################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 3634505 Genus_species: Chromohalobacter salexigens DSM 3043 Taxid: 158080 Genome size: 3900 Libraries: AIFB, AIFC, AIFA ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 3634505 ------------------------------------------------------------------- ID=3634505 Lineage for 'Chromohalobacter salexigens': Chromohalobacter salexigens species Chromohalobacter genus Halomonadaceae family Oceanospirillales order Gammaproteobacteria class Proteobacteria phylum Bacteria superkingdom cellular organisms no rank root no rank ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 3685675 # phrap: 3790920 # db: 3900000 3792198 +/- 87502 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length AIFA.5-72 326 97.34 728.08 AIFB.5-44 20 87.55 479.20 AIFC.5-28 48 94.86 646.79 QCMC.5-24 80 94.09 635.19 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s AIFB 20 10 85.57 443.40 10 89.53 515.00 AIFC 48 24 94.88 651.12 24 94.84 642.46 AIFA 326 162 97.78 733.72 164 96.90 722.50 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 3634505_fasta.screen ../SCREENME_TOO.fasta -minmatch 40 -minscore 80 -screen > screen.out.ME_TOO /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634505_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 3634505_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634505_fasta.screen -new_ace -minmatch 55 -maxmatch 80 -minscore 75 -penalty -8 -trim_qual 20 -max_subclone_size 50000 -vector_bound 50 > phrap.out /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 3634505_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634505.out /home/copeland/scripts/librariesInfoTxt.sh 3634505 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 3634505+3635208_fasta.screen /usr/local/sequences/LRS.fasta -minmatch 20 -minscore 50 -screen > screen.out.std /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 3634505+3635208_fasta.screen ../SCREENME_TOO.fasta -minmatch 40 -minscore 80 -screen > screen.out.ME_TOO /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634505+3635208_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 3634505+3635208_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634505.out /home/copeland/scripts/librariesInfoTxt.sh 3634505 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 3634505_fasta.screen /usr/local/sequences/LRS.fasta -minmatch 20 -minscore 50 -screen > screen.out.std /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 3634505_fasta.screen ../SCREENME_TOO.fasta -minmatch 40 -minscore 80 -screen > screen.out.ME_TOO /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634505_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 3634505_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634505.out /home/copeland/scripts/librariesInfoTxt.sh 3634505 phrap.out > librariesInfo.txt ################################################################### Library vector screening AIFA.000001.000100 screen.out.1 3634505_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634505_fasta.screen /usr/local/sequences/LRS.fasta AIFA.000101.000200 screen.out.1 3634505_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634505_fasta.screen /usr/local/sequences/LRS.fasta AIFB.000001.000100 screen.out.1 3634505_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634505_fasta.screen /usr/local/sequences/LRS.fasta AIFC.000001.000100 screen.out.1 3634505_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634505_fasta.screen /usr/local/sequences/LRS.fasta QCMC.000001.000100 screen.out.1 3634505_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634505_fasta.screen /usr/local/sequences/LRS.fasta AIFA.000001.000100 screen.out.1 3634505_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634505_fasta.screen /usr/local/sequences/LRS.fasta AIFA.000101.000200 screen.out.1 3634505_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634505_fasta.screen /usr/local/sequences/LRS.fasta AIFB.000001.000100 screen.out.1 3634505_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634505_fasta.screen /usr/local/sequences/LRS.fasta AIFC.000001.000100 screen.out.1 3634505_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634505_fasta.screen /usr/local/sequences/LRS.fasta QCMC.000001.000100 screen.out.1 3634505_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634505_fasta.screen /usr/local/sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 3634505_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 47899 total values totalling 32414064.0000. <676.716925 +/- 173.463952> #Range: [ 22 - 932 ] #Most likely bin: [ 750 - 800 ] 11398 counts #Median bin: [ 700 - 750 ] 8694 counts | 0 - 50 : [ 107 0.00 0.00 ] |XX 50 - 100 : [ 450 0.01 0.01 ] |XX 100 - 150 : [ 518 0.01 0.02 ] |XX 150 - 200 : [ 569 0.01 0.03 ] |XX 200 - 250 : [ 594 0.01 0.05 ] |XXX 250 - 300 : [ 735 0.02 0.06 ] |XXX 300 - 350 : [ 776 0.02 0.08 ] |XXX 350 - 400 : [ 899 0.02 0.10 ] |XXX 400 - 450 : [ 947 0.02 0.12 ] |XXX 450 - 500 : [ 963 0.02 0.14 ] |XXXXX 500 - 550 : [ 1301 0.03 0.16 ] |XXXXXXX 550 - 600 : [ 1952 0.04 0.20 ] |XXXXXXXXXXX 600 - 650 : [ 3129 0.07 0.27 ] |XXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5320 0.11 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8694 0.18 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 11398 0.24 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7950 0.17 0.97 ] |XXXXXX 850 - 900 : [ 1570 0.03 1.00 ] | 900 - 950 : [ 27 0.00 1.00 ] JAZZ trim 15 readlength histogram for AIFA Command: /usr/xpg4/bin/grep AIFA 3634505_fasta.screen.screen.ids > reads.trim15.AIFA.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFA.rl 2 50 #Found 35181 total values totalling 25189513.0000. <715.997641 +/- 131.719506> #Range: [ 24 - 932 ] #Most likely bin: [ 750 - 800 ] 9248 counts #Median bin: [ 750 - 800 ] 9248 counts | 0 - 50 : [ 23 0.00 0.00 ] | 50 - 100 : [ 85 0.00 0.00 ] | 100 - 150 : [ 112 0.00 0.01 ] |X 150 - 200 : [ 139 0.00 0.01 ] |X 200 - 250 : [ 183 0.01 0.02 ] |X 250 - 300 : [ 247 0.01 0.02 ] |X 300 - 350 : [ 303 0.01 0.03 ] |XX 350 - 400 : [ 374 0.01 0.04 ] |XX 400 - 450 : [ 446 0.01 0.05 ] |XX 450 - 500 : [ 553 0.02 0.07 ] |XXX 500 - 550 : [ 805 0.02 0.09 ] |XXXXXX 550 - 600 : [ 1367 0.04 0.13 ] |XXXXXXXXXX 600 - 650 : [ 2326 0.07 0.20 ] |XXXXXXXXXXXXXXXX 650 - 700 : [ 3802 0.11 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6303 0.18 0.49 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 9248 0.26 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7317 0.21 0.96 ] |XXXXXXX 850 - 900 : [ 1521 0.04 1.00 ] | 900 - 950 : [ 27 0.00 1.00 ] JAZZ trim 15 readlength histogram for AIFB Command: /usr/xpg4/bin/grep AIFB 3634505_fasta.screen.screen.ids > reads.trim15.AIFB.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFB.rl 2 50 #Found 3770 total values totalling 1292575.0000. <342.858090 +/- 183.128659> #Range: [ 25 - 797 ] #Most likely bin: [ 150 - 200 ] 339 counts #Median bin: [ 300 - 350 ] 280 counts |XXXXXXX 0 - 50 : [ 60 0.02 0.02 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 50 - 100 : [ 322 0.09 0.10 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 100 - 150 : [ 336 0.09 0.19 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 150 - 200 : [ 339 0.09 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 200 - 250 : [ 315 0.08 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 300 0.08 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 300 - 350 : [ 280 0.07 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 350 - 400 : [ 311 0.08 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 400 - 450 : [ 313 0.08 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 450 - 500 : [ 272 0.07 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 290 0.08 0.83 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 279 0.07 0.91 ] |XXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 194 0.05 0.96 ] |XXXXXXXXXXXXXX 650 - 700 : [ 119 0.03 0.99 ] |XXXX 700 - 750 : [ 34 0.01 1.00 ] |X 750 - 800 : [ 6 0.00 1.00 ] JAZZ trim 15 readlength histogram for AIFC Command: /usr/xpg4/bin/grep AIFC 3634505_fasta.screen.screen.ids > reads.trim15.AIFC.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFC.rl 2 50 #Found 4288 total values totalling 2823760.0000. <658.526119 +/- 174.593664> #Range: [ 22 - 881 ] #Most likely bin: [ 750 - 800 ] 1071 counts #Median bin: [ 700 - 750 ] 966 counts |X 0 - 50 : [ 19 0.00 0.00 ] |X 50 - 100 : [ 34 0.01 0.01 ] |X 100 - 150 : [ 31 0.01 0.02 ] |X 150 - 200 : [ 40 0.01 0.03 ] |X 200 - 250 : [ 40 0.01 0.04 ] |XXXXX 250 - 300 : [ 127 0.03 0.07 ] |XXXXX 300 - 350 : [ 129 0.03 0.10 ] |XXXXX 350 - 400 : [ 136 0.03 0.13 ] |XXXX 400 - 450 : [ 96 0.02 0.15 ] |XX 450 - 500 : [ 63 0.01 0.17 ] |XXX 500 - 550 : [ 88 0.02 0.19 ] |XXXXX 550 - 600 : [ 138 0.03 0.22 ] |XXXXXXXXXX 600 - 650 : [ 263 0.06 0.28 ] |XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 557 0.13 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 966 0.23 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1071 0.25 0.89 ] |XXXXXXXXXXXXXXXXX 800 - 850 : [ 442 0.10 0.99 ] |XX 850 - 900 : [ 48 0.01 1.00 ] ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.3634505_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.3634505_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 47788 total values totalling 30303.0730. <0.634115 +/- 0.053579> #Range: [ 0.2877 - 0.8644 ] #Most likely bin: [ 0.64 - 0.645 ] 2691 counts #Median bin: [ 0.64 - 0.645 ] 2691 counts | 0.285 - 0.29 : [ 1 0.00 0.00 ] | 0.29 - 0.295 : [ 1 0.00 0.00 ] #... | 0.3 - 0.305 : [ 3 0.00 0.00 ] #... | 0.32 - 0.325 : [ 2 0.00 0.00 ] #... | 0.335 - 0.34 : [ 1 0.00 0.00 ] | 0.34 - 0.345 : [ 3 0.00 0.00 ] | 0.345 - 0.35 : [ 4 0.00 0.00 ] | 0.35 - 0.355 : [ 2 0.00 0.00 ] | 0.355 - 0.36 : [ 12 0.00 0.00 ] | 0.36 - 0.365 : [ 13 0.00 0.00 ] | 0.365 - 0.37 : [ 20 0.00 0.00 ] | 0.37 - 0.375 : [ 23 0.00 0.00 ] | 0.375 - 0.38 : [ 27 0.00 0.00 ] | 0.38 - 0.385 : [ 26 0.00 0.00 ] |X 0.385 - 0.39 : [ 44 0.00 0.00 ] |X 0.39 - 0.395 : [ 51 0.00 0.00 ] |X 0.395 - 0.4 : [ 43 0.00 0.01 ] |X 0.4 - 0.405 : [ 60 0.00 0.01 ] |X 0.405 - 0.41 : [ 52 0.00 0.01 ] |X 0.41 - 0.415 : [ 44 0.00 0.01 ] |X 0.415 - 0.42 : [ 57 0.00 0.01 ] |X 0.42 - 0.425 : [ 51 0.00 0.01 ] |X 0.425 - 0.43 : [ 61 0.00 0.01 ] |X 0.43 - 0.435 : [ 64 0.00 0.01 ] |X 0.435 - 0.44 : [ 43 0.00 0.01 ] |X 0.44 - 0.445 : [ 63 0.00 0.02 ] |X 0.445 - 0.45 : [ 65 0.00 0.02 ] |X 0.45 - 0.455 : [ 57 0.00 0.02 ] |X 0.455 - 0.46 : [ 53 0.00 0.02 ] |X 0.46 - 0.465 : [ 57 0.00 0.02 ] |X 0.465 - 0.47 : [ 64 0.00 0.02 ] |X 0.47 - 0.475 : [ 78 0.00 0.02 ] |X 0.475 - 0.48 : [ 45 0.00 0.02 ] |X 0.48 - 0.485 : [ 50 0.00 0.03 ] |X 0.485 - 0.49 : [ 68 0.00 0.03 ] |X 0.49 - 0.495 : [ 99 0.00 0.03 ] |X 0.495 - 0.5 : [ 64 0.00 0.03 ] |X 0.5 - 0.505 : [ 100 0.00 0.03 ] |X 0.505 - 0.51 : [ 92 0.00 0.03 ] |X 0.51 - 0.515 : [ 99 0.00 0.04 ] |XX 0.515 - 0.52 : [ 127 0.00 0.04 ] |XX 0.52 - 0.525 : [ 124 0.00 0.04 ] |XX 0.525 - 0.53 : [ 158 0.00 0.05 ] |XXX 0.53 - 0.535 : [ 173 0.00 0.05 ] |XXX 0.535 - 0.54 : [ 204 0.00 0.05 ] |XXX 0.54 - 0.545 : [ 224 0.00 0.06 ] |XXXX 0.545 - 0.55 : [ 256 0.01 0.06 ] |XXXXX 0.55 - 0.555 : [ 305 0.01 0.07 ] |XXXX 0.555 - 0.56 : [ 283 0.01 0.08 ] |XXXXX 0.56 - 0.565 : [ 348 0.01 0.08 ] |XXXXXX 0.565 - 0.57 : [ 376 0.01 0.09 ] |XXXXXX 0.57 - 0.575 : [ 430 0.01 0.10 ] |XXXXXXX 0.575 - 0.58 : [ 486 0.01 0.11 ] |XXXXXXXXX 0.58 - 0.585 : [ 576 0.01 0.12 ] |XXXXXXXXXX 0.585 - 0.59 : [ 669 0.01 0.14 ] |XXXXXXXXXXXX 0.59 - 0.595 : [ 836 0.02 0.15 ] |XXXXXXXXXXXXXX 0.595 - 0.6 : [ 923 0.02 0.17 ] |XXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1159 0.02 0.20 ] |XXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1232 0.03 0.22 ] |XXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1366 0.03 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1645 0.03 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1628 0.03 0.32 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 2125 0.04 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 2281 0.05 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 2445 0.05 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 2691 0.06 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 2655 0.06 0.58 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 2608 0.05 0.63 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 2595 0.05 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 2411 0.05 0.73 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 2138 0.04 0.78 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 1988 0.04 0.82 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 1736 0.04 0.86 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 1603 0.03 0.89 ] |XXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 1277 0.03 0.92 ] |XXXXXXXXXXXXXX 0.69 - 0.695 : [ 955 0.02 0.94 ] |XXXXXXXXXXXX 0.695 - 0.7 : [ 782 0.02 0.95 ] |XXXXXXXXXX 0.7 - 0.705 : [ 659 0.01 0.97 ] |XXXXXX 0.705 - 0.71 : [ 430 0.01 0.98 ] |XXXXX 0.71 - 0.715 : [ 349 0.01 0.98 ] |XXX 0.715 - 0.72 : [ 229 0.00 0.99 ] |XXX 0.72 - 0.725 : [ 170 0.00 0.99 ] |X 0.725 - 0.73 : [ 100 0.00 0.99 ] |X 0.73 - 0.735 : [ 62 0.00 1.00 ] |X 0.735 - 0.74 : [ 63 0.00 1.00 ] |X 0.74 - 0.745 : [ 48 0.00 1.00 ] | 0.745 - 0.75 : [ 21 0.00 1.00 ] | 0.75 - 0.755 : [ 17 0.00 1.00 ] | 0.755 - 0.76 : [ 17 0.00 1.00 ] | 0.76 - 0.765 : [ 9 0.00 1.00 ] | 0.765 - 0.77 : [ 11 0.00 1.00 ] | 0.77 - 0.775 : [ 3 0.00 1.00 ] | 0.775 - 0.78 : [ 3 0.00 1.00 ] | 0.78 - 0.785 : [ 3 0.00 1.00 ] | 0.785 - 0.79 : [ 1 0.00 1.00 ] | 0.79 - 0.795 : [ 3 0.00 1.00 ] #... | 0.8 - 0.805 : [ 1 0.00 1.00 ] | 0.805 - 0.81 : [ 1 0.00 1.00 ] | 0.81 - 0.815 : [ 1 0.00 1.00 ] | 0.815 - 0.82 : [ 3 0.00 1.00 ] | 0.82 - 0.825 : [ 1 0.00 1.00 ] | 0.825 - 0.83 : [ 1 0.00 1.00 ] #... | 0.855 - 0.86 : [ 1 0.00 1.00 ] | 0.86 - 0.865 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones N/plate avg% LIBRARY @ 20 4660 1202 60.10 62.60 QCMC @ 192 35182 17555 91.43 95.24 AIFA @ 40 3770 2155 53.88 56.12 AIFB @ 24 4289 2203 91.79 95.62 AIFC @ ] 47901 23115 83.75 cumulative total@@ LIBRARY PLATE ID COUNT [ QCMC 20 AIFA 192 AIFB 40 AIFC 24 ] for 276 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 = 1037 HQ Discrepant reads = 16 Chimeric reads = 194 Suspect alignments = 4027 ################################################################### C O N T I G I N F O R M A T I O N Mon Sep 6 02:25:03 2004 File: /psf/project/microbe3/3634505/edit_dir.02Jun04.QD/phrap.out Contig 46. 437 reads; 32212 bp (untrimmed), 32082 (trimmed). Contig 47. 489 reads; 38805 bp (untrimmed), 38699 (trimmed). Contig 48. 627 reads; 51600 bp (untrimmed), 51597 (trimmed). Contig 49. 661 reads; 50118 bp (untrimmed), 49929 (trimmed). Contig 50. 680 reads; 54726 bp (untrimmed), 54676 (trimmed). Contig 51. 838 reads; 64536 bp (untrimmed), 64460 (trimmed). Contig 52. 873 reads; 63039 bp (untrimmed), 62546 (trimmed). Contig 53. 947 reads; 72275 bp (untrimmed), 72184 (trimmed). Contig 54. 972 reads; 77220 bp (untrimmed), 77002 (trimmed). Contig 55. 983 reads; 73240 bp (untrimmed), 73174 (trimmed). Contig 56. 1080 reads; 85493 bp (untrimmed), 85393 (trimmed). Contig 57. 1139 reads; 96718 bp (untrimmed), 96599 (trimmed). Contig 58. 1361 reads; 104325 bp (untrimmed), 104303 (trimmed). Contig 59. 1384 reads; 96056 bp (untrimmed), 95906 (trimmed). Contig 60. 1390 reads; 101870 bp (untrimmed), 101776 (trimmed). Contig 61. 1393 reads; 120851 bp (untrimmed), 120422 (trimmed). Contig 62. 1412 reads; 110401 bp (untrimmed), 110276 (trimmed). Contig 63. 1450 reads; 123726 bp (untrimmed), 123672 (trimmed). Contig 64. 1519 reads; 112802 bp (untrimmed), 112665 (trimmed). Contig 65. 1714 reads; 134868 bp (untrimmed), 134735 (trimmed). Contig 66. 1790 reads; 146680 bp (untrimmed), 146678 (trimmed). Contig 67. 1939 reads; 155290 bp (untrimmed), 154963 (trimmed). Contig 68. 2184 reads; 159302 bp (untrimmed), 159246 (trimmed). Contig 69. 2363 reads; 162379 bp (untrimmed), 161548 (trimmed). Contig 70. 2464 reads; 181190 bp (untrimmed), 180853 (trimmed). Contig 71. 4706 reads; 349896 bp (untrimmed), 349669 (trimmed). Contig 72. 6964 reads; 507709 bp (untrimmed), 507577 (trimmed). -------------------------------------------------------------- Totals 47831 reads; 3702702 bp (untrimmed), 3685675 (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 47 total values totalling 3671024.0000. <78106.893617 +/- 90699.128889> #Range: [ 2205 - 507577 ] #Most likely bin: [ 26000 - 28000 ] 4 counts #Median bin: [ 50000 - 52000 ] 1 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 4 0.09 0.09 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 8000 : [ 4 0.09 0.17 ] #... |XXXXXXXXXX 12000 - 14000 : [ 1 0.02 0.19 ] #... |XXXXXXXXXX 18000 - 20000 : [ 1 0.02 0.21 ] |XXXXXXXXXX 20000 - 22000 : [ 1 0.02 0.23 ] |XXXXXXXXXX 22000 - 24000 : [ 1 0.02 0.26 ] |XXXXXXXXXX 24000 - 26000 : [ 1 0.02 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 26000 - 28000 : [ 4 0.09 0.36 ] #... |XXXXXXXXXX 30000 - 32000 : [ 1 0.02 0.38 ] |XXXXXXXXXXXXXXXXXXXX 32000 - 34000 : [ 2 0.04 0.43 ] #... |XXXXXXXXXX 36000 - 38000 : [ 1 0.02 0.45 ] |XXXXXXXXXX 38000 - 40000 : [ 1 0.02 0.47 ] #... |XXXXXXXXXX 48000 - 50000 : [ 1 0.02 0.49 ] |XXXXXXXXXX 50000 - 52000 : [ 1 0.02 0.51 ] #... |XXXXXXXXXX 54000 - 56000 : [ 1 0.02 0.53 ] #... |XXXXXXXXXX 62000 - 64000 : [ 1 0.02 0.55 ] |XXXXXXXXXX 64000 - 66000 : [ 1 0.02 0.57 ] #... |XXXXXXXXXXXXXXXXXXXX 72000 - 74000 : [ 2 0.04 0.62 ] #... |XXXXXXXXXX 76000 - 78000 : [ 1 0.02 0.64 ] #... |XXXXXXXXXX 84000 - 86000 : [ 1 0.02 0.66 ] #... |XXXXXXXXXX 94000 - 96000 : [ 1 0.02 0.68 ] |XXXXXXXXXX 96000 - 98000 : [ 1 0.02 0.70 ] #... |XXXXXXXXXX 100000 - 102000 : [ 1 0.02 0.72 ] #... |XXXXXXXXXX 104000 - 106000 : [ 1 0.02 0.74 ] #... |XXXXXXXXXX 110000 - 112000 : [ 1 0.02 0.77 ] |XXXXXXXXXX 112000 - 114000 : [ 1 0.02 0.79 ] #... |XXXXXXXXXX 120000 - 122000 : [ 1 0.02 0.81 ] |XXXXXXXXXX 122000 - 124000 : [ 1 0.02 0.83 ] #... |XXXXXXXXXX 134000 - 136000 : [ 1 0.02 0.85 ] #... |XXXXXXXXXX 146000 - 148000 : [ 1 0.02 0.87 ] #... |XXXXXXXXXX 154000 - 156000 : [ 1 0.02 0.89 ] #... |XXXXXXXXXX 158000 - 160000 : [ 1 0.02 0.91 ] |XXXXXXXXXX 160000 - 162000 : [ 1 0.02 0.94 ] #... |XXXXXXXXXX 180000 - 182000 : [ 1 0.02 0.96 ] #... |XXXXXXXXXX 348000 - 350000 : [ 1 0.02 0.98 ] #... |XXXXXXXXXX 506000 - 508000 : [ 1 0.02 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 8103643 C = 13793823 G = 13808719 T = 8037365 N = 218161 X = 867532 GC fraction = 0.62 Total = 44829243 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 3634505_fasta.screen.contigs A 668736 C 1184099 G 1181374 N 76 T 666891 X 1526 fraction GC = 0.64 total bases = 3702702 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 3698509 bases = 11.30 +- 4.47 = 0.16 +- 4.35 m1 = 1.77 m2 = 0.28 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 53 total values totalling 491.2100. <9.268113 +/- 7.323758> #Range: [ 1.40 - 54.24 ] #Most likely bin: [ 11.5 - 12 ] 8 counts #Median bin: [ 10 - 10.5 ] 4 counts |XXXXX 1 - 1.5 : [ 1 0.02 0.02 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 6 0.11 0.13 ] |XXXXX 2 - 2.5 : [ 1 0.02 0.15 ] |XXXXXXXXXX 2.5 - 3 : [ 2 0.04 0.19 ] |XXXXXXXXXX 3 - 3.5 : [ 2 0.04 0.23 ] #... |XXXXXXXXXX 5 - 5.5 : [ 2 0.04 0.26 ] #... |XXXXXXXXXX 6 - 6.5 : [ 2 0.04 0.30 ] #... |XXXXXXXXXX 7.5 - 8 : [ 2 0.04 0.34 ] #... |XXXXXXXXXX 8.5 - 9 : [ 2 0.04 0.38 ] |XXXXXXXXXXXXXXX 9 - 9.5 : [ 3 0.06 0.43 ] |XXXXXXXXXX 9.5 - 10 : [ 2 0.04 0.47 ] |XXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 4 0.08 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 6 0.11 0.66 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 5 0.09 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 8 0.15 0.91 ] |XXXXX 12 - 12.5 : [ 1 0.02 0.92 ] |XXXXXXXXXX 12.5 - 13 : [ 2 0.04 0.96 ] #... |XXXXX 14 - 14.5 : [ 1 0.02 0.98 ] #... |XXXXX 54 - 54.5 : [ 1 0.02 1.00 ] Histogram of Major Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000 #Found 40 total values totalling 411.4700. <10.286750 +/- 2.015214> #Range: [ 5.23 - 14.18 ] #Most likely bin: [ 11.5 - 12 ] 8 counts #Median bin: [ 10.5 - 11 ] 6 counts |XXXXXXXXXX 5 - 5.5 : [ 2 0.05 0.05 ] #... |XXXXXXXXXX 6 - 6.5 : [ 2 0.05 0.10 ] #... |XXXXXXXXXX 7.5 - 8 : [ 2 0.05 0.15 ] #... |XXXXXXXXXX 8.5 - 9 : [ 2 0.05 0.20 ] |XXXXXXXXXXXXXXX 9 - 9.5 : [ 3 0.07 0.28 ] |XXXXXXXXXX 9.5 - 10 : [ 2 0.05 0.33 ] |XXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 4 0.10 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 6 0.15 0.57 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 5 0.12 0.70 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 8 0.20 0.90 ] |XXXXX 12 - 12.5 : [ 1 0.03 0.93 ] |XXXXXXXXXX 12.5 - 13 : [ 2 0.05 0.97 ] #... |XXXXX 14 - 14.5 : [ 1 0.03 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 3 2 reads 1156 bases = 1.40 +- 0.49 = 1.40 +- 0.49 m1 = 0.17 m2 = 0.00 Contig 10 2 reads 1037 bases = 1.56 +- 0.50 = 1.56 +- 0.50 m1 = 0.16 m2 = 0.00 Contig 11 2 reads 942 bases = 1.59 +- 0.49 = 1.59 +- 0.49 m1 = 0.15 m2 = 0.00 Contig 13 2 reads 1034 bases = 1.72 +- 0.45 = 1.72 +- 0.45 m1 = 0.12 m2 = 0.00 Contig 14 2 reads 995 bases = 1.80 +- 0.40 = 1.80 +- 0.40 m1 = 0.09 m2 = 0.00 Contig 9 2 reads 976 bases = 1.80 +- 0.40 = 1.80 +- 0.40 m1 = 0.09 m2 = 0.00 Contig 8 2 reads 528 bases = 1.95 +- 0.21 = 0.05 +- 0.21 m1 = 0.02 m2 = 0.00 Contig 17 3 reads 1277 bases = 2.10 +- 0.85 = 2.10 +- 0.85 m1 = 0.34 m2 = 0.00 Contig 20 5 reads 1706 bases = 2.58 +- 1.44 = 1.67 +- 0.70 m1 = 0.81 m2 = 0.40 Contig 18 3 reads 970 bases = 2.85 +- 0.40 = 2.85 +- 0.40 m1 = 0.06 m2 = 0.00 Contig 24 7 reads 2086 bases = 3.05 +- 1.31 = 1.38 +- 1.78 m1 = 0.57 m2 = -0.36 Contig 19 4 reads 1165 bases = 3.10 +- 1.10 = 3.10 +- 1.10 m1 = 0.39 m2 = 0.00 Contig 29 45 reads 7257 bases = 5.23 +- 2.76 = 1.08 +- 3.28 m1 = 1.45 m2 = -0.79 Contig 25 17 reads 2810 bases = 5.24 +- 2.25 = 0.27 +- 2.41 m1 = 0.97 m2 = -0.18 Contig 27 27 reads 3892 bases = 6.14 +- 2.58 = 1.58 +- 1.86 m1 = 1.09 m2 = 0.80 Contig 31 59 reads 7698 bases = 6.26 +- 3.38 = 0.77 +- 5.21 m1 = 1.83 m2 = -3.92 Contig 32 64 reads 7195 bases = 7.59 +- 3.40 = 1.78 +- 3.64 m1 = 1.52 m2 = -0.43 Contig 34 118 reads 12770 bases = 7.85 +- 3.91 = 0.41 +- 3.75 m1 = 1.95 m2 = 0.30 Contig 39 378 reads 38029 bases = 8.55 +- 3.05 = 0.41 +- 4.17 m1 = 1.09 m2 = -2.03 Contig 35 212 reads 20940 bases = 8.71 +- 3.47 = 0.89 +- 4.78 m1 = 1.38 m2 = -2.70 Contig 45 685 reads 54724 bases = 10.89 +- 4.13 = 0.45 +- 4.14 m1 = 1.57 m2 = -0.01 Contig 59 1979 reads 155293 bases = 10.89 +- 4.16 = 0.13 +- 4.27 m1 = 1.59 m2 = -0.24 Contig 49 1124 reads 85931 bases = 11.05 +- 4.48 = 0.36 +- 4.53 m1 = 1.82 m2 = -0.11 Contig 47 960 reads 72316 bases = 11.34 +- 4.41 = 0.23 +- 4.53 m1 = 1.71 m2 = -0.28 Contig 53 1386 reads 104335 bases = 11.35 +- 4.09 = 0.18 +- 4.34 m1 = 1.47 m2 = -0.54 Contig 46 857 reads 64536 bases = 11.38 +- 4.43 = -0.03 +- 3.83 m1 = 1.72 m2 = 1.24 Contig 64 5261 reads 392882 bases = 11.49 +- 4.08 = -0.00 +- 4.02 m1 = 1.45 m2 = 0.11 Contig 50 1148 reads 50119 bases = 11.68 +- 6.14 = -0.48 +- 6.30 m1 = 3.23 m2 = -0.50 Contig 58 1572 reads 115038 bases = 11.69 +- 3.93 = 0.23 +- 4.28 m1 = 1.32 m2 = -0.73 Contig 62 4615 reads 338744 bases = 11.73 +- 4.53 = 0.22 +- 4.28 m1 = 1.75 m2 = 0.55 Contig 63 4707 reads 342862 bases = 11.80 +- 4.50 = 0.06 +- 4.47 m1 = 1.72 m2 = 0.08 Contig 43 443 reads 32212 bases = 11.92 +- 4.72 = 0.62 +- 4.99 m1 = 1.87 m2 = -0.65 Contig 65 7397 reads 534933 bases = 11.95 +- 4.19 = 0.04 +- 4.39 m1 = 1.47 m2 = -0.43 Contig 52 1342 reads 96591 bases = 11.97 +- 4.56 = 0.01 +- 4.33 m1 = 1.74 m2 = 0.51 Contig 54 1405 reads 101870 bases = 11.98 +- 4.52 = 0.19 +- 4.81 m1 = 1.70 m2 = -0.67 Contig 40 384 reads 27620 bases = 12.20 +- 4.96 = 0.44 +- 4.43 m1 = 2.02 m2 = 1.25 Contig 56 1468 reads 99622 bases = 12.55 +- 4.46 = 0.18 +- 4.84 m1 = 1.59 m2 = -0.87 Contig 61 2405 reads 162379 bases = 12.72 +- 4.72 = 0.05 +- 4.56 m1 = 1.75 m2 = 0.38 Contig 28 33 reads 2059 bases = 14.18 +- 8.37 = 2.76 +- 5.14 m1 = 4.94 m2 = 10.91 Contig 30 55 reads 635 bases = 54.24 +- 3.79 = 0.24 +- 3.79 m1 = 0.26 m2 = 0.00 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 72 total values totalling 47831.0000. <664.319444 +/- 1110.998010> #Range: [ 1 - 6964 ] #Most likely bin: [ 1 - 2 ] 12 counts #Median bin: [ 243 - 244 ] 1 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 2 : [ 12 0.17 0.17 ] |XXXXXXX 2 - 3 : [ 2 0.03 0.19 ] |XXXXXXXXXXXXX 3 - 4 : [ 4 0.06 0.25 ] #... |XXXXXXXXXX 5 - 6 : [ 3 0.04 0.29 ] |XXXXXXX 6 - 7 : [ 2 0.03 0.32 ] |XXX 7 - 8 : [ 1 0.01 0.33 ] #... |XXX 17 - 18 : [ 1 0.01 0.35 ] |XXX 18 - 19 : [ 1 0.01 0.36 ] #... |XXX 20 - 21 : [ 1 0.01 0.38 ] #... |XXX 27 - 28 : [ 1 0.01 0.39 ] #... |XXX 42 - 43 : [ 1 0.01 0.40 ] #... |XXXXXXX 55 - 56 : [ 2 0.03 0.43 ] #... |XXX 63 - 64 : [ 1 0.01 0.44 ] #... |XXX 115 - 116 : [ 1 0.01 0.46 ] #... |XXX 131 - 132 : [ 1 0.01 0.47 ] #... |XXX 193 - 194 : [ 1 0.01 0.49 ] #... |XXX 243 - 244 : [ 1 0.01 0.50 ] #... |XXX 286 - 287 : [ 1 0.01 0.51 ] #... |XXX 296 - 297 : [ 1 0.01 0.53 ] #... |XXX 303 - 304 : [ 1 0.01 0.54 ] #... |XXX 330 - 331 : [ 1 0.01 0.56 ] #... |XXXXXXX 334 - 335 : [ 2 0.03 0.58 ] #... |XXX 374 - 375 : [ 1 0.01 0.60 ] #... |XXX 383 - 384 : [ 1 0.01 0.61 ] #... |XXX 391 - 392 : [ 1 0.01 0.62 ] #... |XXX 437 - 438 : [ 1 0.01 0.64 ] #... |XXX 489 - 490 : [ 1 0.01 0.65 ] #... |XXX 627 - 628 : [ 1 0.01 0.67 ] #... |XXX 661 - 662 : [ 1 0.01 0.68 ] #... |XXX 680 - 681 : [ 1 0.01 0.69 ] #... |XXX 838 - 839 : [ 1 0.01 0.71 ] #... |XXX 873 - 874 : [ 1 0.01 0.72 ] #... |XXX 947 - 948 : [ 1 0.01 0.74 ] #... |XXX 972 - 973 : [ 1 0.01 0.75 ] #... |XXX 983 - 984 : [ 1 0.01 0.76 ] #... |XXX 1080 - 1081 : [ 1 0.01 0.78 ] #... |XXX 1139 - 1140 : [ 1 0.01 0.79 ] #... |XXX 1361 - 1362 : [ 1 0.01 0.81 ] #... |XXX 1384 - 1385 : [ 1 0.01 0.82 ] #... |XXX 1390 - 1391 : [ 1 0.01 0.83 ] #... |XXX 1393 - 1394 : [ 1 0.01 0.85 ] #... |XXX 1412 - 1413 : [ 1 0.01 0.86 ] #... |XXX 1450 - 1451 : [ 1 0.01 0.88 ] #... |XXX 1519 - 1520 : [ 1 0.01 0.89 ] #... |XXX 1714 - 1715 : [ 1 0.01 0.90 ] #... |XXX 1790 - 1791 : [ 1 0.01 0.92 ] #... |XXX 1939 - 1940 : [ 1 0.01 0.93 ] #... |XXX 2184 - 2185 : [ 1 0.01 0.94 ] #... |XXX 2363 - 2364 : [ 1 0.01 0.96 ] #... |XXX 2464 - 2465 : [ 1 0.01 0.97 ] #... |XXX 4706 - 4707 : [ 1 0.01 0.99 ] #... |XXX 6964 - 6965 : [ 1 0.01 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 72 total values totalling 3702702.0000. <51426.416667 +/- 82028.633122> #Range: [ 178 - 507709 ] #Most likely bin: [ 0 - 1000 ] 21 counts #Median bin: [ 22000 - 23000 ] 1 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 1000 : [ 21 0.29 0.29 ] |XXXXXX 1000 - 2000 : [ 3 0.04 0.33 ] |XXXXXXXX 2000 - 3000 : [ 4 0.06 0.39 ] |XX 3000 - 4000 : [ 1 0.01 0.40 ] #... |XX 6000 - 7000 : [ 1 0.01 0.42 ] |XXXXXX 7000 - 8000 : [ 3 0.04 0.46 ] #... |XX 12000 - 13000 : [ 1 0.01 0.47 ] #... |XX 18000 - 19000 : [ 1 0.01 0.49 ] #... |XX 22000 - 23000 : [ 1 0.01 0.50 ] |XX 23000 - 24000 : [ 1 0.01 0.51 ] |XX 24000 - 25000 : [ 1 0.01 0.53 ] #... |XXXX 26000 - 27000 : [ 2 0.03 0.56 ] |XXXX 27000 - 28000 : [ 2 0.03 0.58 ] #... |XX 31000 - 32000 : [ 1 0.01 0.60 ] |XX 32000 - 33000 : [ 1 0.01 0.61 ] |XX 33000 - 34000 : [ 1 0.01 0.62 ] #... |XXXX 38000 - 39000 : [ 2 0.03 0.65 ] #... |XX 50000 - 51000 : [ 1 0.01 0.67 ] |XX 51000 - 52000 : [ 1 0.01 0.68 ] #... |XX 54000 - 55000 : [ 1 0.01 0.69 ] #... |XX 63000 - 64000 : [ 1 0.01 0.71 ] |XX 64000 - 65000 : [ 1 0.01 0.72 ] #... |XX 72000 - 73000 : [ 1 0.01 0.74 ] |XX 73000 - 74000 : [ 1 0.01 0.75 ] #... |XX 77000 - 78000 : [ 1 0.01 0.76 ] #... |XX 85000 - 86000 : [ 1 0.01 0.78 ] #... |XXXX 96000 - 97000 : [ 2 0.03 0.81 ] #... |XX 101000 - 102000 : [ 1 0.01 0.82 ] #... |XX 104000 - 105000 : [ 1 0.01 0.83 ] #... |XX 110000 - 111000 : [ 1 0.01 0.85 ] #... |XX 112000 - 113000 : [ 1 0.01 0.86 ] #... |XX 120000 - 121000 : [ 1 0.01 0.88 ] #... |XX 123000 - 124000 : [ 1 0.01 0.89 ] #... |XX 134000 - 135000 : [ 1 0.01 0.90 ] #... |XX 146000 - 147000 : [ 1 0.01 0.92 ] #... |XX 155000 - 156000 : [ 1 0.01 0.93 ] #... |XX 159000 - 160000 : [ 1 0.01 0.94 ] #... |XX 162000 - 163000 : [ 1 0.01 0.96 ] #... |XX 181000 - 182000 : [ 1 0.01 0.97 ] #... |XX 349000 - 350000 : [ 1 0.01 0.99 ] #... |XX 507000 - 508000 : [ 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 AIFA reads.list > grep.reads.list.AIFA Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFA 4 500 #Found 15743 total values totalling 63029423.0000. <4003.647526 +/- 2113.448500> #Range: [ - 202579 ] #Most likely bin: [ 4000 - 4500 ] 5069 counts #Median bin: [ 3500 - 4000 ] 4673 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 10 0.00 0.00 ] | 1000 - 1500 : [ 38 0.00 0.00 ] | 1500 - 2000 : [ 35 0.00 0.01 ] | 2000 - 2500 : [ 41 0.00 0.01 ] |XX 2500 - 3000 : [ 267 0.02 0.02 ] |XXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2814 0.18 0.20 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 4673 0.30 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 5069 0.32 0.82 ] |XXXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 2554 0.16 0.98 ] |XX 5000 - 5500 : [ 223 0.01 1.00 ] | 5500 - 6000 : [ 4 0.00 1.00 ] | 6000 - 6500 : [ 2 0.00 1.00 ] #... | 7000 - 7500 : [ 2 0.00 1.00 ] | 7500 - 8000 : [ 1 0.00 1.00 ] #... | 8500 - 9000 : [ 1 0.00 1.00 ] #... | 12000 - 12500 : [ 1 0.00 1.00 ] #... | 18000 - 18500 : [ 1 0.00 1.00 ] #... | 33000 - 33500 : [ 1 0.00 1.00 ] #... | 51500 - 52000 : [ 1 0.00 1.00 ] | 52000 - 52500 : [ 1 0.00 1.00 ] #... | 71000 - 71500 : [ 1 0.00 1.00 ] #... | 129000 - 129500 : [ 1 0.00 1.00 ] #... | 202500 - 203000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AIFB reads.list > grep.reads.list.AIFB Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFB 4 500 #Found 1395 total values totalling 11127490.0000. <7976.695341 +/- 2101.559017> #Range: [ - 41492 ] #Most likely bin: [ 8000 - 8500 ] 245 counts #Median bin: [ 8000 - 8500 ] 245 counts | 0 - 500 : [ 1 0.00 0.00 ] |X 500 - 1000 : [ 4 0.00 0.00 ] |XX 1000 - 1500 : [ 15 0.01 0.01 ] |XX 1500 - 2000 : [ 10 0.01 0.02 ] |XX 2000 - 2500 : [ 13 0.01 0.03 ] |XX 2500 - 3000 : [ 10 0.01 0.04 ] |XXX 3000 - 3500 : [ 17 0.01 0.05 ] |XX 3500 - 4000 : [ 13 0.01 0.06 ] |XXX 4000 - 4500 : [ 16 0.01 0.07 ] |XXXX 4500 - 5000 : [ 22 0.02 0.09 ] |XXX 5000 - 5500 : [ 19 0.01 0.10 ] |XXX 5500 - 6000 : [ 21 0.02 0.12 ] |XXXXXX 6000 - 6500 : [ 35 0.03 0.14 ] |XXXXXXXXXX 6500 - 7000 : [ 62 0.04 0.18 ] |XXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 118 0.08 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 165 0.12 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 245 0.18 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 238 0.17 0.73 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 159 0.11 0.85 ] |XXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 110 0.08 0.93 ] |XXXXXXXXX 10000 - 10500 : [ 56 0.04 0.97 ] |XXXXX 10500 - 11000 : [ 28 0.02 0.99 ] |XX 11000 - 11500 : [ 12 0.01 1.00 ] |X 11500 - 12000 : [ 5 0.00 1.00 ] #... | 41000 - 41500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AIFC reads.list > grep.reads.list.AIFC Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFC 4 500 #Found 1302 total values totalling 51087089.0000. <39237.395545 +/- 3334.123329> #Range: [ - 53546 ] #Most likely bin: [ 39500 - 40000 ] 85 counts #Median bin: [ 39000 - 39500 ] 82 counts | 0 - 500 : [ 1 0.00 0.00 ] #... | 29000 - 29500 : [ 1 0.00 0.00 ] |X 29500 - 30000 : [ 2 0.00 0.00 ] #... |X 30500 - 31000 : [ 3 0.00 0.01 ] |XX 31000 - 31500 : [ 5 0.00 0.01 ] |X 31500 - 32000 : [ 3 0.00 0.01 ] |XXXX 32000 - 32500 : [ 8 0.01 0.02 ] |XXXX 32500 - 33000 : [ 8 0.01 0.02 ] |XXXXXX 33000 - 33500 : [ 12 0.01 0.03 ] |XXXXXXXX 33500 - 34000 : [ 16 0.01 0.05 ] |XXXXXXXXXXX 34000 - 34500 : [ 24 0.02 0.06 ] |XXXXXXXXXXXXXXXX 34500 - 35000 : [ 34 0.03 0.09 ] |XXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 40 0.03 0.12 ] |XXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 46 0.04 0.16 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 58 0.04 0.20 ] |XXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 51 0.04 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 83 0.06 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 58 0.04 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 83 0.06 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 65 0.05 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 82 0.06 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 85 0.07 0.59 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 75 0.06 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 54 0.04 0.69 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 64 0.05 0.74 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 75 0.06 0.80 ] |XXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 40 0.03 0.83 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 59 0.05 0.87 ] |XXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 43 0.03 0.90 ] |XXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 42 0.03 0.94 ] |XXXXXXXXXXXXXXX 44000 - 44500 : [ 32 0.02 0.96 ] |XXXXXXXX 44500 - 45000 : [ 17 0.01 0.97 ] |XXXXXXXX 45000 - 45500 : [ 17 0.01 0.99 ] |XXXX 45500 - 46000 : [ 9 0.01 0.99 ] |X 46000 - 46500 : [ 3 0.00 1.00 ] | 46500 - 47000 : [ 1 0.00 1.00 ] | 47000 - 47500 : [ 1 0.00 1.00 ] #... | 48000 - 48500 : [ 1 0.00 1.00 ] #... | 53500 - 54000 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # AIFB 7594 +- 2687 (n=730) # QCMC 7580 +- 2427 (n=483) # AIFC 39365 +- 3066 (n=642) # AIFA 3861 +- 712 (n=7996) ################################################################### 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 676.716925 bp, 47831 reads, genome size 3792198 bp Command: idealAssembly 3792198 47831 676.716925 ------------------------------------------------------------------- Genome = 3792198 bases Nreads = 47831 readLength = 676.716925 Depth = 8.54 N_contigs = N_gaps = 9 mean gap size = 78 bases mean contig size = 5092 reads (~ 403713 bases) %cover = 99.98 %singlet = 0.00 assembly size = 3791452 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 2 contigs containing at least 8544 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: