO Command: /usr/xpg4/bin/grep LAO 2351472_fasta.screen.screen.ids > reads.trim15.LAO.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.LAO.rl 2 50 #Found 743 total values totalling 375231.0000. <505.021534 +/- 187.339802> #Range: [ 26 - 728 ] #Most likely bin: [ 600 - 650 ] 176 counts #Median bin: [ 550 - 600 ] 129 counts |X 0 - 50 : [ 5 0.01 0.01 ] |XXXXX 50 - 100 : [ 24 0.03 0.04 ] |XXXXXXXXX 100 - 150 : [ 39 0.05 0.09 ] |XXXXXXX 150 - 200 : [ 31 0.04 0.13 ] |XXXXX 200 - 250 : [ 24 0.03 0.17 ] |XXX 250 - 300 : [ 15 0.02 0.19 ] |XXXXX 300 - 350 : [ 22 0.03 0.22 ] |XXXX 350 - 400 : [ 17 0.02 0.24 ] |XXXXXX 400 - 450 : [ 26 0.03 0.27 ] |XXXXXX 450 - 500 : [ 27 0.04 0.31 ] |XXXXXXXXXXXXXX 500 - 550 : [ 60 0.08 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 129 0.17 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 176 0.24 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 135 0.18 0.98 ] |XXX 700 - 750 : [ 13 0.02 1.00 ] JAZZ trim 15 readlength histogram for KPP Command: /usr/xpg4/bin/grep KPP 2351472_fasta.screen.screen.ids > reads.trim15.KPP.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.KPP.rl 2 50 #Found 1512 total values totalling 724198.0000. <478.966931 +/- 214.496782> #Range: [ 24 - 785 ] #Most likely bin: [ 650 - 700 ] 247 counts #Median bin: [ 550 - 600 ] 124 counts |XX 0 - 50 : [ 10 0.01 0.01 ] |XXXXXXXXX 50 - 100 : [ 58 0.04 0.04 ] |XXXXXXXXXXXX 100 - 150 : [ 73 0.05 0.09 ] |XXXXXXXXXXXXXXXXXXX 150 - 200 : [ 120 0.08 0.17 ] |XXXXXXXXXXXX 200 - 250 : [ 73 0.05 0.22 ] |XXXXXXXXXXX 250 - 300 : [ 68 0.04 0.27 ] |XXXXXXXXXXX 300 - 350 : [ 65 0.04 0.31 ] |XXXXXXXXXXXX 350 - 400 : [ 75 0.05 0.36 ] |XXXXXXXXX 400 - 450 : [ 55 0.04 0.39 ] |XXXXXXXXXXX 450 - 500 : [ 71 0.05 0.44 ] |XXXXXXXXXXXX 500 - 550 : [ 76 0.05 0.49 ] |XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 124 0.08 0.57 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 185 0.12 0.70 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 247 0.16 0.86 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 184 0.12 0.98 ] |XXXXX 750 - 800 : [ 28 0.02 1.00 ] JAZZ trim 15 readlength histogram for KXP Command: /usr/xpg4/bin/grep KXP 2351472_fasta.screen.screen.ids > reads.trim15.KXP.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.KXP.rl 2 50 #Found 413 total values totalling 93271.0000. <225.837772 +/- 144.482865> #Range: [ 35 - 750 ] #Most likely bin: [ 150 - 200 ] 235 counts #Median bin: [ 150 - 200 ] 235 counts |X 0 - 50 : [ 3 0.01 0.01 ] |XXXX 50 - 100 : [ 21 0.05 0.06 ] |XXXXXXXXXX 100 - 150 : [ 58 0.14 0.20 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 150 - 200 : [ 235 0.57 0.77 ] |XXXXXX 200 - 250 : [ 35 0.08 0.85 ] |X 250 - 300 : [ 4 0.01 0.86 ] |X 300 - 350 : [ 8 0.02 0.88 ] |X 350 - 400 : [ 8 0.02 0.90 ] |X 400 - 450 : [ 6 0.01 0.92 ] | 450 - 500 : [ 1 0.00 0.92 ] |X 500 - 550 : [ 4 0.01 0.93 ] |X 550 - 600 : [ 3 0.01 0.93 ] | 600 - 650 : [ 2 0.00 0.94 ] |XX 650 - 700 : [ 12 0.03 0.97 ] |XX 700 - 750 : [ 12 0.03 1.00 ] | 750 - 800 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for TQX Command: /usr/xpg4/bin/grep TQX 2351472_fasta.screen.screen.ids > reads.trim15.TQX.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.TQX.rl 2 50 #Found 1010 total values totalling 735073.0000. <727.795050 +/- 145.926146> #Range: [ 37 - 938 ] #Most likely bin: [ 700 - 750 ] 442 counts #Median bin: [ 700 - 750 ] 442 counts | 0 - 50 : [ 4 0.00 0.00 ] |X 50 - 100 : [ 8 0.01 0.01 ] | 100 - 150 : [ 5 0.00 0.02 ] |X 150 - 200 : [ 10 0.01 0.03 ] |X 200 - 250 : [ 6 0.01 0.03 ] |X 250 - 300 : [ 6 0.01 0.04 ] | 300 - 350 : [ 3 0.00 0.04 ] |X 350 - 400 : [ 9 0.01 0.05 ] | 400 - 450 : [ 2 0.00 0.05 ] |X 450 - 500 : [ 6 0.01 0.06 ] | 500 - 550 : [ 5 0.00 0.06 ] |X 550 - 600 : [ 7 0.01 0.07 ] |XX 600 - 650 : [ 21 0.02 0.09 ] |XXXXXXXXXXXX 650 - 700 : [ 129 0.13 0.22 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 442 0.44 0.66 ] |XXXXXXXXX 750 - 800 : [ 94 0.09 0.75 ] |XXXXX 800 - 850 : [ 59 0.06 0.81 ] |XXXXXXXXXXXXXXX 850 - 900 : [ 164 0.16 0.97 ] |XXX 900 - 950 : [ 30 0.03 1.00 ] JAZZ trim 15 readlength histogram for WSV Command: /usr/xpg4/bin/grep WSV 2351472_fasta.screen.screen.ids > reads.trim15.WSV.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.WSV.rl 2 50 #Found 20874 total values totalling 11073005.0000. <530.468765 +/- 173.057209> #Range: [ 23 - 841 ] #Most likely bin: [ 650 - 700 ] 3845 counts #Median bin: [ 550 - 600 ] 2623 counts |X 0 - 50 : [ 80 0.00 0.00 ] |XXXX 50 - 100 : [ 405 0.02 0.02 ] |XXXXX 100 - 150 : [ 464 0.02 0.05 ] |XXXXXX 150 - 200 : [ 537 0.03 0.07 ] |XXXXXX 200 - 250 : [ 558 0.03 0.10 ] |XXXXXXX 250 - 300 : [ 678 0.03 0.13 ] |XXXXXXXX 300 - 350 : [ 760 0.04 0.17 ] |XXXXXXXXX 350 - 400 : [ 905 0.04 0.21 ] |XXXXXXXXXXXX 400 - 450 : [ 1151 0.06 0.27 ] |XXXXXXXXXXXXXX 450 - 500 : [ 1355 0.06 0.33 ] |XXXXXXXXXXXXXXXXXXX 500 - 550 : [ 1788 0.09 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 2623 0.13 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3477 0.17 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3845 0.18 0.89 ] |XXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1795 0.09 0.98 ] |XXXX 750 - 800 : [ 388 0.02 1.00 ] |X 800 - 850 : [ 65 0.00 1.00 ] JAZZ trim 15 readlength histogram for LAQ JAZZ trim 15 readlength histogram for PKV Command: /usr/xpg4/bin/grep PKV 2351472_fasta.screen.screen.ids > reads.trim15.PKV.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.PKV.rl 2 50 #Found 72871 total values totalling 37202184.0000. <510.521113 +/- 168.711586> #Range: [ 22 - 783 ] #Most likely bin: [ 600 - 650 ] 15685 counts #Median bin: [ 550 - 600 ] 10469 counts |X 0 - 50 : [ 335 0.00 0.00 ] |XXXX 50 - 100 : [ 1677 0.02 0.03 ] |XXXXX 100 - 150 : [ 2039 0.03 0.06 ] |XXXXX 150 - 200 : [ 1969 0.03 0.08 ] |XXXXX 200 - 250 : [ 2141 0.03 0.11 ] |XXXXXX 250 - 300 : [ 2329 0.03 0.14 ] |XXXXXXX 300 - 350 : [ 2715 0.04 0.18 ] |XXXXXXXX 350 - 400 : [ 3295 0.05 0.23 ] |XXXXXXXXXX 400 - 450 : [ 3923 0.05 0.28 ] |XXXXXXXXXXXXX 450 - 500 : [ 5099 0.07 0.35 ] |XXXXXXXXXXXXXXXXXX 500 - 550 : [ 7001 0.10 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 10469 0.14 0.59 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 15685 0.22 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 12126 0.17 0.97 ] |XXXXX 700 - 750 : [ 2036 0.03 1.00 ] | 750 - 800 : [ 32 0.00 1.00 ] JAZZ trim 15 readlength histogram for LCL JAZZ trim 15 readlength histogram for XUC Command: /usr/xpg4/bin/grep XUC 2351472_fasta.screen.screen.ids > reads.trim15.XUC.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.XUC.rl 2 50 #Found 3823 total values totalling 1632341.0000. <426.979074 +/- 215.922784> #Range: [ 22 - 929 ] #Most likely bin: [ 550 - 600 ] 346 counts #Median bin: [ 400 - 450 ] 293 counts |XXXXXXXXXXXXXXXXXXX 0 - 50 : [ 164 0.04 0.04 ] |XXXXXXXXXXXXXXXXXXXX 50 - 100 : [ 169 0.04 0.09 ] |XXXXXXXXXXXXXXXXXXXXXXX 100 - 150 : [ 200 0.05 0.14 ] |XXXXXXXXXXXXXXXXXXXXXX 150 - 200 : [ 192 0.05 0.19 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 200 - 250 : [ 221 0.06 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 219 0.06 0.30 ] |XXXXXXXXXXXXXXXXXXXXXX 300 - 350 : [ 192 0.05 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 350 - 400 : [ 277 0.07 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 400 - 450 : [ 293 0.08 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 450 - 500 : [ 293 0.08 0.58 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 340 0.09 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 346 0.09 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 275 0.07 0.83 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 244 0.06 0.90 ] |XXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 172 0.04 0.94 ] |XXXXXXXXXXXXXXXX 750 - 800 : [ 137 0.04 0.98 ] |XXXXXXXX 800 - 850 : [ 67 0.02 0.99 ] |XX 850 - 900 : [ 21 0.01 1.00 ] | 900 - 950 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for AKBA JAZZ trim 15 readlength histogram for AONA ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.2351472_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.2351472_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 100672 total values totalling 39241.7325. <0.389798 +/- 0.058397> #Range: [ 0.0466 - 1 ] #Most likely bin: [ 0.4 - 0.405 ] 3862 counts #Median bin: [ 0.39 - 0.395 ] 3570 counts | 0.045 - 0.05 : [ 1 0.00 0.00 ] #... | 0.08 - 0.085 : [ 1 0.00 0.00 ] | 0.085 - 0.09 : [ 1 0.00 0.00 ] #... | 0.095 - 0.1 : [ 1 0.00 0.00 ] | 0.1 - 0.105 : [ 2 0.00 0.00 ] #... | 0.115 - 0.12 : [ 1 0.00 0.00 ] #... | 0.125 - 0.13 : [ 2 0.00 0.00 ] | 0.13 - 0.135 : [ 2 0.00 0.00 ] | 0.135 - 0.14 : [ 1 0.00 0.00 ] | 0.14 - 0.145 : [ 4 0.00 0.00 ] | 0.145 - 0.15 : [ 3 0.00 0.00 ] | 0.15 - 0.155 : [ 5 0.00 0.00 ] | 0.155 - 0.16 : [ 4 0.00 0.00 ] | 0.16 - 0.165 : [ 8 0.00 0.00 ] | 0.165 - 0.17 : [ 6 0.00 0.00 ] | 0.17 - 0.175 : [ 12 0.00 0.00 ] | 0.175 - 0.18 : [ 11 0.00 0.00 ] | 0.18 - 0.185 : [ 15 0.00 0.00 ] | 0.185 - 0.19 : [ 14 0.00 0.00 ] | 0.19 - 0.195 : [ 23 0.00 0.00 ] | 0.195 - 0.2 : [ 18 0.00 0.00 ] | 0.2 - 0.205 : [ 24 0.00 0.00 ] | 0.205 - 0.21 : [ 35 0.00 0.00 ] | 0.21 - 0.215 : [ 44 0.00 0.00 ] |X 0.215 - 0.22 : [ 53 0.00 0.00 ] |X 0.22 - 0.225 : [ 68 0.00 0.00 ] |X 0.225 - 0.23 : [ 83 0.00 0.00 ] |X 0.23 - 0.235 : [ 100 0.00 0.01 ] |X 0.235 - 0.24 : [ 124 0.00 0.01 ] |XX 0.24 - 0.245 : [ 185 0.00 0.01 ] |XX 0.245 - 0.25 : [ 146 0.00 0.01 ] |XX 0.25 - 0.255 : [ 228 0.00 0.01 ] |XXX 0.255 - 0.26 : [ 245 0.00 0.01 ] |XXX 0.26 - 0.265 : [ 316 0.00 0.02 ] |XXXX 0.265 - 0.27 : [ 368 0.00 0.02 ] |XXXX 0.27 - 0.275 : [ 405 0.00 0.03 ] |XXXXX 0.275 - 0.28 : [ 505 0.01 0.03 ] |XXXXXX 0.28 - 0.285 : [ 622 0.01 0.04 ] |XXXXXXXX 0.285 - 0.29 : [ 732 0.01 0.04 ] |XXXXXXXXX 0.29 - 0.295 : [ 828 0.01 0.05 ] |XXXXXXXXX 0.295 - 0.3 : [ 903 0.01 0.06 ] |XXXXXXXXXXX 0.3 - 0.305 : [ 1049 0.01 0.07 ] |XXXXXXXXXXXX 0.305 - 0.31 : [ 1161 0.01 0.08 ] |XXXXXXXXXXXXXX 0.31 - 0.315 : [ 1341 0.01 0.10 ] |XXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 1595 0.02 0.11 ] |XXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 1611 0.02 0.13 ] |XXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 1892 0.02 0.15 ] |XXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 2165 0.02 0.17 ] |XXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 2185 0.02 0.19 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 2328 0.02 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 2526 0.03 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 2784 0.03 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 2817 0.03 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 3050 0.03 0.32 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 3191 0.03 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 3140 0.03 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 3325 0.03 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 3362 0.03 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 3502 0.03 0.49 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 3570 0.04 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 3520 0.03 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 3862 0.04 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 3525 0.04 0.63 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 3581 0.04 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 3531 0.04 0.70 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 3377 0.03 0.74 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 3068 0.03 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 2890 0.03 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 2673 0.03 0.82 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 2422 0.02 0.85 ] |XXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 2100 0.02 0.87 ] |XXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 1938 0.02 0.89 ] |XXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 1707 0.02 0.90 ] |XXXXXXXXXXXXXXX 0.46 - 0.465 : [ 1495 0.01 0.92 ] |XXXXXXXXXXXXX 0.465 - 0.47 : [ 1286 0.01 0.93 ] |XXXXXXXXXXX 0.47 - 0.475 : [ 1051 0.01 0.94 ] |XXXXXXXXX 0.475 - 0.48 : [ 899 0.01 0.95 ] |XXXXXXXX 0.48 - 0.485 : [ 781 0.01 0.96 ] |XXXXXX 0.485 - 0.49 : [ 603 0.01 0.96 ] |XXXXX 0.49 - 0.495 : [ 506 0.01 0.97 ] |XXX 0.495 - 0.5 : [ 285 0.00 0.97 ] |XXXXX 0.5 - 0.505 : [ 520 0.01 0.98 ] |XXX 0.505 - 0.51 : [ 268 0.00 0.98 ] |XX 0.51 - 0.515 : [ 229 0.00 0.98 ] |XX 0.515 - 0.52 : [ 191 0.00 0.98 ] |XX 0.52 - 0.525 : [ 159 0.00 0.99 ] |X 0.525 - 0.53 : [ 127 0.00 0.99 ] |X 0.53 - 0.535 : [ 131 0.00 0.99 ] |X 0.535 - 0.54 : [ 131 0.00 0.99 ] |X 0.54 - 0.545 : [ 117 0.00 0.99 ] |X 0.545 - 0.55 : [ 106 0.00 0.99 ] |X 0.55 - 0.555 : [ 86 0.00 0.99 ] |XX 0.555 - 0.56 : [ 240 0.00 0.99 ] |X 0.56 - 0.565 : [ 117 0.00 1.00 ] |X 0.565 - 0.57 : [ 75 0.00 1.00 ] |X 0.57 - 0.575 : [ 55 0.00 1.00 ] | 0.575 - 0.58 : [ 36 0.00 1.00 ] | 0.58 - 0.585 : [ 18 0.00 1.00 ] | 0.585 - 0.59 : [ 29 0.00 1.00 ] | 0.59 - 0.595 : [ 18 0.00 1.00 ] | 0.595 - 0.6 : [ 6 0.00 1.00 ] | 0.6 - 0.605 : [ 22 0.00 1.00 ] | 0.605 - 0.61 : [ 13 0.00 1.00 ] | 0.61 - 0.615 : [ 11 0.00 1.00 ] | 0.615 - 0.62 : [ 10 0.00 1.00 ] | 0.62 - 0.625 : [ 3 0.00 1.00 ] | 0.625 - 0.63 : [ 13 0.00 1.00 ] | 0.63 - 0.635 : [ 5 0.00 1.00 ] | 0.635 - 0.64 : [ 11 0.00 1.00 ] | 0.64 - 0.645 : [ 5 0.00 1.00 ] | 0.645 - 0.65 : [ 9 0.00 1.00 ] | 0.65 - 0.655 : [ 7 0.00 1.00 ] | 0.655 - 0.66 : [ 10 0.00 1.00 ] | 0.66 - 0.665 : [ 4 0.00 1.00 ] | 0.665 - 0.67 : [ 6 0.00 1.00 ] | 0.67 - 0.675 : [ 2 0.00 1.00 ] | 0.675 - 0.68 : [ 4 0.00 1.00 ] | 0.68 - 0.685 : [ 3 0.00 1.00 ] | 0.685 - 0.69 : [ 3 0.00 1.00 ] | 0.69 - 0.695 : [ 7 0.00 1.00 ] #... | 0.7 - 0.705 : [ 4 0.00 1.00 ] | 0.705 - 0.71 : [ 2 0.00 1.00 ] | 0.71 - 0.715 : [ 2 0.00 1.00 ] #... | 0.72 - 0.725 : [ 1 0.00 1.00 ] #... | 0.73 - 0.735 : [ 4 0.00 1.00 ] #... | 0.74 - 0.745 : [ 1 0.00 1.00 ] #... | 0.75 - 0.755 : [ 2 0.00 1.00 ] #... | 0.76 - 0.765 : [ 1 0.00 1.00 ] #... | 0.79 - 0.795 : [ 1 0.00 1.00 ] #... | 1 - 1.005 : [ 4 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones LIBRARY @ ] 101327 55632 86.92 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 = 38 HQ Discrepant reads = 263 Chimeric reads = 892 Suspect alignments = 20255 ################################################################### C O N T I G I N F O R M A T I O N Wed Sep 8 02:07:21 2004 File: /psf/project/microbe1/2351472/edit_dir.14Nov03.QD/phrap.out Contig 230. 1109 reads; 42782 bp (untrimmed), 42742 (trimmed). Contig 231. 1125 reads; 46016 bp (untrimmed), 45913 (trimmed). Contig 232. 1134 reads; 40096 bp (untrimmed), 39842 (trimmed). Contig 233. 1153 reads; 42726 bp (untrimmed), 42680 (trimmed). Contig 234. 1283 reads; 47946 bp (untrimmed), 47946 (trimmed). Contig 235. 1469 reads; 55498 bp (untrimmed), 55266 (trimmed). Contig 236. 1636 reads; 59216 bp (untrimmed), 59185 (trimmed). Contig 237. 1642 reads; 53992 bp (untrimmed), 53869 (trimmed). Contig 238. 1707 reads; 66430 bp (untrimmed), 66234 (trimmed). Contig 239. 1707 reads; 59265 bp (untrimmed), 58978 (trimmed). Contig 240. 1764 reads; 64163 bp (untrimmed), 63854 (trimmed). Contig 241. 1767 reads; 65148 bp (untrimmed), 64941 (trimmed). Contig 242. 1819 reads; 58713 bp (untrimmed), 58659 (trimmed). Contig 243. 1948 reads; 59407 bp (untrimmed), 59122 (trimmed). Contig 244. 2064 reads; 73272 bp (untrimmed), 72551 (trimmed). Contig 245. 2096 reads; 85406 bp (untrimmed), 84798 (trimmed). Contig 246. 2107 reads; 52159 bp (untrimmed), 52062 (trimmed). Contig 247. 2221 reads; 78494 bp (untrimmed), 78463 (trimmed). Contig 248. 2308 reads; 81353 bp (untrimmed), 81312 (trimmed). Contig 249. 2462 reads; 89699 bp (untrimmed), 89359 (trimmed). Contig 250. 2482 reads; 98490 bp (untrimmed), 98029 (trimmed). Contig 251. 3213 reads; 106925 bp (untrimmed), 106909 (trimmed). Contig 252. 3340 reads; 119171 bp (untrimmed), 118945 (trimmed). Contig 253. 4496 reads; 152763 bp (untrimmed), 152743 (trimmed). Contig 254. 4581 reads; 127823 bp (untrimmed), 127390 (trimmed). Contig 255. 5122 reads; 160635 bp (untrimmed), 160635 (trimmed). Contig 256. 8951 reads; 316981 bp (untrimmed), 316950 (trimmed). -------------------------------------------------------------- Totals 100864 reads; 3894953 bp (untrimmed), 3843457 (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 130 total values totalling 3737586.0000. <28750.661538 +/- 39629.515100> #Range: [ 2023 - 316950 ] #Most likely bin: [ 2000 - 4000 ] 24 counts #Median bin: [ 14000 - 16000 ] 4 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 24 0.18 0.18 ] |XXXXXXXXXXXXXXXXXXXX 4000 - 6000 : [ 12 0.09 0.28 ] |XXXXXXXXXXXX 6000 - 8000 : [ 7 0.05 0.33 ] |XXXXXXXX 8000 - 10000 : [ 5 0.04 0.37 ] |XXXXXXX 10000 - 12000 : [ 4 0.03 0.40 ] |XXXXXXXXXXXXXXX 12000 - 14000 : [ 9 0.07 0.47 ] |XXXXXXX 14000 - 16000 : [ 4 0.03 0.50 ] |XXXXXXXX 16000 - 18000 : [ 5 0.04 0.54 ] |XXX 18000 - 20000 : [ 2 0.02 0.55 ] |XXXXXXXXXXXXX 20000 - 22000 : [ 8 0.06 0.62 ] |XXXXX 22000 - 24000 : [ 3 0.02 0.64 ] |XXXXXXX 24000 - 26000 : [ 4 0.03 0.67 ] |XXXXXXX 26000 - 28000 : [ 4 0.03 0.70 ] |XXXXX 28000 - 30000 : [ 3 0.02 0.72 ] |XX 30000 - 32000 : [ 1 0.01 0.73 ] |XX 32000 - 34000 : [ 1 0.01 0.74 ] |XX 34000 - 36000 : [ 1 0.01 0.75 ] |XXX 36000 - 38000 : [ 2 0.02 0.76 ] |XXXXXXX 38000 - 40000 : [ 4 0.03 0.79 ] #... |XXX 42000 - 44000 : [ 2 0.02 0.81 ] |XX 44000 - 46000 : [ 1 0.01 0.82 ] |XX 46000 - 48000 : [ 1 0.01 0.82 ] #... |XX 50000 - 52000 : [ 1 0.01 0.83 ] |XXX 52000 - 54000 : [ 2 0.02 0.85 ] |XX 54000 - 56000 : [ 1 0.01 0.85 ] #... |XXXXXXX 58000 - 60000 : [ 4 0.03 0.88 ] #... |XX 62000 - 64000 : [ 1 0.01 0.89 ] |XX 64000 - 66000 : [ 1 0.01 0.90 ] |XX 66000 - 68000 : [ 1 0.01 0.91 ] #... |XX 72000 - 74000 : [ 1 0.01 0.92 ] #... |XX 78000 - 80000 : [ 1 0.01 0.92 ] |XX 80000 - 82000 : [ 1 0.01 0.93 ] #... |XX 84000 - 86000 : [ 1 0.01 0.94 ] #... |XX 88000 - 90000 : [ 1 0.01 0.95 ] #... |XX 98000 - 100000 : [ 1 0.01 0.95 ] #... |XX 106000 - 108000 : [ 1 0.01 0.96 ] #... |XX 118000 - 120000 : [ 1 0.01 0.97 ] #... |XX 126000 - 128000 : [ 1 0.01 0.98 ] #... |XX 152000 - 154000 : [ 1 0.01 0.98 ] #... |XX 160000 - 162000 : [ 1 0.01 0.99 ] #... |XX 316000 - 318000 : [ 1 0.01 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 28505021 C = 19506526 G = 19210228 T = 27129157 N = 278867 X = 1582524 GC fraction = 0.40 Total = 96212323 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 2351472_fasta.screen.contigs A 1164488 C 791208 G 735246 N 288 T 1203257 X 466 fraction GC = 0.39 total bases = 3894953 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 3882610 bases = 19.65 +- 12.02 = 0.94 +- 9.42 m1 = 7.35 m2 = 13.93 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 226 total values totalling 2707.2300. <11.978894 +/- 14.265542> #Range: [ 1.07 - 139.35 ] #Most likely bin: [ 1.5 - 2 ] 25 counts #Median bin: [ 8.5 - 9 ] 2 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 18 0.08 0.08 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 25 0.11 0.19 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 21 0.09 0.28 ] |XXXXXXXXXX 2.5 - 3 : [ 6 0.03 0.31 ] |XXXXX 3 - 3.5 : [ 3 0.01 0.32 ] |XXXXXX 3.5 - 4 : [ 4 0.02 0.34 ] |XXXXXXXXXX 4 - 4.5 : [ 6 0.03 0.37 ] |XXXXXXXX 4.5 - 5 : [ 5 0.02 0.39 ] |XXX 5 - 5.5 : [ 2 0.01 0.40 ] |XXXXXX 5.5 - 6 : [ 4 0.02 0.42 ] |XXXXX 6 - 6.5 : [ 3 0.01 0.43 ] |XXXXXXXXXXX 6.5 - 7 : [ 7 0.03 0.46 ] |XX 7 - 7.5 : [ 1 0.00 0.46 ] |XXXXXXXX 7.5 - 8 : [ 5 0.02 0.49 ] |XX 8 - 8.5 : [ 1 0.00 0.49 ] |XXX 8.5 - 9 : [ 2 0.01 0.50 ] #... |XXX 9.5 - 10 : [ 2 0.01 0.51 ] |XXXXX 10 - 10.5 : [ 3 0.01 0.52 ] |XXX 10.5 - 11 : [ 2 0.01 0.53 ] |XXXXXX 11 - 11.5 : [ 4 0.02 0.55 ] |XXXXX 11.5 - 12 : [ 3 0.01 0.56 ] |XXXXX 12 - 12.5 : [ 3 0.01 0.58 ] |XXX 12.5 - 13 : [ 2 0.01 0.58 ] |XXXXXXXX 13 - 13.5 : [ 5 0.02 0.61 ] |XXXXXXXX 13.5 - 14 : [ 5 0.02 0.63 ] |XXX 14 - 14.5 : [ 2 0.01 0.64 ] |XXXXX 14.5 - 15 : [ 3 0.01 0.65 ] |XX 15 - 15.5 : [ 1 0.00 0.65 ] #... |XXXXX 16 - 16.5 : [ 3 0.01 0.67 ] |XX 16.5 - 17 : [ 1 0.00 0.67 ] |XXXXX 17 - 17.5 : [ 3 0.01 0.69 ] |XXXXXXXX 17.5 - 18 : [ 5 0.02 0.71 ] |XXX 18 - 18.5 : [ 2 0.01 0.72 ] |XXXXXXXX 18.5 - 19 : [ 5 0.02 0.74 ] |XXXXX 19 - 19.5 : [ 3 0.01 0.75 ] |XXXXXXXX 19.5 - 20 : [ 5 0.02 0.77 ] |XXXXXX 20 - 20.5 : [ 4 0.02 0.79 ] |XXXXXXXXXXXXX 20.5 - 21 : [ 8 0.04 0.83 ] |XXXXXXXXXXXXXX 21 - 21.5 : [ 9 0.04 0.87 ] |XXXXXXXX 21.5 - 22 : [ 5 0.02 0.89 ] |XXX 22 - 22.5 : [ 2 0.01 0.90 ] |XX 22.5 - 23 : [ 1 0.00 0.90 ] |XXXXXX 23 - 23.5 : [ 4 0.02 0.92 ] |XXXXX 23.5 - 24 : [ 3 0.01 0.93 ] |XXX 24 - 24.5 : [ 2 0.01 0.94 ] |XXXXX 24.5 - 25 : [ 3 0.01 0.96 ] |XX 25 - 25.5 : [ 1 0.00 0.96 ] #... |XX 26 - 26.5 : [ 1 0.00 0.96 ] |XX 26.5 - 27 : [ 1 0.00 0.97 ] |XX 27 - 27.5 : [ 1 0.00 0.97 ] #... |XX 29 - 29.5 : [ 1 0.00 0.98 ] #... |XX 30.5 - 31 : [ 1 0.00 0.98 ] #... |XX 34.5 - 35 : [ 1 0.00 0.99 ] #... |XX 35.5 - 36 : [ 1 0.00 0.99 ] #... |XX 125 - 125.5 : [ 1 0.00 1.00 ] #... |XX 139 - 139.5 : [ 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 132 total values totalling 2121.6100. <16.072803 +/- 6.736870> #Range: [ 2.42 - 34.64 ] #Most likely bin: [ 21 - 21.5 ] 8 counts #Median bin: [ 17 - 17.5 ] 3 counts |XXXXX 2 - 2.5 : [ 1 0.01 0.01 ] #... |XXXXX 3.5 - 4 : [ 1 0.01 0.02 ] |XXXXXXXXXXXXXXX 4 - 4.5 : [ 3 0.02 0.04 ] |XXXXXXXXXXXXXXX 4.5 - 5 : [ 3 0.02 0.06 ] |XXXXX 5 - 5.5 : [ 1 0.01 0.07 ] |XXXXXXXXXXXXXXX 5.5 - 6 : [ 3 0.02 0.09 ] |XXXXXXXXXX 6 - 6.5 : [ 2 0.02 0.11 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 7 0.05 0.16 ] |XXXXX 7 - 7.5 : [ 1 0.01 0.17 ] |XXXXXXXXXX 7.5 - 8 : [ 2 0.02 0.18 ] |XXXXX 8 - 8.5 : [ 1 0.01 0.19 ] |XXXXX 8.5 - 9 : [ 1 0.01 0.20 ] #... |XXXXXXXXXX 9.5 - 10 : [ 2 0.02 0.21 ] |XXXXXXXXXXXXXXX 10 - 10.5 : [ 3 0.02 0.23 ] |XXXXXXXXXX 10.5 - 11 : [ 2 0.02 0.25 ] |XXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.03 0.28 ] |XXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.02 0.30 ] |XXXXXXXXXXXXXXX 12 - 12.5 : [ 3 0.02 0.33 ] |XXXXXXXXXX 12.5 - 13 : [ 2 0.02 0.34 ] |XXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 4 0.03 0.37 ] |XXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 4 0.03 0.40 ] |XXXXXXXXXX 14 - 14.5 : [ 2 0.02 0.42 ] |XXXXXXXXXXXXXXX 14.5 - 15 : [ 3 0.02 0.44 ] |XXXXX 15 - 15.5 : [ 1 0.01 0.45 ] #... |XXXXXXXXXXXXXXX 16 - 16.5 : [ 3 0.02 0.47 ] |XXXXX 16.5 - 17 : [ 1 0.01 0.48 ] |XXXXXXXXXXXXXXX 17 - 17.5 : [ 3 0.02 0.50 ] |XXXXXXXXXXXXXXXXXXXX 17.5 - 18 : [ 4 0.03 0.53 ] |XXXXXXXXXX 18 - 18.5 : [ 2 0.02 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 18.5 - 19 : [ 5 0.04 0.58 ] |XXXXXXXXXXXXXXX 19 - 19.5 : [ 3 0.02 0.61 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 19.5 - 20 : [ 5 0.04 0.64 ] |XXXXXXXXXXXXXXXXXXXX 20 - 20.5 : [ 4 0.03 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 20.5 - 21 : [ 8 0.06 0.73 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 21 - 21.5 : [ 8 0.06 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 21.5 - 22 : [ 5 0.04 0.83 ] |XXXXXXXXXX 22 - 22.5 : [ 2 0.02 0.85 ] |XXXXX 22.5 - 23 : [ 1 0.01 0.86 ] |XXXXXXXXXXXXXXXXXXXX 23 - 23.5 : [ 4 0.03 0.89 ] |XXXXXXXXXXXXXXX 23.5 - 24 : [ 3 0.02 0.91 ] |XXXXXXXXXX 24 - 24.5 : [ 2 0.02 0.92 ] |XXXXXXXXXXXXXXX 24.5 - 25 : [ 3 0.02 0.95 ] |XXXXX 25 - 25.5 : [ 1 0.01 0.95 ] #... |XXXXX 26 - 26.5 : [ 1 0.01 0.96 ] |XXXXX 26.5 - 27 : [ 1 0.01 0.97 ] |XXXXX 27 - 27.5 : [ 1 0.01 0.98 ] #... |XXXXX 29 - 29.5 : [ 1 0.01 0.98 ] #... |XXXXX 30.5 - 31 : [ 1 0.01 0.99 ] #... |XXXXX 34.5 - 35 : [ 1 0.01 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 52 2 reads 2287 bases = 1.07 +- 0.26 = -0.01 +- 0.96 m1 = 0.06 m2 = -0.21 Contig 10 2 reads 1146 bases = 1.10 +- 0.30 = 1.10 +- 0.30 m1 = 0.08 m2 = 0.00 Contig 32 2 reads 807 bases = 1.13 +- 0.34 = 0.87 +- 0.34 m1 = 0.10 m2 = -0.00 Contig 78 4 reads 2492 bases = 1.20 +- 0.73 = 0.13 +- 1.12 m1 = 0.44 m2 = -0.18 Contig 13 2 reads 1283 bases = 1.22 +- 0.41 = 1.22 +- 0.41 m1 = 0.14 m2 = 0.00 Contig 28 2 reads 1189 bases = 1.27 +- 0.44 = 0.12 +- 0.85 m1 = 0.15 m2 = -0.13 Contig 17 2 reads 1045 bases = 1.28 +- 0.45 = -0.16 +- 0.83 m1 = 0.16 m2 = -0.12 Contig 23 2 reads 1162 bases = 1.29 +- 0.46 = 0.02 +- 0.84 m1 = 0.16 m2 = -0.12 Contig 56 2 reads 1487 bases = 1.30 +- 0.46 = 1.30 +- 0.46 m1 = 0.16 m2 = 0.00 Contig 12 2 reads 1341 bases = 1.32 +- 0.46 = 1.32 +- 0.46 m1 = 0.16 m2 = 0.00 Contig 31 2 reads 760 bases = 1.32 +- 0.47 = -0.68 +- 0.47 m1 = 0.17 m2 = -0.00 Contig 50 2 reads 1158 bases = 1.34 +- 0.47 = 1.34 +- 0.47 m1 = 0.17 m2 = 0.00 Contig 25 2 reads 1155 bases = 1.35 +- 0.48 = 1.35 +- 0.48 m1 = 0.17 m2 = 0.00 Contig 40 2 reads 661 bases = 1.38 +- 0.49 = 1.38 +- 0.49 m1 = 0.17 m2 = 0.00 Contig 39 2 reads 1019 bases = 1.40 +- 0.49 = -0.02 +- 0.77 m1 = 0.17 m2 = -0.09 Contig 15 2 reads 1303 bases = 1.41 +- 0.49 = -0.07 +- 0.76 m1 = 0.17 m2 = -0.09 Contig 20 2 reads 765 bases = 1.48 +- 0.50 = -0.52 +- 0.50 m1 = 0.17 m2 = -0.00 Contig 34 2 reads 925 bases = 1.48 +- 0.50 = 0.17 +- 0.70 m1 = 0.17 m2 = -0.06 Contig 71 3 reads 964 bases = 1.50 +- 0.81 = 1.03 +- 0.30 m1 = 0.44 m2 = 0.14 Contig 19 2 reads 882 bases = 1.51 +- 0.50 = 0.27 +- 0.64 m1 = 0.17 m2 = -0.04 Contig 172 184 reads 5996 bases = 23.38 +- 10.58 = 1.64 +- 10.88 m1 = 4.78 m2 = -1.64 Contig 221 817 reads 26306 bases = 23.49 +- 7.82 = 0.44 +- 10.61 m1 = 2.61 m2 = -12.84 Contig 242 1819 reads 58713 bases = 23.54 +- 10.29 = 1.38 +- 10.58 m1 = 4.49 m2 = -1.56 Contig 211 619 reads 19734 bases = 23.76 +- 9.02 = 3.07 +- 9.32 m1 = 3.43 m2 = -1.38 Contig 193 374 reads 11894 bases = 23.87 +- 9.89 = 5.14 +- 5.98 m1 = 4.10 m2 = 15.50 Contig 223 830 reads 26118 bases = 24.07 +- 12.27 = 0.20 +- 9.95 m1 = 6.25 m2 = 12.87 Contig 255 5122 reads 160635 bases = 24.26 +- 11.07 = -0.06 +- 10.06 m1 = 5.05 m2 = 5.32 Contig 171 183 reads 5426 bases = 24.69 +- 10.55 = 8.70 +- 6.53 m1 = 4.51 m2 = 17.17 Contig 216 744 reads 22388 bases = 24.77 +- 13.31 = 1.58 +- 11.68 m1 = 7.15 m2 = 10.16 Contig 243 1948 reads 59407 bases = 24.86 +- 10.95 = 2.38 +- 10.41 m1 = 4.83 m2 = 2.92 Contig 210 614 reads 18844 bases = 25.11 +- 9.03 = 1.12 +- 8.07 m1 = 3.25 m2 = 4.11 Contig 217 744 reads 21830 bases = 26.00 +- 8.33 = 0.14 +- 7.76 m1 = 2.67 m2 = 2.30 Contig 254 4581 reads 127823 bases = 26.94 +- 11.24 = 0.10 +- 9.58 m1 = 4.69 m2 = 8.61 Contig 219 757 reads 20948 bases = 27.34 +- 8.67 = 2.42 +- 8.44 m1 = 2.75 m2 = 0.95 Contig 200 492 reads 13212 bases = 29.01 +- 11.43 = 4.54 +- 9.22 m1 = 4.50 m2 = 11.36 Contig 246 2107 reads 52159 bases = 30.70 +- 27.14 = 0.63 +- 12.46 m1 = 23.99 m2 = 145.31 Contig 183 281 reads 6074 bases = 34.64 +- 33.78 = 3.28 +- 11.12 m1 = 32.95 m2 = 254.46 Contig 165 149 reads 1701 bases = 35.87 +- 28.15 = 0.56 +- 8.25 m1 = 22.09 m2 = 181.05 Contig 189 343 reads 1306 bases = 125.39 +- 119.27 = -17.23 +- 27.37 m1 = 113.45 m2 = 3368.80 Contig 174 201 reads 988 bases = 139.35 +- 78.47 = 139.35 +- 78.47 m1 = 44.19 m2 = 0.00 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 256 total values totalling 100864.0000. <394.000000 +/- 922.084650> #Range: [ 1 - 8951 ] #Most likely bin: [ 2 - 3 ] 52 counts #Median bin: [ 21 - 22 ] 3 counts |XXXXXXX 1 - 2 : [ 9 0.04 0.04 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 3 : [ 52 0.20 0.24 ] |XXXXXXXXXXXX 3 - 4 : [ 16 0.06 0.30 ] |XXXXXX 4 - 5 : [ 8 0.03 0.33 ] |XXXXXXXX 5 - 6 : [ 11 0.04 0.38 ] |XXX 6 - 7 : [ 4 0.02 0.39 ] |XXX 7 - 8 : [ 4 0.02 0.41 ] |XX 8 - 9 : [ 2 0.01 0.41 ] |XX 9 - 10 : [ 2 0.01 0.42 ] #... |XX 11 - 12 : [ 3 0.01 0.43 ] |XXX 12 - 13 : [ 4 0.02 0.45 ] |X 13 - 14 : [ 1 0.00 0.45 ] |XX 14 - 15 : [ 2 0.01 0.46 ] |X 15 - 16 : [ 1 0.00 0.46 ] #... |XXX 17 - 18 : [ 4 0.02 0.48 ] #... |X 19 - 20 : [ 1 0.00 0.48 ] |X 20 - 21 : [ 1 0.00 0.49 ] |XX 21 - 22 : [ 3 0.01 0.50 ] #... |XX 23 - 24 : [ 2 0.01 0.51 ] #... |XX 25 - 26 : [ 3 0.01 0.52 ] #... |XX 28 - 29 : [ 2 0.01 0.53 ] #... |XX 32 - 33 : [ 2 0.01 0.54 ] #... |X 34 - 35 : [ 1 0.00 0.54 ] #... |X 37 - 38 : [ 1 0.00 0.54 ] #... |X 43 - 44 : [ 1 0.00 0.55 ] #... |X 45 - 46 : [ 1 0.00 0.55 ] |XX 46 - 47 : [ 2 0.01 0.56 ] |X 47 - 48 : [ 1 0.00 0.56 ] |X 48 - 49 : [ 1 0.00 0.57 ] #... |X 51 - 52 : [ 1 0.00 0.57 ] #... |X 56 - 57 : [ 1 0.00 0.57 ] #... |X 58 - 59 : [ 1 0.00 0.58 ] |X 59 - 60 : [ 1 0.00 0.58 ] #... |XX 62 - 63 : [ 2 0.01 0.59 ] #... |X 64 - 65 : [ 1 0.00 0.59 ] #... |X 72 - 73 : [ 1 0.00 0.60 ] #... |X 74 - 75 : [ 1 0.00 0.60 ] #... |X 78 - 79 : [ 1 0.00 0.61 ] |X 79 - 80 : [ 1 0.00 0.61 ] #... |X 81 - 82 : [ 1 0.00 0.61 ] #... |X 90 - 91 : [ 1 0.00 0.62 ] |X 91 - 92 : [ 1 0.00 0.62 ] #... |X 95 - 96 : [ 1 0.00 0.62 ] #... |X 114 - 115 : [ 1 0.00 0.63 ] #... |X 133 - 134 : [ 1 0.00 0.63 ] #... |X 138 - 139 : [ 1 0.00 0.64 ] #... |X 142 - 143 : [ 1 0.00 0.64 ] #... |X 149 - 150 : [ 1 0.00 0.64 ] |X 150 - 151 : [ 1 0.00 0.65 ] |X 151 - 152 : [ 1 0.00 0.65 ] |XX 152 - 153 : [ 2 0.01 0.66 ] #... |X 177 - 178 : [ 1 0.00 0.66 ] #... |X 183 - 184 : [ 1 0.00 0.67 ] |X 184 - 185 : [ 1 0.00 0.67 ] #... |X 187 - 188 : [ 1 0.00 0.68 ] #... |X 201 - 202 : [ 1 0.00 0.68 ] #... |X 226 - 227 : [ 1 0.00 0.68 ] #... |X 231 - 232 : [ 1 0.00 0.69 ] #... |X 246 - 247 : [ 1 0.00 0.69 ] |X 247 - 248 : [ 1 0.00 0.70 ] #... |X 254 - 255 : [ 1 0.00 0.70 ] #... |X 257 - 258 : [ 1 0.00 0.70 ] #... |X 261 - 262 : [ 1 0.00 0.71 ] #... |X 279 - 280 : [ 1 0.00 0.71 ] #... |X 281 - 282 : [ 1 0.00 0.71 ] #... |X 283 - 284 : [ 1 0.00 0.72 ] #... |X 318 - 319 : [ 1 0.00 0.72 ] #... |X 333 - 334 : [ 1 0.00 0.73 ] #... |X 336 - 337 : [ 1 0.00 0.73 ] #... |X 342 - 343 : [ 1 0.00 0.73 ] |X 343 - 344 : [ 1 0.00 0.74 ] #... |X 353 - 354 : [ 1 0.00 0.74 ] #... |X 370 - 371 : [ 1 0.00 0.75 ] #... |X 372 - 373 : [ 1 0.00 0.75 ] #... |X 374 - 375 : [ 1 0.00 0.75 ] #... |X 381 - 382 : [ 1 0.00 0.76 ] #... |X 394 - 395 : [ 1 0.00 0.76 ] #... |X 408 - 409 : [ 1 0.00 0.77 ] #... |X 448 - 449 : [ 1 0.00 0.77 ] #... |X 454 - 455 : [ 1 0.00 0.77 ] #... |X 484 - 485 : [ 1 0.00 0.78 ] #... |XX 492 - 493 : [ 2 0.01 0.79 ] #... |X 495 - 496 : [ 1 0.00 0.79 ] #... |X 512 - 513 : [ 1 0.00 0.79 ] #... |X 531 - 532 : [ 1 0.00 0.80 ] #... |X 569 - 570 : [ 1 0.00 0.80 ] #... |X 590 - 591 : [ 1 0.00 0.80 ] |X 591 - 592 : [ 1 0.00 0.81 ] |X 592 - 593 : [ 1 0.00 0.81 ] #... |X 595 - 596 : [ 1 0.00 0.82 ] #... |X 614 - 615 : [ 1 0.00 0.82 ] #... |X 619 - 620 : [ 1 0.00 0.82 ] #... |X 629 - 630 : [ 1 0.00 0.83 ] #... |X 645 - 646 : [ 1 0.00 0.83 ] #... |X 661 - 662 : [ 1 0.00 0.84 ] #... |X 689 - 690 : [ 1 0.00 0.84 ] #... |XX 744 - 745 : [ 2 0.01 0.85 ] #... |X 755 - 756 : [ 1 0.00 0.85 ] #... |X 757 - 758 : [ 1 0.00 0.86 ] #... |X 798 - 799 : [ 1 0.00 0.86 ] #... |X 817 - 818 : [ 1 0.00 0.86 ] #... |X 819 - 820 : [ 1 0.00 0.87 ] #... |X 830 - 831 : [ 1 0.00 0.87 ] #... |X 894 - 895 : [ 1 0.00 0.88 ] |X 895 - 896 : [ 1 0.00 0.88 ] #... |X 942 - 943 : [ 1 0.00 0.88 ] #... |X 968 - 969 : [ 1 0.00 0.89 ] #... |X 1040 - 1041 : [ 1 0.00 0.89 ] #... |X 1051 - 1052 : [ 1 0.00 0.89 ] #... |X 1109 - 1110 : [ 1 0.00 0.90 ] #... |X 1125 - 1126 : [ 1 0.00 0.90 ] #... |X 1134 - 1135 : [ 1 0.00 0.91 ] #... |X 1153 - 1154 : [ 1 0.00 0.91 ] #... |X 1283 - 1284 : [ 1 0.00 0.91 ] #... |X 1469 - 1470 : [ 1 0.00 0.92 ] #... |X 1636 - 1637 : [ 1 0.00 0.92 ] #... |X 1642 - 1643 : [ 1 0.00 0.93 ] #... |XX 1707 - 1708 : [ 2 0.01 0.93 ] #... |X 1764 - 1765 : [ 1 0.00 0.94 ] #... |X 1767 - 1768 : [ 1 0.00 0.94 ] #... |X 1819 - 1820 : [ 1 0.00 0.95 ] #... |X 1948 - 1949 : [ 1 0.00 0.95 ] #... |X 2064 - 2065 : [ 1 0.00 0.95 ] #... |X 2096 - 2097 : [ 1 0.00 0.96 ] #... |X 2107 - 2108 : [ 1 0.00 0.96 ] #... |X 2221 - 2222 : [ 1 0.00 0.96 ] #... |X 2308 - 2309 : [ 1 0.00 0.97 ] #... |X 2462 - 2463 : [ 1 0.00 0.97 ] #... |X 2482 - 2483 : [ 1 0.00 0.98 ] #... |X 3213 - 3214 : [ 1 0.00 0.98 ] #... |X 3340 - 3341 : [ 1 0.00 0.98 ] #... |X 4496 - 4497 : [ 1 0.00 0.99 ] #... |X 4581 - 4582 : [ 1 0.00 0.99 ] #... |X 5122 - 5123 : [ 1 0.00 1.00 ] #... |X 8951 - 8952 : [ 1 0.00 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 256 total values totalling 3894953.0000. <15214.660156 +/- 31489.674335> #Range: [ 106 - 316981 ] #Most likely bin: [ 1000 - 2000 ] 63 counts #Median bin: [ 2000 - 3000 ] 22 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 1000 : [ 55 0.21 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 63 0.25 0.46 ] |XXXXXXXXXXXXXX 2000 - 3000 : [ 22 0.09 0.55 ] |XXXXX 3000 - 4000 : [ 8 0.03 0.58 ] |XXXX 4000 - 5000 : [ 6 0.02 0.60 ] |XXXX 5000 - 6000 : [ 7 0.03 0.63 ] |XXXX 6000 - 7000 : [ 6 0.02 0.65 ] |X 7000 - 8000 : [ 2 0.01 0.66 ] |X 8000 - 9000 : [ 2 0.01 0.67 ] |X 9000 - 10000 : [ 2 0.01 0.68 ] |X 10000 - 11000 : [ 1 0.00 0.68 ] |XXX 11000 - 12000 : [ 4 0.02 0.70 ] |X 12000 - 13000 : [ 1 0.00 0.70 ] |XXXX 13000 - 14000 : [ 6 0.02 0.72 ] |XXX 14000 - 15000 : [ 5 0.02 0.74 ] |X 15000 - 16000 : [ 1 0.00 0.75 ] |X 16000 - 17000 : [ 2 0.01 0.75 ] |XX 17000 - 18000 : [ 3 0.01 0.77 ] |X 18000 - 19000 : [ 1 0.00 0.77 ] |X 19000 - 20000 : [ 1 0.00 0.77 ] |XXX 20000 - 21000 : [ 5 0.02 0.79 ] |XX 21000 - 22000 : [ 3 0.01 0.80 ] |X 22000 - 23000 : [ 2 0.01 0.81 ] |X 23000 - 24000 : [ 1 0.00 0.82 ] #... |XXX 25000 - 26000 : [ 4 0.02 0.83 ] |XXX 26000 - 27000 : [ 4 0.02 0.85 ] #... |XX 29000 - 30000 : [ 3 0.01 0.86 ] #... |X 31000 - 32000 : [ 1 0.00 0.86 ] #... |X 33000 - 34000 : [ 1 0.00 0.87 ] |X 34000 - 35000 : [ 1 0.00 0.87 ] #... |X 36000 - 37000 : [ 1 0.00 0.88 ] #... |X 38000 - 39000 : [ 2 0.01 0.88 ] |X 39000 - 40000 : [ 2 0.01 0.89 ] |X 40000 - 41000 : [ 1 0.00 0.89 ] #... |X 42000 - 43000 : [ 2 0.01 0.90 ] #... |X 46000 - 47000 : [ 1 0.00 0.91 ] |X 47000 - 48000 : [ 1 0.00 0.91 ] #... |X 51000 - 52000 : [ 1 0.00 0.91 ] |X 52000 - 53000 : [ 1 0.00 0.92 ] |X 53000 - 54000 : [ 1 0.00 0.92 ] #... |X 55000 - 56000 : [ 1 0.00 0.93 ] #... |X 58000 - 59000 : [ 1 0.00 0.93 ] |XX 59000 - 60000 : [ 3 0.01 0.94 ] #... |X 64000 - 65000 : [ 1 0.00 0.95 ] |X 65000 - 66000 : [ 1 0.00 0.95 ] |X 66000 - 67000 : [ 1 0.00 0.95 ] #... |X 73000 - 74000 : [ 1 0.00 0.96 ] #... |X 78000 - 79000 : [ 1 0.00 0.96 ] #... |X 81000 - 82000 : [ 1 0.00 0.96 ] #... |X 85000 - 86000 : [ 1 0.00 0.97 ] #... |X 89000 - 90000 : [ 1 0.00 0.97 ] #... |X 98000 - 99000 : [ 1 0.00 0.98 ] #... |X 106000 - 107000 : [ 1 0.00 0.98 ] #... |X 119000 - 120000 : [ 1 0.00 0.98 ] #... |X 127000 - 128000 : [ 1 0.00 0.99 ] #... |X 152000 - 153000 : [ 1 0.00 0.99 ] #... |X 160000 - 161000 : [ 1 0.00 1.00 ] #... |X 316000 - 317000 : [ 1 0.00 1.00 ] ################################################################### Histogram of Assembled Average Insert Sizes Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list ------------------------------------------------------------------- ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # PKV 3548 +- 697 (n=14283) # XUC 36099 +- 5084 (n=153) # WSV 5827 +- 1136 (n=3752) # LAO 3636 +- 982 (n=179) # KPP 2631 +- 1147 (n=325) # KXP 730 +- 839 (n=63) ################################################################### 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 511.973836 bp, 100864 reads, genome size 4185395 bp Command: idealAssembly 4185395 100864 511.973836 ------------------------------------------------------------------- Genome = 4185395 bases Nreads = 100864 readLength = 511.973836 Depth = 12.34 N_contigs = N_gaps = 0 mean gap size = 40 bases mean contig size = 228223 reads (~ 9470204 bases) %cover = 100.00 %singlet = 0.00 assembly size = 4185377 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 0 contigs containing at least 382958 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: