################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 3634483 Genus_species: Anaeromyxobacter dehalogenans 2CP-C Taxid: 161493 Genome size: 3380 Libraries: AHZN, AHZI, AHZK ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 3634483 ------------------------------------------------------------------- ID=3634483 Lineage for 'Anaeromyxobacter dehalogenans': Anaeromyxobacter dehalogenans species Anaeromyxobacter genus Myxococcaceae family Cystobacterineae suborder Myxococcales order Deltaproteobacteria class delta/epsilon subdivisions subphylum Proteobacteria phylum Bacteria superkingdom cellular organisms no rank root no rank ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 5002096 # phrap: 6497607 # db: 3380000 4959901 +/- 1273107 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length AHZI.5-44 304 90.80 563.02 AHZK.5-68 372 87.48 493.94 AHZN.5-24 40 56.35 250.50 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s AHZN 40 20 49.74 211.85 20 62.97 289.15 AHZI 304 150 91.84 574.77 154 89.79 551.58 AHZK 372 188 91.14 535.56 184 83.75 451.41 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634483_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 3634483_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634483.out /home/copeland/scripts/librariesInfoTxt.sh 3634483 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634483_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 3634483_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634483.out /home/copeland/scripts/librariesInfoTxt.sh 3634483 phrap.out > librariesInfo.txt ################################################################### Library vector screening AHZI.000001.000100 screen.out.1 3634483_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634483_fasta.screen /usr/local/sequences/LRS.fasta AHZI.000101.000200 screen.out.1 3634483_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634483_fasta.screen /usr/local/sequences/LRS.fasta AHZK.000001.000100 screen.out.1 3634483_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634483_fasta.screen /usr/local/sequences/LRS.fasta AHZK.000101.000200 screen.out.1 3634483_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634483_fasta.screen /usr/local/sequences/LRS.fasta AHZN.000001.000100 screen.out.1 3634483_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634483_fasta.screen /usr/local/sequences/LRS.fasta AHZI.000001.000100 screen.out.1 3634483_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634483_fasta.screen /usr/local/sequences/LRS.fasta AHZI.000101.000200 screen.out.1 3634483_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634483_fasta.screen /usr/local/sequences/LRS.fasta AHZK.000001.000100 screen.out.1 3634483_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634483_fasta.screen /usr/local/sequences/LRS.fasta AHZK.000101.000200 screen.out.1 3634483_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634483_fasta.screen /usr/local/sequences/LRS.fasta AHZN.000001.000100 screen.out.1 3634483_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634483_fasta.screen /usr/local/sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 3634483_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 59627 total values totalling 34396465.0000. <576.860567 +/- 211.883819> #Range: [ 22 - 933 ] #Most likely bin: [ 700 - 750 ] 8833 counts #Median bin: [ 650 - 700 ] 7258 counts |X 0 - 50 : [ 278 0.00 0.00 ] |XXXXX 50 - 100 : [ 1133 0.02 0.02 ] |XXXXXXX 100 - 150 : [ 1454 0.02 0.05 ] |XXXXXXX 150 - 200 : [ 1569 0.03 0.07 ] |XXXXXXXX 200 - 250 : [ 1756 0.03 0.10 ] |XXXXXXXXXXX 250 - 300 : [ 2433 0.04 0.14 ] |XXXXXXXXXXXXXX 300 - 350 : [ 3198 0.05 0.20 ] |XXXXXXXXXXX 350 - 400 : [ 2338 0.04 0.24 ] |XXXXXXXXXX 400 - 450 : [ 2134 0.04 0.27 ] |XXXXXXXXXX 450 - 500 : [ 2123 0.04 0.31 ] |XXXXXXXXXXXX 500 - 550 : [ 2684 0.05 0.35 ] |XXXXXXXXXXXXXXX 550 - 600 : [ 3403 0.06 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 5030 0.08 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 7258 0.12 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8833 0.15 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8720 0.15 0.91 ] |XXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4606 0.08 0.99 ] |XXX 850 - 900 : [ 665 0.01 1.00 ] | 900 - 950 : [ 12 0.00 1.00 ] JAZZ trim 15 readlength histogram for AHZI Command: /usr/xpg4/bin/grep AHZI 3634483_fasta.screen.screen.ids > reads.trim15.AHZI.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZI.rl 2 50 #Found 29252 total values totalling 17670544.0000. <604.079858 +/- 205.105640> #Range: [ 22 - 933 ] #Most likely bin: [ 750 - 800 ] 4927 counts #Median bin: [ 650 - 700 ] 3702 counts |X 0 - 50 : [ 65 0.00 0.00 ] |XXXX 50 - 100 : [ 446 0.02 0.02 ] |XXXXXX 100 - 150 : [ 678 0.02 0.04 ] |XXXXXX 150 - 200 : [ 766 0.03 0.07 ] |XXXXXX 200 - 250 : [ 788 0.03 0.09 ] |XXXXXXX 250 - 300 : [ 889 0.03 0.12 ] |XXXXXXXX 300 - 350 : [ 1006 0.03 0.16 ] |XXXXXXX 350 - 400 : [ 920 0.03 0.19 ] |XXXXXXX 400 - 450 : [ 917 0.03 0.22 ] |XXXXXXXX 450 - 500 : [ 965 0.03 0.25 ] |XXXXXXXXXX 500 - 550 : [ 1276 0.04 0.30 ] |XXXXXXXXXXXXX 550 - 600 : [ 1599 0.05 0.35 ] |XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2495 0.09 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3702 0.13 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4476 0.15 0.72 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4927 0.17 0.89 ] |XXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2885 0.10 0.98 ] |XXXX 850 - 900 : [ 443 0.02 1.00 ] | 900 - 950 : [ 9 0.00 1.00 ] JAZZ trim 15 readlength histogram for AHZK Command: /usr/xpg4/bin/grep AHZK 3634483_fasta.screen.screen.ids > reads.trim15.AHZK.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZK.rl 2 50 #Found 28398 total values totalling 15887805.0000. <559.469153 +/- 212.539151> #Range: [ 22 - 911 ] #Most likely bin: [ 700 - 750 ] 4222 counts #Median bin: [ 600 - 650 ] 2385 counts |XX 0 - 50 : [ 185 0.01 0.01 ] |XXXXX 50 - 100 : [ 576 0.02 0.03 ] |XXXXXX 100 - 150 : [ 680 0.02 0.05 ] |XXXXXXX 150 - 200 : [ 702 0.02 0.08 ] |XXXXXXXX 200 - 250 : [ 866 0.03 0.11 ] |XXXXXXXXXXXXX 250 - 300 : [ 1324 0.05 0.15 ] |XXXXXXXXXXXXXXXXXXXX 300 - 350 : [ 2065 0.07 0.23 ] |XXXXXXXXXXXX 350 - 400 : [ 1265 0.04 0.27 ] |XXXXXXXXXX 400 - 450 : [ 1033 0.04 0.31 ] |XXXXXXXXXX 450 - 500 : [ 1048 0.04 0.34 ] |XXXXXXXXXXXX 500 - 550 : [ 1307 0.05 0.39 ] |XXXXXXXXXXXXXXXX 550 - 600 : [ 1693 0.06 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2385 0.08 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3404 0.12 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4222 0.15 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3719 0.13 0.93 ] |XXXXXXXXXXXXXXXX 800 - 850 : [ 1700 0.06 0.99 ] |XX 850 - 900 : [ 221 0.01 1.00 ] | 900 - 950 : [ 3 0.00 1.00 ] JAZZ trim 15 readlength histogram for AHZN Command: /usr/xpg4/bin/grep AHZN 3634483_fasta.screen.screen.ids > reads.trim15.AHZN.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZN.rl 2 50 #Found 1977 total values totalling 838116.0000. <423.933232 +/- 209.823995> #Range: [ 23 - 859 ] #Most likely bin: [ 250 - 300 ] 220 counts #Median bin: [ 400 - 450 ] 184 counts |XXXXX 0 - 50 : [ 28 0.01 0.01 ] |XXXXXXXXXXXXXXXXXXXX 50 - 100 : [ 111 0.06 0.07 ] |XXXXXXXXXXXXXXXXX 100 - 150 : [ 96 0.05 0.12 ] |XXXXXXXXXXXXXXXXXX 150 - 200 : [ 101 0.05 0.17 ] |XXXXXXXXXXXXXXXXXXX 200 - 250 : [ 102 0.05 0.22 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 220 0.11 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXX 300 - 350 : [ 127 0.06 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 350 - 400 : [ 153 0.08 0.47 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 400 - 450 : [ 184 0.09 0.57 ] |XXXXXXXXXXXXXXXXXXXX 450 - 500 : [ 110 0.06 0.62 ] |XXXXXXXXXXXXXXXXXX 500 - 550 : [ 101 0.05 0.67 ] |XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 111 0.06 0.73 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 150 0.08 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 152 0.08 0.88 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 135 0.07 0.95 ] |XXXXXXXXXXXXX 750 - 800 : [ 74 0.04 0.99 ] |XXXX 800 - 850 : [ 21 0.01 1.00 ] | 850 - 900 : [ 1 0.00 1.00 ] ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.3634483_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.3634483_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 59232 total values totalling 43901.2362. <0.741174 +/- 0.049847> #Range: [ 0 - 1 ] #Most likely bin: [ 0.75 - 0.755 ] 2774 counts #Median bin: [ 0.74 - 0.745 ] 2455 counts | 0 - 0.005 : [ 1 0.00 0.00 ] #... | 0.34 - 0.345 : [ 1 0.00 0.00 ] | 0.345 - 0.35 : [ 1 0.00 0.00 ] #... | 0.395 - 0.4 : [ 1 0.00 0.00 ] #... | 0.42 - 0.425 : [ 2 0.00 0.00 ] | 0.425 - 0.43 : [ 2 0.00 0.00 ] #... | 0.465 - 0.47 : [ 1 0.00 0.00 ] #... | 0.48 - 0.485 : [ 3 0.00 0.00 ] #... | 0.5 - 0.505 : [ 6 0.00 0.00 ] #... | 0.51 - 0.515 : [ 5 0.00 0.00 ] | 0.515 - 0.52 : [ 6 0.00 0.00 ] | 0.52 - 0.525 : [ 5 0.00 0.00 ] | 0.525 - 0.53 : [ 9 0.00 0.00 ] | 0.53 - 0.535 : [ 10 0.00 0.00 ] | 0.535 - 0.54 : [ 7 0.00 0.00 ] | 0.54 - 0.545 : [ 10 0.00 0.00 ] | 0.545 - 0.55 : [ 6 0.00 0.00 ] | 0.55 - 0.555 : [ 8 0.00 0.00 ] | 0.555 - 0.56 : [ 18 0.00 0.00 ] | 0.56 - 0.565 : [ 26 0.00 0.00 ] | 0.565 - 0.57 : [ 20 0.00 0.00 ] | 0.57 - 0.575 : [ 31 0.00 0.00 ] | 0.575 - 0.58 : [ 28 0.00 0.00 ] |X 0.58 - 0.585 : [ 52 0.00 0.00 ] |X 0.585 - 0.59 : [ 61 0.00 0.01 ] |X 0.59 - 0.595 : [ 87 0.00 0.01 ] |X 0.595 - 0.6 : [ 90 0.00 0.01 ] |XX 0.6 - 0.605 : [ 106 0.00 0.01 ] |XX 0.605 - 0.61 : [ 106 0.00 0.01 ] |X 0.61 - 0.615 : [ 95 0.00 0.01 ] |XX 0.615 - 0.62 : [ 119 0.00 0.02 ] |XX 0.62 - 0.625 : [ 120 0.00 0.02 ] |XXX 0.625 - 0.63 : [ 219 0.00 0.02 ] |XXXX 0.63 - 0.635 : [ 251 0.00 0.03 ] |XXXX 0.635 - 0.64 : [ 245 0.00 0.03 ] |XXXX 0.64 - 0.645 : [ 270 0.00 0.03 ] |XXXXX 0.645 - 0.65 : [ 323 0.01 0.04 ] |XXXXX 0.65 - 0.655 : [ 380 0.01 0.05 ] |XXXXXXX 0.655 - 0.66 : [ 452 0.01 0.05 ] |XXXXXXX 0.66 - 0.665 : [ 511 0.01 0.06 ] |XXXXXXXXX 0.665 - 0.67 : [ 657 0.01 0.07 ] |XXXXXXXXXXX 0.67 - 0.675 : [ 762 0.01 0.09 ] |XXXXXXXXXXXX 0.675 - 0.68 : [ 838 0.01 0.10 ] |XXXXXXXXXXXXXXX 0.68 - 0.685 : [ 1072 0.02 0.12 ] |XXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 1131 0.02 0.14 ] |XXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 1343 0.02 0.16 ] |XXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 1429 0.02 0.18 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 1678 0.03 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 1805 0.03 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 1966 0.03 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 2086 0.04 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 2114 0.04 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.725 - 0.73 : [ 2343 0.04 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.73 - 0.735 : [ 2450 0.04 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.735 - 0.74 : [ 2437 0.04 0.47 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.74 - 0.745 : [ 2455 0.04 0.51 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.745 - 0.75 : [ 2409 0.04 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.75 - 0.755 : [ 2774 0.05 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.755 - 0.76 : [ 2573 0.04 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.76 - 0.765 : [ 2536 0.04 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.765 - 0.77 : [ 2287 0.04 0.72 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.77 - 0.775 : [ 2130 0.04 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.775 - 0.78 : [ 2070 0.03 0.79 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.78 - 0.785 : [ 1891 0.03 0.83 ] |XXXXXXXXXXXXXXXXXXXXXXX 0.785 - 0.79 : [ 1612 0.03 0.85 ] |XXXXXXXXXXXXXXXXXXXXX 0.79 - 0.795 : [ 1439 0.02 0.88 ] |XXXXXXXXXXXXXXXXX 0.795 - 0.8 : [ 1159 0.02 0.90 ] |XXXXXXXXXXXXXXXXX 0.8 - 0.805 : [ 1154 0.02 0.92 ] |XXXXXXXXXXXXX 0.805 - 0.81 : [ 898 0.02 0.93 ] |XXXXXXXXXXX 0.81 - 0.815 : [ 763 0.01 0.94 ] |XXXXXXXXX 0.815 - 0.82 : [ 628 0.01 0.96 ] |XXXXXXXX 0.82 - 0.825 : [ 543 0.01 0.96 ] |XXXXXX 0.825 - 0.83 : [ 405 0.01 0.97 ] |XXXXX 0.83 - 0.835 : [ 352 0.01 0.98 ] |XXXX 0.835 - 0.84 : [ 268 0.00 0.98 ] |XXX 0.84 - 0.845 : [ 197 0.00 0.99 ] |XX 0.845 - 0.85 : [ 161 0.00 0.99 ] |XX 0.85 - 0.855 : [ 147 0.00 0.99 ] |X 0.855 - 0.86 : [ 101 0.00 0.99 ] |X 0.86 - 0.865 : [ 94 0.00 0.99 ] |X 0.865 - 0.87 : [ 77 0.00 0.99 ] |X 0.87 - 0.875 : [ 46 0.00 1.00 ] |X 0.875 - 0.88 : [ 54 0.00 1.00 ] |X 0.88 - 0.885 : [ 42 0.00 1.00 ] | 0.885 - 0.89 : [ 33 0.00 1.00 ] | 0.89 - 0.895 : [ 18 0.00 1.00 ] | 0.895 - 0.9 : [ 12 0.00 1.00 ] | 0.9 - 0.905 : [ 16 0.00 1.00 ] | 0.905 - 0.91 : [ 10 0.00 1.00 ] | 0.91 - 0.915 : [ 15 0.00 1.00 ] | 0.915 - 0.92 : [ 10 0.00 1.00 ] | 0.92 - 0.925 : [ 5 0.00 1.00 ] | 0.925 - 0.93 : [ 10 0.00 1.00 ] | 0.93 - 0.935 : [ 5 0.00 1.00 ] | 0.935 - 0.94 : [ 5 0.00 1.00 ] | 0.94 - 0.945 : [ 3 0.00 1.00 ] | 0.945 - 0.95 : [ 1 0.00 1.00 ] | 0.95 - 0.955 : [ 4 0.00 1.00 ] | 0.955 - 0.96 : [ 3 0.00 1.00 ] | 0.96 - 0.965 : [ 3 0.00 1.00 ] | 0.965 - 0.97 : [ 2 0.00 1.00 ] | 0.97 - 0.975 : [ 2 0.00 1.00 ] | 0.975 - 0.98 : [ 1 0.00 1.00 ] #... | 1 - 1.005 : [ 4 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones N/plate avg% LIBRARY @ 136 29257 12531 92.14 95.98 AHZI @ 160 28400 14046 87.79 91.45 AHZK @ 20 1977 1344 67.20 70.00 AHZN @ ] 59634 27921 88.36 cumulative total@@ LIBRARY PLATE ID COUNT [ AHZI 136 AHZK 160 AHZN 20 ] for 316 total 96 well plate ids. Only indicates plates present in input file. Make no assumption regarding plates (not) present in project that do not appear above. ################################################################### Reads in assembly summary Small Inserts = 863 HQ Discrepant reads = 91 Chimeric reads = 337 Suspect alignments = 3529 ################################################################### C O N T I G I N F O R M A T I O N Sun Sep 5 22:01:06 2004 File: /psf/project/microbe3/3634483/edit_dir.20Aug04.QD/phrap.out Contig 71. 746 reads; 60757 bp (untrimmed), 60565 (trimmed). Contig 72. 785 reads; 64186 bp (untrimmed), 63918 (trimmed). Contig 73. 807 reads; 70589 bp (untrimmed), 70538 (trimmed). Contig 74. 850 reads; 73113 bp (untrimmed), 72787 (trimmed). Contig 75. 895 reads; 82288 bp (untrimmed), 81975 (trimmed). Contig 76. 950 reads; 83323 bp (untrimmed), 83195 (trimmed). Contig 77. 1016 reads; 86437 bp (untrimmed), 85442 (trimmed). Contig 78. 1025 reads; 87897 bp (untrimmed), 87667 (trimmed). Contig 79. 1047 reads; 83163 bp (untrimmed), 83122 (trimmed). Contig 80. 1143 reads; 96355 bp (untrimmed), 96153 (trimmed). Contig 81. 1167 reads; 97960 bp (untrimmed), 97640 (trimmed). Contig 82. 1350 reads; 123073 bp (untrimmed), 122579 (trimmed). Contig 83. 1453 reads; 134180 bp (untrimmed), 133660 (trimmed). Contig 84. 1453 reads; 127540 bp (untrimmed), 127035 (trimmed). Contig 85. 1495 reads; 136389 bp (untrimmed), 135542 (trimmed). Contig 86. 1628 reads; 139284 bp (untrimmed), 138967 (trimmed). Contig 87. 1642 reads; 130661 bp (untrimmed), 130388 (trimmed). Contig 88. 1663 reads; 131971 bp (untrimmed), 131874 (trimmed). Contig 89. 1676 reads; 159607 bp (untrimmed), 159336 (trimmed). Contig 90. 1813 reads; 135231 bp (untrimmed), 135120 (trimmed). Contig 91. 1945 reads; 158337 bp (untrimmed), 157972 (trimmed). Contig 92. 1978 reads; 173837 bp (untrimmed), 173066 (trimmed). Contig 93. 2054 reads; 160663 bp (untrimmed), 160412 (trimmed). Contig 94. 2647 reads; 206819 bp (untrimmed), 206771 (trimmed). Contig 95. 2697 reads; 199202 bp (untrimmed), 198380 (trimmed). Contig 96. 3066 reads; 250850 bp (untrimmed), 250022 (trimmed). Contig 97. 3574 reads; 282718 bp (untrimmed), 282688 (trimmed). -------------------------------------------------------------- Totals 59419 reads; 5033117 bp (untrimmed), 5002096 (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 89 total values totalling 4996326.0000. <56138.494382 +/- 59526.638523> #Range: [ 2070 - 282688 ] #Most likely bin: [ 4000 - 6000 ] 9 counts #Median bin: [ 34000 - 36000 ] 2 counts |XXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 5 0.06 0.06 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 6000 : [ 9 0.10 0.16 ] #... |XXXXXXXXXXXXX 8000 - 10000 : [ 3 0.03 0.19 ] |XXXXXXXXXXXXX 10000 - 12000 : [ 3 0.03 0.22 ] |XXXXXXXXX 12000 - 14000 : [ 2 0.02 0.25 ] |XXXXXXXXXXXXXXXXXXXXXX 14000 - 16000 : [ 5 0.06 0.30 ] |XXXXXXXXXXXXXXXXXX 16000 - 18000 : [ 4 0.04 0.35 ] |XXXXXXXXX 18000 - 20000 : [ 2 0.02 0.37 ] |XXXXXXXXX 20000 - 22000 : [ 2 0.02 0.39 ] #... |XXXXXXXXXXXXXXXXXX 24000 - 26000 : [ 4 0.04 0.44 ] |XXXX 26000 - 28000 : [ 1 0.01 0.45 ] |XXXXXXXXX 28000 - 30000 : [ 2 0.02 0.47 ] |XXXXXXXXX 30000 - 32000 : [ 2 0.02 0.49 ] #... |XXXXXXXXX 34000 - 36000 : [ 2 0.02 0.52 ] #... |XXXX 38000 - 40000 : [ 1 0.01 0.53 ] |XXXXXXXXXXXXX 40000 - 42000 : [ 3 0.03 0.56 ] |XXXXXXXXX 42000 - 44000 : [ 2 0.02 0.58 ] |XXXX 44000 - 46000 : [ 1 0.01 0.60 ] #... |XXXX 48000 - 50000 : [ 1 0.01 0.61 ] |XXXX 50000 - 52000 : [ 1 0.01 0.62 ] |XXXXXXXXX 52000 - 54000 : [ 2 0.02 0.64 ] |XXXXXXXXX 54000 - 56000 : [ 2 0.02 0.66 ] |XXXX 56000 - 58000 : [ 1 0.01 0.67 ] |XXXXXXXXX 58000 - 60000 : [ 2 0.02 0.70 ] |XXXX 60000 - 62000 : [ 1 0.01 0.71 ] |XXXX 62000 - 64000 : [ 1 0.01 0.72 ] #... |XXXX 70000 - 72000 : [ 1 0.01 0.73 ] |XXXX 72000 - 74000 : [ 1 0.01 0.74 ] #... |XXXX 80000 - 82000 : [ 1 0.01 0.75 ] |XXXXXXXXX 82000 - 84000 : [ 2 0.02 0.78 ] |XXXX 84000 - 86000 : [ 1 0.01 0.79 ] |XXXX 86000 - 88000 : [ 1 0.01 0.80 ] #... |XXXXXXXXX 96000 - 98000 : [ 2 0.02 0.82 ] #... |XXXX 122000 - 124000 : [ 1 0.01 0.83 ] #... |XXXX 126000 - 128000 : [ 1 0.01 0.84 ] #... |XXXXXXXXX 130000 - 132000 : [ 2 0.02 0.87 ] |XXXX 132000 - 134000 : [ 1 0.01 0.88 ] |XXXXXXXXX 134000 - 136000 : [ 2 0.02 0.90 ] #... |XXXX 138000 - 140000 : [ 1 0.01 0.91 ] #... |XXXX 156000 - 158000 : [ 1 0.01 0.92 ] |XXXX 158000 - 160000 : [ 1 0.01 0.93 ] |XXXX 160000 - 162000 : [ 1 0.01 0.94 ] #... |XXXX 172000 - 174000 : [ 1 0.01 0.96 ] #... |XXXX 198000 - 200000 : [ 1 0.01 0.97 ] #... |XXXX 206000 - 208000 : [ 1 0.01 0.98 ] #... |XXXX 250000 - 252000 : [ 1 0.01 0.99 ] #... |XXXX 282000 - 284000 : [ 1 0.01 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 8246399 C = 20847520 G = 20467648 T = 9777009 N = 172259 X = 572574 GC fraction = 0.69 Total = 60083409 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 3634483_fasta.screen.contigs A 634656 C 1893358 G 1871691 N 55 T 633357 fraction GC = 0.75 total bases = 5033117 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 5031923 bases = 9.82 +- 4.27 = 0.16 +- 3.65 m1 = 1.86 m2 = 1.23 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 95 total values totalling 816.0000. <8.589474 +/- 2.345013> #Range: [ 1.62 - 14.47 ] #Most likely bin: [ 9.5 - 10 ] 16 counts #Median bin: [ 9 - 9.5 ] 11 counts |XXXXX 1.5 - 2 : [ 2 0.02 0.02 ] |XX 2 - 2.5 : [ 1 0.01 0.03 ] |XX 2.5 - 3 : [ 1 0.01 0.04 ] #... |XXXXX 3.5 - 4 : [ 2 0.02 0.06 ] |XXXXXXXX 4 - 4.5 : [ 3 0.03 0.09 ] |XXXXX 4.5 - 5 : [ 2 0.02 0.12 ] #... |XX 5.5 - 6 : [ 1 0.01 0.13 ] |XXXXXXXX 6 - 6.5 : [ 3 0.03 0.16 ] |XXXXX 6.5 - 7 : [ 2 0.02 0.18 ] |XXXXX 7 - 7.5 : [ 2 0.02 0.20 ] |XXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 9 0.09 0.29 ] |XXXXXXXXXX 8 - 8.5 : [ 4 0.04 0.34 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 12 0.13 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 11 0.12 0.58 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 16 0.17 0.75 ] |XXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 9 0.09 0.84 ] |XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 8 0.08 0.93 ] |XXXXXXXX 11 - 11.5 : [ 3 0.03 0.96 ] |XXXXX 11.5 - 12 : [ 2 0.02 0.98 ] |XX 12 - 12.5 : [ 1 0.01 0.99 ] #... |XX 14 - 14.5 : [ 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 89 total values totalling 798.7800. <8.975056 +/- 1.851265> #Range: [ 3.87 - 14.47 ] #Most likely bin: [ 9.5 - 10 ] 16 counts #Median bin: [ 9 - 9.5 ] 11 counts |XX 3.5 - 4 : [ 1 0.01 0.01 ] |XXXXXXXX 4 - 4.5 : [ 3 0.03 0.04 ] |XX 4.5 - 5 : [ 1 0.01 0.06 ] #... |XX 5.5 - 6 : [ 1 0.01 0.07 ] |XXXXXXXX 6 - 6.5 : [ 3 0.03 0.10 ] |XXXXX 6.5 - 7 : [ 2 0.02 0.12 ] |XXXXX 7 - 7.5 : [ 2 0.02 0.15 ] |XXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 9 0.10 0.25 ] |XXXXXXXXXX 8 - 8.5 : [ 4 0.04 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 12 0.13 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 11 0.12 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 16 0.18 0.73 ] |XXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 9 0.10 0.83 ] |XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 8 0.09 0.92 ] |XXXXXXXX 11 - 11.5 : [ 3 0.03 0.96 ] |XXXXX 11.5 - 12 : [ 2 0.02 0.98 ] |XX 12 - 12.5 : [ 1 0.01 0.99 ] #... |XX 14 - 14.5 : [ 1 0.01 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 2 2 reads 697 bases = 1.62 +- 0.49 = 1.62 +- 0.49 m1 = 0.15 m2 = 0.00 Contig 5 4 reads 1424 bases = 1.72 +- 0.83 = 0.33 +- 1.02 m1 = 0.41 m2 = -0.08 Contig 3 3 reads 1012 bases = 2.49 +- 0.80 = 2.49 +- 0.80 m1 = 0.26 m2 = 0.00 Contig 8 7 reads 1761 bases = 2.86 +- 2.06 = -0.08 +- 1.09 m1 = 1.49 m2 = 0.76 Contig 6 5 reads 1066 bases = 3.57 +- 1.10 = 1.94 +- 0.83 m1 = 0.34 m2 = 0.13 Contig 11 18 reads 3602 bases = 3.87 +- 3.14 = 1.45 +- 2.14 m1 = 2.55 m2 = 1.33 Contig 13 29 reads 4756 bases = 4.07 +- 1.77 = -0.07 +- 2.48 m1 = 0.77 m2 = -0.75 Contig 9 12 reads 2317 bases = 4.08 +- 1.74 = 0.28 +- 2.25 m1 = 0.74 m2 = -0.51 Contig 10 18 reads 3086 bases = 4.26 +- 2.03 = 0.01 +- 2.65 m1 = 0.97 m2 = -0.73 Contig 16 40 reads 6146 bases = 4.77 +- 2.28 = 0.12 +- 2.22 m1 = 1.09 m2 = 0.06 Contig 7 6 reads 894 bases = 4.96 +- 1.25 = 4.96 +- 1.25 m1 = 0.32 m2 = 0.00 Contig 17 43 reads 5845 bases = 5.51 +- 2.10 = 1.55 +- 1.78 m1 = 0.80 m2 = 0.31 Contig 12 28 reads 3600 bases = 6.10 +- 4.74 = 0.51 +- 3.61 m1 = 3.69 m2 = 2.36 Contig 28 114 reads 12665 bases = 6.18 +- 2.12 = 0.30 +- 2.59 m1 = 0.73 m2 = -0.56 Contig 18 48 reads 6751 bases = 6.25 +- 3.33 = 0.98 +- 2.28 m1 = 1.77 m2 = 1.47 Contig 14 34 reads 4374 bases = 6.57 +- 2.86 = 1.55 +- 1.65 m1 = 1.24 m2 = 1.36 Contig 23 87 reads 9971 bases = 6.73 +- 2.97 = 0.05 +- 2.86 m1 = 1.31 m2 = 0.15 Contig 34 177 reads 20795 bases = 7.05 +- 2.70 = 0.39 +- 2.48 m1 = 1.03 m2 = 0.28 Contig 20 53 reads 5779 bases = 7.09 +- 3.01 = 0.82 +- 2.89 m1 = 1.28 m2 = 0.18 Contig 29 123 reads 13388 bases = 7.52 +- 3.58 = 0.52 +- 2.30 m1 = 1.71 m2 = 1.88 Contig 68 705 reads 54928 bases = 10.18 +- 3.68 = 0.08 +- 3.64 m1 = 1.33 m2 = 0.07 Contig 91 1945 reads 158337 bases = 10.21 +- 4.01 = 0.05 +- 3.61 m1 = 1.57 m2 = 0.75 Contig 79 1047 reads 83163 bases = 10.33 +- 3.91 = 0.22 +- 3.62 m1 = 1.48 m2 = 0.56 Contig 38 210 reads 16591 bases = 10.37 +- 3.57 = -0.07 +- 3.57 m1 = 1.23 m2 = 0.01 Contig 66 645 reads 52811 bases = 10.42 +- 4.18 = 0.23 +- 3.96 m1 = 1.68 m2 = 0.46 Contig 87 1642 reads 130661 bases = 10.51 +- 4.28 = -0.05 +- 3.79 m1 = 1.74 m2 = 0.98 Contig 94 2647 reads 206819 bases = 10.51 +- 4.35 = 0.20 +- 3.96 m1 = 1.80 m2 = 0.80 Contig 70 731 reads 59148 bases = 10.54 +- 4.53 = 0.27 +- 4.06 m1 = 1.95 m2 = 1.02 Contig 88 1663 reads 131971 bases = 10.57 +- 4.70 = 0.07 +- 4.05 m1 = 2.09 m2 = 1.42 Contig 50 338 reads 27013 bases = 10.61 +- 4.29 = 0.51 +- 3.97 m1 = 1.74 m2 = 0.67 Contig 97 3574 reads 282718 bases = 10.62 +- 3.84 = 0.07 +- 3.86 m1 = 1.39 m2 = -0.04 Contig 36 190 reads 14635 bases = 10.81 +- 5.27 = 0.78 +- 3.21 m1 = 2.57 m2 = 4.38 Contig 93 2054 reads 160663 bases = 10.86 +- 4.41 = 0.01 +- 3.97 m1 = 1.79 m2 = 0.92 Contig 62 548 reads 41347 bases = 11.00 +- 4.85 = 0.07 +- 4.20 m1 = 2.14 m2 = 1.47 Contig 69 706 reads 53660 bases = 11.19 +- 4.60 = 0.19 +- 3.20 m1 = 1.89 m2 = 2.72 Contig 37 201 reads 14652 bases = 11.42 +- 5.49 = 1.23 +- 5.10 m1 = 2.64 m2 = 1.02 Contig 90 1813 reads 135231 bases = 11.54 +- 5.16 = 0.07 +- 4.11 m1 = 2.31 m2 = 2.44 Contig 95 2697 reads 199202 bases = 11.96 +- 5.01 = 0.20 +- 4.03 m1 = 2.10 m2 = 2.20 Contig 51 355 reads 24455 bases = 12.39 +- 9.58 = 0.86 +- 3.18 m1 = 7.41 m2 = 20.42 Contig 47 312 reads 19604 bases = 14.47 +- 5.29 = 0.34 +- 5.43 m1 = 1.94 m2 = -0.37 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 97 total values totalling 59419.0000. <612.567010 +/- 731.183448> #Range: [ 1 - 3574 ] #Most likely bin: [ 18 - 19 ] 2 counts #Median bin: [ 318 - 319 ] 1 counts |XXXXXXXXXXXXXXXXXXXX 1 - 2 : [ 1 0.01 0.01 ] |XXXXXXXXXXXXXXXXXXXX 2 - 3 : [ 1 0.01 0.02 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 4 : [ 2 0.02 0.04 ] |XXXXXXXXXXXXXXXXXXXX 4 - 5 : [ 1 0.01 0.05 ] |XXXXXXXXXXXXXXXXXXXX 5 - 6 : [ 1 0.01 0.06 ] |XXXXXXXXXXXXXXXXXXXX 6 - 7 : [ 1 0.01 0.07 ] |XXXXXXXXXXXXXXXXXXXX 7 - 8 : [ 1 0.01 0.08 ] #... |XXXXXXXXXXXXXXXXXXXX 12 - 13 : [ 1 0.01 0.09 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 18 - 19 : [ 2 0.02 0.11 ] #... |XXXXXXXXXXXXXXXXXXXX 28 - 29 : [ 1 0.01 0.12 ] |XXXXXXXXXXXXXXXXXXXX 29 - 30 : [ 1 0.01 0.13 ] #... |XXXXXXXXXXXXXXXXXXXX 34 - 35 : [ 1 0.01 0.14 ] #... |XXXXXXXXXXXXXXXXXXXX 38 - 39 : [ 1 0.01 0.15 ] #... |XXXXXXXXXXXXXXXXXXXX 40 - 41 : [ 1 0.01 0.16 ] #... |XXXXXXXXXXXXXXXXXXXX 43 - 44 : [ 1 0.01 0.18 ] #... |XXXXXXXXXXXXXXXXXXXX 48 - 49 : [ 1 0.01 0.19 ] #... |XXXXXXXXXXXXXXXXXXXX 52 - 53 : [ 1 0.01 0.20 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 53 - 54 : [ 2 0.02 0.22 ] #... |XXXXXXXXXXXXXXXXXXXX 61 - 62 : [ 1 0.01 0.23 ] #... |XXXXXXXXXXXXXXXXXXXX 87 - 88 : [ 1 0.01 0.24 ] |XXXXXXXXXXXXXXXXXXXX 88 - 89 : [ 1 0.01 0.25 ] |XXXXXXXXXXXXXXXXXXXX 89 - 90 : [ 1 0.01 0.26 ] #... |XXXXXXXXXXXXXXXXXXXX 105 - 106 : [ 1 0.01 0.27 ] #... |XXXXXXXXXXXXXXXXXXXX 107 - 108 : [ 1 0.01 0.28 ] #... |XXXXXXXXXXXXXXXXXXXX 114 - 115 : [ 1 0.01 0.29 ] #... |XXXXXXXXXXXXXXXXXXXX 123 - 124 : [ 1 0.01 0.30 ] #... |XXXXXXXXXXXXXXXXXXXX 132 - 133 : [ 1 0.01 0.31 ] #... |XXXXXXXXXXXXXXXXXXXX 149 - 150 : [ 1 0.01 0.32 ] #... |XXXXXXXXXXXXXXXXXXXX 176 - 177 : [ 1 0.01 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 177 - 178 : [ 2 0.02 0.35 ] #... |XXXXXXXXXXXXXXXXXXXX 185 - 186 : [ 1 0.01 0.36 ] #... |XXXXXXXXXXXXXXXXXXXX 190 - 191 : [ 1 0.01 0.37 ] #... |XXXXXXXXXXXXXXXXXXXX 201 - 202 : [ 1 0.01 0.38 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 210 - 211 : [ 2 0.02 0.40 ] #... |XXXXXXXXXXXXXXXXXXXX 216 - 217 : [ 1 0.01 0.41 ] |XXXXXXXXXXXXXXXXXXXX 217 - 218 : [ 1 0.01 0.42 ] #... |XXXXXXXXXXXXXXXXXXXX 238 - 239 : [ 1 0.01 0.43 ] #... |XXXXXXXXXXXXXXXXXXXX 254 - 255 : [ 1 0.01 0.44 ] #... |XXXXXXXXXXXXXXXXXXXX 259 - 260 : [ 1 0.01 0.45 ] #... |XXXXXXXXXXXXXXXXXXXX 288 - 289 : [ 1 0.01 0.46 ] #... |XXXXXXXXXXXXXXXXXXXX 293 - 294 : [ 1 0.01 0.47 ] #... |XXXXXXXXXXXXXXXXXXXX 312 - 313 : [ 1 0.01 0.48 ] |XXXXXXXXXXXXXXXXXXXX 313 - 314 : [ 1 0.01 0.49 ] #... |XXXXXXXXXXXXXXXXXXXX 318 - 319 : [ 1 0.01 0.51 ] #... |XXXXXXXXXXXXXXXXXXXX 338 - 339 : [ 1 0.01 0.52 ] #... |XXXXXXXXXXXXXXXXXXXX 355 - 356 : [ 1 0.01 0.53 ] #... |XXXXXXXXXXXXXXXXXXXX 371 - 372 : [ 1 0.01 0.54 ] #... |XXXXXXXXXXXXXXXXXXXX 403 - 404 : [ 1 0.01 0.55 ] #... |XXXXXXXXXXXXXXXXXXXX 415 - 416 : [ 1 0.01 0.56 ] #... |XXXXXXXXXXXXXXXXXXXX 445 - 446 : [ 1 0.01 0.57 ] #... |XXXXXXXXXXXXXXXXXXXX 466 - 467 : [ 1 0.01 0.58 ] #... |XXXXXXXXXXXXXXXXXXXX 468 - 469 : [ 1 0.01 0.59 ] #... |XXXXXXXXXXXXXXXXXXXX 470 - 471 : [ 1 0.01 0.60 ] #... |XXXXXXXXXXXXXXXXXXXX 489 - 490 : [ 1 0.01 0.61 ] #... |XXXXXXXXXXXXXXXXXXXX 503 - 504 : [ 1 0.01 0.62 ] #... |XXXXXXXXXXXXXXXXXXXX 545 - 546 : [ 1 0.01 0.63 ] #... |XXXXXXXXXXXXXXXXXXXX 548 - 549 : [ 1 0.01 0.64 ] #... |XXXXXXXXXXXXXXXXXXXX 582 - 583 : [ 1 0.01 0.65 ] #... |XXXXXXXXXXXXXXXXXXXX 593 - 594 : [ 1 0.01 0.66 ] #... |XXXXXXXXXXXXXXXXXXXX 618 - 619 : [ 1 0.01 0.67 ] #... |XXXXXXXXXXXXXXXXXXXX 645 - 646 : [ 1 0.01 0.68 ] #... |XXXXXXXXXXXXXXXXXXXX 672 - 673 : [ 1 0.01 0.69 ] #... |XXXXXXXXXXXXXXXXXXXX 705 - 706 : [ 1 0.01 0.70 ] |XXXXXXXXXXXXXXXXXXXX 706 - 707 : [ 1 0.01 0.71 ] #... |XXXXXXXXXXXXXXXXXXXX 731 - 732 : [ 1 0.01 0.72 ] #... |XXXXXXXXXXXXXXXXXXXX 746 - 747 : [ 1 0.01 0.73 ] #... |XXXXXXXXXXXXXXXXXXXX 785 - 786 : [ 1 0.01 0.74 ] #... |XXXXXXXXXXXXXXXXXXXX 807 - 808 : [ 1 0.01 0.75 ] #... |XXXXXXXXXXXXXXXXXXXX 850 - 851 : [ 1 0.01 0.76 ] #... |XXXXXXXXXXXXXXXXXXXX 895 - 896 : [ 1 0.01 0.77 ] #... |XXXXXXXXXXXXXXXXXXXX 950 - 951 : [ 1 0.01 0.78 ] #... |XXXXXXXXXXXXXXXXXXXX 1016 - 1017 : [ 1 0.01 0.79 ] #... |XXXXXXXXXXXXXXXXXXXX 1025 - 1026 : [ 1 0.01 0.80 ] #... |XXXXXXXXXXXXXXXXXXXX 1047 - 1048 : [ 1 0.01 0.81 ] #... |XXXXXXXXXXXXXXXXXXXX 1143 - 1144 : [ 1 0.01 0.82 ] #... |XXXXXXXXXXXXXXXXXXXX 1167 - 1168 : [ 1 0.01 0.84 ] #... |XXXXXXXXXXXXXXXXXXXX 1350 - 1351 : [ 1 0.01 0.85 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1453 - 1454 : [ 2 0.02 0.87 ] #... |XXXXXXXXXXXXXXXXXXXX 1495 - 1496 : [ 1 0.01 0.88 ] #... |XXXXXXXXXXXXXXXXXXXX 1628 - 1629 : [ 1 0.01 0.89 ] #... |XXXXXXXXXXXXXXXXXXXX 1642 - 1643 : [ 1 0.01 0.90 ] #... |XXXXXXXXXXXXXXXXXXXX 1663 - 1664 : [ 1 0.01 0.91 ] #... |XXXXXXXXXXXXXXXXXXXX 1676 - 1677 : [ 1 0.01 0.92 ] #... |XXXXXXXXXXXXXXXXXXXX 1813 - 1814 : [ 1 0.01 0.93 ] #... |XXXXXXXXXXXXXXXXXXXX 1945 - 1946 : [ 1 0.01 0.94 ] #... |XXXXXXXXXXXXXXXXXXXX 1978 - 1979 : [ 1 0.01 0.95 ] #... |XXXXXXXXXXXXXXXXXXXX 2054 - 2055 : [ 1 0.01 0.96 ] #... |XXXXXXXXXXXXXXXXXXXX 2647 - 2648 : [ 1 0.01 0.97 ] #... |XXXXXXXXXXXXXXXXXXXX 2697 - 2698 : [ 1 0.01 0.98 ] #... |XXXXXXXXXXXXXXXXXXXX 3066 - 3067 : [ 1 0.01 0.99 ] #... |XXXXXXXXXXXXXXXXXXXX 3574 - 3575 : [ 1 0.01 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 97 total values totalling 5033117.0000. <51887.804124 +/- 59049.643259> #Range: [ 132 - 282718 ] #Most likely bin: [ 1000 - 2000 ] 5 counts #Median bin: [ 28000 - 29000 ] 1 counts |XXXXXXXXXXXXXXXXXXXXXXXX 0 - 1000 : [ 3 0.03 0.03 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 5 0.05 0.08 ] |XXXXXXXX 2000 - 3000 : [ 1 0.01 0.09 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 4000 : [ 4 0.04 0.13 ] |XXXXXXXXXXXXXXXX 4000 - 5000 : [ 2 0.02 0.15 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5000 - 6000 : [ 5 0.05 0.21 ] |XXXXXXXXXXXXXXXX 6000 - 7000 : [ 2 0.02 0.23 ] #... |XXXXXXXX 8000 - 9000 : [ 1 0.01 0.24 ] |XXXXXXXXXXXXXXXX 9000 - 10000 : [ 2 0.02 0.26 ] |XXXXXXXX 10000 - 11000 : [ 1 0.01 0.27 ] |XXXXXXXX 11000 - 12000 : [ 1 0.01 0.28 ] |XXXXXXXXXXXXXXXX 12000 - 13000 : [ 2 0.02 0.30 ] |XXXXXXXX 13000 - 14000 : [ 1 0.01 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 14000 - 15000 : [ 4 0.04 0.35 ] |XXXXXXXX 15000 - 16000 : [ 1 0.01 0.36 ] |XXXXXXXXXXXXXXXX 16000 - 17000 : [ 2 0.02 0.38 ] |XXXXXXXX 17000 - 18000 : [ 1 0.01 0.39 ] |XXXXXXXX 18000 - 19000 : [ 1 0.01 0.40 ] |XXXXXXXXXXXXXXXX 19000 - 20000 : [ 2 0.02 0.42 ] |XXXXXXXX 20000 - 21000 : [ 1 0.01 0.43 ] |XXXXXXXX 21000 - 22000 : [ 1 0.01 0.44 ] #... |XXXXXXXXXXXXXXXX 24000 - 25000 : [ 2 0.02 0.46 ] |XXXXXXXX 25000 - 26000 : [ 1 0.01 0.47 ] |XXXXXXXX 26000 - 27000 : [ 1 0.01 0.48 ] |XXXXXXXX 27000 - 28000 : [ 1 0.01 0.49 ] |XXXXXXXX 28000 - 29000 : [ 1 0.01 0.51 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 30000 - 31000 : [ 3 0.03 0.54 ] #... |XXXXXXXX 34000 - 35000 : [ 1 0.01 0.55 ] #... |XXXXXXXX 36000 - 37000 : [ 1 0.01 0.56 ] #... |XXXXXXXX 38000 - 39000 : [ 1 0.01 0.57 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 41000 - 42000 : [ 3 0.03 0.60 ] #... |XXXXXXXXXXXXXXXX 43000 - 44000 : [ 2 0.02 0.62 ] |XXXXXXXX 44000 - 45000 : [ 1 0.01 0.63 ] #... |XXXXXXXXXXXXXXXX 50000 - 51000 : [ 2 0.02 0.65 ] #... |XXXXXXXX 52000 - 53000 : [ 1 0.01 0.66 ] |XXXXXXXX 53000 - 54000 : [ 1 0.01 0.67 ] |XXXXXXXX 54000 - 55000 : [ 1 0.01 0.68 ] |XXXXXXXX 55000 - 56000 : [ 1 0.01 0.69 ] #... |XXXXXXXX 57000 - 58000 : [ 1 0.01 0.70 ] #... |XXXXXXXX 59000 - 60000 : [ 1 0.01 0.71 ] |XXXXXXXXXXXXXXXX 60000 - 61000 : [ 2 0.02 0.73 ] #... |XXXXXXXX 64000 - 65000 : [ 1 0.01 0.74 ] #... |XXXXXXXX 70000 - 71000 : [ 1 0.01 0.75 ] #... |XXXXXXXX 73000 - 74000 : [ 1 0.01 0.76 ] #... |XXXXXXXX 82000 - 83000 : [ 1 0.01 0.77 ] |XXXXXXXXXXXXXXXX 83000 - 84000 : [ 2 0.02 0.79 ] #... |XXXXXXXX 86000 - 87000 : [ 1 0.01 0.80 ] |XXXXXXXX 87000 - 88000 : [ 1 0.01 0.81 ] #... |XXXXXXXX 96000 - 97000 : [ 1 0.01 0.82 ] |XXXXXXXX 97000 - 98000 : [ 1 0.01 0.84 ] #... |XXXXXXXX 123000 - 124000 : [ 1 0.01 0.85 ] #... |XXXXXXXX 127000 - 128000 : [ 1 0.01 0.86 ] #... |XXXXXXXX 130000 - 131000 : [ 1 0.01 0.87 ] |XXXXXXXX 131000 - 132000 : [ 1 0.01 0.88 ] #... |XXXXXXXX 134000 - 135000 : [ 1 0.01 0.89 ] |XXXXXXXX 135000 - 136000 : [ 1 0.01 0.90 ] |XXXXXXXX 136000 - 137000 : [ 1 0.01 0.91 ] #... |XXXXXXXX 139000 - 140000 : [ 1 0.01 0.92 ] #... |XXXXXXXX 158000 - 159000 : [ 1 0.01 0.93 ] |XXXXXXXX 159000 - 160000 : [ 1 0.01 0.94 ] |XXXXXXXX 160000 - 161000 : [ 1 0.01 0.95 ] #... |XXXXXXXX 173000 - 174000 : [ 1 0.01 0.96 ] #... |XXXXXXXX 199000 - 200000 : [ 1 0.01 0.97 ] #... |XXXXXXXX 206000 - 207000 : [ 1 0.01 0.98 ] #... |XXXXXXXX 250000 - 251000 : [ 1 0.01 0.99 ] #... |XXXXXXXX 282000 - 283000 : [ 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 AHZI reads.list > grep.reads.list.AHZI Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZI 4 500 #Found 10123 total values totalling 29337391.0000. <2898.092561 +/- 1858.191837> #Range: [ - 173431 ] #Most likely bin: [ 2500 - 3000 ] 5732 counts #Median bin: [ 2500 - 3000 ] 5732 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 4 0.00 0.00 ] | 1000 - 1500 : [ 68 0.01 0.01 ] |X 1500 - 2000 : [ 110 0.01 0.02 ] |XXXX 2000 - 2500 : [ 634 0.06 0.08 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 5732 0.57 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3457 0.34 0.99 ] |X 3500 - 4000 : [ 112 0.01 1.00 ] #... | 5000 - 5500 : [ 1 0.00 1.00 ] #... | 6000 - 6500 : [ 1 0.00 1.00 ] | 6500 - 7000 : [ 1 0.00 1.00 ] #... | 71500 - 72000 : [ 1 0.00 1.00 ] #... | 173000 - 173500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AHZK reads.list > grep.reads.list.AHZK Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZK 4 500 #Found 9529 total values totalling 59046833.0000. <6196.540351 +/- 1669.683887> #Range: [ - 122036 ] #Most likely bin: [ 6000 - 6500 ] 2477 counts #Median bin: [ 6000 - 6500 ] 2477 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 3 0.00 0.00 ] |X 1000 - 1500 : [ 78 0.01 0.01 ] |X 1500 - 2000 : [ 81 0.01 0.02 ] |X 2000 - 2500 : [ 85 0.01 0.03 ] |XX 2500 - 3000 : [ 94 0.01 0.04 ] |X 3000 - 3500 : [ 73 0.01 0.04 ] |X 3500 - 4000 : [ 85 0.01 0.05 ] |XX 4000 - 4500 : [ 127 0.01 0.07 ] |XXXX 4500 - 5000 : [ 240 0.03 0.09 ] |XXXXXXXXXX 5000 - 5500 : [ 608 0.06 0.15 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1617 0.17 0.32 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2477 0.26 0.58 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2072 0.22 0.80 ] |XXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1293 0.14 0.94 ] |XXXXXXXXX 7500 - 8000 : [ 548 0.06 1.00 ] |X 8000 - 8500 : [ 42 0.00 1.00 ] #... | 10000 - 10500 : [ 1 0.00 1.00 ] #... | 19500 - 20000 : [ 1 0.00 1.00 ] #... | 21000 - 21500 : [ 1 0.00 1.00 ] | 21500 - 22000 : [ 1 0.00 1.00 ] #... | 122000 - 122500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AHZN reads.list > grep.reads.list.AHZN Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZN 4 500 #Found 324 total values totalling 13416145.0000. <41407.854938 +/- 6280.578521> #Range: [ - 125138 ] #Most likely bin: [ 40000 - 40500 ] 25 counts #Median bin: [ 41000 - 41500 ] 12 counts |XX 0 - 500 : [ 1 0.00 0.00 ] #... |XX 27000 - 27500 : [ 1 0.00 0.01 ] #... |XX 31500 - 32000 : [ 1 0.00 0.01 ] |XX 32000 - 32500 : [ 1 0.00 0.01 ] |XXXXX 32500 - 33000 : [ 3 0.01 0.02 ] |XXXXX 33000 - 33500 : [ 3 0.01 0.03 ] #... |XX 34000 - 34500 : [ 1 0.00 0.03 ] |XXXXXXXXXXXXX 34500 - 35000 : [ 8 0.02 0.06 ] |XX 35000 - 35500 : [ 1 0.00 0.06 ] |XXXXXXXXXXX 35500 - 36000 : [ 7 0.02 0.08 ] |XXXXXXXX 36000 - 36500 : [ 5 0.02 0.10 ] |XXXXXXXX 36500 - 37000 : [ 5 0.02 0.11 ] |XXXXXXXXXXX 37000 - 37500 : [ 7 0.02 0.14 ] |XXXXXXXXXXXXXXXX 37500 - 38000 : [ 10 0.03 0.17 ] |XXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 14 0.04 0.21 ] |XXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 12 0.04 0.25 ] |XXXXXXXXXXXXXX 39000 - 39500 : [ 9 0.03 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 20 0.06 0.34 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 25 0.08 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 16 0.05 0.46 ] |XXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 12 0.04 0.50 ] |XXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 14 0.04 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 20 0.06 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 21 0.06 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 15 0.05 0.72 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 20 0.06 0.78 ] |XXXXXXXXXXXXXX 44000 - 44500 : [ 9 0.03 0.81 ] |XXXXXXXXXXXXXXXXXXXXX 44500 - 45000 : [ 13 0.04 0.85 ] |XXXXXXXXXXXXXXXXXXXXX 45000 - 45500 : [ 13 0.04 0.89 ] |XXXXXXXXXXXXXXXXXXXXX 45500 - 46000 : [ 13 0.04 0.93 ] |XXXXXXXXXXXXXXXXXX 46000 - 46500 : [ 11 0.03 0.96 ] |XXXXXXXXXX 46500 - 47000 : [ 6 0.02 0.98 ] |XXXXXX 47000 - 47500 : [ 4 0.01 0.99 ] |XX 47500 - 48000 : [ 1 0.00 0.99 ] #... |XX 57500 - 58000 : [ 1 0.00 1.00 ] #... |XX 125000 - 125500 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # AHZN 41107 +- 3545 (n=164) # AHZI 2766 +- 417 (n=6074) # AHZK 6088 +- 1350 (n=4957) ################################################################### 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 576.860567 bp, 59419 reads, genome size 4959901 bp Command: idealAssembly 4959901 59419 576.860567 ------------------------------------------------------------------- Genome = 4959901 bases Nreads = 59419 readLength = 576.860567 Depth = 6.91 N_contigs = N_gaps = 59 mean gap size = 82 bases mean contig size = 1003 reads (~ 83721 bases) %cover = 99.90 %singlet = 0.00 assembly size = 4954922 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 11 contigs containing at least 1683 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: