################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 3634606 Genus_species: Shewanella frigidimarina NCMIB400 Taxid: 56812 Genome size: 4500 Libraries: AIOH, AIOK, AIOI ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 3634606 ------------------------------------------------------------------- ID=3634606 Lineage for 'Shewanella frigidimarina': Shewanella frigidimarina species Shewanella genus Alteromonadaceae family Alteromonadales order Gammaproteobacteria class Proteobacteria phylum Bacteria superkingdom cellular organisms no rank root no rank ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 4770085 # phrap: 4429007 # db: -1 3066363 +/- 2172713 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length AIOH.5-56 272 98.00 750.34 AIOI.5-44 332 92.04 689.12 AIOK.5-28 48 88.00 499.27 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s AIOH 272 136 98.25 753.31 136 97.74 747.37 AIOK 48 24 87.11 494.54 24 88.89 504.00 AIOI 332 166 92.31 687.27 166 91.78 690.98 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634606_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 3634606_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634606.out /home/copeland/scripts/librariesInfoTxt.sh 3634606 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634606_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 3634606_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634606.out /home/copeland/scripts/librariesInfoTxt.sh 3634606 phrap.out > librariesInfo.txt ################################################################### Library vector screening AIOH.000001.000100 screen.out.1 3634606_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta AIOH.000101.000200 screen.out.1 3634606_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta AIOI.000001.000100 screen.out.1 3634606_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta AIOI.000101.000200 screen.out.1 3634606_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta AIOI.000201.000300 screen.out.1 3634606_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta AIOK.000001.000100 screen.out.1 3634606_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta AIOH.000001.000100 screen.out.1 3634606_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta AIOH.000101.000200 screen.out.1 3634606_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta AIOI.000001.000100 screen.out.1 3634606_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta AIOI.000101.000200 screen.out.1 3634606_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta AIOI.000201.000300 screen.out.1 3634606_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta AIOK.000001.000100 screen.out.1 3634606_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634606_fasta.screen /usr/local/sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 3634606_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 58571 total values totalling 42398359.0000. <723.879719 +/- 157.375957> #Range: [ 22 - 937 ] #Most likely bin: [ 800 - 850 ] 16367 counts #Median bin: [ 750 - 800 ] 15361 counts | 0 - 50 : [ 128 0.00 0.00 ] |X 50 - 100 : [ 397 0.01 0.01 ] |X 100 - 150 : [ 429 0.01 0.02 ] |X 150 - 200 : [ 419 0.01 0.02 ] |X 200 - 250 : [ 484 0.01 0.03 ] |XX 250 - 300 : [ 638 0.01 0.04 ] |X 300 - 350 : [ 588 0.01 0.05 ] |X 350 - 400 : [ 613 0.01 0.06 ] |XX 400 - 450 : [ 709 0.01 0.08 ] |XX 450 - 500 : [ 809 0.01 0.09 ] |XXX 500 - 550 : [ 1113 0.02 0.11 ] |XXXX 550 - 600 : [ 1587 0.03 0.14 ] |XXXXXX 600 - 650 : [ 2339 0.04 0.18 ] |XXXXXXXXXX 650 - 700 : [ 3981 0.07 0.24 ] |XXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8105 0.14 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 15361 0.26 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 16367 0.28 0.92 ] |XXXXXXXXXXX 850 - 900 : [ 4384 0.07 1.00 ] | 900 - 950 : [ 120 0.00 1.00 ] JAZZ trim 15 readlength histogram for AIOH Command: /usr/xpg4/bin/grep AIOH 3634606_fasta.screen.screen.ids > reads.trim15.AIOH.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOH.rl 2 50 #Found 25266 total values totalling 19266033.0000. <762.528022 +/- 102.863162> #Range: [ 22 - 937 ] #Most likely bin: [ 750 - 800 ] 8217 counts #Median bin: [ 750 - 800 ] 8217 counts | 0 - 50 : [ 22 0.00 0.00 ] | 50 - 100 : [ 51 0.00 0.00 ] | 100 - 150 : [ 48 0.00 0.00 ] | 150 - 200 : [ 60 0.00 0.01 ] | 200 - 250 : [ 69 0.00 0.01 ] | 250 - 300 : [ 96 0.00 0.01 ] | 300 - 350 : [ 79 0.00 0.02 ] | 350 - 400 : [ 92 0.00 0.02 ] |X 400 - 450 : [ 127 0.01 0.03 ] |X 450 - 500 : [ 124 0.00 0.03 ] |X 500 - 550 : [ 144 0.01 0.04 ] |X 550 - 600 : [ 191 0.01 0.04 ] |XX 600 - 650 : [ 481 0.02 0.06 ] |XXXXXXXX 650 - 700 : [ 1543 0.06 0.12 ] |XXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4497 0.18 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8217 0.33 0.63 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7305 0.29 0.92 ] |XXXXXXXXXX 850 - 900 : [ 2045 0.08 1.00 ] | 900 - 950 : [ 75 0.00 1.00 ] JAZZ trim 15 readlength histogram for AIOI Command: /usr/xpg4/bin/grep AIOI 3634606_fasta.screen.screen.ids > reads.trim15.AIOI.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOI.rl 2 50 #Found 29386 total values totalling 20992679.0000. <714.376880 +/- 173.689720> #Range: [ 22 - 923 ] #Most likely bin: [ 800 - 850 ] 9038 counts #Median bin: [ 750 - 800 ] 6984 counts | 0 - 50 : [ 73 0.00 0.00 ] |X 50 - 100 : [ 253 0.01 0.01 ] |X 100 - 150 : [ 309 0.01 0.02 ] |X 150 - 200 : [ 286 0.01 0.03 ] |X 200 - 250 : [ 315 0.01 0.04 ] |X 250 - 300 : [ 334 0.01 0.05 ] |XX 300 - 350 : [ 373 0.01 0.07 ] |XX 350 - 400 : [ 402 0.01 0.08 ] |XX 400 - 450 : [ 443 0.02 0.09 ] |XX 450 - 500 : [ 510 0.02 0.11 ] |XXX 500 - 550 : [ 697 0.02 0.14 ] |XXXX 550 - 600 : [ 946 0.03 0.17 ] |XXXXX 600 - 650 : [ 1238 0.04 0.21 ] |XXXXXXXX 650 - 700 : [ 1736 0.06 0.27 ] |XXXXXXXXXXXXXX 700 - 750 : [ 3065 0.10 0.37 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6984 0.24 0.61 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 9038 0.31 0.92 ] |XXXXXXXXXX 850 - 900 : [ 2339 0.08 1.00 ] | 900 - 950 : [ 45 0.00 1.00 ] JAZZ trim 15 readlength histogram for AIOK Command: /usr/xpg4/bin/grep AIOK 3634606_fasta.screen.screen.ids > reads.trim15.AIOK.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOK.rl 2 50 #Found 3919 total values totalling 2139647.0000. <545.967594 +/- 183.765227> #Range: [ 26 - 836 ] #Most likely bin: [ 650 - 700 ] 702 counts #Median bin: [ 600 - 650 ] 620 counts |XX 0 - 50 : [ 33 0.01 0.01 ] |XXXXX 50 - 100 : [ 93 0.02 0.03 ] |XXXX 100 - 150 : [ 72 0.02 0.05 ] |XXXX 150 - 200 : [ 73 0.02 0.07 ] |XXXXXX 200 - 250 : [ 100 0.03 0.09 ] |XXXXXXXXXXXX 250 - 300 : [ 208 0.05 0.15 ] |XXXXXXXX 300 - 350 : [ 136 0.03 0.18 ] |XXXXXXX 350 - 400 : [ 119 0.03 0.21 ] |XXXXXXXX 400 - 450 : [ 139 0.04 0.25 ] |XXXXXXXXXX 450 - 500 : [ 175 0.04 0.29 ] |XXXXXXXXXXXXXXX 500 - 550 : [ 272 0.07 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 450 0.11 0.48 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 620 0.16 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 702 0.18 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 543 0.14 0.95 ] |XXXXXXXXX 750 - 800 : [ 160 0.04 0.99 ] |X 800 - 850 : [ 24 0.01 1.00 ] ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.3634606_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.3634606_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 58427 total values totalling 24367.4837. <0.417059 +/- 0.039125> #Range: [ 0.0769 - 0.9259 ] #Most likely bin: [ 0.425 - 0.43 ] 3573 counts #Median bin: [ 0.415 - 0.42 ] 3513 counts | 0.075 - 0.08 : [ 1 0.00 0.00 ] #... | 0.135 - 0.14 : [ 1 0.00 0.00 ] #... | 0.15 - 0.155 : [ 1 0.00 0.00 ] | 0.155 - 0.16 : [ 1 0.00 0.00 ] #... | 0.18 - 0.185 : [ 2 0.00 0.00 ] | 0.185 - 0.19 : [ 1 0.00 0.00 ] | 0.19 - 0.195 : [ 1 0.00 0.00 ] #... | 0.205 - 0.21 : [ 2 0.00 0.00 ] | 0.21 - 0.215 : [ 1 0.00 0.00 ] | 0.215 - 0.22 : [ 2 0.00 0.00 ] | 0.22 - 0.225 : [ 1 0.00 0.00 ] | 0.225 - 0.23 : [ 3 0.00 0.00 ] | 0.23 - 0.235 : [ 5 0.00 0.00 ] | 0.235 - 0.24 : [ 4 0.00 0.00 ] | 0.24 - 0.245 : [ 7 0.00 0.00 ] | 0.245 - 0.25 : [ 5 0.00 0.00 ] | 0.25 - 0.255 : [ 7 0.00 0.00 ] | 0.255 - 0.26 : [ 8 0.00 0.00 ] | 0.26 - 0.265 : [ 24 0.00 0.00 ] | 0.265 - 0.27 : [ 21 0.00 0.00 ] | 0.27 - 0.275 : [ 22 0.00 0.00 ] | 0.275 - 0.28 : [ 16 0.00 0.00 ] | 0.28 - 0.285 : [ 26 0.00 0.00 ] | 0.285 - 0.29 : [ 37 0.00 0.00 ] |X 0.29 - 0.295 : [ 58 0.00 0.00 ] |X 0.295 - 0.3 : [ 68 0.00 0.01 ] |X 0.3 - 0.305 : [ 69 0.00 0.01 ] |X 0.305 - 0.31 : [ 82 0.00 0.01 ] |X 0.31 - 0.315 : [ 95 0.00 0.01 ] |XX 0.315 - 0.32 : [ 138 0.00 0.01 ] |XX 0.32 - 0.325 : [ 164 0.00 0.01 ] |XX 0.325 - 0.33 : [ 188 0.00 0.02 ] |XXX 0.33 - 0.335 : [ 238 0.00 0.02 ] |XXX 0.335 - 0.34 : [ 266 0.00 0.03 ] |XXXX 0.34 - 0.345 : [ 381 0.01 0.03 ] |XXXXX 0.345 - 0.35 : [ 472 0.01 0.04 ] |XXXXXXX 0.35 - 0.355 : [ 597 0.01 0.05 ] |XXXXXXXX 0.355 - 0.36 : [ 720 0.01 0.06 ] |XXXXXXXXXX 0.36 - 0.365 : [ 860 0.01 0.08 ] |XXXXXXXXXXXX 0.365 - 0.37 : [ 1034 0.02 0.10 ] |XXXXXXXXXXXXXX 0.37 - 0.375 : [ 1281 0.02 0.12 ] |XXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 1523 0.03 0.14 ] |XXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 1730 0.03 0.17 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 2131 0.04 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 2394 0.04 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 2682 0.05 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 3028 0.05 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 3122 0.05 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 3351 0.06 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 3513 0.06 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 3537 0.06 0.58 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 3573 0.06 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 3285 0.06 0.70 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 3088 0.05 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 2742 0.05 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 2427 0.04 0.84 ] |XXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 2004 0.03 0.87 ] |XXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 1741 0.03 0.90 ] |XXXXXXXXXXXXXX 0.46 - 0.465 : [ 1221 0.02 0.92 ] |XXXXXXXXXXX 0.465 - 0.47 : [ 1010 0.02 0.94 ] |XXXXXXXXX 0.47 - 0.475 : [ 814 0.01 0.96 ] |XXXXXX 0.475 - 0.48 : [ 555 0.01 0.96 ] |XXXX 0.48 - 0.485 : [ 395 0.01 0.97 ] |XXX 0.485 - 0.49 : [ 309 0.01 0.98 ] |XX 0.49 - 0.495 : [ 206 0.00 0.98 ] |XX 0.495 - 0.5 : [ 148 0.00 0.98 ] |XX 0.5 - 0.505 : [ 164 0.00 0.99 ] |X 0.505 - 0.51 : [ 78 0.00 0.99 ] |X 0.51 - 0.515 : [ 66 0.00 0.99 ] |X 0.515 - 0.52 : [ 48 0.00 0.99 ] |X 0.52 - 0.525 : [ 49 0.00 0.99 ] | 0.525 - 0.53 : [ 40 0.00 0.99 ] | 0.53 - 0.535 : [ 41 0.00 0.99 ] | 0.535 - 0.54 : [ 24 0.00 0.99 ] | 0.54 - 0.545 : [ 27 0.00 0.99 ] | 0.545 - 0.55 : [ 21 0.00 0.99 ] | 0.55 - 0.555 : [ 25 0.00 0.99 ] |X 0.555 - 0.56 : [ 46 0.00 0.99 ] |X 0.56 - 0.565 : [ 92 0.00 1.00 ] |X 0.565 - 0.57 : [ 55 0.00 1.00 ] | 0.57 - 0.575 : [ 21 0.00 1.00 ] | 0.575 - 0.58 : [ 14 0.00 1.00 ] | 0.58 - 0.585 : [ 19 0.00 1.00 ] | 0.585 - 0.59 : [ 12 0.00 1.00 ] | 0.59 - 0.595 : [ 11 0.00 1.00 ] | 0.595 - 0.6 : [ 8 0.00 1.00 ] | 0.6 - 0.605 : [ 13 0.00 1.00 ] | 0.605 - 0.61 : [ 9 0.00 1.00 ] | 0.61 - 0.615 : [ 21 0.00 1.00 ] | 0.615 - 0.62 : [ 12 0.00 1.00 ] | 0.62 - 0.625 : [ 13 0.00 1.00 ] | 0.625 - 0.63 : [ 11 0.00 1.00 ] | 0.63 - 0.635 : [ 15 0.00 1.00 ] | 0.635 - 0.64 : [ 10 0.00 1.00 ] | 0.64 - 0.645 : [ 10 0.00 1.00 ] | 0.645 - 0.65 : [ 2 0.00 1.00 ] | 0.65 - 0.655 : [ 2 0.00 1.00 ] #... | 0.66 - 0.665 : [ 1 0.00 1.00 ] #... | 0.67 - 0.675 : [ 2 0.00 1.00 ] | 0.675 - 0.68 : [ 1 0.00 1.00 ] #... | 0.685 - 0.69 : [ 1 0.00 1.00 ] | 0.69 - 0.695 : [ 1 0.00 1.00 ] #... | 0.705 - 0.71 : [ 2 0.00 1.00 ] #... | 0.925 - 0.93 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones N/plate avg% LIBRARY @ 24 3919 2087 86.96 90.58 AIOK @ 136 25269 12817 94.24 98.17 AIOH @ 196 29392 15411 78.63 81.90 AIOI @ ] 58580 30315 85.15 cumulative total@@ LIBRARY PLATE ID COUNT [ AIOK 24 AIOH 136 AIOI 196 ] for 356 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 = 2008 HQ Discrepant reads = 42 Chimeric reads = 117 Suspect alignments = 5791 ################################################################### C O N T I G I N F O R M A T I O N Mon Sep 6 04:03:57 2004 File: /psf/project/microbe3/3634606/edit_dir.26Jul04.QD/phrap.out Contig 64. 636 reads; 61624 bp (untrimmed), 61605 (trimmed). Contig 65. 641 reads; 60929 bp (untrimmed), 60811 (trimmed). Contig 66. 648 reads; 56769 bp (untrimmed), 56615 (trimmed). Contig 67. 650 reads; 57626 bp (untrimmed), 57151 (trimmed). Contig 68. 676 reads; 62970 bp (untrimmed), 62727 (trimmed). Contig 69. 683 reads; 57256 bp (untrimmed), 57201 (trimmed). Contig 70. 687 reads; 61758 bp (untrimmed), 61664 (trimmed). Contig 71. 746 reads; 62343 bp (untrimmed), 62178 (trimmed). Contig 72. 762 reads; 58562 bp (untrimmed), 58460 (trimmed). Contig 73. 776 reads; 61761 bp (untrimmed), 61727 (trimmed). Contig 74. 818 reads; 73133 bp (untrimmed), 73085 (trimmed). Contig 75. 931 reads; 91082 bp (untrimmed), 91057 (trimmed). Contig 76. 968 reads; 83615 bp (untrimmed), 83492 (trimmed). Contig 77. 1286 reads; 101078 bp (untrimmed), 100848 (trimmed). Contig 78. 1345 reads; 97882 bp (untrimmed), 97866 (trimmed). Contig 79. 2042 reads; 172744 bp (untrimmed), 172724 (trimmed). Contig 80. 2080 reads; 148647 bp (untrimmed), 148603 (trimmed). Contig 81. 2118 reads; 169292 bp (untrimmed), 169244 (trimmed). Contig 82. 2405 reads; 200925 bp (untrimmed), 200892 (trimmed). Contig 83. 2574 reads; 208417 bp (untrimmed), 208399 (trimmed). Contig 84. 2588 reads; 172006 bp (untrimmed), 171922 (trimmed). Contig 85. 2769 reads; 210670 bp (untrimmed), 210626 (trimmed). Contig 86. 2809 reads; 226823 bp (untrimmed), 226791 (trimmed). Contig 87. 3365 reads; 238599 bp (untrimmed), 238576 (trimmed). Contig 88. 4104 reads; 300947 bp (untrimmed), 300643 (trimmed). Contig 89. 5251 reads; 414092 bp (untrimmed), 413818 (trimmed). Contig 90. 5631 reads; 423697 bp (untrimmed), 423656 (trimmed). -------------------------------------------------------------- Totals 58506 reads; 4782427 bp (untrimmed), 4770085 (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 67 total values totalling 4741115.0000. <70762.910448 +/- 91092.423919> #Range: [ 2018 - 423656 ] #Most likely bin: [ 2000 - 4000 ] 8 counts #Median bin: [ 40000 - 42000 ] 3 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 8 0.12 0.12 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 6000 : [ 7 0.10 0.22 ] |XXXXX 6000 - 8000 : [ 1 0.01 0.24 ] #... |XXXXXXXXXXXXXXX 10000 - 12000 : [ 3 0.04 0.28 ] #... |XXXXX 14000 - 16000 : [ 1 0.01 0.30 ] #... |XXXXXXXXXX 18000 - 20000 : [ 2 0.03 0.33 ] #... |XXXXX 22000 - 24000 : [ 1 0.01 0.34 ] |XXXXXXXXXXXXXXXXXXXX 24000 - 26000 : [ 4 0.06 0.40 ] #... |XXXXXXXXXX 30000 - 32000 : [ 2 0.03 0.43 ] #... |XXXXXXXXXX 36000 - 38000 : [ 2 0.03 0.46 ] |XXXXX 38000 - 40000 : [ 1 0.01 0.48 ] |XXXXXXXXXXXXXXX 40000 - 42000 : [ 3 0.04 0.52 ] |XXXXX 42000 - 44000 : [ 1 0.01 0.54 ] |XXXXX 44000 - 46000 : [ 1 0.01 0.55 ] #... |XXXXX 48000 - 50000 : [ 1 0.01 0.57 ] |XXXXX 50000 - 52000 : [ 1 0.01 0.58 ] |XXXXX 52000 - 54000 : [ 1 0.01 0.60 ] #... |XXXXXXXXXXXXXXX 56000 - 58000 : [ 3 0.04 0.64 ] |XXXXX 58000 - 60000 : [ 1 0.01 0.66 ] |XXXXXXXXXXXXXXXXXXXX 60000 - 62000 : [ 4 0.06 0.72 ] |XXXXXXXXXX 62000 - 64000 : [ 2 0.03 0.75 ] #... |XXXXX 72000 - 74000 : [ 1 0.01 0.76 ] #... |XXXXX 82000 - 84000 : [ 1 0.01 0.78 ] #... |XXXXX 90000 - 92000 : [ 1 0.01 0.79 ] #... |XXXXX 96000 - 98000 : [ 1 0.01 0.81 ] #... |XXXXX 100000 - 102000 : [ 1 0.01 0.82 ] #... |XXXXX 148000 - 150000 : [ 1 0.01 0.84 ] #... |XXXXX 168000 - 170000 : [ 1 0.01 0.85 ] |XXXXX 170000 - 172000 : [ 1 0.01 0.87 ] |XXXXX 172000 - 174000 : [ 1 0.01 0.88 ] #... |XXXXX 200000 - 202000 : [ 1 0.01 0.90 ] #... |XXXXX 208000 - 210000 : [ 1 0.01 0.91 ] |XXXXX 210000 - 212000 : [ 1 0.01 0.93 ] #... |XXXXX 226000 - 228000 : [ 1 0.01 0.94 ] #... |XXXXX 238000 - 240000 : [ 1 0.01 0.96 ] #... |XXXXX 300000 - 302000 : [ 1 0.01 0.97 ] #... |XXXXX 412000 - 414000 : [ 1 0.01 0.99 ] #... |XXXXX 422000 - 424000 : [ 1 0.01 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 16369948 C = 11969795 G = 11922526 T = 16265662 N = 193034 X = 588125 GC fraction = 0.42 Total = 57309090 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 3634606_fasta.screen.contigs A 1408344 C 1001729 G 986319 N 30 T 1386005 fraction GC = 0.42 total bases = 4782427 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 4781939 bases = 11.31 +- 4.63 = 0.21 +- 4.12 m1 = 1.89 m2 = 1.10 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 88 total values totalling 699.2100. <7.945568 +/- 3.577961> #Range: [ 1.25 - 13.96 ] #Most likely bin: [ 9.5 - 10 ] 9 counts #Median bin: [ 8.5 - 9 ] 3 counts |XXXXXXXXX 1 - 1.5 : [ 2 0.02 0.02 ] |XXXXXXXXXXXXX 1.5 - 2 : [ 3 0.03 0.06 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 7 0.08 0.14 ] |XXXXXXXXX 2.5 - 3 : [ 2 0.02 0.16 ] |XXXXXXXXX 3 - 3.5 : [ 2 0.02 0.18 ] |XXXXXXXXXXXXX 3.5 - 4 : [ 3 0.03 0.22 ] |XXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 4 0.05 0.26 ] |XXXX 4.5 - 5 : [ 1 0.01 0.27 ] |XXXXXXXXX 5 - 5.5 : [ 2 0.02 0.30 ] #... |XXXX 6 - 6.5 : [ 1 0.01 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 6 0.07 0.38 ] |XXXXXXXXX 7 - 7.5 : [ 2 0.02 0.40 ] |XXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 4 0.05 0.44 ] |XXXXXXXXX 8 - 8.5 : [ 2 0.02 0.47 ] |XXXXXXXXXXXXX 8.5 - 9 : [ 3 0.03 0.50 ] |XXXXXXXXX 9 - 9.5 : [ 2 0.02 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 9 0.10 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 7 0.08 0.70 ] |XXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 4 0.05 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 7 0.08 0.83 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.08 0.91 ] |XXXXXXXXXXXXX 12 - 12.5 : [ 3 0.03 0.94 ] |XXXXXXXXXXXXX 12.5 - 13 : [ 3 0.03 0.98 ] |XXXX 13 - 13.5 : [ 1 0.01 0.99 ] |XXXX 13.5 - 14 : [ 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 67 total values totalling 637.1500. <9.509701 +/- 2.443984> #Range: [ 3.44 - 13.96 ] #Most likely bin: [ 9.5 - 10 ] 9 counts #Median bin: [ 9.5 - 10 ] 9 counts |XXXXXXXXX 3 - 3.5 : [ 2 0.03 0.03 ] |XXXX 3.5 - 4 : [ 1 0.01 0.04 ] |XXXX 4 - 4.5 : [ 1 0.01 0.06 ] |XXXX 4.5 - 5 : [ 1 0.01 0.07 ] |XXXX 5 - 5.5 : [ 1 0.01 0.09 ] #... |XXXX 6 - 6.5 : [ 1 0.01 0.10 ] |XXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 5 0.07 0.18 ] |XXXXXXXXX 7 - 7.5 : [ 2 0.03 0.21 ] |XXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 4 0.06 0.27 ] |XXXXXXXXX 8 - 8.5 : [ 2 0.03 0.30 ] |XXXXXXXXXXXXX 8.5 - 9 : [ 3 0.04 0.34 ] |XXXXXXXXX 9 - 9.5 : [ 2 0.03 0.37 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 9 0.13 0.51 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 7 0.10 0.61 ] |XXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 4 0.06 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 7 0.10 0.78 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.10 0.88 ] |XXXXXXXXXXXXX 12 - 12.5 : [ 3 0.04 0.93 ] |XXXXXXXXXXXXX 12.5 - 13 : [ 3 0.04 0.97 ] |XXXX 13 - 13.5 : [ 1 0.01 0.99 ] |XXXX 13.5 - 14 : [ 1 0.01 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 2 2 reads 1484 bases = 1.25 +- 0.43 = 1.25 +- 0.43 m1 = 0.15 m2 = 0.00 Contig 7 3 reads 1921 bases = 1.48 +- 0.50 = 1.48 +- 0.50 m1 = 0.17 m2 = 0.00 Contig 9 4 reads 2513 bases = 1.54 +- 0.57 = 0.76 +- 1.05 m1 = 0.21 m2 = -0.19 Contig 10 4 reads 2194 bases = 1.66 +- 0.52 = 0.87 +- 1.18 m1 = 0.16 m2 = -0.28 Contig 11 4 reads 1743 bases = 1.90 +- 0.96 = -0.31 +- 0.65 m1 = 0.49 m2 = 0.12 Contig 3 3 reads 1191 bases = 2.23 +- 0.89 = 2.23 +- 0.89 m1 = 0.35 m2 = 0.00 Contig 17 6 reads 1924 bases = 2.27 +- 1.34 = 0.09 +- 0.83 m1 = 0.79 m2 = 0.28 Contig 12 4 reads 1707 bases = 2.29 +- 1.00 = 1.07 +- 0.69 m1 = 0.44 m2 = 0.13 Contig 6 3 reads 1267 bases = 2.35 +- 0.85 = 0.82 +- 0.59 m1 = 0.31 m2 = 0.09 Contig 13 4 reads 1521 bases = 2.36 +- 0.79 = 2.36 +- 0.79 m1 = 0.27 m2 = 0.00 Contig 8 3 reads 1206 bases = 2.37 +- 0.87 = 0.70 +- 0.64 m1 = 0.32 m2 = 0.09 Contig 5 3 reads 998 bases = 2.41 +- 0.70 = 2.41 +- 0.70 m1 = 0.20 m2 = 0.00 Contig 18 6 reads 1977 bases = 2.87 +- 1.42 = 2.87 +- 1.42 m1 = 0.70 m2 = 0.00 Contig 19 7 reads 2202 bases = 2.92 +- 2.05 = 0.43 +- 1.15 m1 = 1.44 m2 = 0.72 Contig 23 10 reads 2720 bases = 3.44 +- 2.12 = 2.73 +- 2.57 m1 = 1.31 m2 = -0.52 Contig 29 23 reads 6197 bases = 3.44 +- 1.55 = 0.78 +- 3.28 m1 = 0.70 m2 = -2.08 Contig 15 5 reads 1183 bases = 3.67 +- 1.44 = 3.67 +- 1.44 m1 = 0.56 m2 = 0.00 Contig 14 5 reads 1218 bases = 3.81 +- 1.43 = 2.38 +- 1.13 m1 = 0.54 m2 = 0.19 Contig 27 15 reads 3554 bases = 3.98 +- 2.10 = 2.89 +- 1.28 m1 = 1.11 m2 = 0.69 Contig 20 8 reads 1669 bases = 4.01 +- 1.39 = 3.36 +- 1.91 m1 = 0.48 m2 = -0.43 Contig 60 512 reads 42875 bases = 11.12 +- 4.36 = 0.31 +- 4.44 m1 = 1.71 m2 = -0.18 Contig 71 746 reads 62343 bases = 11.12 +- 4.88 = 0.78 +- 5.82 m1 = 2.14 m2 = -2.51 Contig 47 235 reads 19532 bases = 11.18 +- 4.53 = 1.03 +- 3.87 m1 = 1.84 m2 = 1.39 Contig 86 2809 reads 226823 bases = 11.40 +- 4.63 = 0.06 +- 3.55 m1 = 1.88 m2 = 2.20 Contig 83 2574 reads 208417 bases = 11.44 +- 4.63 = 0.04 +- 4.40 m1 = 1.87 m2 = 0.52 Contig 63 613 reads 49035 bases = 11.57 +- 5.13 = 0.12 +- 4.94 m1 = 2.27 m2 = 0.47 Contig 81 2118 reads 169292 bases = 11.61 +- 4.04 = 0.10 +- 4.05 m1 = 1.41 m2 = -0.01 Contig 73 776 reads 61761 bases = 11.62 +- 3.59 = 0.48 +- 3.42 m1 = 1.11 m2 = 0.29 Contig 89 5251 reads 414092 bases = 11.70 +- 4.07 = 0.13 +- 3.81 m1 = 1.42 m2 = 0.52 Contig 77 1286 reads 101078 bases = 11.72 +- 4.28 = -0.01 +- 3.67 m1 = 1.57 m2 = 1.21 Contig 72 762 reads 58562 bases = 11.97 +- 4.57 = 0.01 +- 3.69 m1 = 1.74 m2 = 1.80 Contig 51 314 reads 24256 bases = 11.99 +- 3.87 = 0.53 +- 3.83 m1 = 1.25 m2 = 0.07 Contig 85 2769 reads 210670 bases = 12.17 +- 4.75 = 0.04 +- 4.20 m1 = 1.85 m2 = 1.23 Contig 59 503 reads 38219 bases = 12.24 +- 3.53 = 0.11 +- 4.30 m1 = 1.02 m2 = -1.51 Contig 90 5631 reads 423697 bases = 12.28 +- 4.89 = 0.05 +- 3.90 m1 = 1.94 m2 = 2.16 Contig 88 4104 reads 300947 bases = 12.60 +- 4.25 = 0.12 +- 4.25 m1 = 1.44 m2 = 0.01 Contig 78 1345 reads 97882 bases = 12.69 +- 4.62 = 0.21 +- 3.62 m1 = 1.68 m2 = 2.05 Contig 80 2080 reads 148647 bases = 12.87 +- 5.07 = 0.10 +- 4.16 m1 = 2.00 m2 = 2.11 Contig 87 3365 reads 238599 bases = 13.08 +- 5.32 = 0.32 +- 5.37 m1 = 2.16 m2 = -0.13 Contig 84 2588 reads 172006 bases = 13.96 +- 4.81 = 0.03 +- 4.03 m1 = 1.65 m2 = 1.71 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 90 total values totalling 58506.0000. <650.066667 +/- 1110.732109> #Range: [ 2 - 5631 ] #Most likely bin: [ 3 - 4 ] 6 counts #Median bin: [ 212 - 213 ] 1 counts |XXXXXXXXXXXXX 2 - 3 : [ 2 0.02 0.02 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 4 : [ 6 0.07 0.09 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 5 : [ 5 0.06 0.14 ] |XXXXXXXXXXXXX 5 - 6 : [ 2 0.02 0.17 ] |XXXXXXXXXXXXXXXXXXXX 6 - 7 : [ 3 0.03 0.20 ] |XXXXXXX 7 - 8 : [ 1 0.01 0.21 ] |XXXXXXXXXXXXX 8 - 9 : [ 2 0.02 0.23 ] |XXXXXXX 9 - 10 : [ 1 0.01 0.24 ] |XXXXXXX 10 - 11 : [ 1 0.01 0.26 ] #... |XXXXXXX 13 - 14 : [ 1 0.01 0.27 ] |XXXXXXX 14 - 15 : [ 1 0.01 0.28 ] |XXXXXXXXXXXXX 15 - 16 : [ 2 0.02 0.30 ] #... |XXXXXXX 20 - 21 : [ 1 0.01 0.31 ] #... |XXXXXXX 23 - 24 : [ 1 0.01 0.32 ] #... |XXXXXXX 25 - 26 : [ 1 0.01 0.33 ] #... |XXXXXXX 27 - 28 : [ 1 0.01 0.34 ] #... |XXXXXXX 32 - 33 : [ 1 0.01 0.36 ] |XXXXXXXXXXXXX 33 - 34 : [ 2 0.02 0.38 ] #... |XXXXXXX 35 - 36 : [ 1 0.01 0.39 ] |XXXXXXX 36 - 37 : [ 1 0.01 0.40 ] #... |XXXXXXX 45 - 46 : [ 1 0.01 0.41 ] #... |XXXXXXX 52 - 53 : [ 1 0.01 0.42 ] #... |XXXXXXX 65 - 66 : [ 1 0.01 0.43 ] #... |XXXXXXX 78 - 79 : [ 1 0.01 0.44 ] #... |XXXXXXX 84 - 85 : [ 1 0.01 0.46 ] #... |XXXXXXX 88 - 89 : [ 1 0.01 0.47 ] #... |XXXXXXX 105 - 106 : [ 1 0.01 0.48 ] #... |XXXXXXX 153 - 154 : [ 1 0.01 0.49 ] #... |XXXXXXX 212 - 213 : [ 1 0.01 0.50 ] #... |XXXXXXX 231 - 232 : [ 1 0.01 0.51 ] #... |XXXXXXX 235 - 236 : [ 1 0.01 0.52 ] #... |XXXXXXX 260 - 261 : [ 1 0.01 0.53 ] #... |XXXXXXX 275 - 276 : [ 1 0.01 0.54 ] #... |XXXXXXX 311 - 312 : [ 1 0.01 0.56 ] #... |XXXXXXX 314 - 315 : [ 1 0.01 0.57 ] #... |XXXXXXX 328 - 329 : [ 1 0.01 0.58 ] #... |XXXXXXX 362 - 363 : [ 1 0.01 0.59 ] #... |XXXXXXX 395 - 396 : [ 1 0.01 0.60 ] #... |XXXXXXX 417 - 418 : [ 1 0.01 0.61 ] #... |XXXXXXX 427 - 428 : [ 1 0.01 0.62 ] #... |XXXXXXX 432 - 433 : [ 1 0.01 0.63 ] #... |XXXXXXX 448 - 449 : [ 1 0.01 0.64 ] #... |XXXXXXX 503 - 504 : [ 1 0.01 0.66 ] #... |XXXXXXX 512 - 513 : [ 1 0.01 0.67 ] #... |XXXXXXX 539 - 540 : [ 1 0.01 0.68 ] #... |XXXXXXX 600 - 601 : [ 1 0.01 0.69 ] #... |XXXXXXX 613 - 614 : [ 1 0.01 0.70 ] #... |XXXXXXX 636 - 637 : [ 1 0.01 0.71 ] #... |XXXXXXX 641 - 642 : [ 1 0.01 0.72 ] #... |XXXXXXX 648 - 649 : [ 1 0.01 0.73 ] #... |XXXXXXX 650 - 651 : [ 1 0.01 0.74 ] #... |XXXXXXX 676 - 677 : [ 1 0.01 0.76 ] #... |XXXXXXX 683 - 684 : [ 1 0.01 0.77 ] #... |XXXXXXX 687 - 688 : [ 1 0.01 0.78 ] #... |XXXXXXX 746 - 747 : [ 1 0.01 0.79 ] #... |XXXXXXX 762 - 763 : [ 1 0.01 0.80 ] #... |XXXXXXX 776 - 777 : [ 1 0.01 0.81 ] #... |XXXXXXX 818 - 819 : [ 1 0.01 0.82 ] #... |XXXXXXX 931 - 932 : [ 1 0.01 0.83 ] #... |XXXXXXX 968 - 969 : [ 1 0.01 0.84 ] #... |XXXXXXX 1286 - 1287 : [ 1 0.01 0.86 ] #... |XXXXXXX 1345 - 1346 : [ 1 0.01 0.87 ] #... |XXXXXXX 2042 - 2043 : [ 1 0.01 0.88 ] #... |XXXXXXX 2080 - 2081 : [ 1 0.01 0.89 ] #... |XXXXXXX 2118 - 2119 : [ 1 0.01 0.90 ] #... |XXXXXXX 2405 - 2406 : [ 1 0.01 0.91 ] #... |XXXXXXX 2574 - 2575 : [ 1 0.01 0.92 ] #... |XXXXXXX 2588 - 2589 : [ 1 0.01 0.93 ] #... |XXXXXXX 2769 - 2770 : [ 1 0.01 0.94 ] #... |XXXXXXX 2809 - 2810 : [ 1 0.01 0.96 ] #... |XXXXXXX 3365 - 3366 : [ 1 0.01 0.97 ] #... |XXXXXXX 4104 - 4105 : [ 1 0.01 0.98 ] #... |XXXXXXX 5251 - 5252 : [ 1 0.01 0.99 ] #... |XXXXXXX 5631 - 5632 : [ 1 0.01 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 90 total values totalling 4782427.0000. <53138.077778 +/- 84221.163548> #Range: [ 229 - 423697 ] #Most likely bin: [ 1000 - 2000 ] 15 counts #Median bin: [ 19000 - 20000 ] 1 counts |XXXXXXXXXXXXX 0 - 1000 : [ 5 0.06 0.06 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 15 0.17 0.22 ] |XXXXXXXXXXXXXXXXXXX 2000 - 3000 : [ 7 0.08 0.30 ] |XXXXXXXXXXX 3000 - 4000 : [ 4 0.04 0.34 ] |XXXXX 4000 - 5000 : [ 2 0.02 0.37 ] |XXXXXXXX 5000 - 6000 : [ 3 0.03 0.40 ] |XXXXX 6000 - 7000 : [ 2 0.02 0.42 ] |XXX 7000 - 8000 : [ 1 0.01 0.43 ] #... |XXXXX 10000 - 11000 : [ 2 0.02 0.46 ] |XXX 11000 - 12000 : [ 1 0.01 0.47 ] #... |XXX 14000 - 15000 : [ 1 0.01 0.48 ] #... |XXX 18000 - 19000 : [ 1 0.01 0.49 ] |XXX 19000 - 20000 : [ 1 0.01 0.50 ] #... |XXX 22000 - 23000 : [ 1 0.01 0.51 ] #... |XXX 24000 - 25000 : [ 1 0.01 0.52 ] |XXXXXXXX 25000 - 26000 : [ 3 0.03 0.56 ] #... |XXXXX 30000 - 31000 : [ 2 0.02 0.58 ] #... |XXX 37000 - 38000 : [ 1 0.01 0.59 ] |XXXXX 38000 - 39000 : [ 2 0.02 0.61 ] #... |XXX 40000 - 41000 : [ 1 0.01 0.62 ] |XXXXX 41000 - 42000 : [ 2 0.02 0.64 ] |XXX 42000 - 43000 : [ 1 0.01 0.66 ] #... |XXX 44000 - 45000 : [ 1 0.01 0.67 ] #... |XXX 49000 - 50000 : [ 1 0.01 0.68 ] #... |XXX 51000 - 52000 : [ 1 0.01 0.69 ] #... |XXX 53000 - 54000 : [ 1 0.01 0.70 ] #... |XXX 56000 - 57000 : [ 1 0.01 0.71 ] |XXXXX 57000 - 58000 : [ 2 0.02 0.73 ] |XXX 58000 - 59000 : [ 1 0.01 0.74 ] #... |XXX 60000 - 61000 : [ 1 0.01 0.76 ] |XXXXXXXX 61000 - 62000 : [ 3 0.03 0.79 ] |XXXXX 62000 - 63000 : [ 2 0.02 0.81 ] #... |XXX 73000 - 74000 : [ 1 0.01 0.82 ] #... |XXX 83000 - 84000 : [ 1 0.01 0.83 ] #... |XXX 91000 - 92000 : [ 1 0.01 0.84 ] #... |XXX 97000 - 98000 : [ 1 0.01 0.86 ] #... |XXX 101000 - 102000 : [ 1 0.01 0.87 ] #... |XXX 148000 - 149000 : [ 1 0.01 0.88 ] #... |XXX 169000 - 170000 : [ 1 0.01 0.89 ] #... |XXXXX 172000 - 173000 : [ 2 0.02 0.91 ] #... |XXX 200000 - 201000 : [ 1 0.01 0.92 ] #... |XXX 208000 - 209000 : [ 1 0.01 0.93 ] #... |XXX 210000 - 211000 : [ 1 0.01 0.94 ] #... |XXX 226000 - 227000 : [ 1 0.01 0.96 ] #... |XXX 238000 - 239000 : [ 1 0.01 0.97 ] #... |XXX 300000 - 301000 : [ 1 0.01 0.98 ] #... |XXX 414000 - 415000 : [ 1 0.01 0.99 ] #... |XXX 423000 - 424000 : [ 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 AIOH reads.list > grep.reads.list.AIOH Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOH 4 500 #Found 10672 total values totalling 40204643.0000. <3767.301630 +/- 5621.743911> #Range: [ - 361969 ] #Most likely bin: [ 3000 - 3500 ] 3795 counts #Median bin: [ 3500 - 4000 ] 3193 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 3 0.00 0.00 ] | 1000 - 1500 : [ 22 0.00 0.00 ] | 1500 - 2000 : [ 46 0.00 0.01 ] |XX 2000 - 2500 : [ 185 0.02 0.02 ] |XXXXXXXXX 2500 - 3000 : [ 814 0.08 0.10 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3795 0.36 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3193 0.30 0.76 ] |XXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1801 0.17 0.92 ] |XXXXXXX 4500 - 5000 : [ 631 0.06 0.98 ] |XX 5000 - 5500 : [ 162 0.02 1.00 ] | 5500 - 6000 : [ 8 0.00 1.00 ] #... | 21500 - 22000 : [ 1 0.00 1.00 ] #... | 54500 - 55000 : [ 1 0.00 1.00 ] #... | 77500 - 78000 : [ 1 0.00 1.00 ] #... | 82000 - 82500 : [ 1 0.00 1.00 ] #... | 117500 - 118000 : [ 1 0.00 1.00 ] #... | 137500 - 138000 : [ 1 0.00 1.00 ] #... | 138500 - 139000 : [ 1 0.00 1.00 ] | 139000 - 139500 : [ 1 0.00 1.00 ] #... | 221500 - 222000 : [ 1 0.00 1.00 ] #... | 278000 - 278500 : [ 1 0.00 1.00 ] #... | 361500 - 362000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AIOI reads.list > grep.reads.list.AIOI Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOI 4 500 #Found 13076 total values totalling 88338248.0000. <6755.754665 +/- 5611.774979> #Range: [ - 281546 ] #Most likely bin: [ 6000 - 6500 ] 3455 counts #Median bin: [ 6500 - 7000 ] 3305 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 1 0.00 0.00 ] | 1000 - 1500 : [ 35 0.00 0.00 ] | 1500 - 2000 : [ 36 0.00 0.01 ] | 2000 - 2500 : [ 33 0.00 0.01 ] | 2500 - 3000 : [ 35 0.00 0.01 ] |X 3000 - 3500 : [ 57 0.00 0.02 ] |X 3500 - 4000 : [ 44 0.00 0.02 ] | 4000 - 4500 : [ 41 0.00 0.02 ] |X 4500 - 5000 : [ 106 0.01 0.03 ] |XX 5000 - 5500 : [ 185 0.01 0.04 ] |XXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1464 0.11 0.16 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 3455 0.26 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 3305 0.25 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 2710 0.21 0.88 ] |XXXXXXXXXXXXXXXX 7500 - 8000 : [ 1422 0.11 0.99 ] |X 8000 - 8500 : [ 123 0.01 1.00 ] | 8500 - 9000 : [ 5 0.00 1.00 ] | 9000 - 9500 : [ 1 0.00 1.00 ] | 9500 - 10000 : [ 3 0.00 1.00 ] | 10000 - 10500 : [ 1 0.00 1.00 ] | 10500 - 11000 : [ 1 0.00 1.00 ] #... | 11500 - 12000 : [ 1 0.00 1.00 ] #... | 48000 - 48500 : [ 1 0.00 1.00 ] #... | 102000 - 102500 : [ 1 0.00 1.00 ] #... | 140000 - 140500 : [ 2 0.00 1.00 ] | 140500 - 141000 : [ 3 0.00 1.00 ] #... | 280000 - 280500 : [ 1 0.00 1.00 ] #... | 281000 - 281500 : [ 2 0.00 1.00 ] | 281500 - 282000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AIOK reads.list > grep.reads.list.AIOK Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOK 4 500 #Found 1203 total values totalling 43361954.0000. <36044.849543 +/- 4877.507360> #Range: [ - 170407 ] #Most likely bin: [ 35500 - 36000 ] 103 counts #Median bin: [ 35500 - 36000 ] 103 counts | 0 - 500 : [ 1 0.00 0.00 ] #... | 27500 - 28000 : [ 1 0.00 0.00 ] |X 28000 - 28500 : [ 2 0.00 0.00 ] |X 28500 - 29000 : [ 2 0.00 0.00 ] |XX 29000 - 29500 : [ 6 0.00 0.01 ] |X 29500 - 30000 : [ 3 0.00 0.01 ] |XX 30000 - 30500 : [ 6 0.00 0.02 ] |XXXXXX 30500 - 31000 : [ 16 0.01 0.03 ] |XXXXX 31000 - 31500 : [ 14 0.01 0.04 ] |XXXXXXXXXX 31500 - 32000 : [ 27 0.02 0.06 ] |XXXXXXXXXXXXXX 32000 - 32500 : [ 35 0.03 0.09 ] |XXXXXXXXXXXXXXXXX 32500 - 33000 : [ 43 0.04 0.13 ] |XXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 53 0.04 0.17 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 78 0.06 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 89 0.07 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 81 0.07 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 91 0.08 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 103 0.09 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 79 0.07 0.61 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 75 0.06 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 76 0.06 0.73 ] |XXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 60 0.05 0.78 ] |XXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 54 0.04 0.83 ] |XXXXXXXXXXXXXXXXX 38500 - 39000 : [ 43 0.04 0.86 ] |XXXXXXXXXXXXXXXX 39000 - 39500 : [ 42 0.03 0.90 ] |XXXXXXX 39500 - 40000 : [ 18 0.01 0.91 ] |XXXXXXXXX 40000 - 40500 : [ 24 0.02 0.93 ] |XXXXXXX 40500 - 41000 : [ 18 0.01 0.95 ] |XXXXXXX 41000 - 41500 : [ 18 0.01 0.96 ] |XXXX 41500 - 42000 : [ 11 0.01 0.97 ] |XXXX 42000 - 42500 : [ 11 0.01 0.98 ] |XXXX 42500 - 43000 : [ 10 0.01 0.99 ] |XX 43000 - 43500 : [ 4 0.00 0.99 ] |XX 43500 - 44000 : [ 4 0.00 1.00 ] |X 44000 - 44500 : [ 2 0.00 1.00 ] |X 44500 - 45000 : [ 2 0.00 1.00 ] #... | 170000 - 170500 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # AIOH 3548 +- 647 (n=5356) # AIOK 35904 +- 2657 (n=588) # AIOI 6529 +- 1111 (n=6590) ################################################################### 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 723.879719 bp, 58506 reads, genome size 3066363 bp Command: idealAssembly 3066363 58506 723.879719 ------------------------------------------------------------------- Genome = 3066363 bases Nreads = 58506 readLength = 723.879719 Depth = 13.81 N_contigs = N_gaps = 0 mean gap size = 51 bases mean contig size = 996074 reads (~ 52205298 bases) %cover = 100.00 %singlet = 0.00 assembly size = 3066360 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 0 contigs containing at least 1671411 reads each * N50 Contig Sizes * Total Assemb Size: 1/2 (Tot.Assemb. Size): Command: hist contig.grep 5 1000 5 (2200) (15000) Result: Half of the total Assembled Size of the genome is contained in n of the largest contigs equaling n bps. ################################################################### Contam Summary with *.contigs: Command: contam_summary -c -s ------------------------------------------------------------------- Contamination Summary for JGI id: 3634606 Command line options used were: -c -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 12673 Number of reads with percent X's >= 20%: 250 = 0.4% Number of reads with percent X's >= 50%: 158 = 0.3% Number of reads with percent X's >= 80%: 47 = 0.1% Total nr of reads in project is: 58580 Total nr of X's: 588125 Total nr not found in screened files: 0 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with L09136-pUC18 11168 54 32 2 Nr with pCC1Fos 1225 6 4 0 Nr with pMCL200 280 190 122 45 ################################################################### Contam Summary with *.singlets: Command: contam_summary -c -s -g ------------------------------------------------------------------- Contamination Summary for JGI id: 3634606 Command line options used were: -c -g -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 13 Number of reads with percent X's >= 20%: 2 = 2.7% Number of reads with percent X's >= 50%: 2 = 2.7% Number of reads with percent X's >= 80%: 0 = 0.0% Total nr of reads in project is: 74 Total nr of X's: 1759 Total nr not found in screened files: 0 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with L09136-pUC18 5 0 0 0 Nr with pCC1Fos 6 0 0 0 Nr with pMCL200 2 2 2 0 ################################################################### Bad M1 Contigs ------------------------------------------------------------------- ################################################################### Bad M2 Contigs ------------------------------------------------------------------- ################################################################### Ran Plates2contigs: Output Location: Ran in.dir: Output Location: Viewed Contigs with Phrapview: ################################################################### Conclusions: