################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 2351481 Genus_species: Xylella fastidiosa Taxid: 2371 Genome size: 2600 Libraries: APOZ, KPX ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 2351481 ------------------------------------------------------------------- ID=2351481 ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 2583634 # phrap: 2450563 # db: 2600000 2544732 +/- 66922 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length KPX.5-77 649 82.90 459.46 XIC.5-8 7 71.28 271.29 XIF.5-22 54 63.00 302.78 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s APOZ 160 80 96.62 643.79 80 97.10 651.61 KPX 3 1 87.50 456.00 2 81.25 410.50 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 2351481_fasta.screen /usr/local/sequences/LRS.fasta -minmatch 20 -minscore 50 -screen > screen.out.std /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 2351481_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa -minmatch 12 -minscore 18 -screen > screen.out.1 /usr/local/src/assembly/pphrap/pphrap.SUN3.57 2351481_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 2351481_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out /usr/local/src/assembly/pphrap/pphrap.SUN3.57 2351481_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 2351481_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.2351481.out /home/copeland/scripts/librariesInfoTxt.sh 2351481 phrap.out > librariesInfo.txt ################################################################### Library vector screening APOZ.000001.000100 screen.out.1 2351481_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 2351481_fasta.screen /usr/local/sequences/LRS.fasta KPX.000001.000100 screen.out.1 2351481_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 2351481_fasta.screen /usr/local/sequences/LRS.fasta KPX.000101.000200 screen.out.1 2351481_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 2351481_fasta.screen /usr/local/sequences/LRS.fasta KPX.000201.000300 screen.out.1 2351481_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 2351481_fasta.screen /usr/local/sequences/LRS.fasta KPX.000301.000400 screen.out.1 2351481_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 2351481_fasta.screen /usr/local/sequences/LRS.fasta APOZ.000001.000100 screen.out.1 2351481_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 2351481_fasta.screen /usr/local/sequences/LRS.fasta KPX.000001.000100 screen.out.1 2351481_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 2351481_fasta.screen /usr/local/sequences/LRS.fasta KPX.000101.000200 screen.out.1 2351481_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 2351481_fasta.screen /usr/local/sequences/LRS.fasta KPX.000201.000300 screen.out.1 2351481_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 2351481_fasta.screen /usr/local/sequences/LRS.fasta KPX.000301.000400 screen.out.1 2351481_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 2351481_fasta.screen /usr/local/sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 2351481_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 49473 total values totalling 23796310.0000. <480.995897 +/- 209.323444> #Range: [ 22 - 805 ] #Most likely bin: [ 600 - 650 ] 10465 counts #Median bin: [ 550 - 600 ] 5114 counts |XXXXXXX 0 - 50 : [ 1705 0.03 0.03 ] |XXXXXXXXX 50 - 100 : [ 2286 0.05 0.08 ] |XXXXXXXXX 100 - 150 : [ 2296 0.05 0.13 ] |XXXXXXX 150 - 200 : [ 1840 0.04 0.16 ] |XXXXXX 200 - 250 : [ 1612 0.03 0.20 ] |XXXXXX 250 - 300 : [ 1566 0.03 0.23 ] |XXXXXX 300 - 350 : [ 1670 0.03 0.26 ] |XXXXXXX 350 - 400 : [ 1937 0.04 0.30 ] |XXXXXXXX 400 - 450 : [ 2105 0.04 0.34 ] |XXXXXXXXXX 450 - 500 : [ 2489 0.05 0.39 ] |XXXXXXXXXXXX 500 - 550 : [ 3099 0.06 0.46 ] |XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 5114 0.10 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 10465 0.21 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 9062 0.18 0.95 ] |XXXXXXXX 700 - 750 : [ 1998 0.04 1.00 ] |X 750 - 800 : [ 227 0.00 1.00 ] | 800 - 850 : [ 2 0.00 1.00 ] JAZZ trim 15 readlength histogram for KPX Command: /usr/xpg4/bin/grep KPX 2351481_fasta.screen.screen.ids > reads.trim15.KPX.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.KPX.rl 2 50 #Found 46289 total values totalling 22566827.0000. <487.520296 +/- 207.801243> #Range: [ 22 - 805 ] #Most likely bin: [ 600 - 650 ] 9958 counts #Median bin: [ 550 - 600 ] 4750 counts |XXXXXX 0 - 50 : [ 1532 0.03 0.03 ] |XXXXXXXX 50 - 100 : [ 2044 0.04 0.08 ] |XXXXXXXX 100 - 150 : [ 2045 0.04 0.12 ] |XXXXXXX 150 - 200 : [ 1662 0.04 0.16 ] |XXXXXX 200 - 250 : [ 1449 0.03 0.19 ] |XXXXXX 250 - 300 : [ 1424 0.03 0.22 ] |XXXXXX 300 - 350 : [ 1490 0.03 0.25 ] |XXXXXXX 350 - 400 : [ 1761 0.04 0.29 ] |XXXXXXXX 400 - 450 : [ 1918 0.04 0.33 ] |XXXXXXXXX 450 - 500 : [ 2273 0.05 0.38 ] |XXXXXXXXXXX 500 - 550 : [ 2854 0.06 0.44 ] |XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 4750 0.10 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 9958 0.22 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 8905 0.19 0.95 ] |XXXXXXXX 700 - 750 : [ 1995 0.04 1.00 ] |X 750 - 800 : [ 227 0.00 1.00 ] | 800 - 850 : [ 2 0.00 1.00 ] JAZZ trim 15 readlength histogram for APOZ ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.2351481_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.2351481_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 48222 total values totalling 25739.7931. <0.533777 +/- 0.058916> #Range: [ 0 - 0.8572 ] #Most likely bin: [ 0.535 - 0.54 ] 2001 counts #Median bin: [ 0.535 - 0.54 ] 2001 counts | 0 - 0.005 : [ 1 0.00 0.00 ] #... | 0.08 - 0.085 : [ 1 0.00 0.00 ] #... | 0.165 - 0.17 : [ 1 0.00 0.00 ] #... | 0.185 - 0.19 : [ 1 0.00 0.00 ] #... | 0.2 - 0.205 : [ 3 0.00 0.00 ] | 0.205 - 0.21 : [ 3 0.00 0.00 ] | 0.21 - 0.215 : [ 7 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 : [ 5 0.00 0.00 ] | 0.235 - 0.24 : [ 3 0.00 0.00 ] | 0.24 - 0.245 : [ 3 0.00 0.00 ] #... | 0.25 - 0.255 : [ 6 0.00 0.00 ] | 0.255 - 0.26 : [ 2 0.00 0.00 ] | 0.26 - 0.265 : [ 5 0.00 0.00 ] | 0.265 - 0.27 : [ 5 0.00 0.00 ] | 0.27 - 0.275 : [ 6 0.00 0.00 ] | 0.275 - 0.28 : [ 12 0.00 0.00 ] | 0.28 - 0.285 : [ 10 0.00 0.00 ] | 0.285 - 0.29 : [ 8 0.00 0.00 ] | 0.29 - 0.295 : [ 8 0.00 0.00 ] | 0.295 - 0.3 : [ 4 0.00 0.00 ] | 0.3 - 0.305 : [ 12 0.00 0.00 ] | 0.305 - 0.31 : [ 10 0.00 0.00 ] | 0.31 - 0.315 : [ 22 0.00 0.00 ] | 0.315 - 0.32 : [ 23 0.00 0.00 ] | 0.32 - 0.325 : [ 21 0.00 0.00 ] |X 0.325 - 0.33 : [ 26 0.00 0.00 ] |X 0.33 - 0.335 : [ 43 0.00 0.01 ] |X 0.335 - 0.34 : [ 35 0.00 0.01 ] |X 0.34 - 0.345 : [ 41 0.00 0.01 ] |X 0.345 - 0.35 : [ 43 0.00 0.01 ] |X 0.35 - 0.355 : [ 50 0.00 0.01 ] |X 0.355 - 0.36 : [ 60 0.00 0.01 ] |XX 0.36 - 0.365 : [ 77 0.00 0.01 ] |X 0.365 - 0.37 : [ 74 0.00 0.01 ] |X 0.37 - 0.375 : [ 65 0.00 0.01 ] |XX 0.375 - 0.38 : [ 83 0.00 0.02 ] |XX 0.38 - 0.385 : [ 89 0.00 0.02 ] |XX 0.385 - 0.39 : [ 97 0.00 0.02 ] |XX 0.39 - 0.395 : [ 104 0.00 0.02 ] |XX 0.395 - 0.4 : [ 87 0.00 0.02 ] |XXX 0.4 - 0.405 : [ 166 0.00 0.03 ] |XXX 0.405 - 0.41 : [ 146 0.00 0.03 ] |XXX 0.41 - 0.415 : [ 165 0.00 0.03 ] |XXXX 0.415 - 0.42 : [ 224 0.00 0.04 ] |XXXX 0.42 - 0.425 : [ 214 0.00 0.04 ] |XXXX 0.425 - 0.43 : [ 212 0.00 0.05 ] |XXXXXX 0.43 - 0.435 : [ 296 0.01 0.05 ] |XXXXXX 0.435 - 0.44 : [ 304 0.01 0.06 ] |XXXXXXX 0.44 - 0.445 : [ 332 0.01 0.07 ] |XXXXXXXX 0.445 - 0.45 : [ 384 0.01 0.07 ] |XXXXXXXX 0.45 - 0.455 : [ 410 0.01 0.08 ] |XXXXXXXXXX 0.455 - 0.46 : [ 500 0.01 0.09 ] |XXXXXXXXXXXX 0.46 - 0.465 : [ 592 0.01 0.11 ] |XXXXXXXXXXXX 0.465 - 0.47 : [ 590 0.01 0.12 ] |XXXXXXXXXXXXXX 0.47 - 0.475 : [ 717 0.01 0.13 ] |XXXXXXXXXXXXXXX 0.475 - 0.48 : [ 765 0.02 0.15 ] |XXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 965 0.02 0.17 ] |XXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1021 0.02 0.19 ] |XXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1141 0.02 0.21 ] |XXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 996 0.02 0.23 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1612 0.03 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1445 0.03 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1601 0.03 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1728 0.04 0.37 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1786 0.04 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1945 0.04 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1912 0.04 0.48 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 2001 0.04 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1970 0.04 0.57 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1937 0.04 0.61 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1870 0.04 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1730 0.04 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1603 0.03 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1563 0.03 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1342 0.03 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1277 0.03 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1145 0.02 0.82 ] |XXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1152 0.02 0.85 ] |XXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 1050 0.02 0.87 ] |XXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 861 0.02 0.89 ] |XXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 906 0.02 0.91 ] |XXXXXXXXXXXXXX 0.605 - 0.61 : [ 714 0.01 0.92 ] |XXXXXXXXXXXX 0.61 - 0.615 : [ 625 0.01 0.93 ] |XXXXXXXXXXX 0.615 - 0.62 : [ 546 0.01 0.95 ] |XXXXXXXX 0.62 - 0.625 : [ 384 0.01 0.95 ] |XXXXXXXXX 0.625 - 0.63 : [ 435 0.01 0.96 ] |XXXXXX 0.63 - 0.635 : [ 293 0.01 0.97 ] |XXXXX 0.635 - 0.64 : [ 269 0.01 0.97 ] |XXXX 0.64 - 0.645 : [ 224 0.00 0.98 ] |XXXX 0.645 - 0.65 : [ 189 0.00 0.98 ] |XXX 0.65 - 0.655 : [ 144 0.00 0.99 ] |XX 0.655 - 0.66 : [ 108 0.00 0.99 ] |XX 0.66 - 0.665 : [ 119 0.00 0.99 ] |XX 0.665 - 0.67 : [ 106 0.00 0.99 ] |X 0.67 - 0.675 : [ 62 0.00 0.99 ] |X 0.675 - 0.68 : [ 43 0.00 1.00 ] |X 0.68 - 0.685 : [ 42 0.00 1.00 ] | 0.685 - 0.69 : [ 25 0.00 1.00 ] | 0.69 - 0.695 : [ 21 0.00 1.00 ] | 0.695 - 0.7 : [ 19 0.00 1.00 ] | 0.7 - 0.705 : [ 14 0.00 1.00 ] | 0.705 - 0.71 : [ 19 0.00 1.00 ] | 0.71 - 0.715 : [ 10 0.00 1.00 ] | 0.715 - 0.72 : [ 11 0.00 1.00 ] | 0.72 - 0.725 : [ 10 0.00 1.00 ] | 0.725 - 0.73 : [ 12 0.00 1.00 ] | 0.73 - 0.735 : [ 3 0.00 1.00 ] | 0.735 - 0.74 : [ 5 0.00 1.00 ] | 0.74 - 0.745 : [ 6 0.00 1.00 ] #... | 0.75 - 0.755 : [ 6 0.00 1.00 ] | 0.755 - 0.76 : [ 2 0.00 1.00 ] | 0.76 - 0.765 : [ 3 0.00 1.00 ] | 0.765 - 0.77 : [ 5 0.00 1.00 ] #... | 0.775 - 0.78 : [ 1 0.00 1.00 ] | 0.78 - 0.785 : [ 4 0.00 1.00 ] | 0.785 - 0.79 : [ 1 0.00 1.00 ] | 0.79 - 0.795 : [ 1 0.00 1.00 ] #... | 0.805 - 0.81 : [ 2 0.00 1.00 ] #... | 0.815 - 0.82 : [ 1 0.00 1.00 ] #... | 0.825 - 0.83 : [ 1 0.00 1.00 ] #... | 0.84 - 0.845 : [ 1 0.00 1.00 ] #... | 0.85 - 0.855 : [ 1 0.00 1.00 ] | 0.855 - 0.86 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones LIBRARY @ ] 62886 33426 89.61 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 = 6290 HQ Discrepant reads = 291 Chimeric reads = 1063 Suspect alignments = 4669 ################################################################### C O N T I G I N F O R M A T I O N Sun Sep 5 08:20:18 2004 File: /psf/project/microbe3/2351481/edit_dir.30Mar04.QD/phrap.out Contig 293. 581 reads; 30932 bp (untrimmed), 30932 (trimmed). Contig 294. 583 reads; 33168 bp (untrimmed), 33146 (trimmed). Contig 295. 595 reads; 37244 bp (untrimmed), 37093 (trimmed). Contig 296. 605 reads; 28355 bp (untrimmed), 28272 (trimmed). Contig 297. 609 reads; 18791 bp (untrimmed), 18765 (trimmed). Contig 298. 629 reads; 28028 bp (untrimmed), 27550 (trimmed). Contig 299. 649 reads; 34641 bp (untrimmed), 34422 (trimmed). Contig 300. 756 reads; 43937 bp (untrimmed), 43794 (trimmed). Contig 301. 792 reads; 41655 bp (untrimmed), 41635 (trimmed). Contig 302. 797 reads; 43489 bp (untrimmed), 43482 (trimmed). Contig 303. 800 reads; 49721 bp (untrimmed), 49687 (trimmed). Contig 304. 816 reads; 37110 bp (untrimmed), 36817 (trimmed). Contig 305. 823 reads; 21722 bp (untrimmed), 21202 (trimmed). Contig 306. 843 reads; 19725 bp (untrimmed), 19700 (trimmed). Contig 307. 922 reads; 43170 bp (untrimmed), 43136 (trimmed). Contig 308. 1074 reads; 64385 bp (untrimmed), 64141 (trimmed). Contig 309. 1145 reads; 56553 bp (untrimmed), 56335 (trimmed). Contig 310. 1227 reads; 54081 bp (untrimmed), 53557 (trimmed). Contig 311. 1248 reads; 21246 bp (untrimmed), 20735 (trimmed). Contig 312. 1257 reads; 39905 bp (untrimmed), 39830 (trimmed). Contig 313. 1283 reads; 71882 bp (untrimmed), 71816 (trimmed). Contig 314. 1611 reads; 96476 bp (untrimmed), 96182 (trimmed). Contig 315. 1840 reads; 85353 bp (untrimmed), 85352 (trimmed). Contig 316. 1921 reads; 92480 bp (untrimmed), 92294 (trimmed). Contig 317. 2586 reads; 102654 bp (untrimmed), 102549 (trimmed). Contig 318. 2894 reads; 84570 bp (untrimmed), 84561 (trimmed). Contig 319. 2901 reads; 98914 bp (untrimmed), 98862 (trimmed). -------------------------------------------------------------- Totals 49279 reads; 2630460 bp (untrimmed), 2583634 (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 143 total values totalling 2490120.0000. <17413.426573 +/- 21357.707704> #Range: [ 2070 - 102549 ] #Most likely bin: [ 2000 - 4000 ] 46 counts #Median bin: [ 8000 - 10000 ] 8 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 46 0.32 0.32 ] |XXXXXXXXXXXXXXXX 4000 - 6000 : [ 18 0.13 0.45 ] |XXXX 6000 - 8000 : [ 5 0.03 0.48 ] |XXXXXXX 8000 - 10000 : [ 8 0.06 0.54 ] |XXX 10000 - 12000 : [ 3 0.02 0.56 ] |XXXXXXX 12000 - 14000 : [ 8 0.06 0.62 ] |XXX 14000 - 16000 : [ 4 0.03 0.64 ] |XXX 16000 - 18000 : [ 3 0.02 0.66 ] |XXXXXXX 18000 - 20000 : [ 8 0.06 0.72 ] |XXXX 20000 - 22000 : [ 5 0.03 0.76 ] |XXX 22000 - 24000 : [ 3 0.02 0.78 ] #... |XXX 26000 - 28000 : [ 3 0.02 0.80 ] |XX 28000 - 30000 : [ 2 0.01 0.81 ] |XX 30000 - 32000 : [ 2 0.01 0.83 ] |XX 32000 - 34000 : [ 2 0.01 0.84 ] |X 34000 - 36000 : [ 1 0.01 0.85 ] |XXXX 36000 - 38000 : [ 5 0.03 0.88 ] |XX 38000 - 40000 : [ 2 0.01 0.90 ] |X 40000 - 42000 : [ 1 0.01 0.90 ] |XXX 42000 - 44000 : [ 3 0.02 0.92 ] #... |X 48000 - 50000 : [ 1 0.01 0.93 ] #... |X 52000 - 54000 : [ 1 0.01 0.94 ] #... |X 56000 - 58000 : [ 1 0.01 0.94 ] #... |X 64000 - 66000 : [ 1 0.01 0.95 ] #... |X 70000 - 72000 : [ 1 0.01 0.96 ] #... |XX 84000 - 86000 : [ 2 0.01 0.97 ] #... |X 92000 - 94000 : [ 1 0.01 0.98 ] #... |X 96000 - 98000 : [ 1 0.01 0.99 ] |X 98000 - 100000 : [ 1 0.01 0.99 ] #... |X 102000 - 104000 : [ 1 0.01 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 13155748 C = 13442595 G = 13953866 T = 11601303 N = 275468 X = 3074013 GC fraction = 0.49 Total = 55502993 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 2351481_fasta.screen.contigs A 606588 C 655373 G 714869 N 630 T 652771 X 229 fraction GC = 0.52 total bases = 2630460 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 2606052 bases = 12.04 +- 9.84 = 0.57 +- 5.99 m1 = 8.04 m2 = 15.21 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 228 total values totalling 1625.1200. <7.127719 +/- 6.681518> #Range: [ 1.11 - 44.86 ] #Most likely bin: [ 1.5 - 2 ] 28 counts #Median bin: [ 4.5 - 5 ] 10 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 19 0.08 0.08 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 28 0.12 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 17 0.07 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 17 0.07 0.36 ] |XXXXXXXXXXX 3 - 3.5 : [ 8 0.04 0.39 ] |XXXXXXXXX 3.5 - 4 : [ 6 0.03 0.42 ] |XXXXXXXXXXXXX 4 - 4.5 : [ 9 0.04 0.46 ] |XXXXXXXXXXXXXX 4.5 - 5 : [ 10 0.04 0.50 ] |XXXXXXXXX 5 - 5.5 : [ 6 0.03 0.53 ] |XXXX 5.5 - 6 : [ 3 0.01 0.54 ] |XXXXXXXXXXXXXX 6 - 6.5 : [ 10 0.04 0.58 ] |XXXXXXX 6.5 - 7 : [ 5 0.02 0.61 ] |XXXXXXXXXX 7 - 7.5 : [ 7 0.03 0.64 ] |XXXXXXXXXX 7.5 - 8 : [ 7 0.03 0.67 ] |XXXXXXX 8 - 8.5 : [ 5 0.02 0.69 ] |X 8.5 - 9 : [ 1 0.00 0.69 ] |XXXXXX 9 - 9.5 : [ 4 0.02 0.71 ] |XXXX 9.5 - 10 : [ 3 0.01 0.72 ] |XXXXXXXXXX 10 - 10.5 : [ 7 0.03 0.75 ] |XXXXXXXXXX 10.5 - 11 : [ 7 0.03 0.79 ] |XXXXXXXXX 11 - 11.5 : [ 6 0.03 0.81 ] |XXXXXXXXX 11.5 - 12 : [ 6 0.03 0.84 ] |XXXXXX 12 - 12.5 : [ 4 0.02 0.86 ] |XXXXXX 12.5 - 13 : [ 4 0.02 0.87 ] |XXXXXXXXX 13 - 13.5 : [ 6 0.03 0.90 ] |XXX 13.5 - 14 : [ 2 0.01 0.91 ] |XXXX 14 - 14.5 : [ 3 0.01 0.92 ] |X 14.5 - 15 : [ 1 0.00 0.93 ] #... |X 15.5 - 16 : [ 1 0.00 0.93 ] |X 16 - 16.5 : [ 1 0.00 0.93 ] |XXXX 16.5 - 17 : [ 3 0.01 0.95 ] #... |X 19 - 19.5 : [ 1 0.00 0.95 ] |X 19.5 - 20 : [ 1 0.00 0.96 ] |X 20 - 20.5 : [ 1 0.00 0.96 ] |X 20.5 - 21 : [ 1 0.00 0.96 ] #... |X 21.5 - 22 : [ 1 0.00 0.97 ] #... |X 24.5 - 25 : [ 1 0.00 0.97 ] #... |XXX 27 - 27.5 : [ 2 0.01 0.98 ] #... |X 35.5 - 36 : [ 1 0.00 0.99 ] |X 36 - 36.5 : [ 1 0.00 0.99 ] #... |X 37.5 - 38 : [ 1 0.00 1.00 ] #... |X 44.5 - 45 : [ 1 0.00 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 144 total values totalling 1406.6600. <9.768472 +/- 7.029078> #Range: [ 2.06 - 44.86 ] #Most likely bin: [ 2.5 - 3 ] 10 counts #Median bin: [ 8 - 8.5 ] 5 counts |XXXXXXXXXXXXXXXX 2 - 2.5 : [ 4 0.03 0.03 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 10 0.07 0.10 ] |XXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 5 0.03 0.13 ] |XXXXXXXXXXXXXXXX 3.5 - 4 : [ 4 0.03 0.16 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 8 0.06 0.22 ] |XXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 5 0.03 0.25 ] |XXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 5 0.03 0.28 ] |XXXXXXXXXXXX 5.5 - 6 : [ 3 0.02 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 9 0.06 0.37 ] |XXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 5 0.03 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 7 0.05 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 6 0.04 0.49 ] |XXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 5 0.03 0.53 ] |XXXX 8.5 - 9 : [ 1 0.01 0.53 ] |XXXXXXXXXXXXXXXX 9 - 9.5 : [ 4 0.03 0.56 ] |XXXXXXXX 9.5 - 10 : [ 2 0.01 0.58 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 7 0.05 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 6 0.04 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 6 0.04 0.71 ] |XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 5 0.03 0.74 ] |XXXXXXXXXXXXXXXX 12 - 12.5 : [ 4 0.03 0.77 ] |XXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.03 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 6 0.04 0.84 ] |XXXXXXXX 13.5 - 14 : [ 2 0.01 0.85 ] |XXXXXXXXXXXX 14 - 14.5 : [ 3 0.02 0.88 ] |XXXX 14.5 - 15 : [ 1 0.01 0.88 ] #... |XXXX 15.5 - 16 : [ 1 0.01 0.89 ] |XXXX 16 - 16.5 : [ 1 0.01 0.90 ] |XXXXXXXXXXXX 16.5 - 17 : [ 3 0.02 0.92 ] #... |XXXX 19 - 19.5 : [ 1 0.01 0.92 ] |XXXX 19.5 - 20 : [ 1 0.01 0.93 ] |XXXX 20 - 20.5 : [ 1 0.01 0.94 ] |XXXX 20.5 - 21 : [ 1 0.01 0.94 ] #... |XXXX 21.5 - 22 : [ 1 0.01 0.95 ] #... |XXXX 24.5 - 25 : [ 1 0.01 0.96 ] #... |XXXXXXXX 27 - 27.5 : [ 2 0.01 0.97 ] #... |XXXX 35.5 - 36 : [ 1 0.01 0.98 ] |XXXX 36 - 36.5 : [ 1 0.01 0.99 ] #... |XXXX 37.5 - 38 : [ 1 0.01 0.99 ] #... |XXXX 44.5 - 45 : [ 1 0.01 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 47 2 reads 786 bases = 1.11 +- 0.31 = -0.89 +- 0.31 m1 = 0.09 m2 = 0.00 Contig 12 2 reads 743 bases = 1.15 +- 0.36 = 1.15 +- 0.36 m1 = 0.11 m2 = 0.00 Contig 91 2 reads 1253 bases = 1.15 +- 0.36 = 1.15 +- 0.36 m1 = 0.11 m2 = 0.00 Contig 40 2 reads 1199 bases = 1.19 +- 0.40 = 0.09 +- 0.89 m1 = 0.13 m2 = -0.16 Contig 22 2 reads 661 bases = 1.21 +- 0.41 = 1.21 +- 0.41 m1 = 0.14 m2 = 0.00 Contig 111 2 reads 846 bases = 1.25 +- 0.44 = 1.25 +- 0.44 m1 = 0.15 m2 = 0.00 Contig 74 2 reads 984 bases = 1.25 +- 0.43 = 1.25 +- 0.43 m1 = 0.15 m2 = 0.00 Contig 28 2 reads 828 bases = 1.26 +- 0.44 = 0.74 +- 0.44 m1 = 0.15 m2 = -0.00 Contig 13 2 reads 1113 bases = 1.27 +- 0.44 = 1.27 +- 0.44 m1 = 0.15 m2 = 0.00 Contig 14 2 reads 1311 bases = 1.27 +- 0.45 = 1.27 +- 0.45 m1 = 0.16 m2 = 0.00 Contig 32 2 reads 1608 bases = 1.28 +- 0.45 = 1.28 +- 0.45 m1 = 0.16 m2 = 0.00 Contig 87 2 reads 918 bases = 1.30 +- 0.46 = 1.30 +- 0.46 m1 = 0.16 m2 = 0.00 Contig 68 2 reads 1122 bases = 1.33 +- 0.47 = 1.33 +- 0.47 m1 = 0.17 m2 = 0.00 Contig 133 3 reads 1191 bases = 1.39 +- 0.59 = 0.43 +- 0.73 m1 = 0.25 m2 = -0.05 Contig 30 2 reads 1027 bases = 1.41 +- 0.49 = 1.41 +- 0.49 m1 = 0.17 m2 = 0.00 Contig 108 2 reads 1193 bases = 1.42 +- 0.49 = 1.42 +- 0.49 m1 = 0.17 m2 = 0.00 Contig 150 5 reads 1712 bases = 1.42 +- 1.01 = 0.16 +- 0.96 m1 = 0.72 m2 = 0.03 Contig 93 2 reads 678 bases = 1.44 +- 0.50 = 1.44 +- 0.50 m1 = 0.17 m2 = 0.00 Contig 50 2 reads 785 bases = 1.48 +- 0.50 = 1.48 +- 0.50 m1 = 0.17 m2 = 0.00 Contig 127 3 reads 1240 bases = 1.50 +- 0.70 = 0.74 +- 0.45 m1 = 0.33 m2 = 0.07 Contig 242 100 reads 4847 bases = 14.10 +- 6.60 = 8.41 +- 4.55 m1 = 3.09 m2 = 5.70 Contig 310 1227 reads 54081 bases = 14.35 +- 7.84 = 0.86 +- 7.22 m1 = 4.29 m2 = 2.37 Contig 298 629 reads 28028 bases = 14.85 +- 6.36 = 0.70 +- 4.78 m1 = 2.72 m2 = 4.40 Contig 256 193 reads 7174 bases = 15.92 +- 9.06 = 3.95 +- 7.42 m1 = 5.16 m2 = 6.77 Contig 317 2586 reads 102654 bases = 16.32 +- 8.47 = -0.18 +- 6.31 m1 = 4.40 m2 = 7.98 Contig 278 355 reads 13152 bases = 16.67 +- 9.60 = 1.15 +- 5.02 m1 = 5.53 m2 = 16.72 Contig 243 104 reads 3984 bases = 16.85 +- 6.76 = 1.34 +- 3.50 m1 = 2.71 m2 = 8.36 Contig 284 496 reads 19019 bases = 16.86 +- 8.15 = 0.76 +- 6.19 m1 = 3.94 m2 = 7.02 Contig 319 2901 reads 98914 bases = 19.40 +- 10.23 = -0.13 +- 8.85 m1 = 5.39 m2 = 6.56 Contig 312 1257 reads 39905 bases = 19.75 +- 14.71 = 1.26 +- 10.45 m1 = 10.96 m2 = 26.79 Contig 248 141 reads 4703 bases = 20.06 +- 22.89 = 3.36 +- 3.78 m1 = 26.11 m2 = 127.38 Contig 297 609 reads 18791 bases = 20.77 +- 8.85 = 1.75 +- 6.72 m1 = 3.77 m2 = 8.30 Contig 318 2894 reads 84570 bases = 21.71 +- 21.20 = -0.11 +- 7.70 m1 = 20.70 m2 = 97.52 Contig 305 823 reads 21722 bases = 24.64 +- 18.80 = 1.08 +- 7.06 m1 = 14.35 m2 = 75.91 Contig 267 237 reads 5346 bases = 27.02 +- 12.57 = 6.03 +- 9.97 m1 = 5.85 m2 = 14.64 Contig 306 843 reads 19725 bases = 27.22 +- 16.22 = 0.05 +- 11.66 m1 = 9.67 m2 = 31.81 Contig 274 303 reads 5391 bases = 35.65 +- 15.47 = 3.96 +- 9.43 m1 = 6.71 m2 = 37.60 Contig 311 1248 reads 21246 bases = 36.05 +- 27.11 = 1.35 +- 12.43 m1 = 20.38 m2 = 145.11 Contig 282 438 reads 2403 bases = 37.79 +- 30.54 = 13.74 +- 12.79 m1 = 24.69 m2 = 192.32 Contig 252 170 reads 2387 bases = 44.86 +- 24.44 = 6.45 +- 4.72 m1 = 13.31 m2 = 143.73 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 319 total values totalling 49279.0000. <154.479624 +/- 386.196369> #Range: [ 1 - 2901 ] #Most likely bin: [ 2 - 3 ] 102 counts #Median bin: [ 8 - 9 ] 2 counts |XXXX 1 - 2 : [ 11 0.03 0.03 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 3 : [ 102 0.32 0.35 ] |XXXXXXXXX 3 - 4 : [ 23 0.07 0.43 ] |XXXX 4 - 5 : [ 9 0.03 0.45 ] |XX 5 - 6 : [ 5 0.02 0.47 ] |XX 6 - 7 : [ 4 0.01 0.48 ] |XX 7 - 8 : [ 4 0.01 0.50 ] |X 8 - 9 : [ 2 0.01 0.50 ] |XX 9 - 10 : [ 5 0.02 0.52 ] |XX 10 - 11 : [ 5 0.02 0.53 ] |XXX 11 - 12 : [ 8 0.03 0.56 ] |XX 12 - 13 : [ 4 0.01 0.57 ] #... |X 14 - 15 : [ 3 0.01 0.58 ] |X 15 - 16 : [ 2 0.01 0.59 ] | 16 - 17 : [ 1 0.00 0.59 ] |XX 17 - 18 : [ 4 0.01 0.60 ] |X 18 - 19 : [ 3 0.01 0.61 ] |X 19 - 20 : [ 3 0.01 0.62 ] |X 20 - 21 : [ 2 0.01 0.63 ] #... |XX 22 - 23 : [ 4 0.01 0.64 ] |X 23 - 24 : [ 2 0.01 0.65 ] | 24 - 25 : [ 1 0.00 0.65 ] | 25 - 26 : [ 1 0.00 0.65 ] |X 26 - 27 : [ 2 0.01 0.66 ] #... | 28 - 29 : [ 1 0.00 0.66 ] | 29 - 30 : [ 1 0.00 0.66 ] | 30 - 31 : [ 1 0.00 0.67 ] |X 31 - 32 : [ 2 0.01 0.67 ] #... | 34 - 35 : [ 1 0.00 0.68 ] #... | 36 - 37 : [ 1 0.00 0.68 ] | 37 - 38 : [ 1 0.00 0.68 ] #... |X 39 - 40 : [ 2 0.01 0.69 ] #... |X 43 - 44 : [ 2 0.01 0.70 ] #... | 46 - 47 : [ 1 0.00 0.70 ] #... | 49 - 50 : [ 1 0.00 0.70 ] | 50 - 51 : [ 1 0.00 0.71 ] #... | 52 - 53 : [ 1 0.00 0.71 ] #... | 54 - 55 : [ 1 0.00 0.71 ] | 55 - 56 : [ 1 0.00 0.71 ] #... | 57 - 58 : [ 1 0.00 0.72 ] #... | 60 - 61 : [ 1 0.00 0.72 ] | 61 - 62 : [ 1 0.00 0.72 ] | 62 - 63 : [ 1 0.00 0.73 ] | 63 - 64 : [ 1 0.00 0.73 ] #... | 65 - 66 : [ 1 0.00 0.73 ] | 66 - 67 : [ 1 0.00 0.74 ] #... | 72 - 73 : [ 1 0.00 0.74 ] #... | 79 - 80 : [ 1 0.00 0.74 ] #... | 86 - 87 : [ 1 0.00 0.75 ] #... | 88 - 89 : [ 1 0.00 0.75 ] | 89 - 90 : [ 1 0.00 0.75 ] #... | 98 - 99 : [ 1 0.00 0.76 ] #... | 100 - 101 : [ 1 0.00 0.76 ] #... | 104 - 105 : [ 1 0.00 0.76 ] #... | 106 - 107 : [ 1 0.00 0.76 ] #... |X 113 - 114 : [ 2 0.01 0.77 ] #... | 126 - 127 : [ 1 0.00 0.77 ] #... | 141 - 142 : [ 1 0.00 0.78 ] #... | 152 - 153 : [ 1 0.00 0.78 ] #... | 160 - 161 : [ 1 0.00 0.78 ] | 161 - 162 : [ 1 0.00 0.79 ] #... | 170 - 171 : [ 1 0.00 0.79 ] #... | 182 - 183 : [ 1 0.00 0.79 ] #... | 185 - 186 : [ 1 0.00 0.80 ] #... | 187 - 188 : [ 1 0.00 0.80 ] #... | 193 - 194 : [ 1 0.00 0.80 ] #... | 203 - 204 : [ 1 0.00 0.81 ] #... | 206 - 207 : [ 1 0.00 0.81 ] #... | 208 - 209 : [ 1 0.00 0.81 ] #... | 210 - 211 : [ 1 0.00 0.82 ] #... | 215 - 216 : [ 1 0.00 0.82 ] #... | 218 - 219 : [ 1 0.00 0.82 ] | 219 - 220 : [ 1 0.00 0.82 ] #... | 229 - 230 : [ 1 0.00 0.83 ] | 230 - 231 : [ 1 0.00 0.83 ] #... | 232 - 233 : [ 1 0.00 0.83 ] #... | 237 - 238 : [ 1 0.00 0.84 ] | 238 - 239 : [ 1 0.00 0.84 ] #... | 240 - 241 : [ 1 0.00 0.84 ] #... | 250 - 251 : [ 1 0.00 0.85 ] #... | 255 - 256 : [ 1 0.00 0.85 ] #... | 268 - 269 : [ 1 0.00 0.85 ] #... | 287 - 288 : [ 1 0.00 0.86 ] #... | 303 - 304 : [ 1 0.00 0.86 ] #... | 309 - 310 : [ 1 0.00 0.86 ] | 310 - 311 : [ 1 0.00 0.87 ] #... | 327 - 328 : [ 1 0.00 0.87 ] #... | 355 - 356 : [ 1 0.00 0.87 ] #... | 410 - 411 : [ 1 0.00 0.87 ] #... | 412 - 413 : [ 1 0.00 0.88 ] #... | 418 - 419 : [ 1 0.00 0.88 ] #... | 438 - 439 : [ 1 0.00 0.88 ] #... | 462 - 463 : [ 1 0.00 0.89 ] #... | 496 - 497 : [ 1 0.00 0.89 ] #... | 505 - 506 : [ 1 0.00 0.89 ] #... | 508 - 509 : [ 1 0.00 0.90 ] #... | 511 - 512 : [ 1 0.00 0.90 ] #... | 537 - 538 : [ 1 0.00 0.90 ] #... |X 543 - 544 : [ 2 0.01 0.91 ] #... | 553 - 554 : [ 1 0.00 0.91 ] #... | 556 - 557 : [ 1 0.00 0.92 ] #... | 581 - 582 : [ 1 0.00 0.92 ] #... | 583 - 584 : [ 1 0.00 0.92 ] #... | 595 - 596 : [ 1 0.00 0.92 ] #... | 605 - 606 : [ 1 0.00 0.93 ] #... | 609 - 610 : [ 1 0.00 0.93 ] #... | 629 - 630 : [ 1 0.00 0.93 ] #... | 649 - 650 : [ 1 0.00 0.94 ] #... | 756 - 757 : [ 1 0.00 0.94 ] #... | 792 - 793 : [ 1 0.00 0.94 ] #... | 797 - 798 : [ 1 0.00 0.95 ] #... | 800 - 801 : [ 1 0.00 0.95 ] #... | 816 - 817 : [ 1 0.00 0.95 ] #... | 823 - 824 : [ 1 0.00 0.96 ] #... | 843 - 844 : [ 1 0.00 0.96 ] #... | 922 - 923 : [ 1 0.00 0.96 ] #... | 1074 - 1075 : [ 1 0.00 0.97 ] #... | 1145 - 1146 : [ 1 0.00 0.97 ] #... | 1227 - 1228 : [ 1 0.00 0.97 ] #... | 1248 - 1249 : [ 1 0.00 0.97 ] #... | 1257 - 1258 : [ 1 0.00 0.98 ] #... | 1283 - 1284 : [ 1 0.00 0.98 ] #... | 1611 - 1612 : [ 1 0.00 0.98 ] #... | 1840 - 1841 : [ 1 0.00 0.99 ] #... | 1921 - 1922 : [ 1 0.00 0.99 ] #... | 2586 - 2587 : [ 1 0.00 0.99 ] #... | 2894 - 2895 : [ 1 0.00 1.00 ] #... | 2901 - 2902 : [ 1 0.00 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 319 total values totalling 2630460.0000. <8245.956113 +/- 16579.611560> #Range: [ 63 - 102654 ] #Most likely bin: [ 0 - 1000 ] 134 counts #Median bin: [ 1000 - 2000 ] 40 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 1000 : [ 134 0.42 0.42 ] |XXXXXXXXXXXX 1000 - 2000 : [ 40 0.13 0.55 ] |XXXXXXXXXX 2000 - 3000 : [ 33 0.10 0.65 ] |XXXX 3000 - 4000 : [ 14 0.04 0.69 ] |XXX 4000 - 5000 : [ 9 0.03 0.72 ] |XX 5000 - 6000 : [ 8 0.03 0.75 ] |X 6000 - 7000 : [ 4 0.01 0.76 ] |X 7000 - 8000 : [ 3 0.01 0.77 ] |X 8000 - 9000 : [ 2 0.01 0.77 ] |XX 9000 - 10000 : [ 6 0.02 0.79 ] #... |X 11000 - 12000 : [ 2 0.01 0.80 ] |X 12000 - 13000 : [ 3 0.01 0.81 ] |XX 13000 - 14000 : [ 6 0.02 0.83 ] #... |X 15000 - 16000 : [ 3 0.01 0.84 ] |X 16000 - 17000 : [ 3 0.01 0.85 ] | 17000 - 18000 : [ 1 0.00 0.85 ] |X 18000 - 19000 : [ 5 0.02 0.87 ] |X 19000 - 20000 : [ 3 0.01 0.87 ] | 20000 - 21000 : [ 1 0.00 0.88 ] |X 21000 - 22000 : [ 4 0.01 0.89 ] #... |X 23000 - 24000 : [ 3 0.01 0.90 ] #... |X 27000 - 28000 : [ 2 0.01 0.91 ] |X 28000 - 29000 : [ 2 0.01 0.91 ] | 29000 - 30000 : [ 1 0.00 0.92 ] |X 30000 - 31000 : [ 2 0.01 0.92 ] #... | 32000 - 33000 : [ 1 0.00 0.92 ] | 33000 - 34000 : [ 1 0.00 0.93 ] | 34000 - 35000 : [ 1 0.00 0.93 ] #... |X 36000 - 37000 : [ 3 0.01 0.94 ] |X 37000 - 38000 : [ 2 0.01 0.95 ] #... |X 39000 - 40000 : [ 2 0.01 0.95 ] #... | 41000 - 42000 : [ 1 0.00 0.96 ] #... |X 43000 - 44000 : [ 3 0.01 0.97 ] #... | 49000 - 50000 : [ 1 0.00 0.97 ] #... | 54000 - 55000 : [ 1 0.00 0.97 ] #... | 56000 - 57000 : [ 1 0.00 0.97 ] #... | 64000 - 65000 : [ 1 0.00 0.98 ] #... | 71000 - 72000 : [ 1 0.00 0.98 ] #... | 84000 - 85000 : [ 1 0.00 0.98 ] | 85000 - 86000 : [ 1 0.00 0.99 ] #... | 92000 - 93000 : [ 1 0.00 0.99 ] #... | 96000 - 97000 : [ 1 0.00 0.99 ] #... | 98000 - 99000 : [ 1 0.00 1.00 ] #... | 102000 - 103000 : [ 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 KPX reads.list > grep.reads.list.KPX Command: /home/copeland/scripts/histogram2.pl grep.reads.list.KPX 4 500 #Found 15702 total values totalling 57204456.0000. <3643.131830 +/- 616.226055> #Range: [ - 18977 ] #Most likely bin: [ 3000 - 3500 ] 6080 counts #Median bin: [ 3500 - 4000 ] 4889 counts | 0 - 500 : [ 5 0.00 0.00 ] | 500 - 1000 : [ 62 0.00 0.00 ] |X 1000 - 1500 : [ 105 0.01 0.01 ] |X 1500 - 2000 : [ 79 0.01 0.02 ] | 2000 - 2500 : [ 67 0.00 0.02 ] |XXXX 2500 - 3000 : [ 631 0.04 0.06 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 6080 0.39 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 4889 0.31 0.76 ] |XXXXXXXXXXXXXXXX 4000 - 4500 : [ 2461 0.16 0.92 ] |XXXXXXX 4500 - 5000 : [ 1027 0.07 0.98 ] |XX 5000 - 5500 : [ 283 0.02 1.00 ] | 5500 - 6000 : [ 12 0.00 1.00 ] #... | 18500 - 19000 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # KPX 3522 +- 775 (n=7801) ################################################################### 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 480.995897 bp, 49279 reads, genome size 2544732 bp Command: idealAssembly 2544732 49279 480.995897 ------------------------------------------------------------------- Genome = 2544732 bases Nreads = 49279 readLength = 480.995897 Depth = 9.31 N_contigs = N_gaps = 4 mean gap size = 51 bases mean contig size = 11098 reads (~ 573102 bases) %cover = 99.99 %singlet = 0.00 assembly size = 2544503 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 1 contigs containing at least 18623 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: 2351481 Command line options used were: -c -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 24352 Number of reads with percent X's >= 20%: 3651 = 5.8% Number of reads with percent X's >= 50%: 3255 = 5.2% Number of reads with percent X's >= 80%: 2196 = 3.5% Total nr of reads in project is: 62886 Total nr of X's: 3074013 Total nr not found in screened files: 1 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with L09136-pUC18 24351 3651 3255 2196 ################################################################### Contam Summary with *.singlets: Command: contam_summary -c -s -g ------------------------------------------------------------------- Contamination Summary for JGI id: 2351481 Command line options used were: -c -g -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 3535 Number of reads with percent X's >= 20%: 2885 = 21.2% Number of reads with percent X's >= 50%: 2749 = 20.2% Number of reads with percent X's >= 80%: 2121 = 15.6% Total nr of reads in project is: 13607 Total nr of X's: 2070571 Total nr not found in screened files: 0 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with L09136-pUC18 3535 2885 2749 2121 ################################################################### Bad M1 Contigs ------------------------------------------------------------------- ################################################################### Bad M2 Contigs ------------------------------------------------------------------- ################################################################### Ran Plates2contigs: Output Location: Ran in.dir: Output Location: Viewed Contigs with Phrapview: ################################################################### Conclusions: