################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 2662189 Genus_species: Trichodesmium erythraeum Taxid: 1206 Genome size: 6500 Libraries: ABSU, SUT, AGPT, AIZO, ABTK, POM, SRU, PPO, TQZ ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 2662189 ------------------------------------------------------------------- ID=2662189 Lineage for 'Trichodesmium erythraeum': Trichodesmium erythraeum species Trichodesmium genus Oscillatoriales order Cyanobacteria phylum Bacteria superkingdom cellular organisms no rank root no rank ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 7822344 # phrap: 7523424 # db: 6500000 7281922 +/- 566209 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s AIZO 0 0 0.00 0.00 0 0.00 0.00 ABSU 166 84 96.30 719.43 82 97.83 724.05 SUT 181 90 89.48 545.20 91 78.11 413.52 ABTK 32 16 47.59 282.50 16 73.31 501.69 POM 560 281 94.51 617.32 279 93.68 595.18 SRU 107 53 88.83 513.81 54 84.80 450.76 PPO 0 0 0.00 0.00 0 0.00 0.00 AGPT 80 40 80.16 560.10 40 97.03 684.80 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 2662189_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 2662189_fasta.screen.contigs /sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out /home/copeland/scripts/asseminfo phrap.out > asseminfo.2662189.out /home/copeland/scripts/librariesInfoTxt.sh 2662189 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pphrap.SUN3.57 2662189_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 2662189_fasta.screen.contigs /sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out /home/copeland/scripts/asseminfo phrap.out > asseminfo.2662189.out /home/copeland/scripts/librariesInfoTxt.sh 2662189 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pphrap.SUN3.57 2662189_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 2662189_fasta.screen.contigs /sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out /home/copeland/scripts/asseminfo phrap.out > asseminfo.2662189.out /home/copeland/scripts/librariesInfoTxt.sh 2662189 phrap.out > librariesInfo.txt ################################################################### Library vector screening ABSU.000001.000100 screen.out.1 2662189_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2662189_fasta.screen /sequences/LRS.fasta ABSU.000101.000200 screen.out.1 2662189_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2662189_fasta.screen /sequences/LRS.fasta ABTK.000001.000100 screen.out 2662189_fasta.screen /sequences/pCC1FOS.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta AGPT.000001.000100 screen.out.1 2662189_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 2662189_fasta.screen /sequences/LRS.fasta POM.000001.000100 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta POM.000101.000200 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta POM.000201.000300 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta POM.000301.000400 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta POM.000401.000500 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta SRU.000001.000100 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta SUT.000001.000100 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta SUT.000101.000200 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta TQZ.000001.000100 screen.out 2662189_fasta /sequences/microbe_vector.seq ABSU.000001.000100 screen.out.1 2662189_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2662189_fasta.screen /sequences/LRS.fasta ABSU.000101.000200 screen.out.1 2662189_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2662189_fasta.screen /sequences/LRS.fasta ABTK.000001.000100 screen.out 2662189_fasta.screen /sequences/pCC1FOS.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta AGPT.000001.000100 screen.out.1 2662189_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 2662189_fasta.screen /sequences/LRS.fasta POM.000001.000100 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta POM.000101.000200 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta POM.000201.000300 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta POM.000301.000400 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta POM.000401.000500 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta SRU.000001.000100 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta SUT.000001.000100 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta SUT.000101.000200 screen.out 2662189_fasta.screen /sequences/pUC.fasta screen.out.std 2662189_fasta.screen /sequences/LRS.fasta TQZ.000001.000100 screen.out 2662189_fasta /sequences/microbe_vector.seq ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 2662189_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 135777 total values totalling 77142984.0000. <568.159438 +/- 162.886051> #Range: [ 22 - 900 ] #Most likely bin: [ 650 - 700 ] 30129 counts #Median bin: [ 600 - 650 ] 26687 counts |X 0 - 50 : [ 493 0.00 0.00 ] |XX 50 - 100 : [ 1851 0.01 0.02 ] |XXX 100 - 150 : [ 2261 0.02 0.03 ] |XXX 150 - 200 : [ 2284 0.02 0.05 ] |XXX 200 - 250 : [ 2602 0.02 0.07 ] |XXXX 250 - 300 : [ 3111 0.02 0.09 ] |XXXXX 300 - 350 : [ 3702 0.03 0.12 ] |XXXXXX 350 - 400 : [ 4460 0.03 0.15 ] |XXXXXXX 400 - 450 : [ 5272 0.04 0.19 ] |XXXXXXXXX 450 - 500 : [ 6870 0.05 0.24 ] |XXXXXXXXXXXXX 500 - 550 : [ 9737 0.07 0.31 ] |XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 15253 0.11 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 26687 0.20 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 30129 0.22 0.84 ] |XXXXXXXXXXXXXXXXXXX 700 - 750 : [ 14610 0.11 0.95 ] |XXXXXXX 750 - 800 : [ 5345 0.04 0.99 ] |X 800 - 850 : [ 1045 0.01 1.00 ] | 850 - 900 : [ 64 0.00 1.00 ] | 900 - 950 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for ABTK Command: /usr/xpg4/bin/grep ABTK 2662189_fasta.screen.screen.ids > reads.trim15.ABTK.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.ABTK.rl 2 50 #Found 1585 total values totalling 1054109.0000. <665.052997 +/- 150.945156> #Range: [ 28 - 847 ] #Most likely bin: [ 700 - 750 ] 488 counts #Median bin: [ 700 - 750 ] 488 counts |X 0 - 50 : [ 11 0.01 0.01 ] |X 50 - 100 : [ 16 0.01 0.02 ] |X 100 - 150 : [ 10 0.01 0.02 ] |XX 150 - 200 : [ 22 0.01 0.04 ] |XX 200 - 250 : [ 25 0.02 0.05 ] |X 250 - 300 : [ 12 0.01 0.06 ] |X 300 - 350 : [ 9 0.01 0.07 ] | 350 - 400 : [ 6 0.00 0.07 ] |XX 400 - 450 : [ 19 0.01 0.08 ] |XX 450 - 500 : [ 26 0.02 0.10 ] |XXX 500 - 550 : [ 31 0.02 0.12 ] |XXXXX 550 - 600 : [ 63 0.04 0.16 ] |XXXXXXXXXX 600 - 650 : [ 121 0.08 0.23 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 327 0.21 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 488 0.31 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 356 0.22 0.97 ] |XXXX 800 - 850 : [ 43 0.03 1.00 ] JAZZ trim 15 readlength histogram for ABSU Command: /usr/xpg4/bin/grep ABSU 2662189_fasta.screen.screen.ids > reads.trim15.ABSU.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.ABSU.rl 2 50 #Found 21032 total values totalling 13634578.0000. <648.277767 +/- 144.873478> #Range: [ 24 - 862 ] #Most likely bin: [ 700 - 750 ] 6529 counts #Median bin: [ 650 - 700 ] 4425 counts | 0 - 50 : [ 42 0.00 0.00 ] |X 50 - 100 : [ 106 0.01 0.01 ] |X 100 - 150 : [ 239 0.01 0.02 ] |X 150 - 200 : [ 179 0.01 0.03 ] |X 200 - 250 : [ 214 0.01 0.04 ] |XX 250 - 300 : [ 245 0.01 0.05 ] |XX 300 - 350 : [ 281 0.01 0.06 ] |XX 350 - 400 : [ 371 0.02 0.08 ] |XXX 400 - 450 : [ 418 0.02 0.10 ] |XXX 450 - 500 : [ 503 0.02 0.12 ] |XXXX 500 - 550 : [ 706 0.03 0.16 ] |XXXXXXX 550 - 600 : [ 1142 0.05 0.21 ] |XXXXXXXXXXXXX 600 - 650 : [ 2097 0.10 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4425 0.21 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6529 0.31 0.83 ] |XXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3189 0.15 0.98 ] |XX 800 - 850 : [ 343 0.02 1.00 ] | 850 - 900 : [ 3 0.00 1.00 ] JAZZ trim 15 readlength histogram for TQZ Command: /usr/xpg4/bin/grep TQZ 2662189_fasta.screen.screen.ids > reads.trim15.TQZ.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.TQZ.rl 2 50 #Found 1160 total values totalling 794897.0000. <685.256034 +/- 112.799796> #Range: [ 54 - 788 ] #Most likely bin: [ 700 - 750 ] 685 counts #Median bin: [ 700 - 750 ] 685 counts | 50 - 100 : [ 4 0.00 0.00 ] | 100 - 150 : [ 8 0.01 0.01 ] | 150 - 200 : [ 6 0.01 0.02 ] | 200 - 250 : [ 3 0.00 0.02 ] |X 250 - 300 : [ 10 0.01 0.03 ] |X 300 - 350 : [ 11 0.01 0.04 ] |X 350 - 400 : [ 22 0.02 0.06 ] |X 400 - 450 : [ 10 0.01 0.06 ] |X 450 - 500 : [ 9 0.01 0.07 ] | 500 - 550 : [ 3 0.00 0.07 ] |X 550 - 600 : [ 23 0.02 0.09 ] |XXX 600 - 650 : [ 44 0.04 0.13 ] |XXXXXXXXXXXX 650 - 700 : [ 205 0.18 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 685 0.59 0.90 ] |XXXXXXX 750 - 800 : [ 117 0.10 1.00 ] JAZZ trim 15 readlength histogram for PPO JAZZ trim 15 readlength histogram for SRU Command: /usr/xpg4/bin/grep SRU 2662189_fasta.screen.screen.ids > reads.trim15.SRU.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.SRU.rl 2 50 #Found 12154 total values totalling 5783687.0000. <475.866957 +/- 174.654452> #Range: [ 26 - 771 ] #Most likely bin: [ 600 - 650 ] 2246 counts #Median bin: [ 500 - 550 ] 1314 counts |X 0 - 50 : [ 74 0.01 0.01 ] |XXXXXX 50 - 100 : [ 352 0.03 0.04 ] |XXXXXXXX 100 - 150 : [ 456 0.04 0.07 ] |XXXXXXX 150 - 200 : [ 415 0.03 0.11 ] |XXXXXXXX 200 - 250 : [ 455 0.04 0.14 ] |XXXXXXXXXX 250 - 300 : [ 535 0.04 0.19 ] |XXXXXXXXXX 300 - 350 : [ 581 0.05 0.24 ] |XXXXXXXXXXXXX 350 - 400 : [ 709 0.06 0.29 ] |XXXXXXXXXXXXXX 400 - 450 : [ 794 0.07 0.36 ] |XXXXXXXXXXXXXXXXX 450 - 500 : [ 967 0.08 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 1314 0.11 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1692 0.14 0.69 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2246 0.18 0.87 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1392 0.11 0.99 ] |XXX 700 - 750 : [ 171 0.01 1.00 ] | 750 - 800 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for SUT Command: /usr/xpg4/bin/grep SUT 2662189_fasta.screen.screen.ids > reads.trim15.SUT.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.SUT.rl 2 50 #Found 19762 total values totalling 9555415.0000. <483.524694 +/- 182.839076> #Range: [ 22 - 770 ] #Most likely bin: [ 600 - 650 ] 3389 counts #Median bin: [ 500 - 550 ] 1811 counts |XX 0 - 50 : [ 197 0.01 0.01 ] |XXXXXXXX 50 - 100 : [ 654 0.03 0.04 ] |XXXXXXXX 100 - 150 : [ 689 0.03 0.08 ] |XXXXXXXX 150 - 200 : [ 696 0.04 0.11 ] |XXXXXXXX 200 - 250 : [ 693 0.04 0.15 ] |XXXXXXXXX 250 - 300 : [ 796 0.04 0.19 ] |XXXXXXXXXXX 300 - 350 : [ 923 0.05 0.24 ] |XXXXXXXXXXXX 350 - 400 : [ 1026 0.05 0.29 ] |XXXXXXXXXXXXXXX 400 - 450 : [ 1280 0.06 0.35 ] |XXXXXXXXXXXXXXXXXX 450 - 500 : [ 1512 0.08 0.43 ] |XXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 1811 0.09 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 2320 0.12 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3389 0.17 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3249 0.16 0.97 ] |XXXXXX 700 - 750 : [ 523 0.03 1.00 ] | 750 - 800 : [ 4 0.00 1.00 ] JAZZ trim 15 readlength histogram for POM Command: /usr/xpg4/bin/grep POM 2662189_fasta.screen.screen.ids > reads.trim15.POM.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.POM.rl 2 50 #Found 73775 total values totalling 42037449.0000. <569.806154 +/- 139.789977> #Range: [ 24 - 792 ] #Most likely bin: [ 650 - 700 ] 19564 counts #Median bin: [ 600 - 650 ] 18381 counts | 0 - 50 : [ 143 0.00 0.00 ] |X 50 - 100 : [ 673 0.01 0.01 ] |XX 100 - 150 : [ 817 0.01 0.02 ] |XX 150 - 200 : [ 935 0.01 0.03 ] |XX 200 - 250 : [ 1166 0.02 0.05 ] |XXX 250 - 300 : [ 1425 0.02 0.07 ] |XXXX 300 - 350 : [ 1789 0.02 0.09 ] |XXXX 350 - 400 : [ 2171 0.03 0.12 ] |XXXXX 400 - 450 : [ 2660 0.04 0.16 ] |XXXXXXXX 450 - 500 : [ 3767 0.05 0.21 ] |XXXXXXXXXXXX 500 - 550 : [ 5748 0.08 0.29 ] |XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 9809 0.13 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 18381 0.25 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 19564 0.27 0.94 ] |XXXXXXXXX 700 - 750 : [ 4628 0.06 1.00 ] | 750 - 800 : [ 99 0.00 1.00 ] JAZZ trim 15 readlength histogram for AGPT Command: /usr/xpg4/bin/grep AGPT 2662189_fasta.screen.screen.ids > reads.trim15.AGPT.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AGPT.rl 2 50 #Found 6309 total values totalling 4282849.0000. <678.847519 +/- 153.523675> #Range: [ 26 - 900 ] #Most likely bin: [ 700 - 750 ] 1586 counts #Median bin: [ 700 - 750 ] 1586 counts |X 0 - 50 : [ 26 0.00 0.00 ] |X 50 - 100 : [ 46 0.01 0.01 ] |X 100 - 150 : [ 42 0.01 0.02 ] |X 150 - 200 : [ 31 0.00 0.02 ] |X 200 - 250 : [ 46 0.01 0.03 ] |XX 250 - 300 : [ 88 0.01 0.04 ] |XXX 300 - 350 : [ 108 0.02 0.06 ] |XXXX 350 - 400 : [ 155 0.02 0.09 ] |XX 400 - 450 : [ 91 0.01 0.10 ] |XX 450 - 500 : [ 86 0.01 0.11 ] |XXX 500 - 550 : [ 124 0.02 0.13 ] |XXXXX 550 - 600 : [ 204 0.03 0.17 ] |XXXXXXXXXX 600 - 650 : [ 409 0.06 0.23 ] |XXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 967 0.15 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1586 0.25 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1579 0.25 0.89 ] |XXXXXXXXXXXXXXXXX 800 - 850 : [ 659 0.10 0.99 ] |XX 850 - 900 : [ 61 0.01 1.00 ] | 900 - 950 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for AIZO ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.2662189_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.2662189_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 135322 total values totalling 46779.5936. <0.345691 +/- 0.065764> #Range: [ 0.0435 - 0.9118 ] #Most likely bin: [ 0.325 - 0.33 ] 4758 counts #Median bin: [ 0.335 - 0.34 ] 4591 counts | 0.04 - 0.045 : [ 2 0.00 0.00 ] #... | 0.065 - 0.07 : [ 1 0.00 0.00 ] #... | 0.08 - 0.085 : [ 1 0.00 0.00 ] #... | 0.105 - 0.11 : [ 3 0.00 0.00 ] | 0.11 - 0.115 : [ 2 0.00 0.00 ] | 0.115 - 0.12 : [ 1 0.00 0.00 ] | 0.12 - 0.125 : [ 2 0.00 0.00 ] | 0.125 - 0.13 : [ 2 0.00 0.00 ] | 0.13 - 0.135 : [ 4 0.00 0.00 ] | 0.135 - 0.14 : [ 6 0.00 0.00 ] | 0.14 - 0.145 : [ 11 0.00 0.00 ] | 0.145 - 0.15 : [ 10 0.00 0.00 ] | 0.15 - 0.155 : [ 9 0.00 0.00 ] | 0.155 - 0.16 : [ 14 0.00 0.00 ] | 0.16 - 0.165 : [ 21 0.00 0.00 ] | 0.165 - 0.17 : [ 29 0.00 0.00 ] | 0.17 - 0.175 : [ 31 0.00 0.00 ] | 0.175 - 0.18 : [ 40 0.00 0.00 ] | 0.18 - 0.185 : [ 53 0.00 0.00 ] | 0.185 - 0.19 : [ 42 0.00 0.00 ] |X 0.19 - 0.195 : [ 91 0.00 0.00 ] |X 0.195 - 0.2 : [ 131 0.00 0.00 ] |XX 0.2 - 0.205 : [ 189 0.00 0.01 ] |XX 0.205 - 0.21 : [ 223 0.00 0.01 ] |XX 0.21 - 0.215 : [ 256 0.00 0.01 ] |XX 0.215 - 0.22 : [ 282 0.00 0.01 ] |XXXX 0.22 - 0.225 : [ 446 0.00 0.01 ] |XXXX 0.225 - 0.23 : [ 507 0.00 0.02 ] |XXXXX 0.23 - 0.235 : [ 613 0.00 0.02 ] |XXXXXX 0.235 - 0.24 : [ 747 0.01 0.03 ] |XXXXXXXX 0.24 - 0.245 : [ 947 0.01 0.03 ] |XXXXXXXX 0.245 - 0.25 : [ 1006 0.01 0.04 ] |XXXXXXXXXXX 0.25 - 0.255 : [ 1367 0.01 0.05 ] |XXXXXXXXXXXXX 0.255 - 0.26 : [ 1533 0.01 0.06 ] |XXXXXXXXXXXXXXXX 0.26 - 0.265 : [ 1892 0.01 0.08 ] |XXXXXXXXXXXXXXXXX 0.265 - 0.27 : [ 2068 0.02 0.09 ] |XXXXXXXXXXXXXXXXXXXX 0.27 - 0.275 : [ 2427 0.02 0.11 ] |XXXXXXXXXXXXXXXXXXXXXXX 0.275 - 0.28 : [ 2765 0.02 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.28 - 0.285 : [ 3030 0.02 0.15 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.285 - 0.29 : [ 3277 0.02 0.18 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 3669 0.03 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.295 - 0.3 : [ 3834 0.03 0.23 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 4097 0.03 0.26 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 4446 0.03 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 4497 0.03 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 4695 0.03 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 4661 0.03 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 4758 0.04 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 4733 0.03 0.47 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 4591 0.03 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 4315 0.03 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 4224 0.03 0.57 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 4116 0.03 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 4017 0.03 0.63 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 3821 0.03 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 3662 0.03 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 3602 0.03 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 3559 0.03 0.73 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 3338 0.02 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 3201 0.02 0.78 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 3267 0.02 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 2779 0.02 0.83 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 2959 0.02 0.85 ] |XXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 2624 0.02 0.87 ] |XXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 2410 0.02 0.89 ] |XXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 2146 0.02 0.90 ] |XXXXXXXXXXXXXXX 0.42 - 0.425 : [ 1788 0.01 0.92 ] |XXXXXXXXXXXXX 0.425 - 0.43 : [ 1595 0.01 0.93 ] |XXXXXXXXXXX 0.43 - 0.435 : [ 1297 0.01 0.94 ] |XXXXXXXXX 0.435 - 0.44 : [ 1078 0.01 0.94 ] |XXXXXXX 0.44 - 0.445 : [ 889 0.01 0.95 ] |XXXXXX 0.445 - 0.45 : [ 723 0.01 0.96 ] |XXXXX 0.45 - 0.455 : [ 584 0.00 0.96 ] |XXXX 0.455 - 0.46 : [ 466 0.00 0.96 ] |XXX 0.46 - 0.465 : [ 395 0.00 0.97 ] |XXX 0.465 - 0.47 : [ 359 0.00 0.97 ] |XXX 0.47 - 0.475 : [ 342 0.00 0.97 ] |XX 0.475 - 0.48 : [ 264 0.00 0.97 ] |XX 0.48 - 0.485 : [ 229 0.00 0.98 ] |X 0.485 - 0.49 : [ 164 0.00 0.98 ] |X 0.49 - 0.495 : [ 137 0.00 0.98 ] |X 0.495 - 0.5 : [ 91 0.00 0.98 ] |XX 0.5 - 0.505 : [ 264 0.00 0.98 ] |X 0.505 - 0.51 : [ 94 0.00 0.98 ] |X 0.51 - 0.515 : [ 67 0.00 0.98 ] |X 0.515 - 0.52 : [ 65 0.00 0.98 ] | 0.52 - 0.525 : [ 58 0.00 0.98 ] | 0.525 - 0.53 : [ 58 0.00 0.98 ] | 0.53 - 0.535 : [ 55 0.00 0.98 ] |X 0.535 - 0.54 : [ 76 0.00 0.98 ] |X 0.54 - 0.545 : [ 137 0.00 0.99 ] |X 0.545 - 0.55 : [ 117 0.00 0.99 ] |XX 0.55 - 0.555 : [ 198 0.00 0.99 ] |X 0.555 - 0.56 : [ 162 0.00 0.99 ] |X 0.56 - 0.565 : [ 168 0.00 0.99 ] |X 0.565 - 0.57 : [ 105 0.00 0.99 ] | 0.57 - 0.575 : [ 40 0.00 0.99 ] | 0.575 - 0.58 : [ 35 0.00 0.99 ] | 0.58 - 0.585 : [ 31 0.00 0.99 ] | 0.585 - 0.59 : [ 44 0.00 0.99 ] | 0.59 - 0.595 : [ 28 0.00 0.99 ] | 0.595 - 0.6 : [ 25 0.00 0.99 ] | 0.6 - 0.605 : [ 25 0.00 0.99 ] | 0.605 - 0.61 : [ 18 0.00 0.99 ] | 0.61 - 0.615 : [ 14 0.00 0.99 ] | 0.615 - 0.62 : [ 22 0.00 0.99 ] | 0.62 - 0.625 : [ 24 0.00 0.99 ] | 0.625 - 0.63 : [ 32 0.00 0.99 ] | 0.63 - 0.635 : [ 23 0.00 0.99 ] | 0.635 - 0.64 : [ 35 0.00 0.99 ] | 0.64 - 0.645 : [ 31 0.00 0.99 ] | 0.645 - 0.65 : [ 29 0.00 0.99 ] | 0.65 - 0.655 : [ 36 0.00 0.99 ] | 0.655 - 0.66 : [ 37 0.00 1.00 ] | 0.66 - 0.665 : [ 53 0.00 1.00 ] | 0.665 - 0.67 : [ 52 0.00 1.00 ] | 0.67 - 0.675 : [ 57 0.00 1.00 ] | 0.675 - 0.68 : [ 47 0.00 1.00 ] | 0.68 - 0.685 : [ 54 0.00 1.00 ] | 0.685 - 0.69 : [ 52 0.00 1.00 ] | 0.69 - 0.695 : [ 43 0.00 1.00 ] | 0.695 - 0.7 : [ 52 0.00 1.00 ] | 0.7 - 0.705 : [ 49 0.00 1.00 ] | 0.705 - 0.71 : [ 45 0.00 1.00 ] | 0.71 - 0.715 : [ 36 0.00 1.00 ] | 0.715 - 0.72 : [ 35 0.00 1.00 ] | 0.72 - 0.725 : [ 22 0.00 1.00 ] | 0.725 - 0.73 : [ 23 0.00 1.00 ] | 0.73 - 0.735 : [ 10 0.00 1.00 ] | 0.735 - 0.74 : [ 11 0.00 1.00 ] | 0.74 - 0.745 : [ 11 0.00 1.00 ] | 0.745 - 0.75 : [ 5 0.00 1.00 ] | 0.75 - 0.755 : [ 2 0.00 1.00 ] | 0.755 - 0.76 : [ 1 0.00 1.00 ] #... | 0.77 - 0.775 : [ 2 0.00 1.00 ] | 0.775 - 0.78 : [ 1 0.00 1.00 ] #... | 0.8 - 0.805 : [ 2 0.00 1.00 ] #... | 0.91 - 0.915 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones LIBRARY @ ] 135795 73574 84.96 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 = 1115 HQ Discrepant reads = 138 Chimeric reads = 461 Suspect alignments = 14403 ################################################################### C O N T I G I N F O R M A T I O N Thu Aug 12 10:48:50 2004 File: /psf/project/microbe2/2662189/edit_dir.16Dec03.QD/phrap.out Contig 92. 1310 reads; 77675 bp (untrimmed), 77295 (trimmed). Contig 93. 1437 reads; 86010 bp (untrimmed), 85399 (trimmed). Contig 94. 1533 reads; 85051 bp (untrimmed), 85026 (trimmed). Contig 95. 1693 reads; 104274 bp (untrimmed), 103640 (trimmed). Contig 96. 1816 reads; 102580 bp (untrimmed), 102519 (trimmed). Contig 97. 1838 reads; 104576 bp (untrimmed), 104558 (trimmed). Contig 98. 1900 reads; 117499 bp (untrimmed), 117185 (trimmed). Contig 99. 1918 reads; 110439 bp (untrimmed), 110161 (trimmed). Contig 100. 1952 reads; 110813 bp (untrimmed), 110813 (trimmed). Contig 101. 2100 reads; 122555 bp (untrimmed), 121778 (trimmed). Contig 102. 2220 reads; 126619 bp (untrimmed), 125555 (trimmed). Contig 103. 2437 reads; 139894 bp (untrimmed), 139133 (trimmed). Contig 104. 2760 reads; 149561 bp (untrimmed), 149367 (trimmed). Contig 105. 2887 reads; 173946 bp (untrimmed), 173946 (trimmed). Contig 106. 2890 reads; 168255 bp (untrimmed), 168255 (trimmed). Contig 107. 2971 reads; 170439 bp (untrimmed), 170205 (trimmed). Contig 108. 2999 reads; 162238 bp (untrimmed), 162214 (trimmed). Contig 109. 3034 reads; 174989 bp (untrimmed), 174959 (trimmed). Contig 110. 3305 reads; 188271 bp (untrimmed), 187978 (trimmed). Contig 111. 3992 reads; 238558 bp (untrimmed), 238558 (trimmed). Contig 112. 4009 reads; 232964 bp (untrimmed), 232797 (trimmed). Contig 113. 4035 reads; 235832 bp (untrimmed), 235654 (trimmed). Contig 114. 4970 reads; 276032 bp (untrimmed), 275915 (trimmed). Contig 115. 5150 reads; 307673 bp (untrimmed), 307672 (trimmed). Contig 116. 15968 reads; 928420 bp (untrimmed), 928383 (trimmed). Contig 117. 20462 reads; 1178388 bp (untrimmed), 1178388 (trimmed). Contig 118. 22508 reads; 1319663 bp (untrimmed), 1319662 (trimmed). -------------------------------------------------------------- Totals 134602 reads; 7847528 bp (untrimmed), 7822344 (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 59 total values totalling 7746754.0000. <131300.915254 +/- 249490.287752> #Range: [ 2208 - 1319662 ] #Most likely bin: [ 2000 - 4000 ] 5 counts #Median bin: [ 46000 - 48000 ] 3 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 5 0.08 0.08 ] |XXXXXXXXXXXXXXXX 4000 - 6000 : [ 2 0.03 0.12 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 8000 : [ 5 0.08 0.20 ] |XXXXXXXX 8000 - 10000 : [ 1 0.02 0.22 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10000 - 12000 : [ 4 0.07 0.29 ] |XXXXXXXX 12000 - 14000 : [ 1 0.02 0.31 ] |XXXXXXXXXXXXXXXX 14000 - 16000 : [ 2 0.03 0.34 ] #... |XXXXXXXXXXXXXXXX 20000 - 22000 : [ 2 0.03 0.37 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 24000 - 26000 : [ 3 0.05 0.42 ] |XXXXXXXXXXXXXXXX 26000 - 28000 : [ 2 0.03 0.46 ] #... |XXXXXXXX 34000 - 36000 : [ 1 0.02 0.47 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 46000 - 48000 : [ 3 0.05 0.53 ] #... |XXXXXXXX 60000 - 62000 : [ 1 0.02 0.54 ] #... |XXXXXXXX 76000 - 78000 : [ 1 0.02 0.56 ] #... |XXXXXXXXXXXXXXXX 84000 - 86000 : [ 2 0.03 0.59 ] #... |XXXXXXXXXXXXXXXX 102000 - 104000 : [ 2 0.03 0.63 ] |XXXXXXXX 104000 - 106000 : [ 1 0.02 0.64 ] #... |XXXXXXXXXXXXXXXX 110000 - 112000 : [ 2 0.03 0.68 ] #... |XXXXXXXX 116000 - 118000 : [ 1 0.02 0.69 ] #... |XXXXXXXX 120000 - 122000 : [ 1 0.02 0.71 ] #... |XXXXXXXX 124000 - 126000 : [ 1 0.02 0.73 ] #... |XXXXXXXX 138000 - 140000 : [ 1 0.02 0.75 ] #... |XXXXXXXX 148000 - 150000 : [ 1 0.02 0.76 ] #... |XXXXXXXX 162000 - 164000 : [ 1 0.02 0.78 ] #... |XXXXXXXX 168000 - 170000 : [ 1 0.02 0.80 ] |XXXXXXXX 170000 - 172000 : [ 1 0.02 0.81 ] |XXXXXXXX 172000 - 174000 : [ 1 0.02 0.83 ] |XXXXXXXX 174000 - 176000 : [ 1 0.02 0.85 ] #... |XXXXXXXX 186000 - 188000 : [ 1 0.02 0.86 ] #... |XXXXXXXX 232000 - 234000 : [ 1 0.02 0.88 ] |XXXXXXXX 234000 - 236000 : [ 1 0.02 0.90 ] #... |XXXXXXXX 238000 - 240000 : [ 1 0.02 0.92 ] #... |XXXXXXXX 274000 - 276000 : [ 1 0.02 0.93 ] #... |XXXXXXXX 306000 - 308000 : [ 1 0.02 0.95 ] #... |XXXXXXXX 928000 - 930000 : [ 1 0.02 0.97 ] #... |XXXXXXXX 1178000 - 1180000 : [ 1 0.02 0.98 ] #... |XXXXXXXX 1318000 - 1320000 : [ 1 0.02 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 40804480 C = 23286331 G = 23088665 T = 39533257 N = 367660 X = 3855955 GC fraction = 0.35 Total = 130936348 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 2662189_fasta.screen.contigs A 2572985 C 1352048 G 1348039 N 39 T 2574373 X 44 fraction GC = 0.34 total bases = 7847528 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 7845466 bases = 13.52 +- 7.17 = 0.23 +- 6.64 m1 = 3.80 m2 = 1.82 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 112 total values totalling 1132.8500. <10.114732 +/- 9.184627> #Range: [ 1.19 - 61.63 ] #Most likely bin: [ 13.5 - 14 ] 20 counts #Median bin: [ 11.5 - 12 ] 3 counts |XXXXXXXXXXXX 1 - 1.5 : [ 6 0.05 0.05 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 16 0.14 0.20 ] |XXXXXXXXXXXXXX 2 - 2.5 : [ 7 0.06 0.26 ] |XXXX 2.5 - 3 : [ 2 0.02 0.28 ] |XXXXXXXXXX 3 - 3.5 : [ 5 0.04 0.32 ] |XXXXXXXX 3.5 - 4 : [ 4 0.04 0.36 ] |XX 4 - 4.5 : [ 1 0.01 0.37 ] #... |XXXX 5 - 5.5 : [ 2 0.02 0.38 ] #... |XXXX 6.5 - 7 : [ 2 0.02 0.40 ] #... |XX 8 - 8.5 : [ 1 0.01 0.41 ] #... |XX 9 - 9.5 : [ 1 0.01 0.42 ] #... |XXXX 10 - 10.5 : [ 2 0.02 0.44 ] |XXXXXX 10.5 - 11 : [ 3 0.03 0.46 ] |XXXXXX 11 - 11.5 : [ 3 0.03 0.49 ] |XXXXXX 11.5 - 12 : [ 3 0.03 0.52 ] |XXXXXXXXXXXX 12 - 12.5 : [ 6 0.05 0.57 ] |XXXXXXXXXXXXXX 12.5 - 13 : [ 7 0.06 0.63 ] |XXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 10 0.09 0.72 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 20 0.18 0.90 ] |XXXX 14 - 14.5 : [ 2 0.02 0.92 ] |XXXXXX 14.5 - 15 : [ 3 0.03 0.95 ] #... |XX 15.5 - 16 : [ 1 0.01 0.96 ] #... |XX 28.5 - 29 : [ 1 0.01 0.96 ] #... |XX 34 - 34.5 : [ 1 0.01 0.97 ] #... |XX 43 - 43.5 : [ 1 0.01 0.98 ] #... |XX 49.5 - 50 : [ 1 0.01 0.99 ] #... |XX 61.5 - 62 : [ 1 0.01 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 62 total values totalling 845.3700. <13.635000 +/- 7.133564> #Range: [ 2.17 - 61.63 ] #Most likely bin: [ 13.5 - 14 ] 20 counts #Median bin: [ 13 - 13.5 ] 10 counts |XX 2 - 2.5 : [ 1 0.02 0.02 ] #... |XX 3 - 3.5 : [ 1 0.02 0.03 ] #... |XX 5 - 5.5 : [ 1 0.02 0.05 ] #... |XX 8 - 8.5 : [ 1 0.02 0.06 ] #... |XX 10 - 10.5 : [ 1 0.02 0.08 ] |XXXXXX 10.5 - 11 : [ 3 0.05 0.13 ] |XXXXXX 11 - 11.5 : [ 3 0.05 0.18 ] |XXXX 11.5 - 12 : [ 2 0.03 0.21 ] |XXXXXXXXXXXX 12 - 12.5 : [ 6 0.10 0.31 ] |XXXXXXXXXXXX 12.5 - 13 : [ 6 0.10 0.40 ] |XXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 10 0.16 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 20 0.32 0.89 ] |XXXX 14 - 14.5 : [ 2 0.03 0.92 ] |XXXXXX 14.5 - 15 : [ 3 0.05 0.97 ] #... |XX 34 - 34.5 : [ 1 0.02 0.98 ] #... |XX 61.5 - 62 : [ 1 0.02 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 21 3 reads 2323 bases = 1.19 +- 0.40 = 1.19 +- 0.40 m1 = 0.13 m2 = 0.00 Contig 7 3 reads 2423 bases = 1.23 +- 0.42 = 1.23 +- 0.42 m1 = 0.15 m2 = 0.00 Contig 26 3 reads 1821 bases = 1.36 +- 0.48 = 1.36 +- 0.48 m1 = 0.17 m2 = 0.00 Contig 18 3 reads 1994 bases = 1.44 +- 0.50 = 0.59 +- 1.27 m1 = 0.17 m2 = -0.34 Contig 25 3 reads 2076 bases = 1.44 +- 0.50 = 0.50 +- 0.80 m1 = 0.17 m2 = -0.10 Contig 9 3 reads 1726 bases = 1.48 +- 0.52 = 0.51 +- 0.85 m1 = 0.18 m2 = -0.11 Contig 4 3 reads 1867 bases = 1.51 +- 0.61 = 0.38 +- 1.11 m1 = 0.25 m2 = -0.22 Contig 14 3 reads 1863 bases = 1.56 +- 0.62 = 1.56 +- 0.62 m1 = 0.25 m2 = 0.00 Contig 6 3 reads 2094 bases = 1.61 +- 0.66 = 1.61 +- 0.66 m1 = 0.27 m2 = 0.00 Contig 20 3 reads 1946 bases = 1.69 +- 0.74 = 1.69 +- 0.74 m1 = 0.32 m2 = 0.00 Contig 30 4 reads 2519 bases = 1.71 +- 0.52 = 0.81 +- 1.15 m1 = 0.16 m2 = -0.26 Contig 16 3 reads 1685 bases = 1.73 +- 0.88 = 0.86 +- 0.35 m1 = 0.45 m2 = 0.16 Contig 24 3 reads 1721 bases = 1.76 +- 0.88 = 0.83 +- 0.37 m1 = 0.44 m2 = 0.16 Contig 27 3 reads 1054 bases = 1.76 +- 0.72 = 1.76 +- 0.72 m1 = 0.30 m2 = 0.00 Contig 13 3 reads 1740 bases = 1.85 +- 0.83 = 0.64 +- 1.01 m1 = 0.38 m2 = -0.08 Contig 15 3 reads 1250 bases = 1.90 +- 0.78 = 0.62 +- 0.48 m1 = 0.32 m2 = 0.10 Contig 23 3 reads 1474 bases = 1.90 +- 0.86 = 1.90 +- 0.86 m1 = 0.39 m2 = 0.00 Contig 8 3 reads 1793 bases = 1.90 +- 0.90 = 0.57 +- 0.93 m1 = 0.43 m2 = -0.02 Contig 11 3 reads 1616 bases = 1.92 +- 0.86 = 0.56 +- 0.97 m1 = 0.39 m2 = -0.05 Contig 17 3 reads 1525 bases = 1.93 +- 0.71 = 0.62 +- 0.65 m1 = 0.26 m2 = 0.02 Contig 102 2220 reads 126619 bases = 13.82 +- 4.43 = 0.04 +- 4.19 m1 = 1.42 m2 = 0.50 Contig 97 1838 reads 104576 bases = 13.82 +- 4.13 = 0.12 +- 3.88 m1 = 1.23 m2 = 0.50 Contig 110 3305 reads 188271 bases = 13.86 +- 4.29 = 0.33 +- 4.30 m1 = 1.32 m2 = -0.03 Contig 82 381 reads 21548 bases = 13.86 +- 4.63 = 0.53 +- 4.67 m1 = 1.55 m2 = -0.09 Contig 85 487 reads 26999 bases = 13.88 +- 4.57 = 0.40 +- 3.81 m1 = 1.50 m2 = 1.59 Contig 100 1952 reads 110813 bases = 13.91 +- 3.94 = 0.25 +- 3.80 m1 = 1.12 m2 = 0.26 Contig 74 193 reads 10845 bases = 13.94 +- 5.77 = 0.76 +- 3.95 m1 = 2.39 m2 = 4.44 Contig 79 354 reads 20523 bases = 13.94 +- 4.27 = 0.39 +- 3.63 m1 = 1.30 m2 = 1.25 Contig 96 1816 reads 102580 bases = 13.99 +- 3.97 = 0.29 +- 3.72 m1 = 1.12 m2 = 0.47 Contig 114 4970 reads 276032 bases = 14.13 +- 3.93 = 0.02 +- 3.85 m1 = 1.09 m2 = 0.15 Contig 94 1533 reads 85051 bases = 14.19 +- 4.32 = 0.14 +- 3.68 m1 = 1.32 m2 = 1.30 Contig 104 2760 reads 149561 bases = 14.55 +- 3.72 = -0.06 +- 4.09 m1 = 0.95 m2 = -0.72 Contig 108 2999 reads 162238 bases = 14.59 +- 4.61 = 0.27 +- 4.34 m1 = 1.45 m2 = 0.59 Contig 60 51 reads 2699 bases = 14.82 +- 6.85 = 1.71 +- 4.11 m1 = 3.17 m2 = 7.51 Contig 55 32 reads 1330 bases = 15.72 +- 4.83 = -1.02 +- 5.04 m1 = 1.48 m2 = -0.53 Contig 62 57 reads 1518 bases = 28.63 +- 20.26 = 3.56 +- 3.74 m1 = 14.34 m2 = 99.12 Contig 78 261 reads 6673 bases = 34.44 +- 44.38 = 34.44 +- 44.38 m1 = 57.19 m2 = 0.00 Contig 61 52 reads 945 bases = 43.02 +- 14.81 = 43.02 +- 14.81 m1 = 5.10 m2 = 0.00 Contig 63 60 reads 873 bases = 49.72 +- 17.85 = 49.72 +- 17.85 m1 = 6.41 m2 = 0.00 Contig 88 745 reads 10971 bases = 61.63 +- 120.02 = 61.63 +- 120.02 m1 = 233.74 m2 = 0.00 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 118 total values totalling 134602.0000. <1140.694915 +/- 3236.347600> #Range: [ 1 - 22508 ] #Most likely bin: [ 3 - 4 ] 26 counts #Median bin: [ 37 - 38 ] 1 counts |XX 1 - 2 : [ 1 0.01 0.01 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 4 : [ 26 0.22 0.23 ] |XXXXXXXXX 4 - 5 : [ 6 0.05 0.28 ] |XXX 5 - 6 : [ 2 0.02 0.30 ] |XX 6 - 7 : [ 1 0.01 0.31 ] #... |XXXXXX 8 - 9 : [ 4 0.03 0.34 ] |XX 9 - 10 : [ 1 0.01 0.35 ] |XXX 10 - 11 : [ 2 0.02 0.36 ] |XXX 11 - 12 : [ 2 0.02 0.38 ] |XX 12 - 13 : [ 1 0.01 0.39 ] |XXX 13 - 14 : [ 2 0.02 0.41 ] #... |XX 17 - 18 : [ 1 0.01 0.42 ] |XX 18 - 19 : [ 1 0.01 0.42 ] #... |XX 23 - 24 : [ 1 0.01 0.43 ] |XX 24 - 25 : [ 1 0.01 0.44 ] |XX 25 - 26 : [ 1 0.01 0.45 ] |XX 26 - 27 : [ 1 0.01 0.46 ] #... |XXX 32 - 33 : [ 2 0.02 0.47 ] #... |XXX 36 - 37 : [ 2 0.02 0.49 ] |XX 37 - 38 : [ 1 0.01 0.50 ] #... |XX 51 - 52 : [ 1 0.01 0.51 ] |XX 52 - 53 : [ 1 0.01 0.52 ] #... |XX 57 - 58 : [ 1 0.01 0.53 ] #... |XX 60 - 61 : [ 1 0.01 0.53 ] #... |XX 70 - 71 : [ 1 0.01 0.54 ] #... |XX 78 - 79 : [ 1 0.01 0.55 ] #... |XX 89 - 90 : [ 1 0.01 0.56 ] #... |XX 93 - 94 : [ 1 0.01 0.57 ] #... |XX 106 - 107 : [ 1 0.01 0.58 ] #... |XX 109 - 110 : [ 1 0.01 0.58 ] #... |XX 120 - 121 : [ 1 0.01 0.59 ] #... |XX 145 - 146 : [ 1 0.01 0.60 ] #... |XX 155 - 156 : [ 1 0.01 0.61 ] #... |XX 184 - 185 : [ 1 0.01 0.62 ] #... |XX 193 - 194 : [ 1 0.01 0.63 ] #... |XX 202 - 203 : [ 1 0.01 0.64 ] #... |XX 210 - 211 : [ 1 0.01 0.64 ] #... |XX 228 - 229 : [ 1 0.01 0.65 ] #... |XX 261 - 262 : [ 1 0.01 0.66 ] #... |XX 354 - 355 : [ 1 0.01 0.67 ] #... |XX 369 - 370 : [ 1 0.01 0.68 ] #... |XX 374 - 375 : [ 1 0.01 0.69 ] #... |XX 381 - 382 : [ 1 0.01 0.69 ] #... |XX 391 - 392 : [ 1 0.01 0.70 ] #... |XX 414 - 415 : [ 1 0.01 0.71 ] #... |XX 487 - 488 : [ 1 0.01 0.72 ] #... |XX 599 - 600 : [ 1 0.01 0.73 ] #... |XX 730 - 731 : [ 1 0.01 0.74 ] #... |XX 745 - 746 : [ 1 0.01 0.75 ] #... |XX 773 - 774 : [ 1 0.01 0.75 ] #... |XX 806 - 807 : [ 1 0.01 0.76 ] #... |XX 1076 - 1077 : [ 1 0.01 0.77 ] #... |XX 1310 - 1311 : [ 1 0.01 0.78 ] #... |XX 1437 - 1438 : [ 1 0.01 0.79 ] #... |XX 1533 - 1534 : [ 1 0.01 0.80 ] #... |XX 1693 - 1694 : [ 1 0.01 0.81 ] #... |XX 1816 - 1817 : [ 1 0.01 0.81 ] #... |XX 1838 - 1839 : [ 1 0.01 0.82 ] #... |XX 1900 - 1901 : [ 1 0.01 0.83 ] #... |XX 1918 - 1919 : [ 1 0.01 0.84 ] #... |XX 1952 - 1953 : [ 1 0.01 0.85 ] #... |XX 2100 - 2101 : [ 1 0.01 0.86 ] #... |XX 2220 - 2221 : [ 1 0.01 0.86 ] #... |XX 2437 - 2438 : [ 1 0.01 0.87 ] #... |XX 2760 - 2761 : [ 1 0.01 0.88 ] #... |XX 2887 - 2888 : [ 1 0.01 0.89 ] #... |XX 2890 - 2891 : [ 1 0.01 0.90 ] #... |XX 2971 - 2972 : [ 1 0.01 0.91 ] #... |XX 2999 - 3000 : [ 1 0.01 0.92 ] #... |XX 3034 - 3035 : [ 1 0.01 0.92 ] #... |XX 3305 - 3306 : [ 1 0.01 0.93 ] #... |XX 3992 - 3993 : [ 1 0.01 0.94 ] #... |XX 4009 - 4010 : [ 1 0.01 0.95 ] #... |XX 4035 - 4036 : [ 1 0.01 0.96 ] #... |XX 4970 - 4971 : [ 1 0.01 0.97 ] #... |XX 5150 - 5151 : [ 1 0.01 0.97 ] #... |XX 15968 - 15969 : [ 1 0.01 0.98 ] #... |XX 20462 - 20463 : [ 1 0.01 0.99 ] #... |XX 22508 - 22509 : [ 1 0.01 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 118 total values totalling 7847528.0000. <66504.474576 +/- 187981.185167> #Range: [ 100 - 1319663 ] #Most likely bin: [ 1000 - 2000 ] 32 counts #Median bin: [ 2000 - 3000 ] 17 counts |XXXXXXXXXXXXXXXXXX 0 - 1000 : [ 14 0.12 0.12 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 32 0.27 0.39 ] |XXXXXXXXXXXXXXXXXXXXX 2000 - 3000 : [ 17 0.14 0.53 ] |X 3000 - 4000 : [ 1 0.01 0.54 ] #... |XX 5000 - 6000 : [ 2 0.02 0.56 ] |XXXXX 6000 - 7000 : [ 4 0.03 0.59 ] |X 7000 - 8000 : [ 1 0.01 0.60 ] #... |X 9000 - 10000 : [ 1 0.01 0.61 ] |XXXX 10000 - 11000 : [ 3 0.03 0.64 ] |X 11000 - 12000 : [ 1 0.01 0.64 ] #... |X 13000 - 14000 : [ 1 0.01 0.65 ] |X 14000 - 15000 : [ 1 0.01 0.66 ] |X 15000 - 16000 : [ 1 0.01 0.67 ] #... |X 20000 - 21000 : [ 1 0.01 0.68 ] |X 21000 - 22000 : [ 1 0.01 0.69 ] #... |XX 24000 - 25000 : [ 2 0.02 0.70 ] |X 25000 - 26000 : [ 1 0.01 0.71 ] |XX 26000 - 27000 : [ 2 0.02 0.73 ] #... |X 35000 - 36000 : [ 1 0.01 0.74 ] #... |X 46000 - 47000 : [ 1 0.01 0.75 ] |XX 47000 - 48000 : [ 2 0.02 0.76 ] #... |X 62000 - 63000 : [ 1 0.01 0.77 ] #... |X 77000 - 78000 : [ 1 0.01 0.78 ] #... |X 85000 - 86000 : [ 1 0.01 0.79 ] |X 86000 - 87000 : [ 1 0.01 0.80 ] #... |X 102000 - 103000 : [ 1 0.01 0.81 ] #... |XX 104000 - 105000 : [ 2 0.02 0.82 ] #... |XX 110000 - 111000 : [ 2 0.02 0.84 ] #... |X 117000 - 118000 : [ 1 0.01 0.85 ] #... |X 122000 - 123000 : [ 1 0.01 0.86 ] #... |X 126000 - 127000 : [ 1 0.01 0.86 ] #... |X 139000 - 140000 : [ 1 0.01 0.87 ] #... |X 149000 - 150000 : [ 1 0.01 0.88 ] #... |X 162000 - 163000 : [ 1 0.01 0.89 ] #... |X 168000 - 169000 : [ 1 0.01 0.90 ] #... |X 170000 - 171000 : [ 1 0.01 0.91 ] #... |X 173000 - 174000 : [ 1 0.01 0.92 ] |X 174000 - 175000 : [ 1 0.01 0.92 ] #... |X 188000 - 189000 : [ 1 0.01 0.93 ] #... |X 232000 - 233000 : [ 1 0.01 0.94 ] #... |X 235000 - 236000 : [ 1 0.01 0.95 ] #... |X 238000 - 239000 : [ 1 0.01 0.96 ] #... |X 276000 - 277000 : [ 1 0.01 0.97 ] #... |X 307000 - 308000 : [ 1 0.01 0.97 ] #... |X 928000 - 929000 : [ 1 0.01 0.98 ] #... |X 1178000 - 1179000 : [ 1 0.01 0.99 ] #... |X 1319000 - 1320000 : [ 1 0.01 1.00 ] ################################################################### Histogram of Assembled Average Insert Sizes Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list ------------------------------------------------------------------- Command: /usr/xpg4/bin/grep ABTK reads.list > grep.reads.list.ABTK Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ABTK 4 500 #Found 267 total values totalling 9884794.0000. <37021.700375 +/- 23144.155865> #Range: [ - 407792 ] #Most likely bin: [ 35500 - 36000 ] 23 counts #Median bin: [ 35500 - 36000 ] 23 counts |XX 0 - 500 : [ 1 0.00 0.00 ] #... |XX 15500 - 16000 : [ 1 0.00 0.01 ] #... |XX 18500 - 19000 : [ 1 0.00 0.01 ] #... |XXX 24000 - 24500 : [ 2 0.01 0.02 ] |XXX 24500 - 25000 : [ 2 0.01 0.03 ] #... |XX 26500 - 27000 : [ 1 0.00 0.03 ] |XX 27000 - 27500 : [ 1 0.00 0.03 ] |XX 27500 - 28000 : [ 1 0.00 0.04 ] |XX 28000 - 28500 : [ 1 0.00 0.04 ] |XXX 28500 - 29000 : [ 2 0.01 0.05 ] #... |XXXXX 29500 - 30000 : [ 3 0.01 0.06 ] |XXX 30000 - 30500 : [ 2 0.01 0.07 ] |XX 30500 - 31000 : [ 1 0.00 0.07 ] |XXXXX 31000 - 31500 : [ 3 0.01 0.08 ] |XXXXXXX 31500 - 32000 : [ 4 0.01 0.10 ] |XXXXXXXXXXXXXXXX 32000 - 32500 : [ 9 0.03 0.13 ] |XXXXXXXXXXXXXX 32500 - 33000 : [ 8 0.03 0.16 ] |XXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 12 0.04 0.21 ] |XXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 11 0.04 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 14 0.05 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 18 0.07 0.37 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 19 0.07 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 23 0.09 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 22 0.08 0.61 ] |XXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 12 0.04 0.65 ] |XXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 12 0.04 0.70 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 20 0.07 0.77 ] |XXXXXXXXXXXX 38000 - 38500 : [ 7 0.03 0.80 ] |XXXXXXXXXX 38500 - 39000 : [ 6 0.02 0.82 ] |XXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 11 0.04 0.86 ] |XXXXXXXXXXXXXX 39500 - 40000 : [ 8 0.03 0.89 ] |XXXXXXX 40000 - 40500 : [ 4 0.01 0.91 ] |XXXXXXXXXXXXXXXXX 40500 - 41000 : [ 10 0.04 0.94 ] |XXXXX 41000 - 41500 : [ 3 0.01 0.96 ] |XXXXX 41500 - 42000 : [ 3 0.01 0.97 ] |XXX 42000 - 42500 : [ 2 0.01 0.97 ] |XXX 42500 - 43000 : [ 2 0.01 0.98 ] #... |XX 43500 - 44000 : [ 1 0.00 0.99 ] |XX 44000 - 44500 : [ 1 0.00 0.99 ] |XX 44500 - 45000 : [ 1 0.00 0.99 ] |XX 45000 - 45500 : [ 1 0.00 1.00 ] #... |XX 407500 - 408000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep ABSU reads.list > grep.reads.list.ABSU Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ABSU 4 500 #Found 8664 total values totalling 59427991.0000. <6859.186404 +/- 15655.614369> #Range: [ - 733864 ] #Most likely bin: [ 6000 - 6500 ] 2463 counts #Median bin: [ 6000 - 6500 ] 2463 counts | 0 - 500 : [ 12 0.00 0.00 ] #... |X 1000 - 1500 : [ 38 0.00 0.01 ] |X 1500 - 2000 : [ 54 0.01 0.01 ] |X 2000 - 2500 : [ 64 0.01 0.02 ] |X 2500 - 3000 : [ 59 0.01 0.03 ] |X 3000 - 3500 : [ 66 0.01 0.03 ] |X 3500 - 4000 : [ 78 0.01 0.04 ] |XX 4000 - 4500 : [ 101 0.01 0.05 ] |XXX 4500 - 5000 : [ 166 0.02 0.07 ] |XXXXXX 5000 - 5500 : [ 367 0.04 0.12 ] |XXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1081 0.12 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2463 0.28 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2280 0.26 0.79 ] |XXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1406 0.16 0.95 ] |XXXXXX 7500 - 8000 : [ 399 0.05 1.00 ] | 8000 - 8500 : [ 12 0.00 1.00 ] | 8500 - 9000 : [ 3 0.00 1.00 ] | 9000 - 9500 : [ 1 0.00 1.00 ] | 9500 - 10000 : [ 1 0.00 1.00 ] #... | 66000 - 66500 : [ 1 0.00 1.00 ] #... | 136000 - 136500 : [ 1 0.00 1.00 ] #... | 343500 - 344000 : [ 1 0.00 1.00 ] #... | 378000 - 378500 : [ 1 0.00 1.00 ] | 378500 - 379000 : [ 2 0.00 1.00 ] | 379000 - 379500 : [ 3 0.00 1.00 ] | 379500 - 380000 : [ 1 0.00 1.00 ] | 380000 - 380500 : [ 1 0.00 1.00 ] #... | 589000 - 589500 : [ 1 0.00 1.00 ] #... | 733500 - 734000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep TQZ reads.list > grep.reads.list.TQZ Command: /home/copeland/scripts/histogram2.pl grep.reads.list.TQZ 4 500 #Found 1 total values totalling 0.0000. <0.000000 +/- 0.000000> #Range: [ - ] #Most likely bin: [ 0 - 500 ] 1 counts #Median bin: [ 0 - 500 ] 1 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 500 : [ 1 1.00 1.00 ] Command: /usr/xpg4/bin/grep SRU reads.list > grep.reads.list.SRU Command: /home/copeland/scripts/histogram2.pl grep.reads.list.SRU 4 500 #Found 5043 total values totalling 16478564.0000. <3267.611342 +/- 9047.072734> #Range: [ - 439210 ] #Most likely bin: [ 2500 - 3000 ] 2094 counts #Median bin: [ 2500 - 3000 ] 2094 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 5 0.00 0.00 ] | 1000 - 1500 : [ 23 0.00 0.01 ] |X 1500 - 2000 : [ 68 0.01 0.02 ] |XXXXXXXXXXX 2000 - 2500 : [ 574 0.11 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2094 0.42 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1334 0.26 0.81 ] |XXXXXXXXXXXX 3500 - 4000 : [ 639 0.13 0.94 ] |XXXXX 4000 - 4500 : [ 236 0.05 0.99 ] |X 4500 - 5000 : [ 60 0.01 1.00 ] | 5000 - 5500 : [ 4 0.00 1.00 ] #... | 87500 - 88000 : [ 1 0.00 1.00 ] #... | 91000 - 91500 : [ 1 0.00 1.00 ] #... | 261000 - 261500 : [ 1 0.00 1.00 ] #... | 376500 - 377000 : [ 1 0.00 1.00 ] #... | 439000 - 439500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep SUT reads.list > grep.reads.list.SUT Command: /home/copeland/scripts/histogram2.pl grep.reads.list.SUT 4 500 #Found 8076 total values totalling 26757124.0000. <3313.165428 +/- 11482.681485> #Range: [ - 463138 ] #Most likely bin: [ 2500 - 3000 ] 3486 counts #Median bin: [ 2500 - 3000 ] 3486 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 6 0.00 0.00 ] |X 1000 - 1500 : [ 46 0.01 0.01 ] |X 1500 - 2000 : [ 92 0.01 0.02 ] |XXXXXXXXXXX 2000 - 2500 : [ 979 0.12 0.14 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 3486 0.43 0.57 ] |XXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2051 0.25 0.82 ] |XXXXXXXXXXX 3500 - 4000 : [ 955 0.12 0.94 ] |XXXX 4000 - 4500 : [ 354 0.04 0.99 ] |X 4500 - 5000 : [ 95 0.01 1.00 ] | 5000 - 5500 : [ 5 0.00 1.00 ] #... | 375500 - 376000 : [ 1 0.00 1.00 ] #... | 376500 - 377000 : [ 1 0.00 1.00 ] #... | 427500 - 428000 : [ 1 0.00 1.00 ] | 428000 - 428500 : [ 1 0.00 1.00 ] #... | 462500 - 463000 : [ 1 0.00 1.00 ] | 463000 - 463500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep POM reads.list > grep.reads.list.POM Command: /home/copeland/scripts/histogram2.pl grep.reads.list.POM 4 500 #Found 33179 total values totalling 110747432.0000. <3337.877332 +/- 11580.318364> #Range: [ - 962322 ] #Most likely bin: [ 2500 - 3000 ] 13706 counts #Median bin: [ 2500 - 3000 ] 13706 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 21 0.00 0.00 ] | 1000 - 1500 : [ 137 0.00 0.00 ] |X 1500 - 2000 : [ 347 0.01 0.02 ] |XXXXXXXXXXX 2000 - 2500 : [ 3711 0.11 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 13706 0.41 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 8729 0.26 0.80 ] |XXXXXXXXXXXXX 3500 - 4000 : [ 4320 0.13 0.93 ] |XXXXX 4000 - 4500 : [ 1641 0.05 0.98 ] |X 4500 - 5000 : [ 507 0.02 1.00 ] | 5000 - 5500 : [ 31 0.00 1.00 ] #... | 85000 - 85500 : [ 1 0.00 1.00 ] #... | 86000 - 86500 : [ 2 0.00 1.00 ] #... | 91000 - 91500 : [ 1 0.00 1.00 ] | 91500 - 92000 : [ 1 0.00 1.00 ] #... | 132000 - 132500 : [ 1 0.00 1.00 ] #... | 256000 - 256500 : [ 1 0.00 1.00 ] #... | 262000 - 262500 : [ 1 0.00 1.00 ] #... | 294500 - 295000 : [ 1 0.00 1.00 ] #... | 375000 - 375500 : [ 5 0.00 1.00 ] | 375500 - 376000 : [ 4 0.00 1.00 ] | 376000 - 376500 : [ 3 0.00 1.00 ] #... | 427500 - 428000 : [ 1 0.00 1.00 ] #... | 428500 - 429000 : [ 1 0.00 1.00 ] #... | 439000 - 439500 : [ 1 0.00 1.00 ] #... | 462500 - 463000 : [ 1 0.00 1.00 ] #... | 551500 - 552000 : [ 1 0.00 1.00 ] #... | 725000 - 725500 : [ 1 0.00 1.00 ] #... | 962000 - 962500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AGPT reads.list > grep.reads.list.AGPT Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AGPT 4 500 #Found 1548 total values totalling 56688363.0000. <36620.389535 +/- 15054.074619> #Range: [ - 411111 ] #Most likely bin: [ 35500 - 36000 ] 139 counts #Median bin: [ 35500 - 36000 ] 139 counts | 0 - 500 : [ 1 0.00 0.00 ] #... | 12000 - 12500 : [ 1 0.00 0.00 ] #... | 13500 - 14000 : [ 1 0.00 0.00 ] | 14000 - 14500 : [ 1 0.00 0.00 ] #... | 15000 - 15500 : [ 1 0.00 0.00 ] #... | 17500 - 18000 : [ 1 0.00 0.00 ] #... | 21000 - 21500 : [ 1 0.00 0.00 ] #... | 22000 - 22500 : [ 1 0.00 0.01 ] #... | 23000 - 23500 : [ 1 0.00 0.01 ] |X 23500 - 24000 : [ 2 0.00 0.01 ] |X 24000 - 24500 : [ 2 0.00 0.01 ] #... | 26000 - 26500 : [ 1 0.00 0.01 ] | 26500 - 27000 : [ 1 0.00 0.01 ] #... |X 27500 - 28000 : [ 3 0.00 0.01 ] #... |X 28500 - 29000 : [ 2 0.00 0.01 ] | 29000 - 29500 : [ 1 0.00 0.01 ] |XX 29500 - 30000 : [ 7 0.00 0.02 ] |XX 30000 - 30500 : [ 6 0.00 0.02 ] |XXX 30500 - 31000 : [ 10 0.01 0.03 ] |XXXX 31000 - 31500 : [ 14 0.01 0.04 ] |XXXXX 31500 - 32000 : [ 18 0.01 0.05 ] |XXXXXXXXXXXX 32000 - 32500 : [ 40 0.03 0.07 ] |XXXXXXXXXXXXXX 32500 - 33000 : [ 48 0.03 0.11 ] |XXXXXXXXXXXXXXXXX 33000 - 33500 : [ 59 0.04 0.14 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 89 0.06 0.20 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 112 0.07 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 120 0.08 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 130 0.08 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 139 0.09 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 106 0.07 0.59 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 120 0.08 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 87 0.06 0.73 ] |XXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 77 0.05 0.78 ] |XXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 64 0.04 0.82 ] |XXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 63 0.04 0.86 ] |XXXXXXXXXXXXXX 39000 - 39500 : [ 48 0.03 0.89 ] |XXXXXXXXXXXXX 39500 - 40000 : [ 46 0.03 0.92 ] |XXXXXXXX 40000 - 40500 : [ 29 0.02 0.94 ] |XXXXXXX 40500 - 41000 : [ 25 0.02 0.95 ] |XXX 41000 - 41500 : [ 10 0.01 0.96 ] |XXX 41500 - 42000 : [ 9 0.01 0.97 ] |XXXX 42000 - 42500 : [ 15 0.01 0.98 ] |XX 42500 - 43000 : [ 8 0.01 0.98 ] |XXXX 43000 - 43500 : [ 13 0.01 0.99 ] |X 43500 - 44000 : [ 5 0.00 0.99 ] |X 44000 - 44500 : [ 4 0.00 1.00 ] |X 44500 - 45000 : [ 3 0.00 1.00 ] #... | 277000 - 277500 : [ 1 0.00 1.00 ] #... | 405500 - 406000 : [ 1 0.00 1.00 ] #... | 411000 - 411500 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # ABSU 6067 +- 1151 (n=4308) # ABTK 35230 +- 3847 (n=141) # SUT 2856 +- 581 (n=4027) # POM 2935 +- 591 (n=16601) # SRU 2889 +- 593 (n=2485) # AGPT 35936 +- 3135 (n=773) ################################################################### 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 568.159438 bp, 134602 reads, genome size 7281922 bp Command: idealAssembly 7281922 134602 568.159438 ------------------------------------------------------------------- Genome = 7281922 bases Nreads = 134602 readLength = 568.159438 Depth = 10.50 N_contigs = N_gaps = 4 mean gap size = 53 bases mean contig size = 36391 reads (~ 1968766 bases) %cover = 100.00 %singlet = 0.00 assembly size = 7281722 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 1 contigs containing at least 61065 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: