################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 2351488 Genus_species: Pseudomonas fluorescens Taxid: 294 Genome size: 5500 Libraries: LAR, AAOZ, LAP, KQD, ANXS, TAH, AFYT ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 2351488 ------------------------------------------------------------------- ID=2351488 Lineage for 'Pseudomonas fluorescens': Pseudomonas fluorescens species Pseudomonas fluorescens group species group Pseudomonas genus Pseudomonadaceae family Pseudomonadales order Gammaproteobacteria class Proteobacteria phylum Bacteria superkingdom cellular organisms no rank root no rank ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 6607019 # phrap: 6183608 # db: 5500000 6096875 +/- 456080 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length AAOZ.5-124 392 98.18 650.65 KQD.5-8 0 0.00 0.00 LAP.5-30 1294 72.35 376.56 LAP.577-608 1294 72.35 376.56 TAH.5-48 84 77.21 414.63 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s AAOZ 392 196 98.15 650.88 196 98.20 650.41 LAP 7 4 70.05 367.50 3 50.00 303.00 TAH 84 44 77.27 424.52 40 77.14 403.75 ANXS 0 0 0.00 0.00 0 0.00 0.00 AFYT 5 3 88.96 666.67 2 91.81 673.50 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 2351488_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 2351488_fasta.screen.contigs /sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out /home/copeland/scripts/asseminfo phrap.out > asseminfo.2351488.out ################################################################### Library vector screening AAOZ.000001.000100 screen.out.1 2351488_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta AAOZ.000101.000200 screen.out.1 2351488_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta AAOZ.000201.000300 screen.out.1 2351488_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta KQD.000001.000100 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000001.000100 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000101.000200 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000201.000300 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000301.000400 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000401.000500 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000501.000600 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000601.000700 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta TAH.000001.000100 screen.out.1 2351488_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta AAOZ.000001.000100 screen.out.1 2351488_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta AAOZ.000101.000200 screen.out.1 2351488_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta AAOZ.000201.000300 screen.out.1 2351488_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta KQD.000001.000100 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000001.000100 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000101.000200 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000201.000300 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000301.000400 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000401.000500 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000501.000600 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta LAP.000601.000700 screen.out.1 2351488_fasta.screen /tmp/pUC18.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta TAH.000001.000100 screen.out.1 2351488_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 2351488_fasta.screen /sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 2351488_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 115692 total values totalling 60407409.0000. <522.139897 +/- 189.140929> #Range: [ 22 - 936 ] #Most likely bin: [ 600 - 650 ] 26534 counts #Median bin: [ 600 - 650 ] 26534 counts |X 0 - 50 : [ 792 0.01 0.01 ] |XXXXX 50 - 100 : [ 3417 0.03 0.04 ] |XXXXXXX 100 - 150 : [ 4822 0.04 0.08 ] |XXXXXX 150 - 200 : [ 4216 0.04 0.11 ] |XXXXX 200 - 250 : [ 3453 0.03 0.14 ] |XXXXX 250 - 300 : [ 3339 0.03 0.17 ] |XXXXX 300 - 350 : [ 3390 0.03 0.20 ] |XXXXX 350 - 400 : [ 3469 0.03 0.23 ] |XXXXXX 400 - 450 : [ 3792 0.03 0.27 ] |XXXXXXX 450 - 500 : [ 4842 0.04 0.31 ] |XXXXXXXXXXX 500 - 550 : [ 7097 0.06 0.37 ] |XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 12904 0.11 0.48 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 26534 0.23 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 26514 0.23 0.94 ] |XXXXXXXXXX 700 - 750 : [ 6372 0.06 0.99 ] |X 750 - 800 : [ 516 0.00 1.00 ] | 800 - 850 : [ 114 0.00 1.00 ] | 850 - 900 : [ 92 0.00 1.00 ] | 900 - 950 : [ 17 0.00 1.00 ] JAZZ trim 15 readlength histogram for AAOZ Command: /usr/xpg4/bin/grep AAOZ 2351488_fasta.screen.screen.ids > reads.trim15.AAOZ.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAOZ.rl 2 50 #Found 34306 total values totalling 20882264.0000. <608.705882 +/- 114.975947> #Range: [ 23 - 900 ] #Most likely bin: [ 600 - 650 ] 10659 counts #Median bin: [ 600 - 650 ] 10659 counts | 0 - 50 : [ 56 0.00 0.00 ] |X 50 - 100 : [ 156 0.00 0.01 ] |XX 100 - 150 : [ 448 0.01 0.02 ] |X 150 - 200 : [ 322 0.01 0.03 ] |X 200 - 250 : [ 265 0.01 0.04 ] |X 250 - 300 : [ 233 0.01 0.04 ] |X 300 - 350 : [ 230 0.01 0.05 ] |X 350 - 400 : [ 231 0.01 0.06 ] |X 400 - 450 : [ 314 0.01 0.07 ] |XX 450 - 500 : [ 627 0.02 0.08 ] |XXXXXXX 500 - 550 : [ 1801 0.05 0.14 ] |XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 5159 0.15 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 10659 0.31 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 10648 0.31 0.91 ] |XXXXXXXXXXX 700 - 750 : [ 3044 0.09 1.00 ] | 750 - 800 : [ 106 0.00 1.00 ] | 800 - 850 : [ 3 0.00 1.00 ] | 850 - 900 : [ 3 0.00 1.00 ] | 900 - 950 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for LAP Command: /usr/xpg4/bin/grep LAP 2351488_fasta.screen.screen.ids > reads.trim15.LAP.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.LAP.rl 2 50 #Found 74969 total values totalling 36359877.0000. <484.998826 +/- 199.699865> #Range: [ 23 - 936 ] #Most likely bin: [ 600 - 650 ] 15097 counts #Median bin: [ 550 - 600 ] 7251 counts |X 0 - 50 : [ 525 0.01 0.01 ] |XXXXXXXX 50 - 100 : [ 2962 0.04 0.05 ] |XXXXXXXXXXX 100 - 150 : [ 4162 0.06 0.10 ] |XXXXXXXXX 150 - 200 : [ 3540 0.05 0.15 ] |XXXXXXXX 200 - 250 : [ 2955 0.04 0.19 ] |XXXXXXX 250 - 300 : [ 2737 0.04 0.23 ] |XXXXXXXX 300 - 350 : [ 2880 0.04 0.26 ] |XXXXXXXX 350 - 400 : [ 3032 0.04 0.30 ] |XXXXXXXXX 400 - 450 : [ 3297 0.04 0.35 ] |XXXXXXXXXXX 450 - 500 : [ 4004 0.05 0.40 ] |XXXXXXXXXXXXX 500 - 550 : [ 4991 0.07 0.47 ] |XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 7251 0.10 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 15097 0.20 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 14785 0.20 0.96 ] |XXXXXX 700 - 750 : [ 2409 0.03 1.00 ] | 750 - 800 : [ 148 0.00 1.00 ] | 800 - 850 : [ 89 0.00 1.00 ] | 850 - 900 : [ 89 0.00 1.00 ] | 900 - 950 : [ 16 0.00 1.00 ] JAZZ trim 15 readlength histogram for KQD Command: /usr/xpg4/bin/grep KQD 2351488_fasta.screen.screen.ids > reads.trim15.KQD.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.KQD.rl 2 50 #Found 535 total values totalling 184251.0000. <344.394393 +/- 223.662286> #Range: [ 29 - 758 ] #Most likely bin: [ 150 - 200 ] 211 counts #Median bin: [ 150 - 200 ] 211 counts |X 0 - 50 : [ 3 0.01 0.01 ] |XXXXX 50 - 100 : [ 25 0.05 0.05 ] |XXXXXX 100 - 150 : [ 31 0.06 0.11 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 150 - 200 : [ 211 0.39 0.50 ] |XXXXXXXXXX 200 - 250 : [ 53 0.10 0.60 ] |XX 250 - 300 : [ 8 0.01 0.62 ] |XX 300 - 350 : [ 8 0.01 0.63 ] |XX 350 - 400 : [ 10 0.02 0.65 ] |XX 400 - 450 : [ 8 0.01 0.67 ] |XX 450 - 500 : [ 12 0.02 0.69 ] |X 500 - 550 : [ 7 0.01 0.70 ] |XXXX 550 - 600 : [ 22 0.04 0.74 ] |XXXXXXX 600 - 650 : [ 36 0.07 0.81 ] |XXXXXXXXXX 650 - 700 : [ 52 0.10 0.91 ] |XXXXXXXXX 700 - 750 : [ 48 0.09 1.00 ] | 750 - 800 : [ 1 0.00 1.00 ] JAZZ trim 15 readlength histogram for TAH Command: /usr/xpg4/bin/grep TAH 2351488_fasta.screen.screen.ids > reads.trim15.TAH.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.TAH.rl 2 50 #Found 5882 total values totalling 2981017.0000. <506.803298 +/- 222.035796> #Range: [ 22 - 847 ] #Most likely bin: [ 650 - 700 ] 1029 counts #Median bin: [ 550 - 600 ] 472 counts |XXXXXXXX 0 - 50 : [ 208 0.04 0.04 ] |XXXXXXXXXXX 50 - 100 : [ 274 0.05 0.08 ] |XXXXXXX 100 - 150 : [ 181 0.03 0.11 ] |XXXXXX 150 - 200 : [ 143 0.02 0.14 ] |XXXXXXX 200 - 250 : [ 180 0.03 0.17 ] |XXXXXXXXXXXXXX 250 - 300 : [ 361 0.06 0.23 ] |XXXXXXXXXXX 300 - 350 : [ 272 0.05 0.28 ] |XXXXXXXX 350 - 400 : [ 196 0.03 0.31 ] |XXXXXXX 400 - 450 : [ 173 0.03 0.34 ] |XXXXXXXX 450 - 500 : [ 199 0.03 0.37 ] |XXXXXXXXXXXX 500 - 550 : [ 298 0.05 0.42 ] |XXXXXXXXXXXXXXXXXX 550 - 600 : [ 472 0.08 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 742 0.13 0.63 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1029 0.17 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 871 0.15 0.95 ] |XXXXXXXXXX 750 - 800 : [ 261 0.04 1.00 ] |X 800 - 850 : [ 22 0.00 1.00 ] JAZZ trim 15 readlength histogram for ANXS JAZZ trim 15 readlength histogram for AFYT JAZZ trim 15 readlength histogram for LAR ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.2351488_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.2351488_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 114976 total values totalling 69308.5276. <0.602809 +/- 0.049545> #Range: [ 0.1818 - 0.9231 ] #Most likely bin: [ 0.615 - 0.62 ] 6611 counts #Median bin: [ 0.61 - 0.615 ] 6124 counts | 0.18 - 0.185 : [ 1 0.00 0.00 ] #... | 0.195 - 0.2 : [ 1 0.00 0.00 ] #... | 0.215 - 0.22 : [ 1 0.00 0.00 ] | 0.22 - 0.225 : [ 1 0.00 0.00 ] #... | 0.23 - 0.235 : [ 1 0.00 0.00 ] #... | 0.26 - 0.265 : [ 1 0.00 0.00 ] | 0.265 - 0.27 : [ 2 0.00 0.00 ] | 0.27 - 0.275 : [ 1 0.00 0.00 ] | 0.275 - 0.28 : [ 1 0.00 0.00 ] | 0.28 - 0.285 : [ 3 0.00 0.00 ] | 0.285 - 0.29 : [ 1 0.00 0.00 ] | 0.29 - 0.295 : [ 3 0.00 0.00 ] | 0.295 - 0.3 : [ 1 0.00 0.00 ] | 0.3 - 0.305 : [ 5 0.00 0.00 ] | 0.305 - 0.31 : [ 3 0.00 0.00 ] | 0.31 - 0.315 : [ 2 0.00 0.00 ] | 0.315 - 0.32 : [ 3 0.00 0.00 ] | 0.32 - 0.325 : [ 11 0.00 0.00 ] | 0.325 - 0.33 : [ 4 0.00 0.00 ] | 0.33 - 0.335 : [ 7 0.00 0.00 ] | 0.335 - 0.34 : [ 3 0.00 0.00 ] | 0.34 - 0.345 : [ 15 0.00 0.00 ] | 0.345 - 0.35 : [ 8 0.00 0.00 ] | 0.35 - 0.355 : [ 19 0.00 0.00 ] | 0.355 - 0.36 : [ 15 0.00 0.00 ] | 0.36 - 0.365 : [ 25 0.00 0.00 ] | 0.365 - 0.37 : [ 25 0.00 0.00 ] | 0.37 - 0.375 : [ 13 0.00 0.00 ] | 0.375 - 0.38 : [ 32 0.00 0.00 ] | 0.38 - 0.385 : [ 34 0.00 0.00 ] | 0.385 - 0.39 : [ 33 0.00 0.00 ] | 0.39 - 0.395 : [ 51 0.00 0.00 ] | 0.395 - 0.4 : [ 36 0.00 0.00 ] | 0.4 - 0.405 : [ 60 0.00 0.00 ] | 0.405 - 0.41 : [ 75 0.00 0.00 ] | 0.41 - 0.415 : [ 74 0.00 0.00 ] |X 0.415 - 0.42 : [ 107 0.00 0.01 ] |X 0.42 - 0.425 : [ 109 0.00 0.01 ] |X 0.425 - 0.43 : [ 124 0.00 0.01 ] |X 0.43 - 0.435 : [ 146 0.00 0.01 ] |X 0.435 - 0.44 : [ 160 0.00 0.01 ] |X 0.44 - 0.445 : [ 173 0.00 0.01 ] |X 0.445 - 0.45 : [ 220 0.00 0.01 ] |X 0.45 - 0.455 : [ 238 0.00 0.02 ] |X 0.455 - 0.46 : [ 192 0.00 0.02 ] |X 0.46 - 0.465 : [ 228 0.00 0.02 ] |XX 0.465 - 0.47 : [ 266 0.00 0.02 ] |XX 0.47 - 0.475 : [ 279 0.00 0.02 ] |XX 0.475 - 0.48 : [ 287 0.00 0.03 ] |XX 0.48 - 0.485 : [ 306 0.00 0.03 ] |XX 0.485 - 0.49 : [ 342 0.00 0.03 ] |XX 0.49 - 0.495 : [ 359 0.00 0.04 ] |XX 0.495 - 0.5 : [ 321 0.00 0.04 ] |XXXX 0.5 - 0.505 : [ 624 0.01 0.04 ] |XXX 0.505 - 0.51 : [ 542 0.00 0.05 ] |XXXX 0.51 - 0.515 : [ 675 0.01 0.05 ] |XXXXX 0.515 - 0.52 : [ 785 0.01 0.06 ] |XXXXX 0.52 - 0.525 : [ 893 0.01 0.07 ] |XXXXXX 0.525 - 0.53 : [ 969 0.01 0.08 ] |XXXXXXX 0.53 - 0.535 : [ 1138 0.01 0.09 ] |XXXXXXX 0.535 - 0.54 : [ 1205 0.01 0.10 ] |XXXXXXXX 0.54 - 0.545 : [ 1352 0.01 0.11 ] |XXXXXXXXX 0.545 - 0.55 : [ 1494 0.01 0.12 ] |XXXXXXXXXXX 0.55 - 0.555 : [ 1739 0.02 0.14 ] |XXXXXXXXXXXXX 0.555 - 0.56 : [ 2087 0.02 0.16 ] |XXXXXXXXXXXXX 0.56 - 0.565 : [ 2138 0.02 0.17 ] |XXXXXXXXXXXXXX 0.565 - 0.57 : [ 2340 0.02 0.19 ] |XXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 2658 0.02 0.22 ] |XXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 3247 0.03 0.25 ] |XXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 3551 0.03 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 3930 0.03 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 4418 0.04 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 4568 0.04 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 5520 0.05 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 5830 0.05 0.49 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 6124 0.05 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 6611 0.06 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 6385 0.06 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 6414 0.06 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 5855 0.05 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 5355 0.05 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 4730 0.04 0.85 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 3948 0.03 0.88 ] |XXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 3222 0.03 0.91 ] |XXXXXXXXXXXXXXX 0.655 - 0.66 : [ 2452 0.02 0.93 ] |XXXXXXXXXXXX 0.66 - 0.665 : [ 1904 0.02 0.95 ] |XXXXXXXXX 0.665 - 0.67 : [ 1421 0.01 0.96 ] |XXXXXX 0.67 - 0.675 : [ 994 0.01 0.97 ] |XXXX 0.675 - 0.68 : [ 734 0.01 0.98 ] |XXX 0.68 - 0.685 : [ 543 0.00 0.98 ] |XXX 0.685 - 0.69 : [ 428 0.00 0.98 ] |XX 0.69 - 0.695 : [ 302 0.00 0.99 ] |X 0.695 - 0.7 : [ 219 0.00 0.99 ] |X 0.7 - 0.705 : [ 218 0.00 0.99 ] |X 0.705 - 0.71 : [ 175 0.00 0.99 ] |X 0.71 - 0.715 : [ 139 0.00 0.99 ] |X 0.715 - 0.72 : [ 110 0.00 1.00 ] |X 0.72 - 0.725 : [ 91 0.00 1.00 ] |X 0.725 - 0.73 : [ 88 0.00 1.00 ] | 0.73 - 0.735 : [ 63 0.00 1.00 ] | 0.735 - 0.74 : [ 48 0.00 1.00 ] | 0.74 - 0.745 : [ 51 0.00 1.00 ] | 0.745 - 0.75 : [ 15 0.00 1.00 ] | 0.75 - 0.755 : [ 50 0.00 1.00 ] | 0.755 - 0.76 : [ 27 0.00 1.00 ] | 0.76 - 0.765 : [ 23 0.00 1.00 ] | 0.765 - 0.77 : [ 18 0.00 1.00 ] | 0.77 - 0.775 : [ 20 0.00 1.00 ] | 0.775 - 0.78 : [ 6 0.00 1.00 ] | 0.78 - 0.785 : [ 6 0.00 1.00 ] | 0.785 - 0.79 : [ 10 0.00 1.00 ] | 0.79 - 0.795 : [ 6 0.00 1.00 ] | 0.795 - 0.8 : [ 2 0.00 1.00 ] | 0.8 - 0.805 : [ 17 0.00 1.00 ] #... | 0.81 - 0.815 : [ 4 0.00 1.00 ] | 0.815 - 0.82 : [ 1 0.00 1.00 ] | 0.82 - 0.825 : [ 1 0.00 1.00 ] | 0.825 - 0.83 : [ 2 0.00 1.00 ] | 0.83 - 0.835 : [ 4 0.00 1.00 ] | 0.835 - 0.84 : [ 1 0.00 1.00 ] | 0.84 - 0.845 : [ 2 0.00 1.00 ] #... | 0.86 - 0.865 : [ 3 0.00 1.00 ] | 0.865 - 0.87 : [ 1 0.00 1.00 ] #... | 0.875 - 0.88 : [ 1 0.00 1.00 ] #... | 0.92 - 0.925 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones LIBRARY @ ] 115702 63462 75.37 cumulative total @@ Only indicates plates present in input file. Make no assumption regarding plates (not) present in project that do not appear above. ################################################################### Reads in assembly summary Small Inserts = 3728 HQ Discrepant reads = 30 Chimeric reads = 1606 Suspect alignments = 6619 ################################################################### C O N T I G I N F O R M A T I O N Wed Sep 8 06:04:03 2004 File: /psf/project/microbe1/2351488/edit_dir.12Nov03.QD/phrap.out Contig 472. 8 reads; 836 bp (untrimmed), 793 (trimmed). Contig 473. 9 reads; 846 bp (untrimmed), 675 (trimmed). Contig 474. 14 reads; 1681 bp (untrimmed), 1681 (trimmed). Contig 475. 20 reads; 2874 bp (untrimmed), 2717 (trimmed). Contig 476. 22 reads; 5086 bp (untrimmed), 4496 (trimmed). Contig 477. 24 reads; 146 bp (untrimmed), 146 (trimmed). Contig 478. 50 reads; 4294 bp (untrimmed), 4211 (trimmed). Contig 479. 168 reads; 14815 bp (untrimmed), 14541 (trimmed). Contig 480. 196 reads; 16535 bp (untrimmed), 16529 (trimmed). Contig 481. 259 reads; 27701 bp (untrimmed), 27448 (trimmed). Contig 482. 424 reads; 1423 bp (untrimmed), 1413 (trimmed). Contig 483. 441 reads; 27385 bp (untrimmed), 27186 (trimmed). Contig 484. 925 reads; 46840 bp (untrimmed), 46836 (trimmed). Contig 485. 1678 reads; 97005 bp (untrimmed), 96986 (trimmed). Contig 486. 1965 reads; 115643 bp (untrimmed), 115551 (trimmed). Contig 487. 2087 reads; 129044 bp (untrimmed), 128833 (trimmed). Contig 488. 2905 reads; 156514 bp (untrimmed), 156514 (trimmed). Contig 489. 3652 reads; 201897 bp (untrimmed), 201376 (trimmed). Contig 490. 5430 reads; 324557 bp (untrimmed), 324218 (trimmed). Contig 491. 5849 reads; 315444 bp (untrimmed), 315433 (trimmed). Contig 492. 6395 reads; 360945 bp (untrimmed), 360945 (trimmed). Contig 493. 7415 reads; 424910 bp (untrimmed), 424837 (trimmed). Contig 494. 7528 reads; 432242 bp (untrimmed), 432224 (trimmed). Contig 495. 8117 reads; 454471 bp (untrimmed), 454470 (trimmed). Contig 496. 9736 reads; 542039 bp (untrimmed), 541686 (trimmed). Contig 497. 10321 reads; 579865 bp (untrimmed), 579838 (trimmed). Contig 498. 38529 reads; 2143218 bp (untrimmed), 2143189 (trimmed). -------------------------------------------------------------- Totals 115211 reads; 6620338 bp (untrimmed), 6607019 (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 22 total values totalling 6420064.0000. <291821.090909 +/- 445520.620309> #Range: [ 2717 - 2143189 ] #Most likely bin: [ 26000 - 28000 ] 2 counts #Median bin: [ 128000 - 130000 ] 1 counts |XXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 1 0.05 0.05 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 6000 : [ 2 0.09 0.14 ] #... |XXXXXXXXXXXXXXXXXXXX 14000 - 16000 : [ 1 0.05 0.18 ] |XXXXXXXXXXXXXXXXXXXX 16000 - 18000 : [ 1 0.05 0.23 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 26000 - 28000 : [ 2 0.09 0.32 ] #... |XXXXXXXXXXXXXXXXXXXX 46000 - 48000 : [ 1 0.05 0.36 ] #... |XXXXXXXXXXXXXXXXXXXX 96000 - 98000 : [ 1 0.05 0.41 ] #... |XXXXXXXXXXXXXXXXXXXX 114000 - 116000 : [ 1 0.05 0.45 ] #... |XXXXXXXXXXXXXXXXXXXX 128000 - 130000 : [ 1 0.05 0.50 ] #... |XXXXXXXXXXXXXXXXXXXX 156000 - 158000 : [ 1 0.05 0.55 ] #... |XXXXXXXXXXXXXXXXXXXX 200000 - 202000 : [ 1 0.05 0.59 ] #... |XXXXXXXXXXXXXXXXXXXX 314000 - 316000 : [ 1 0.05 0.64 ] #... |XXXXXXXXXXXXXXXXXXXX 324000 - 326000 : [ 1 0.05 0.68 ] #... |XXXXXXXXXXXXXXXXXXXX 360000 - 362000 : [ 1 0.05 0.73 ] #... |XXXXXXXXXXXXXXXXXXXX 424000 - 426000 : [ 1 0.05 0.77 ] #... |XXXXXXXXXXXXXXXXXXXX 432000 - 434000 : [ 1 0.05 0.82 ] #... |XXXXXXXXXXXXXXXXXXXX 454000 - 456000 : [ 1 0.05 0.86 ] #... |XXXXXXXXXXXXXXXXXXXX 540000 - 542000 : [ 1 0.05 0.91 ] #... |XXXXXXXXXXXXXXXXXXXX 578000 - 580000 : [ 1 0.05 0.95 ] #... |XXXXXXXXXXXXXXXXXXXX 2142000 - 2144000 : [ 1 0.05 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 18727896 C = 26672210 G = 26879312 T = 17368749 N = 476579 X = 4000406 GC fraction = 0.57 Total = 94125152 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 2351488_fasta.screen.contigs A 1304820 C 2017142 G 1997618 N 145 T 1299575 X 1038 fraction GC = 0.61 total bases = 6620338 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 6538159 bases = 12.16 +- 5.31 = 0.08 +- 4.05 m1 = 2.32 m2 = 2.95 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 150 total values totalling 622.7200. <4.151467 +/- 11.750970> #Range: [ 1.08 - 141.54 ] #Most likely bin: [ 1.5 - 2 ] 43 counts #Median bin: [ 1.5 - 2 ] 43 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 37 0.25 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 43 0.29 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 38 0.25 0.79 ] |X 2.5 - 3 : [ 1 0.01 0.79 ] |XX 3 - 3.5 : [ 2 0.01 0.81 ] #... |XXX 4 - 4.5 : [ 3 0.02 0.83 ] |XX 4.5 - 5 : [ 2 0.01 0.84 ] #... |XX 5.5 - 6 : [ 2 0.01 0.85 ] #... |XX 6.5 - 7 : [ 2 0.01 0.87 ] #... |X 7.5 - 8 : [ 1 0.01 0.87 ] |XX 8 - 8.5 : [ 2 0.01 0.89 ] #... |XX 11 - 11.5 : [ 2 0.01 0.90 ] |XXX 11.5 - 12 : [ 3 0.02 0.92 ] |XXXXXX 12 - 12.5 : [ 6 0.04 0.96 ] |XXXX 12.5 - 13 : [ 4 0.03 0.99 ] #... |X 13.5 - 14 : [ 1 0.01 0.99 ] #... |X 141.5 - 142 : [ 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 22 total values totalling 235.3100. <10.695909 +/- 2.821890> #Range: [ 2.82 - 13.79 ] #Most likely bin: [ 12 - 12.5 ] 6 counts #Median bin: [ 11.5 - 12 ] 3 counts |XXXXXXX 2.5 - 3 : [ 1 0.05 0.05 ] #... |XXXXXXX 4.5 - 5 : [ 1 0.05 0.09 ] #... |XXXXXXX 6.5 - 7 : [ 1 0.05 0.14 ] #... |XXXXXXX 7.5 - 8 : [ 1 0.05 0.18 ] |XXXXXXXXXXXXX 8 - 8.5 : [ 2 0.09 0.27 ] #... |XXXXXXXXXXXXX 11 - 11.5 : [ 2 0.09 0.36 ] |XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.14 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 6 0.27 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.18 0.95 ] #... |XXXXXXX 13.5 - 14 : [ 1 0.05 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 222 2 reads 1437 bases = 1.08 +- 0.26 = 1.08 +- 0.26 m1 = 0.06 m2 = 0.00 Contig 41 2 reads 1276 bases = 1.10 +- 0.29 = -0.02 +- 0.95 m1 = 0.08 m2 = -0.20 Contig 184 2 reads 1187 bases = 1.15 +- 0.36 = -0.01 +- 0.92 m1 = 0.11 m2 = -0.18 Contig 15 2 reads 1293 bases = 1.17 +- 0.38 = 0.04 +- 0.91 m1 = 0.12 m2 = -0.17 Contig 38 2 reads 1395 bases = 1.17 +- 0.38 = 0.00 +- 0.91 m1 = 0.12 m2 = -0.17 Contig 140 2 reads 1335 bases = 1.18 +- 0.39 = -0.02 +- 0.90 m1 = 0.13 m2 = -0.17 Contig 247 2 reads 1300 bases = 1.21 +- 0.41 = -0.02 +- 0.89 m1 = 0.14 m2 = -0.15 Contig 18 2 reads 664 bases = 1.23 +- 0.42 = 1.23 +- 0.42 m1 = 0.14 m2 = 0.00 Contig 162 2 reads 1227 bases = 1.25 +- 0.43 = -0.01 +- 0.87 m1 = 0.15 m2 = -0.14 Contig 244 2 reads 1186 bases = 1.27 +- 0.45 = -0.02 +- 0.85 m1 = 0.16 m2 = -0.13 Contig 426 3 reads 762 bases = 1.27 +- 0.68 = 1.00 +- 0.00 m1 = 0.37 m2 = 0.12 Contig 156 2 reads 1254 bases = 1.28 +- 0.45 = 0.02 +- 0.85 m1 = 0.16 m2 = -0.13 Contig 186 2 reads 1067 bases = 1.28 +- 0.45 = -0.05 +- 0.85 m1 = 0.16 m2 = -0.13 Contig 168 2 reads 735 bases = 1.31 +- 0.46 = -0.62 +- 0.55 m1 = 0.16 m2 = -0.02 Contig 431 3 reads 772 bases = 1.31 +- 0.69 = 0.95 +- 0.21 m1 = 0.37 m2 = 0.11 Contig 446 4 reads 1395 bases = 1.31 +- 0.57 = 0.02 +- 0.90 m1 = 0.25 m2 = -0.12 Contig 432 3 reads 761 bases = 1.32 +- 0.74 = 1.00 +- 0.00 m1 = 0.41 m2 = 0.14 Contig 437 3 reads 656 bases = 1.32 +- 0.73 = 1.00 +- 0.00 m1 = 0.41 m2 = 0.13 Contig 112 2 reads 1175 bases = 1.35 +- 0.48 = -0.02 +- 0.81 m1 = 0.17 m2 = -0.11 Contig 435 3 reads 772 bases = 1.36 +- 0.77 = 1.00 +- 0.00 m1 = 0.44 m2 = 0.15 Contig 478 50 reads 4294 bases = 7.95 +- 3.64 = 5.48 +- 3.54 m1 = 1.66 m2 = 0.17 Contig 479 168 reads 14815 bases = 8.10 +- 3.07 = 1.42 +- 3.54 m1 = 1.16 m2 = -0.78 Contig 480 196 reads 16535 bases = 8.35 +- 3.25 = 1.12 +- 4.60 m1 = 1.27 m2 = -2.65 Contig 483 441 reads 27385 bases = 11.21 +- 4.86 = 0.15 +- 4.40 m1 = 2.11 m2 = 1.05 Contig 487 2087 reads 129044 bases = 11.25 +- 4.02 = 0.25 +- 3.87 m1 = 1.43 m2 = 0.29 Contig 490 5430 reads 324557 bases = 11.65 +- 3.62 = 0.03 +- 3.87 m1 = 1.12 m2 = -0.47 Contig 486 1965 reads 115643 bases = 11.88 +- 4.09 = 0.09 +- 4.39 m1 = 1.41 m2 = -0.63 Contig 485 1678 reads 97005 bases = 11.89 +- 4.22 = 0.19 +- 4.07 m1 = 1.50 m2 = 0.30 Contig 494 7528 reads 432242 bases = 12.13 +- 3.92 = 0.12 +- 4.07 m1 = 1.26 m2 = -0.31 Contig 493 7415 reads 424910 bases = 12.20 +- 4.01 = 0.01 +- 3.97 m1 = 1.32 m2 = 0.08 Contig 495 8117 reads 454471 bases = 12.34 +- 4.13 = 0.01 +- 4.00 m1 = 1.38 m2 = 0.26 Contig 492 6395 reads 360945 bases = 12.37 +- 4.21 = 0.01 +- 3.86 m1 = 1.43 m2 = 0.70 Contig 497 10321 reads 579865 bases = 12.42 +- 4.25 = 0.13 +- 3.89 m1 = 1.46 m2 = 0.74 Contig 496 9736 reads 542039 bases = 12.46 +- 4.17 = 0.01 +- 3.99 m1 = 1.39 m2 = 0.35 Contig 489 3652 reads 201897 bases = 12.51 +- 3.87 = 0.01 +- 4.02 m1 = 1.20 m2 = -0.30 Contig 498 38529 reads 2143218 bases = 12.51 +- 4.61 = 0.07 +- 4.13 m1 = 1.70 m2 = 1.07 Contig 491 5849 reads 315444 bases = 12.79 +- 3.90 = 0.02 +- 3.94 m1 = 1.19 m2 = -0.07 Contig 488 2905 reads 156514 bases = 12.88 +- 4.39 = -0.01 +- 4.45 m1 = 1.50 m2 = -0.13 Contig 484 925 reads 46840 bases = 13.79 +- 4.24 = 0.49 +- 4.20 m1 = 1.30 m2 = 0.08 Contig 482 424 reads 1423 bases = 141.54 +- 143.71 = -14.20 +- 32.41 m1 = 145.91 m2 = 4900.44 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 498 total values totalling 115211.0000. <231.347390 +/- 1991.675637> #Range: [ 1 - 38529 ] #Most likely bin: [ 2 - 3 ] 405 counts #Median bin: [ 2 - 3 ] 405 counts |X 1 - 2 : [ 11 0.02 0.02 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 3 : [ 405 0.81 0.84 ] |XX 3 - 4 : [ 23 0.05 0.88 ] |XX 4 - 5 : [ 20 0.04 0.92 ] | 5 - 6 : [ 4 0.01 0.93 ] | 6 - 7 : [ 4 0.01 0.94 ] | 7 - 8 : [ 2 0.00 0.94 ] | 8 - 9 : [ 3 0.01 0.95 ] | 9 - 10 : [ 1 0.00 0.95 ] #... | 14 - 15 : [ 1 0.00 0.95 ] #... | 20 - 21 : [ 1 0.00 0.95 ] #... | 22 - 23 : [ 1 0.00 0.96 ] #... | 24 - 25 : [ 1 0.00 0.96 ] #... | 50 - 51 : [ 1 0.00 0.96 ] #... | 168 - 169 : [ 1 0.00 0.96 ] #... | 196 - 197 : [ 1 0.00 0.96 ] #... | 259 - 260 : [ 1 0.00 0.97 ] #... | 424 - 425 : [ 1 0.00 0.97 ] #... | 441 - 442 : [ 1 0.00 0.97 ] #... | 925 - 926 : [ 1 0.00 0.97 ] #... | 1678 - 1679 : [ 1 0.00 0.97 ] #... | 1965 - 1966 : [ 1 0.00 0.98 ] #... | 2087 - 2088 : [ 1 0.00 0.98 ] #... | 2905 - 2906 : [ 1 0.00 0.98 ] #... | 3652 - 3653 : [ 1 0.00 0.98 ] #... | 5430 - 5431 : [ 1 0.00 0.98 ] #... | 5849 - 5850 : [ 1 0.00 0.99 ] #... | 6395 - 6396 : [ 1 0.00 0.99 ] #... | 7415 - 7416 : [ 1 0.00 0.99 ] #... | 7528 - 7529 : [ 1 0.00 0.99 ] #... | 8117 - 8118 : [ 1 0.00 0.99 ] #... | 9736 - 9737 : [ 1 0.00 1.00 ] #... | 10321 - 10322 : [ 1 0.00 1.00 ] #... | 38529 - 38530 : [ 1 0.00 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 498 total values totalling 6620338.0000. <13293.851406 +/- 111160.062854> #Range: [ 100 - 2143218 ] #Most likely bin: [ 0 - 1000 ] 438 counts #Median bin: [ 0 - 1000 ] 438 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 1000 : [ 438 0.88 0.88 ] |XXX 1000 - 2000 : [ 36 0.07 0.95 ] | 2000 - 3000 : [ 3 0.01 0.96 ] #... | 4000 - 5000 : [ 1 0.00 0.96 ] | 5000 - 6000 : [ 1 0.00 0.96 ] #... | 14000 - 15000 : [ 1 0.00 0.96 ] #... | 16000 - 17000 : [ 1 0.00 0.97 ] #... | 27000 - 28000 : [ 2 0.00 0.97 ] #... | 46000 - 47000 : [ 1 0.00 0.97 ] #... | 97000 - 98000 : [ 1 0.00 0.97 ] #... | 115000 - 116000 : [ 1 0.00 0.98 ] #... | 129000 - 130000 : [ 1 0.00 0.98 ] #... | 156000 - 157000 : [ 1 0.00 0.98 ] #... | 201000 - 202000 : [ 1 0.00 0.98 ] #... | 315000 - 316000 : [ 1 0.00 0.98 ] #... | 324000 - 325000 : [ 1 0.00 0.99 ] #... | 360000 - 361000 : [ 1 0.00 0.99 ] #... | 424000 - 425000 : [ 1 0.00 0.99 ] #... | 432000 - 433000 : [ 1 0.00 0.99 ] #... | 454000 - 455000 : [ 1 0.00 0.99 ] #... | 542000 - 543000 : [ 1 0.00 1.00 ] #... | 579000 - 580000 : [ 1 0.00 1.00 ] #... | 2143000 - 2144000 : [ 1 0.00 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 AAOZ reads.list > grep.reads.list.AAOZ Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAOZ 4 500 #Found 14994 total values totalling 161369289.0000. <10762.257503 +/- 32121.607995> #Range: [ - 1371342 ] #Most likely bin: [ 8500 - 9000 ] 2143 counts #Median bin: [ 9000 - 9500 ] 1980 counts | 0 - 500 : [ 5 0.00 0.00 ] |X 500 - 1000 : [ 44 0.00 0.00 ] |X 1000 - 1500 : [ 61 0.00 0.01 ] |X 1500 - 2000 : [ 33 0.00 0.01 ] |X 2000 - 2500 : [ 38 0.00 0.01 ] |X 2500 - 3000 : [ 29 0.00 0.01 ] | 3000 - 3500 : [ 23 0.00 0.02 ] | 3500 - 4000 : [ 26 0.00 0.02 ] |X 4000 - 4500 : [ 30 0.00 0.02 ] | 4500 - 5000 : [ 20 0.00 0.02 ] | 5000 - 5500 : [ 22 0.00 0.02 ] | 5500 - 6000 : [ 26 0.00 0.02 ] |X 6000 - 6500 : [ 67 0.00 0.03 ] |XXXX 6500 - 7000 : [ 216 0.01 0.04 ] |XXXXXXXXX 7000 - 7500 : [ 480 0.03 0.07 ] |XXXXXXXXXXXXXXXXX 7500 - 8000 : [ 898 0.06 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1578 0.11 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 2143 0.14 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 1980 0.13 0.51 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 1739 0.12 0.63 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 1445 0.10 0.73 ] |XXXXXXXXXXXXXXXXXXXXX 10500 - 11000 : [ 1140 0.08 0.80 ] |XXXXXXXXXXXXXXXXX 11000 - 11500 : [ 888 0.06 0.86 ] |XXXXXXXXXXXXX 11500 - 12000 : [ 713 0.05 0.91 ] |XXXXXXXXXX 12000 - 12500 : [ 542 0.04 0.95 ] |XXXXXX 12500 - 13000 : [ 315 0.02 0.97 ] |XXX 13000 - 13500 : [ 185 0.01 0.98 ] |XXX 13500 - 14000 : [ 137 0.01 0.99 ] |X 14000 - 14500 : [ 66 0.00 0.99 ] |X 14500 - 15000 : [ 40 0.00 1.00 ] | 15000 - 15500 : [ 12 0.00 1.00 ] | 15500 - 16000 : [ 11 0.00 1.00 ] | 16000 - 16500 : [ 5 0.00 1.00 ] #... | 17000 - 17500 : [ 1 0.00 1.00 ] #... | 27000 - 27500 : [ 1 0.00 1.00 ] #... | 32500 - 33000 : [ 1 0.00 1.00 ] #... | 45000 - 45500 : [ 1 0.00 1.00 ] #... | 57000 - 57500 : [ 1 0.00 1.00 ] #... | 77000 - 77500 : [ 1 0.00 1.00 ] #... | 80000 - 80500 : [ 1 0.00 1.00 ] #... | 91000 - 91500 : [ 1 0.00 1.00 ] #... | 113500 - 114000 : [ 1 0.00 1.00 ] #... | 221500 - 222000 : [ 1 0.00 1.00 ] #... | 229500 - 230000 : [ 1 0.00 1.00 ] #... | 236500 - 237000 : [ 1 0.00 1.00 ] #... | 253500 - 254000 : [ 1 0.00 1.00 ] #... | 272500 - 273000 : [ 1 0.00 1.00 ] #... | 277000 - 277500 : [ 1 0.00 1.00 ] #... | 330500 - 331000 : [ 1 0.00 1.00 ] #... | 350000 - 350500 : [ 1 0.00 1.00 ] #... | 359000 - 359500 : [ 1 0.00 1.00 ] #... | 396000 - 396500 : [ 1 0.00 1.00 ] #... | 460500 - 461000 : [ 1 0.00 1.00 ] #... | 461500 - 462000 : [ 1 0.00 1.00 ] #... | 465000 - 465500 : [ 1 0.00 1.00 ] #... | 471500 - 472000 : [ 1 0.00 1.00 ] #... | 477000 - 477500 : [ 1 0.00 1.00 ] #... | 490500 - 491000 : [ 1 0.00 1.00 ] #... | 549000 - 549500 : [ 1 0.00 1.00 ] #... | 629000 - 629500 : [ 1 0.00 1.00 ] #... | 822500 - 823000 : [ 1 0.00 1.00 ] #... | 906000 - 906500 : [ 1 0.00 1.00 ] #... | 928500 - 929000 : [ 1 0.00 1.00 ] #... | 943000 - 943500 : [ 1 0.00 1.00 ] #... | 1000500 - 1001000 : [ 1 0.00 1.00 ] #... | 1223500 - 1224000 : [ 1 0.00 1.00 ] #... | 1303500 - 1304000 : [ 1 0.00 1.00 ] #... | 1307500 - 1308000 : [ 1 0.00 1.00 ] #... | 1337500 - 1338000 : [ 1 0.00 1.00 ] #... | 1371000 - 1371500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep LAP reads.list > grep.reads.list.LAP Command: /home/copeland/scripts/histogram2.pl grep.reads.list.LAP 4 500 #Found 29880 total values totalling 146986635.0000. <4919.231426 +/- 34469.294042> #Range: [ - 1842951 ] #Most likely bin: [ 3000 - 3500 ] 9057 counts #Median bin: [ 3500 - 4000 ] 7245 counts | 0 - 500 : [ 5 0.00 0.00 ] | 500 - 1000 : [ 28 0.00 0.00 ] | 1000 - 1500 : [ 32 0.00 0.00 ] | 1500 - 2000 : [ 34 0.00 0.00 ] | 2000 - 2500 : [ 36 0.00 0.00 ] |XXXXXXXXXXXXXXX 2500 - 3000 : [ 3464 0.12 0.12 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 9057 0.30 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 7245 0.24 0.67 ] |XXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 4960 0.17 0.83 ] |XXXXXXXXXXXXXX 4500 - 5000 : [ 3219 0.11 0.94 ] |XXXXXX 5000 - 5500 : [ 1458 0.05 0.99 ] |X 5500 - 6000 : [ 271 0.01 1.00 ] | 6000 - 6500 : [ 17 0.00 1.00 ] #... | 14000 - 14500 : [ 1 0.00 1.00 ] #... | 37000 - 37500 : [ 1 0.00 1.00 ] #... | 48500 - 49000 : [ 1 0.00 1.00 ] #... | 56000 - 56500 : [ 1 0.00 1.00 ] #... | 74500 - 75000 : [ 1 0.00 1.00 ] #... | 78000 - 78500 : [ 1 0.00 1.00 ] #... | 96500 - 97000 : [ 1 0.00 1.00 ] #... | 102500 - 103000 : [ 1 0.00 1.00 ] #... | 103500 - 104000 : [ 1 0.00 1.00 ] #... | 173000 - 173500 : [ 1 0.00 1.00 ] #... | 176000 - 176500 : [ 2 0.00 1.00 ] #... | 256000 - 256500 : [ 1 0.00 1.00 ] #... | 265500 - 266000 : [ 1 0.00 1.00 ] | 266000 - 266500 : [ 1 0.00 1.00 ] #... | 269500 - 270000 : [ 1 0.00 1.00 ] #... | 301500 - 302000 : [ 1 0.00 1.00 ] #... | 324500 - 325000 : [ 1 0.00 1.00 ] #... | 365500 - 366000 : [ 1 0.00 1.00 ] #... | 405500 - 406000 : [ 1 0.00 1.00 ] #... | 414500 - 415000 : [ 1 0.00 1.00 ] #... | 447000 - 447500 : [ 1 0.00 1.00 ] #... | 483500 - 484000 : [ 1 0.00 1.00 ] #... | 513500 - 514000 : [ 1 0.00 1.00 ] #... | 516000 - 516500 : [ 1 0.00 1.00 ] #... | 526500 - 527000 : [ 1 0.00 1.00 ] #... | 528000 - 528500 : [ 1 0.00 1.00 ] #... | 546000 - 546500 : [ 1 0.00 1.00 ] #... | 628500 - 629000 : [ 1 0.00 1.00 ] #... | 630000 - 630500 : [ 1 0.00 1.00 ] #... | 653000 - 653500 : [ 1 0.00 1.00 ] #... | 669500 - 670000 : [ 1 0.00 1.00 ] #... | 697000 - 697500 : [ 1 0.00 1.00 ] #... | 723500 - 724000 : [ 1 0.00 1.00 ] #... | 752000 - 752500 : [ 1 0.00 1.00 ] #... | 756000 - 756500 : [ 1 0.00 1.00 ] #... | 760000 - 760500 : [ 1 0.00 1.00 ] #... | 771500 - 772000 : [ 1 0.00 1.00 ] | 772000 - 772500 : [ 1 0.00 1.00 ] #... | 793500 - 794000 : [ 1 0.00 1.00 ] #... | 896000 - 896500 : [ 1 0.00 1.00 ] #... | 911500 - 912000 : [ 1 0.00 1.00 ] #... | 966500 - 967000 : [ 1 0.00 1.00 ] #... | 967500 - 968000 : [ 1 0.00 1.00 ] #... | 1107500 - 1108000 : [ 1 0.00 1.00 ] #... | 1189500 - 1190000 : [ 1 0.00 1.00 ] #... | 1284500 - 1285000 : [ 1 0.00 1.00 ] #... | 1303500 - 1304000 : [ 1 0.00 1.00 ] #... | 1398000 - 1398500 : [ 1 0.00 1.00 ] #... | 1586500 - 1587000 : [ 1 0.00 1.00 ] #... | 1629500 - 1630000 : [ 1 0.00 1.00 ] #... | 1808500 - 1809000 : [ 1 0.00 1.00 ] #... | 1835500 - 1836000 : [ 1 0.00 1.00 ] #... | 1842500 - 1843000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep KQD reads.list > grep.reads.list.KQD Command: /home/copeland/scripts/histogram2.pl grep.reads.list.KQD 4 500 #Found 195 total values totalling 438870.0000. <2250.615385 +/- 1347.516044> #Range: [ - 4699 ] #Most likely bin: [ 500 - 1000 ] 69 counts #Median bin: [ 2500 - 3000 ] 34 counts |XXXXX 0 - 500 : [ 8 0.04 0.04 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 500 - 1000 : [ 69 0.35 0.39 ] |XXX 1000 - 1500 : [ 6 0.03 0.43 ] |X 1500 - 2000 : [ 1 0.01 0.43 ] |X 2000 - 2500 : [ 1 0.01 0.44 ] |XXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 34 0.17 0.61 ] |XXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 38 0.19 0.81 ] |XXXXXXXXXXXXX 3500 - 4000 : [ 22 0.11 0.92 ] |XXXXXXXX 4000 - 4500 : [ 13 0.07 0.98 ] |XX 4500 - 5000 : [ 3 0.02 1.00 ] Command: /usr/xpg4/bin/grep TAH reads.list > grep.reads.list.TAH Command: /home/copeland/scripts/histogram2.pl grep.reads.list.TAH 4 500 #Found 2019 total values totalling 76991640.0000. <38133.551263 +/- 21934.348355> #Range: [ - 781750 ] #Most likely bin: [ 35500 - 36000 ] 95 counts #Median bin: [ 37000 - 37500 ] 87 counts | 0 - 500 : [ 1 0.00 0.00 ] #... | 23500 - 24000 : [ 1 0.00 0.00 ] | 24000 - 24500 : [ 1 0.00 0.00 ] |X 24500 - 25000 : [ 2 0.00 0.00 ] | 25000 - 25500 : [ 1 0.00 0.00 ] | 25500 - 26000 : [ 1 0.00 0.00 ] |X 26000 - 26500 : [ 3 0.00 0.00 ] |X 26500 - 27000 : [ 2 0.00 0.01 ] |XXX 27000 - 27500 : [ 6 0.00 0.01 ] |X 27500 - 28000 : [ 2 0.00 0.01 ] |X 28000 - 28500 : [ 3 0.00 0.01 ] |XX 28500 - 29000 : [ 4 0.00 0.01 ] |XX 29000 - 29500 : [ 4 0.00 0.02 ] |XXXXX 29500 - 30000 : [ 13 0.01 0.02 ] |XXXXXX 30000 - 30500 : [ 15 0.01 0.03 ] |XXXXXXXX 30500 - 31000 : [ 20 0.01 0.04 ] |XXXXXXXXXXX 31000 - 31500 : [ 27 0.01 0.05 ] |XXXXXXXXXXXXXXXXXX 31500 - 32000 : [ 42 0.02 0.07 ] |XXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 47 0.02 0.10 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 69 0.03 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 71 0.04 0.17 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 88 0.04 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 89 0.04 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 88 0.04 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 94 0.05 0.34 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 95 0.05 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 85 0.04 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 93 0.05 0.48 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 87 0.04 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 85 0.04 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 84 0.04 0.61 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 87 0.04 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 76 0.04 0.69 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 86 0.04 0.73 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 59 0.03 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 75 0.04 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 67 0.03 0.83 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 59 0.03 0.86 ] |XXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 58 0.03 0.89 ] |XXXXXXXXXXXXXXXXX 42500 - 43000 : [ 41 0.02 0.91 ] |XXXXXXXXXXXXXXXX 43000 - 43500 : [ 37 0.02 0.93 ] |XXXXXXXXXXXXXXXX 43500 - 44000 : [ 37 0.02 0.94 ] |XXXXXXXX 44000 - 44500 : [ 18 0.01 0.95 ] |XXXXXXXXX 44500 - 45000 : [ 21 0.01 0.96 ] |XXXXXXXXXXX 45000 - 45500 : [ 26 0.01 0.98 ] |XXXXXXXXXX 45500 - 46000 : [ 23 0.01 0.99 ] |XXXX 46000 - 46500 : [ 9 0.00 0.99 ] |XXX 46500 - 47000 : [ 8 0.00 1.00 ] |XX 47000 - 47500 : [ 5 0.00 1.00 ] #... | 52500 - 53000 : [ 1 0.00 1.00 ] #... | 133500 - 134000 : [ 1 0.00 1.00 ] #... | 650000 - 650500 : [ 1 0.00 1.00 ] #... | 781500 - 782000 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # AAOZ 9055 +- 2468 (n=7736) # LAP 3708 +- 720 (n=14899) # KQD 2119 +- 1508 (n=100) # TAH 37356 +- 4160 (n=1023) ################################################################### 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 522.139897 bp, 115211 reads, genome size 6096875 bp Command: idealAssembly 6096875 115211 522.139897 ------------------------------------------------------------------- Genome = 6096875 bases Nreads = 115211 readLength = 522.139897 Depth = 9.87 N_contigs = N_gaps = 6 mean gap size = 52 bases mean contig size = 19278 reads (~ 1020194 bases) %cover = 99.99 %singlet = 0.00 assembly size = 6096559 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 1 contigs containing at least 32349 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: