################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 3634605 Genus_species: Shewanella baltica OS1155 Taxid: 62322 Genome size: 4500 Libraries: AIOG, AIOF, AIOC ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 3634605 ------------------------------------------------------------------- ID=3634605 Lineage for 'Shewanella baltica': Shewanella baltica species Shewanella genus Alteromonadaceae family Alteromonadales order Gammaproteobacteria class Proteobacteria phylum Bacteria superkingdom cellular organisms no rank root no rank ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 5044127 # phrap: 4721774 # db: -1 3255300 +/- 2305604 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length AIOC.5-32 93 94.53 602.77 AIOF.5-64 352 97.41 706.78 AIOG.5-8 56 78.66 386.11 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s AIOG 56 28 76.30 382.86 28 81.03 389.36 AIOF 352 176 97.77 707.23 176 97.05 706.32 AIOC 93 46 93.81 590.70 47 95.25 614.60 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634605_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 3634605_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634605.out /home/copeland/scripts/librariesInfoTxt.sh 3634605 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634605_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 3634605_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634605.out /home/copeland/scripts/librariesInfoTxt.sh 3634605 phrap.out > librariesInfo.txt ################################################################### Library vector screening AIOC.000001.000100 screen.out.1 3634605_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634605_fasta.screen /usr/local/sequences/LRS.fasta AIOC.000101.000200 screen.out.1 3634605_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634605_fasta.screen /usr/local/sequences/LRS.fasta AIOF.000001.000100 screen.out.1 3634605_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634605_fasta.screen /usr/local/sequences/LRS.fasta AIOF.000101.000200 screen.out.1 3634605_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634605_fasta.screen /usr/local/sequences/LRS.fasta AIOG.000001.000100 screen.out.1 3634605_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634605_fasta.screen /usr/local/sequences/LRS.fasta AIOC.000001.000100 screen.out.1 3634605_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634605_fasta.screen /usr/local/sequences/LRS.fasta AIOC.000101.000200 screen.out.1 3634605_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634605_fasta.screen /usr/local/sequences/LRS.fasta AIOF.000001.000100 screen.out.1 3634605_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634605_fasta.screen /usr/local/sequences/LRS.fasta AIOF.000101.000200 screen.out.1 3634605_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634605_fasta.screen /usr/local/sequences/LRS.fasta AIOG.000001.000100 screen.out.1 3634605_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634605_fasta.screen /usr/local/sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 3634605_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 66446 total values totalling 42285302.0000. <636.385968 +/- 183.045080> #Range: [ 22 - 978 ] #Most likely bin: [ 750 - 800 ] 12005 counts #Median bin: [ 650 - 700 ] 9309 counts |X 0 - 50 : [ 217 0.00 0.00 ] |XXX 50 - 100 : [ 789 0.01 0.02 ] |XXX 100 - 150 : [ 1013 0.02 0.03 ] |XXX 150 - 200 : [ 966 0.01 0.04 ] |XXXX 200 - 250 : [ 1157 0.02 0.06 ] |XXXX 250 - 300 : [ 1168 0.02 0.08 ] |XXXXX 300 - 350 : [ 1361 0.02 0.10 ] |XXXXX 350 - 400 : [ 1598 0.02 0.12 ] |XXXXXX 400 - 450 : [ 1940 0.03 0.15 ] |XXXXXXX 450 - 500 : [ 2145 0.03 0.19 ] |XXXXXXXXX 500 - 550 : [ 2696 0.04 0.23 ] |XXXXXXXXXXXXX 550 - 600 : [ 3956 0.06 0.29 ] |XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 6258 0.09 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 9309 0.14 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 11531 0.17 0.69 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 12005 0.18 0.87 ] |XXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7172 0.11 0.98 ] |XXXX 850 - 900 : [ 1065 0.02 1.00 ] | 900 - 950 : [ 98 0.00 1.00 ] | 950 - 1000 : [ 2 0.00 1.00 ] JAZZ trim 15 readlength histogram for AIOC Command: /usr/xpg4/bin/grep AIOC 3634605_fasta.screen.screen.ids > reads.trim15.AIOC.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOC.rl 2 50 #Found 32338 total values totalling 17993229.0000. <556.411312 +/- 182.034035> #Range: [ 23 - 978 ] #Most likely bin: [ 650 - 700 ] 5898 counts #Median bin: [ 600 - 650 ] 4698 counts |X 0 - 50 : [ 78 0.00 0.00 ] |XXX 50 - 100 : [ 490 0.02 0.02 ] |XXXXX 100 - 150 : [ 797 0.02 0.04 ] |XXXXX 150 - 200 : [ 779 0.02 0.07 ] |XXXXXX 200 - 250 : [ 903 0.03 0.09 ] |XXXXXX 250 - 300 : [ 902 0.03 0.12 ] |XXXXXXX 300 - 350 : [ 1068 0.03 0.16 ] |XXXXXXXXX 350 - 400 : [ 1259 0.04 0.19 ] |XXXXXXXXXXX 400 - 450 : [ 1566 0.05 0.24 ] |XXXXXXXXXXXX 450 - 500 : [ 1790 0.06 0.30 ] |XXXXXXXXXXXXXXX 500 - 550 : [ 2206 0.07 0.37 ] |XXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 3163 0.10 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 4698 0.15 0.61 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5898 0.18 0.79 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4573 0.14 0.93 ] |XXXXXXXXXX 750 - 800 : [ 1509 0.05 0.98 ] |XX 800 - 850 : [ 293 0.01 0.99 ] |XX 850 - 900 : [ 271 0.01 1.00 ] |X 900 - 950 : [ 93 0.00 1.00 ] | 950 - 1000 : [ 2 0.00 1.00 ] JAZZ trim 15 readlength histogram for AIOF Command: /usr/xpg4/bin/grep AIOF 3634605_fasta.screen.screen.ids > reads.trim15.AIOF.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOF.rl 2 50 #Found 30691 total values totalling 22490191.0000. <732.794337 +/- 115.770031> #Range: [ 22 - 915 ] #Most likely bin: [ 750 - 800 ] 10095 counts #Median bin: [ 750 - 800 ] 10095 counts | 0 - 50 : [ 19 0.00 0.00 ] | 50 - 100 : [ 47 0.00 0.00 ] | 100 - 150 : [ 83 0.00 0.00 ] | 150 - 200 : [ 96 0.00 0.01 ] |X 200 - 250 : [ 159 0.01 0.01 ] |X 250 - 300 : [ 153 0.00 0.02 ] |X 300 - 350 : [ 201 0.01 0.02 ] |X 350 - 400 : [ 251 0.01 0.03 ] |X 400 - 450 : [ 268 0.01 0.04 ] |X 450 - 500 : [ 252 0.01 0.05 ] |X 500 - 550 : [ 378 0.01 0.06 ] |XX 550 - 600 : [ 599 0.02 0.08 ] |XXXXX 600 - 650 : [ 1223 0.04 0.12 ] |XXXXXXXXXXXX 650 - 700 : [ 2937 0.10 0.22 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6405 0.21 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 10095 0.33 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6738 0.22 0.97 ] |XXX 850 - 900 : [ 782 0.03 1.00 ] | 900 - 950 : [ 5 0.00 1.00 ] JAZZ trim 15 readlength histogram for AIOG Command: /usr/xpg4/bin/grep AIOG 3634605_fasta.screen.screen.ids > reads.trim15.AIOG.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOG.rl 2 50 #Found 3417 total values totalling 1801882.0000. <527.328651 +/- 248.299910> #Range: [ 24 - 887 ] #Most likely bin: [ 700 - 750 ] 553 counts #Median bin: [ 600 - 650 ] 337 counts |XXXXXXXXX 0 - 50 : [ 120 0.04 0.04 ] |XXXXXXXXXXXXXXXXXX 50 - 100 : [ 252 0.07 0.11 ] |XXXXXXXXXX 100 - 150 : [ 133 0.04 0.15 ] |XXXXXXX 150 - 200 : [ 91 0.03 0.17 ] |XXXXXXX 200 - 250 : [ 95 0.03 0.20 ] |XXXXXXXX 250 - 300 : [ 113 0.03 0.24 ] |XXXXXXX 300 - 350 : [ 92 0.03 0.26 ] |XXXXXX 350 - 400 : [ 88 0.03 0.29 ] |XXXXXXXX 400 - 450 : [ 106 0.03 0.32 ] |XXXXXXX 450 - 500 : [ 103 0.03 0.35 ] |XXXXXXXX 500 - 550 : [ 112 0.03 0.38 ] |XXXXXXXXXXXXXX 550 - 600 : [ 194 0.06 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 337 0.10 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 474 0.14 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 553 0.16 0.84 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 401 0.12 0.96 ] |XXXXXXXXXX 800 - 850 : [ 141 0.04 1.00 ] |X 850 - 900 : [ 12 0.00 1.00 ] ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.3634605_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.3634605_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 66191 total values totalling 30466.7958. <0.460286 +/- 0.045733> #Range: [ 0 - 0.84 ] #Most likely bin: [ 0.48 - 0.485 ] 3227 counts #Median bin: [ 0.465 - 0.47 ] 3134 counts | 0 - 0.005 : [ 1 0.00 0.00 ] #... | 0.12 - 0.125 : [ 1 0.00 0.00 ] #... | 0.165 - 0.17 : [ 2 0.00 0.00 ] | 0.17 - 0.175 : [ 1 0.00 0.00 ] #... | 0.18 - 0.185 : [ 1 0.00 0.00 ] #... | 0.19 - 0.195 : [ 1 0.00 0.00 ] #... | 0.2 - 0.205 : [ 5 0.00 0.00 ] | 0.205 - 0.21 : [ 2 0.00 0.00 ] | 0.21 - 0.215 : [ 1 0.00 0.00 ] #... | 0.22 - 0.225 : [ 1 0.00 0.00 ] | 0.225 - 0.23 : [ 6 0.00 0.00 ] | 0.23 - 0.235 : [ 4 0.00 0.00 ] | 0.235 - 0.24 : [ 1 0.00 0.00 ] | 0.24 - 0.245 : [ 7 0.00 0.00 ] | 0.245 - 0.25 : [ 4 0.00 0.00 ] | 0.25 - 0.255 : [ 8 0.00 0.00 ] | 0.255 - 0.26 : [ 15 0.00 0.00 ] | 0.26 - 0.265 : [ 14 0.00 0.00 ] | 0.265 - 0.27 : [ 18 0.00 0.00 ] | 0.27 - 0.275 : [ 16 0.00 0.00 ] | 0.275 - 0.28 : [ 11 0.00 0.00 ] | 0.28 - 0.285 : [ 14 0.00 0.00 ] | 0.285 - 0.29 : [ 22 0.00 0.00 ] |X 0.29 - 0.295 : [ 44 0.00 0.00 ] | 0.295 - 0.3 : [ 34 0.00 0.00 ] |X 0.3 - 0.305 : [ 54 0.00 0.00 ] |X 0.305 - 0.31 : [ 50 0.00 0.01 ] |X 0.31 - 0.315 : [ 60 0.00 0.01 ] |X 0.315 - 0.32 : [ 88 0.00 0.01 ] |X 0.32 - 0.325 : [ 91 0.00 0.01 ] |X 0.325 - 0.33 : [ 112 0.00 0.01 ] |XX 0.33 - 0.335 : [ 150 0.00 0.01 ] |XX 0.335 - 0.34 : [ 150 0.00 0.01 ] |XX 0.34 - 0.345 : [ 174 0.00 0.02 ] |XX 0.345 - 0.35 : [ 193 0.00 0.02 ] |XXX 0.35 - 0.355 : [ 230 0.00 0.02 ] |XXXX 0.355 - 0.36 : [ 287 0.00 0.03 ] |XXXX 0.36 - 0.365 : [ 302 0.00 0.03 ] |XXXX 0.365 - 0.37 : [ 338 0.01 0.04 ] |XXXXX 0.37 - 0.375 : [ 375 0.01 0.04 ] |XXXXXXX 0.375 - 0.38 : [ 530 0.01 0.05 ] |XXXXXXXX 0.38 - 0.385 : [ 618 0.01 0.06 ] |XXXXXXXX 0.385 - 0.39 : [ 646 0.01 0.07 ] |XXXXXXXXX 0.39 - 0.395 : [ 744 0.01 0.08 ] |XXXXXXXXXX 0.395 - 0.4 : [ 802 0.01 0.09 ] |XXXXXXXXXXXXX 0.4 - 0.405 : [ 1043 0.02 0.11 ] |XXXXXXXXXXXXXXX 0.405 - 0.41 : [ 1177 0.02 0.13 ] |XXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 1323 0.02 0.15 ] |XXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 1523 0.02 0.17 ] |XXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 1686 0.03 0.20 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 2005 0.03 0.23 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 2060 0.03 0.26 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 2075 0.03 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 2383 0.04 0.32 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 2531 0.04 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 2951 0.04 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 2993 0.05 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 3069 0.05 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 3134 0.05 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 3146 0.05 0.59 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 3146 0.05 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 3227 0.05 0.69 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 2984 0.05 0.74 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 2905 0.04 0.78 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 2402 0.04 0.82 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 2533 0.04 0.85 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 2040 0.03 0.88 ] |XXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1846 0.03 0.91 ] |XXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1462 0.02 0.93 ] |XXXXXXXXXXXXXX 0.52 - 0.525 : [ 1125 0.02 0.95 ] |XXXXXXXXXXX 0.525 - 0.53 : [ 890 0.01 0.97 ] |XXXXXXXX 0.53 - 0.535 : [ 624 0.01 0.97 ] |XXXXXX 0.535 - 0.54 : [ 459 0.01 0.98 ] |XXXX 0.54 - 0.545 : [ 305 0.00 0.99 ] |XXX 0.545 - 0.55 : [ 230 0.00 0.99 ] |XX 0.55 - 0.555 : [ 182 0.00 0.99 ] |XX 0.555 - 0.56 : [ 131 0.00 0.99 ] |X 0.56 - 0.565 : [ 85 0.00 1.00 ] |X 0.565 - 0.57 : [ 63 0.00 1.00 ] |X 0.57 - 0.575 : [ 49 0.00 1.00 ] | 0.575 - 0.58 : [ 35 0.00 1.00 ] | 0.58 - 0.585 : [ 21 0.00 1.00 ] | 0.585 - 0.59 : [ 17 0.00 1.00 ] | 0.59 - 0.595 : [ 16 0.00 1.00 ] | 0.595 - 0.6 : [ 4 0.00 1.00 ] | 0.6 - 0.605 : [ 12 0.00 1.00 ] | 0.605 - 0.61 : [ 9 0.00 1.00 ] | 0.61 - 0.615 : [ 3 0.00 1.00 ] | 0.615 - 0.62 : [ 9 0.00 1.00 ] | 0.62 - 0.625 : [ 4 0.00 1.00 ] | 0.625 - 0.63 : [ 9 0.00 1.00 ] | 0.63 - 0.635 : [ 3 0.00 1.00 ] | 0.635 - 0.64 : [ 4 0.00 1.00 ] | 0.64 - 0.645 : [ 5 0.00 1.00 ] | 0.645 - 0.65 : [ 4 0.00 1.00 ] | 0.65 - 0.655 : [ 1 0.00 1.00 ] | 0.655 - 0.66 : [ 2 0.00 1.00 ] #... | 0.665 - 0.67 : [ 5 0.00 1.00 ] | 0.67 - 0.675 : [ 1 0.00 1.00 ] | 0.675 - 0.68 : [ 1 0.00 1.00 ] | 0.68 - 0.685 : [ 2 0.00 1.00 ] #... | 0.69 - 0.695 : [ 3 0.00 1.00 ] | 0.695 - 0.7 : [ 1 0.00 1.00 ] #... | 0.715 - 0.72 : [ 2 0.00 1.00 ] #... | 0.77 - 0.775 : [ 1 0.00 1.00 ] #... | 0.79 - 0.795 : [ 1 0.00 1.00 ] #... | 0.84 - 0.845 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones N/plate avg% LIBRARY @ 180 32338 16562 92.01 95.84 AIOC @ 176 30691 15510 88.12 91.80 AIOF @ 28 3418 1974 70.50 73.44 AIOG @ ] 66447 34046 88.66 cumulative total@@ LIBRARY PLATE ID COUNT [ AIOC 180 AIOF 176 AIOG 28 ] for 384 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 = 1319 HQ Discrepant reads = 109 Chimeric reads = 533 Suspect alignments = 7248 ################################################################### C O N T I G I N F O R M A T I O N Mon Sep 6 03:47:18 2004 File: /psf/project/microbe3/3634605/edit_dir.31Aug04.QD/phrap.out Contig 224. 684 reads; 62123 bp (untrimmed), 62116 (trimmed). Contig 225. 704 reads; 52714 bp (untrimmed), 52698 (trimmed). Contig 226. 704 reads; 61077 bp (untrimmed), 60999 (trimmed). Contig 227. 717 reads; 48132 bp (untrimmed), 48132 (trimmed). Contig 228. 828 reads; 68290 bp (untrimmed), 68226 (trimmed). Contig 229. 876 reads; 58771 bp (untrimmed), 58682 (trimmed). Contig 230. 894 reads; 64277 bp (untrimmed), 64200 (trimmed). Contig 231. 899 reads; 55607 bp (untrimmed), 55414 (trimmed). Contig 232. 903 reads; 82051 bp (untrimmed), 81983 (trimmed). Contig 233. 1144 reads; 87893 bp (untrimmed), 87587 (trimmed). Contig 234. 1203 reads; 91434 bp (untrimmed), 91388 (trimmed). Contig 235. 1267 reads; 102240 bp (untrimmed), 102158 (trimmed). Contig 236. 1417 reads; 81600 bp (untrimmed), 81053 (trimmed). Contig 237. 1431 reads; 28535 bp (untrimmed), 28482 (trimmed). Contig 238. 1433 reads; 68427 bp (untrimmed), 68400 (trimmed). Contig 239. 1453 reads; 118284 bp (untrimmed), 117863 (trimmed). Contig 240. 1491 reads; 107961 bp (untrimmed), 107929 (trimmed). Contig 241. 1510 reads; 104915 bp (untrimmed), 104846 (trimmed). Contig 242. 1532 reads; 103928 bp (untrimmed), 103870 (trimmed). Contig 243. 1625 reads; 87530 bp (untrimmed), 87373 (trimmed). Contig 244. 1664 reads; 147907 bp (untrimmed), 147877 (trimmed). Contig 245. 1701 reads; 133530 bp (untrimmed), 133299 (trimmed). Contig 246. 2054 reads; 138772 bp (untrimmed), 138730 (trimmed). Contig 247. 2095 reads; 129274 bp (untrimmed), 128859 (trimmed). Contig 248. 2309 reads; 145004 bp (untrimmed), 144910 (trimmed). Contig 249. 3547 reads; 234066 bp (untrimmed), 233973 (trimmed). Contig 250. 3649 reads; 151914 bp (untrimmed), 151798 (trimmed). -------------------------------------------------------------- Totals 66399 reads; 5084318 bp (untrimmed), 5044127 (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 190 total values totalling 4963890.0000. <26125.736842 +/- 35093.213438> #Range: [ 2012 - 233973 ] #Most likely bin: [ 2000 - 4000 ] 36 counts #Median bin: [ 12000 - 14000 ] 12 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 36 0.19 0.19 ] |XXXXXXXXXXXXXXXXXXXXXXX 4000 - 6000 : [ 21 0.11 0.30 ] |XXXXXXXXXXXXXXXXXX 6000 - 8000 : [ 16 0.08 0.38 ] |XXXXXXXXXXXX 8000 - 10000 : [ 11 0.06 0.44 ] |XXXXXXXXXX 10000 - 12000 : [ 9 0.05 0.49 ] |XXXXXXXXXXXXX 12000 - 14000 : [ 12 0.06 0.55 ] |XXXXXXX 14000 - 16000 : [ 6 0.03 0.58 ] |XXXXXXXX 16000 - 18000 : [ 7 0.04 0.62 ] |X 18000 - 20000 : [ 1 0.01 0.63 ] |XXXXXX 20000 - 22000 : [ 5 0.03 0.65 ] |XXXXXXX 22000 - 24000 : [ 6 0.03 0.68 ] |XXXX 24000 - 26000 : [ 4 0.02 0.71 ] |XXXX 26000 - 28000 : [ 4 0.02 0.73 ] |XX 28000 - 30000 : [ 2 0.01 0.74 ] |XXX 30000 - 32000 : [ 3 0.02 0.75 ] |XXXX 32000 - 34000 : [ 4 0.02 0.77 ] #... |X 36000 - 38000 : [ 1 0.01 0.78 ] |XXXX 38000 - 40000 : [ 4 0.02 0.80 ] |XX 40000 - 42000 : [ 2 0.01 0.81 ] |XXX 42000 - 44000 : [ 3 0.02 0.83 ] |XXX 44000 - 46000 : [ 3 0.02 0.84 ] |X 46000 - 48000 : [ 1 0.01 0.85 ] |X 48000 - 50000 : [ 1 0.01 0.85 ] |X 50000 - 52000 : [ 1 0.01 0.86 ] |X 52000 - 54000 : [ 1 0.01 0.86 ] |XX 54000 - 56000 : [ 2 0.01 0.87 ] |X 56000 - 58000 : [ 1 0.01 0.88 ] |X 58000 - 60000 : [ 1 0.01 0.88 ] |X 60000 - 62000 : [ 1 0.01 0.89 ] |X 62000 - 64000 : [ 1 0.01 0.89 ] |X 64000 - 66000 : [ 1 0.01 0.90 ] #... |XX 68000 - 70000 : [ 2 0.01 0.91 ] #... |XX 80000 - 82000 : [ 2 0.01 0.92 ] #... |XX 86000 - 88000 : [ 2 0.01 0.93 ] #... |X 90000 - 92000 : [ 1 0.01 0.94 ] #... |XX 102000 - 104000 : [ 2 0.01 0.95 ] |X 104000 - 106000 : [ 1 0.01 0.95 ] |X 106000 - 108000 : [ 1 0.01 0.96 ] #... |X 116000 - 118000 : [ 1 0.01 0.96 ] #... |X 128000 - 130000 : [ 1 0.01 0.97 ] #... |X 132000 - 134000 : [ 1 0.01 0.97 ] #... |X 138000 - 140000 : [ 1 0.01 0.98 ] #... |X 144000 - 146000 : [ 1 0.01 0.98 ] |X 146000 - 148000 : [ 1 0.01 0.99 ] #... |X 150000 - 152000 : [ 1 0.01 0.99 ] #... |X 232000 - 234000 : [ 1 0.01 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 16898981 C = 14365865 G = 14433648 T = 16339137 N = 342404 X = 813831 GC fraction = 0.46 Total = 63193866 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 3634605_fasta.screen.contigs A 1363969 C 1180954 G 1170519 N 345 T 1368506 X 25 fraction GC = 0.46 total bases = 5084318 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 5082740 bases = 11.18 +- 9.29 = 0.60 +- 4.47 m1 = 7.71 m2 = 16.56 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 246 total values totalling 1887.9200. <7.674472 +/- 5.124777> #Range: [ 1.16 - 43.21 ] #Most likely bin: [ 3 - 3.5 ] 17 counts #Median bin: [ 7 - 7.5 ] 7 counts |XXXXX 1 - 1.5 : [ 2 0.01 0.01 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 17 0.07 0.08 ] |XXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 10 0.04 0.12 ] |XXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 10 0.04 0.16 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 17 0.07 0.23 ] |XXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 9 0.04 0.26 ] |XXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 10 0.04 0.30 ] |XXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 9 0.04 0.34 ] |XXXXXXXXXXXXXXXX 5 - 5.5 : [ 7 0.03 0.37 ] |XXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 9 0.04 0.41 ] |XXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 9 0.04 0.44 ] |XXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 8 0.03 0.48 ] |XXXXXXXXXXXXXXXX 7 - 7.5 : [ 7 0.03 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 10 0.04 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 13 0.05 0.60 ] |XXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 8 0.03 0.63 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 12 0.05 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 10 0.04 0.72 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 12 0.05 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 15 0.06 0.83 ] |XXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 9 0.04 0.87 ] |XXXXXXXXX 11.5 - 12 : [ 4 0.02 0.88 ] |XXXXXXXXX 12 - 12.5 : [ 4 0.02 0.90 ] |XXXXXXXXXXXXXXXX 12.5 - 13 : [ 7 0.03 0.93 ] |XXXXXXX 13 - 13.5 : [ 3 0.01 0.94 ] |XXXXXXXXX 13.5 - 14 : [ 4 0.02 0.96 ] #... |XX 14.5 - 15 : [ 1 0.00 0.96 ] #... |XX 15.5 - 16 : [ 1 0.00 0.96 ] |XX 16 - 16.5 : [ 1 0.00 0.97 ] #... |XX 17.5 - 18 : [ 1 0.00 0.97 ] #... |XX 19 - 19.5 : [ 1 0.00 0.98 ] #... |XX 20.5 - 21 : [ 1 0.00 0.98 ] #... |XX 21.5 - 22 : [ 1 0.00 0.98 ] |XXXXX 22 - 22.5 : [ 2 0.01 0.99 ] #... |XX 39 - 39.5 : [ 1 0.00 1.00 ] #... |XX 43 - 43.5 : [ 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 190 total values totalling 1698.2600. <8.938211 +/- 4.885462> #Range: [ 2.85 - 43.21 ] #Most likely bin: [ 10.5 - 11 ] 15 counts #Median bin: [ 8.5 - 9 ] 8 counts |XXXXXXXX 2.5 - 3 : [ 3 0.02 0.02 ] |XXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 8 0.04 0.06 ] |XXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 7 0.04 0.09 ] |XXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 8 0.04 0.14 ] |XXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 9 0.05 0.18 ] |XXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 7 0.04 0.22 ] |XXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 9 0.05 0.27 ] |XXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 8 0.04 0.31 ] |XXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 7 0.04 0.35 ] |XXXXXXXXXXXXXXXX 7 - 7.5 : [ 6 0.03 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 9 0.05 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 12 0.06 0.49 ] |XXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 8 0.04 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 12 0.06 0.59 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 10 0.05 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 12 0.06 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 15 0.08 0.79 ] |XXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 9 0.05 0.84 ] |XXXXXXXXXXX 11.5 - 12 : [ 4 0.02 0.86 ] |XXXXXXXX 12 - 12.5 : [ 3 0.02 0.87 ] |XXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 7 0.04 0.91 ] |XXXXXXXX 13 - 13.5 : [ 3 0.02 0.93 ] |XXXXXXXXXXX 13.5 - 14 : [ 4 0.02 0.95 ] #... |XXX 14.5 - 15 : [ 1 0.01 0.95 ] #... |XXX 15.5 - 16 : [ 1 0.01 0.96 ] |XXX 16 - 16.5 : [ 1 0.01 0.96 ] #... |XXX 17.5 - 18 : [ 1 0.01 0.97 ] #... |XXX 19 - 19.5 : [ 1 0.01 0.97 ] #... |XXX 20.5 - 21 : [ 1 0.01 0.98 ] #... |XXX 21.5 - 22 : [ 1 0.01 0.98 ] |XXX 22 - 22.5 : [ 1 0.01 0.99 ] #... |XXX 39 - 39.5 : [ 1 0.01 0.99 ] #... |XXX 43 - 43.5 : [ 1 0.01 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 3 2 reads 1670 bases = 1.16 +- 0.36 = -0.03 +- 0.92 m1 = 0.11 m2 = -0.18 Contig 2 2 reads 1423 bases = 1.27 +- 0.45 = 1.27 +- 0.45 m1 = 0.16 m2 = 0.00 Contig 31 5 reads 2533 bases = 1.55 +- 0.55 = 0.68 +- 1.43 m1 = 0.20 m2 = -0.44 Contig 20 4 reads 2097 bases = 1.61 +- 0.75 = 0.97 +- 1.44 m1 = 0.35 m2 = -0.38 Contig 22 4 reads 2265 bases = 1.64 +- 0.78 = 0.02 +- 0.86 m1 = 0.37 m2 = -0.03 Contig 38 6 reads 2110 bases = 1.64 +- 0.66 = 0.61 +- 0.56 m1 = 0.26 m2 = 0.03 Contig 6 3 reads 1305 bases = 1.64 +- 0.84 = 0.84 +- 0.42 m1 = 0.43 m2 = 0.13 Contig 10 3 reads 1452 bases = 1.67 +- 0.86 = 1.67 +- 0.86 m1 = 0.44 m2 = 0.00 Contig 15 3 reads 1314 bases = 1.68 +- 0.60 = 1.68 +- 0.60 m1 = 0.21 m2 = 0.00 Contig 29 5 reads 2369 bases = 1.73 +- 0.75 = 0.45 +- 1.75 m1 = 0.33 m2 = -0.63 Contig 13 3 reads 1538 bases = 1.76 +- 0.77 = 0.51 +- 1.16 m1 = 0.34 m2 = -0.19 Contig 19 4 reads 2046 bases = 1.76 +- 0.76 = 0.89 +- 0.59 m1 = 0.33 m2 = 0.06 Contig 24 4 reads 1742 bases = 1.78 +- 0.41 = 0.87 +- 1.04 m1 = 0.10 m2 = -0.23 Contig 18 4 reads 2113 bases = 1.83 +- 0.87 = 1.83 +- 0.87 m1 = 0.41 m2 = 0.00 Contig 17 3 reads 1124 bases = 1.90 +- 0.63 = 1.90 +- 0.63 m1 = 0.21 m2 = 0.00 Contig 16 3 reads 1127 bases = 1.92 +- 0.87 = 0.28 +- 1.04 m1 = 0.40 m2 = -0.08 Contig 26 4 reads 1696 bases = 1.97 +- 0.89 = 0.93 +- 0.45 m1 = 0.40 m2 = 0.15 Contig 27 4 reads 1611 bases = 1.97 +- 0.97 = 0.78 +- 0.79 m1 = 0.48 m2 = 0.08 Contig 11 3 reads 1096 bases = 1.98 +- 0.67 = 1.09 +- 0.73 m1 = 0.23 m2 = -0.02 Contig 8 3 reads 1188 bases = 2.12 +- 0.87 = 2.12 +- 0.87 m1 = 0.36 m2 = 0.00 Contig 229 876 reads 58771 bases = 12.95 +- 3.93 = 1.01 +- 4.35 m1 = 1.19 m2 = -0.87 Contig 249 3547 reads 234066 bases = 12.99 +- 14.88 = 0.31 +- 4.23 m1 = 17.06 m2 = 50.91 Contig 206 443 reads 29140 bases = 13.01 +- 3.81 = 0.22 +- 3.97 m1 = 1.12 m2 = -0.31 Contig 216 584 reads 38672 bases = 13.09 +- 4.90 = -0.00 +- 4.78 m1 = 1.84 m2 = 0.30 Contig 220 600 reads 38880 bases = 13.32 +- 3.91 = -0.02 +- 3.68 m1 = 1.15 m2 = 0.44 Contig 189 266 reads 16942 bases = 13.52 +- 4.24 = 0.66 +- 3.92 m1 = 1.33 m2 = 0.66 Contig 248 2309 reads 145004 bases = 13.65 +- 8.18 = 0.55 +- 6.23 m1 = 4.91 m2 = 7.03 Contig 231 899 reads 55607 bases = 13.93 +- 4.24 = 0.28 +- 4.31 m1 = 1.29 m2 = -0.14 Contig 247 2095 reads 129274 bases = 13.97 +- 5.06 = 0.24 +- 4.53 m1 = 1.83 m2 = 1.28 Contig 236 1417 reads 81600 bases = 14.74 +- 20.87 = 0.55 +- 4.50 m1 = 29.56 m2 = 103.88 Contig 243 1625 reads 87530 bases = 15.90 +- 13.77 = 0.42 +- 4.29 m1 = 11.92 m2 = 42.78 Contig 217 588 reads 30710 bases = 16.38 +- 7.48 = 0.14 +- 6.34 m1 = 3.42 m2 = 3.93 Contig 238 1433 reads 68427 bases = 17.99 +- 9.95 = 0.51 +- 5.50 m1 = 5.50 m2 = 17.17 Contig 181 199 reads 8779 bases = 19.00 +- 28.16 = 0.15 +- 3.50 m1 = 41.73 m2 = 195.18 Contig 250 3649 reads 151914 bases = 20.70 +- 25.94 = 0.13 +- 5.16 m1 = 32.51 m2 = 161.57 Contig 135 77 reads 3125 bases = 21.78 +- 18.27 = 20.69 +- 17.99 m1 = 15.33 m2 = 2.52 Contig 146 103 reads 3812 bases = 22.35 +- 17.75 = 5.94 +- 5.94 m1 = 14.10 m2 = 69.95 Contig 120 47 reads 1212 bases = 22.36 +- 20.64 = 22.36 +- 20.64 m1 = 19.06 m2 = 0.00 Contig 200 371 reads 8187 bases = 39.23 +- 15.54 = 3.30 +- 7.03 m1 = 6.16 m2 = 48.05 Contig 237 1431 reads 28535 bases = 43.21 +- 22.95 = 3.83 +- 6.19 m1 = 12.19 m2 = 122.14 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 250 total values totalling 66399.0000. <265.596000 +/- 509.636624> #Range: [ 1 - 3649 ] #Most likely bin: [ 3 - 4 ] 14 counts #Median bin: [ 55 - 56 ] 1 counts |XXX 1 - 2 : [ 1 0.00 0.00 ] |XXXXXX 2 - 3 : [ 2 0.01 0.01 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 4 : [ 14 0.06 0.07 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 5 : [ 10 0.04 0.11 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 6 : [ 10 0.04 0.15 ] |XXXXXXXXXXXXXXXXX 6 - 7 : [ 6 0.02 0.17 ] |XXXXXXXXXXXXXX 7 - 8 : [ 5 0.02 0.19 ] |XXXXXXXXX 8 - 9 : [ 3 0.01 0.20 ] |XXXXXX 9 - 10 : [ 2 0.01 0.21 ] |XXXXXX 10 - 11 : [ 2 0.01 0.22 ] |XXXXXXXXXXX 11 - 12 : [ 4 0.02 0.24 ] |XXXXXXXXXXX 12 - 13 : [ 4 0.02 0.25 ] |XXXXXXXXX 13 - 14 : [ 3 0.01 0.26 ] #... |XXXXXXXXXXX 15 - 16 : [ 4 0.02 0.28 ] |XXX 16 - 17 : [ 1 0.00 0.28 ] |XXXXXXXXXXX 17 - 18 : [ 4 0.02 0.30 ] |XXXXXXXXXXX 18 - 19 : [ 4 0.02 0.32 ] #... |XXX 20 - 21 : [ 1 0.00 0.32 ] |XXXXXX 21 - 22 : [ 2 0.01 0.33 ] |XXXXXX 22 - 23 : [ 2 0.01 0.34 ] |XXXXXX 23 - 24 : [ 2 0.01 0.34 ] |XXX 24 - 25 : [ 1 0.00 0.35 ] |XXXXXX 25 - 26 : [ 2 0.01 0.36 ] #... |XXX 27 - 28 : [ 1 0.00 0.36 ] |XXX 28 - 29 : [ 1 0.00 0.36 ] |XXX 29 - 30 : [ 1 0.00 0.37 ] |XXXXXXXXX 30 - 31 : [ 3 0.01 0.38 ] |XXXXXX 31 - 32 : [ 2 0.01 0.39 ] |XXX 32 - 33 : [ 1 0.00 0.39 ] |XXX 33 - 34 : [ 1 0.00 0.40 ] |XXXXXX 34 - 35 : [ 2 0.01 0.40 ] |XXX 35 - 36 : [ 1 0.00 0.41 ] |XXX 36 - 37 : [ 1 0.00 0.41 ] |XXX 37 - 38 : [ 1 0.00 0.42 ] #... |XXXXXXXXX 39 - 40 : [ 3 0.01 0.43 ] |XXXXXXXXX 40 - 41 : [ 3 0.01 0.44 ] |XXXXXX 41 - 42 : [ 2 0.01 0.45 ] |XXX 42 - 43 : [ 1 0.00 0.45 ] |XXX 43 - 44 : [ 1 0.00 0.46 ] #... |XXXXXX 45 - 46 : [ 2 0.01 0.46 ] |XXXXXX 46 - 47 : [ 2 0.01 0.47 ] |XXXXXX 47 - 48 : [ 2 0.01 0.48 ] #... |XXX 51 - 52 : [ 1 0.00 0.48 ] |XXXXXX 52 - 53 : [ 2 0.01 0.49 ] #... |XXX 54 - 55 : [ 1 0.00 0.50 ] |XXX 55 - 56 : [ 1 0.00 0.50 ] |XXX 56 - 57 : [ 1 0.00 0.50 ] |XXX 57 - 58 : [ 1 0.00 0.51 ] |XXX 58 - 59 : [ 1 0.00 0.51 ] #... |XXX 61 - 62 : [ 1 0.00 0.52 ] |XXX 62 - 63 : [ 1 0.00 0.52 ] #... |XXX 68 - 69 : [ 1 0.00 0.52 ] |XXX 69 - 70 : [ 1 0.00 0.53 ] #... |XXX 72 - 73 : [ 1 0.00 0.53 ] #... |XXX 76 - 77 : [ 1 0.00 0.54 ] |XXXXXX 77 - 78 : [ 2 0.01 0.54 ] |XXXXXX 78 - 79 : [ 2 0.01 0.55 ] #... |XXX 84 - 85 : [ 1 0.00 0.56 ] #... |XXXXXX 88 - 89 : [ 2 0.01 0.56 ] |XXX 89 - 90 : [ 1 0.00 0.57 ] #... |XXX 95 - 96 : [ 1 0.00 0.57 ] #... |XXXXXX 100 - 101 : [ 2 0.01 0.58 ] #... |XXX 103 - 104 : [ 1 0.00 0.58 ] #... |XXX 106 - 107 : [ 1 0.00 0.59 ] |XXX 107 - 108 : [ 1 0.00 0.59 ] #... |XXX 110 - 111 : [ 1 0.00 0.60 ] |XXX 111 - 112 : [ 1 0.00 0.60 ] |XXX 112 - 113 : [ 1 0.00 0.60 ] #... |XXX 114 - 115 : [ 1 0.00 0.61 ] #... |XXX 118 - 119 : [ 1 0.00 0.61 ] |XXX 119 - 120 : [ 1 0.00 0.62 ] #... |XXX 122 - 123 : [ 1 0.00 0.62 ] #... |XXX 126 - 127 : [ 1 0.00 0.62 ] |XXX 127 - 128 : [ 1 0.00 0.63 ] #... |XXX 130 - 131 : [ 1 0.00 0.63 ] #... |XXX 140 - 141 : [ 1 0.00 0.64 ] #... |XXX 144 - 145 : [ 1 0.00 0.64 ] |XXXXXX 145 - 146 : [ 2 0.01 0.65 ] #... |XXX 147 - 148 : [ 1 0.00 0.65 ] |XXX 148 - 149 : [ 1 0.00 0.66 ] |XXX 149 - 150 : [ 1 0.00 0.66 ] #... |XXXXXX 156 - 157 : [ 2 0.01 0.67 ] #... |XXXXXX 158 - 159 : [ 2 0.01 0.68 ] #... |XXX 160 - 161 : [ 1 0.00 0.68 ] #... |XXX 166 - 167 : [ 1 0.00 0.68 ] #... |XXX 168 - 169 : [ 1 0.00 0.69 ] |XXX 169 - 170 : [ 1 0.00 0.69 ] #... |XXX 173 - 174 : [ 1 0.00 0.70 ] #... |XXX 181 - 182 : [ 1 0.00 0.70 ] #... |XXX 184 - 185 : [ 1 0.00 0.70 ] |XXX 185 - 186 : [ 1 0.00 0.71 ] #... |XXX 191 - 192 : [ 1 0.00 0.71 ] #... |XXX 193 - 194 : [ 1 0.00 0.72 ] #... |XXX 197 - 198 : [ 1 0.00 0.72 ] #... |XXX 199 - 200 : [ 1 0.00 0.72 ] #... |XXX 211 - 212 : [ 1 0.00 0.73 ] #... |XXX 216 - 217 : [ 1 0.00 0.73 ] #... |XXX 232 - 233 : [ 1 0.00 0.74 ] #... |XXX 244 - 245 : [ 1 0.00 0.74 ] #... |XXX 247 - 248 : [ 1 0.00 0.74 ] #... |XXX 260 - 261 : [ 1 0.00 0.75 ] #... |XXX 263 - 264 : [ 1 0.00 0.75 ] #... |XXX 266 - 267 : [ 1 0.00 0.76 ] #... |XXX 272 - 273 : [ 1 0.00 0.76 ] #... |XXXXXX 283 - 284 : [ 2 0.01 0.77 ] #... |XXX 287 - 288 : [ 1 0.00 0.77 ] #... |XXX 312 - 313 : [ 1 0.00 0.78 ] #... |XXX 318 - 319 : [ 1 0.00 0.78 ] #... |XXX 325 - 326 : [ 1 0.00 0.78 ] #... |XXX 333 - 334 : [ 1 0.00 0.79 ] #... |XXX 342 - 343 : [ 1 0.00 0.79 ] #... |XXX 348 - 349 : [ 1 0.00 0.80 ] #... |XXX 371 - 372 : [ 1 0.00 0.80 ] #... |XXX 406 - 407 : [ 1 0.00 0.80 ] |XXX 407 - 408 : [ 1 0.00 0.81 ] #... |XXX 425 - 426 : [ 1 0.00 0.81 ] #... |XXX 430 - 431 : [ 1 0.00 0.82 ] #... |XXX 439 - 440 : [ 1 0.00 0.82 ] #... |XXX 443 - 444 : [ 1 0.00 0.82 ] |XXX 444 - 445 : [ 1 0.00 0.83 ] #... |XXX 466 - 467 : [ 1 0.00 0.83 ] #... |XXX 472 - 473 : [ 1 0.00 0.84 ] #... |XXX 516 - 517 : [ 1 0.00 0.84 ] #... |XXX 530 - 531 : [ 1 0.00 0.84 ] #... |XXX 533 - 534 : [ 1 0.00 0.85 ] #... |XXX 553 - 554 : [ 1 0.00 0.85 ] #... |XXX 567 - 568 : [ 1 0.00 0.86 ] #... |XXX 573 - 574 : [ 1 0.00 0.86 ] #... |XXX 584 - 585 : [ 1 0.00 0.86 ] #... |XXX 588 - 589 : [ 1 0.00 0.87 ] #... |XXX 597 - 598 : [ 1 0.00 0.87 ] #... |XXXXXX 600 - 601 : [ 2 0.01 0.88 ] #... |XXX 613 - 614 : [ 1 0.00 0.88 ] #... |XXX 675 - 676 : [ 1 0.00 0.89 ] #... |XXX 677 - 678 : [ 1 0.00 0.89 ] #... |XXX 684 - 685 : [ 1 0.00 0.90 ] #... |XXXXXX 704 - 705 : [ 2 0.01 0.90 ] #... |XXX 717 - 718 : [ 1 0.00 0.91 ] #... |XXX 828 - 829 : [ 1 0.00 0.91 ] #... |XXX 876 - 877 : [ 1 0.00 0.92 ] #... |XXX 894 - 895 : [ 1 0.00 0.92 ] #... |XXX 899 - 900 : [ 1 0.00 0.92 ] #... |XXX 903 - 904 : [ 1 0.00 0.93 ] #... |XXX 1144 - 1145 : [ 1 0.00 0.93 ] #... |XXX 1203 - 1204 : [ 1 0.00 0.94 ] #... |XXX 1267 - 1268 : [ 1 0.00 0.94 ] #... |XXX 1417 - 1418 : [ 1 0.00 0.94 ] #... |XXX 1431 - 1432 : [ 1 0.00 0.95 ] #... |XXX 1433 - 1434 : [ 1 0.00 0.95 ] #... |XXX 1453 - 1454 : [ 1 0.00 0.96 ] #... |XXX 1491 - 1492 : [ 1 0.00 0.96 ] #... |XXX 1510 - 1511 : [ 1 0.00 0.96 ] #... |XXX 1532 - 1533 : [ 1 0.00 0.97 ] #... |XXX 1625 - 1626 : [ 1 0.00 0.97 ] #... |XXX 1664 - 1665 : [ 1 0.00 0.98 ] #... |XXX 1701 - 1702 : [ 1 0.00 0.98 ] #... |XXX 2054 - 2055 : [ 1 0.00 0.98 ] #... |XXX 2095 - 2096 : [ 1 0.00 0.99 ] #... |XXX 2309 - 2310 : [ 1 0.00 0.99 ] #... |XXX 3547 - 3548 : [ 1 0.00 1.00 ] #... |XXX 3649 - 3650 : [ 1 0.00 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 250 total values totalling 5084318.0000. <20337.272000 +/- 32364.457507> #Range: [ 231 - 234066 ] #Most likely bin: [ 1000 - 2000 ] 45 counts #Median bin: [ 6000 - 7000 ] 10 counts |XXXXXX 0 - 1000 : [ 7 0.03 0.03 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 45 0.18 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXX 2000 - 3000 : [ 26 0.10 0.31 ] |XXXXXXXXXXXXXXX 3000 - 4000 : [ 17 0.07 0.38 ] |XXXXXXX 4000 - 5000 : [ 8 0.03 0.41 ] |XXXXXXXXXXXX 5000 - 6000 : [ 13 0.05 0.46 ] |XXXXXXXXX 6000 - 7000 : [ 10 0.04 0.50 ] |XXXX 7000 - 8000 : [ 4 0.02 0.52 ] |XXXXXX 8000 - 9000 : [ 7 0.03 0.55 ] |XXXXXX 9000 - 10000 : [ 7 0.03 0.58 ] |XXXX 10000 - 11000 : [ 4 0.02 0.59 ] |XXXX 11000 - 12000 : [ 5 0.02 0.61 ] |XXXXXX 12000 - 13000 : [ 7 0.03 0.64 ] |XXXX 13000 - 14000 : [ 4 0.02 0.66 ] |XXX 14000 - 15000 : [ 3 0.01 0.67 ] |XXX 15000 - 16000 : [ 3 0.01 0.68 ] |XXXX 16000 - 17000 : [ 5 0.02 0.70 ] |XXX 17000 - 18000 : [ 3 0.01 0.71 ] |X 18000 - 19000 : [ 1 0.00 0.72 ] #... |XX 20000 - 21000 : [ 2 0.01 0.72 ] |XXX 21000 - 22000 : [ 3 0.01 0.74 ] |XXX 22000 - 23000 : [ 3 0.01 0.75 ] |XXX 23000 - 24000 : [ 3 0.01 0.76 ] |X 24000 - 25000 : [ 1 0.00 0.76 ] |XXX 25000 - 26000 : [ 3 0.01 0.78 ] |XX 26000 - 27000 : [ 2 0.01 0.78 ] |XX 27000 - 28000 : [ 2 0.01 0.79 ] |X 28000 - 29000 : [ 1 0.00 0.80 ] |X 29000 - 30000 : [ 1 0.00 0.80 ] |X 30000 - 31000 : [ 1 0.00 0.80 ] |XX 31000 - 32000 : [ 2 0.01 0.81 ] |X 32000 - 33000 : [ 1 0.00 0.82 ] |X 33000 - 34000 : [ 1 0.00 0.82 ] |XX 34000 - 35000 : [ 2 0.01 0.83 ] #... |X 36000 - 37000 : [ 1 0.00 0.83 ] #... |XXX 38000 - 39000 : [ 3 0.01 0.84 ] |X 39000 - 40000 : [ 1 0.00 0.85 ] |X 40000 - 41000 : [ 1 0.00 0.85 ] |X 41000 - 42000 : [ 1 0.00 0.86 ] |XX 42000 - 43000 : [ 2 0.01 0.86 ] |X 43000 - 44000 : [ 1 0.00 0.87 ] |XXX 44000 - 45000 : [ 3 0.01 0.88 ] #... |X 46000 - 47000 : [ 1 0.00 0.88 ] #... |X 48000 - 49000 : [ 1 0.00 0.89 ] #... |X 51000 - 52000 : [ 1 0.00 0.89 ] |X 52000 - 53000 : [ 1 0.00 0.90 ] #... |XX 55000 - 56000 : [ 2 0.01 0.90 ] #... |X 57000 - 58000 : [ 1 0.00 0.91 ] |X 58000 - 59000 : [ 1 0.00 0.91 ] #... |X 61000 - 62000 : [ 1 0.00 0.92 ] |X 62000 - 63000 : [ 1 0.00 0.92 ] #... |X 64000 - 65000 : [ 1 0.00 0.92 ] #... |XX 68000 - 69000 : [ 2 0.01 0.93 ] #... |X 81000 - 82000 : [ 1 0.00 0.94 ] |X 82000 - 83000 : [ 1 0.00 0.94 ] #... |XX 87000 - 88000 : [ 2 0.01 0.95 ] #... |X 91000 - 92000 : [ 1 0.00 0.95 ] #... |X 102000 - 103000 : [ 1 0.00 0.96 ] |X 103000 - 104000 : [ 1 0.00 0.96 ] |X 104000 - 105000 : [ 1 0.00 0.96 ] #... |X 107000 - 108000 : [ 1 0.00 0.97 ] #... |X 118000 - 119000 : [ 1 0.00 0.97 ] #... |X 129000 - 130000 : [ 1 0.00 0.98 ] #... |X 133000 - 134000 : [ 1 0.00 0.98 ] #... |X 138000 - 139000 : [ 1 0.00 0.98 ] #... |X 145000 - 146000 : [ 1 0.00 0.99 ] #... |X 147000 - 148000 : [ 1 0.00 0.99 ] #... |X 151000 - 152000 : [ 1 0.00 1.00 ] #... |X 234000 - 235000 : [ 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 AIOC reads.list > grep.reads.list.AIOC Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOC 4 500 #Found 11595 total values totalling 38876437.0000. <3352.862182 +/- 877.252872> #Range: [ - 51509 ] #Most likely bin: [ 3000 - 3500 ] 5471 counts #Median bin: [ 3000 - 3500 ] 5471 counts | 0 - 500 : [ 2 0.00 0.00 ] | 500 - 1000 : [ 14 0.00 0.00 ] | 1000 - 1500 : [ 54 0.00 0.01 ] |X 1500 - 2000 : [ 77 0.01 0.01 ] |XX 2000 - 2500 : [ 286 0.02 0.04 ] |XXXXXXXXXXX 2500 - 3000 : [ 1555 0.13 0.17 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 5471 0.47 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3583 0.31 0.95 ] |XXXX 4000 - 4500 : [ 536 0.05 1.00 ] | 4500 - 5000 : [ 6 0.00 1.00 ] #... | 8000 - 8500 : [ 1 0.00 1.00 ] #... | 15500 - 16000 : [ 1 0.00 1.00 ] #... | 19000 - 19500 : [ 2 0.00 1.00 ] #... | 21500 - 22000 : [ 1 0.00 1.00 ] | 22000 - 22500 : [ 2 0.00 1.00 ] #... | 24000 - 24500 : [ 1 0.00 1.00 ] #... | 33000 - 33500 : [ 1 0.00 1.00 ] #... | 38000 - 38500 : [ 1 0.00 1.00 ] #... | 51500 - 52000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AIOF reads.list > grep.reads.list.AIOF Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOF 4 500 #Found 11561 total values totalling 84016682.0000. <7267.250411 +/- 1807.859991> #Range: [ - 101692 ] #Most likely bin: [ 7000 - 7500 ] 3098 counts #Median bin: [ 7000 - 7500 ] 3098 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 1 0.00 0.00 ] | 1000 - 1500 : [ 14 0.00 0.00 ] | 1500 - 2000 : [ 20 0.00 0.00 ] | 2000 - 2500 : [ 20 0.00 0.00 ] | 2500 - 3000 : [ 20 0.00 0.01 ] | 3000 - 3500 : [ 23 0.00 0.01 ] | 3500 - 4000 : [ 22 0.00 0.01 ] | 4000 - 4500 : [ 12 0.00 0.01 ] | 4500 - 5000 : [ 16 0.00 0.01 ] |X 5000 - 5500 : [ 54 0.00 0.02 ] |XXXX 5500 - 6000 : [ 297 0.03 0.04 ] |XXXXXXXXXXX 6000 - 6500 : [ 852 0.07 0.12 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2766 0.24 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 3098 0.27 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 2535 0.22 0.84 ] |XXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1523 0.13 0.98 ] |XXXX 8500 - 9000 : [ 278 0.02 1.00 ] #... | 10500 - 11000 : [ 1 0.00 1.00 ] #... | 14500 - 15000 : [ 1 0.00 1.00 ] #... | 23500 - 24000 : [ 1 0.00 1.00 ] #... | 32500 - 33000 : [ 1 0.00 1.00 ] #... | 41500 - 42000 : [ 1 0.00 1.00 ] | 42000 - 42500 : [ 1 0.00 1.00 ] #... | 100500 - 101000 : [ 1 0.00 1.00 ] #... | 101500 - 102000 : [ 2 0.00 1.00 ] Command: /usr/xpg4/bin/grep AIOG reads.list > grep.reads.list.AIOG Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOG 4 500 #Found 353 total values totalling 13225959.0000. <37467.305949 +/- 6772.071117> #Range: [ - 136032 ] #Most likely bin: [ 36500 - 37000 ] 21 counts #Median bin: [ 37000 - 37500 ] 17 counts |XX 0 - 500 : [ 1 0.00 0.00 ] #... |XX 19500 - 20000 : [ 1 0.00 0.01 ] #... |XX 26500 - 27000 : [ 1 0.00 0.01 ] |XX 27000 - 27500 : [ 1 0.00 0.01 ] #... |XX 28500 - 29000 : [ 1 0.00 0.01 ] |XX 29000 - 29500 : [ 1 0.00 0.02 ] |XXXX 29500 - 30000 : [ 2 0.01 0.02 ] |XXXX 30000 - 30500 : [ 2 0.01 0.03 ] |XXXXXXXXXX 30500 - 31000 : [ 5 0.01 0.04 ] |XXXX 31000 - 31500 : [ 2 0.01 0.05 ] |XXXXXXXXXXXXX 31500 - 32000 : [ 7 0.02 0.07 ] |XXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 11 0.03 0.10 ] |XXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 10 0.03 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 12 0.03 0.16 ] |XXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 10 0.03 0.19 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 19 0.05 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 16 0.05 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 14 0.04 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 17 0.05 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 17 0.05 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 21 0.06 0.48 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 17 0.05 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 19 0.05 0.59 ] |XXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 12 0.03 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 17 0.05 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 15 0.04 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 12 0.03 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 19 0.05 0.80 ] |XXXXXXXXXXX 40500 - 41000 : [ 6 0.02 0.82 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 14 0.04 0.86 ] |XXXXXXXXXXXXXXXXX 41500 - 42000 : [ 9 0.03 0.88 ] |XXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 12 0.03 0.92 ] |XXXXXXXX 42500 - 43000 : [ 4 0.01 0.93 ] |XXXXXXXXXXX 43000 - 43500 : [ 6 0.02 0.94 ] |XXXXXXXXXXXXX 43500 - 44000 : [ 7 0.02 0.96 ] |XXXXXXXX 44000 - 44500 : [ 4 0.01 0.97 ] |XXXXXXXXXX 44500 - 45000 : [ 5 0.01 0.99 ] |XX 45000 - 45500 : [ 1 0.00 0.99 ] #... |XX 46000 - 46500 : [ 1 0.00 0.99 ] |XX 46500 - 47000 : [ 1 0.00 1.00 ] #... |XX 136000 - 136500 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # AIOG 37463 +- 3750 (n=173) # AIOF 7170 +- 888 (n=5818) # AIOC 3157 +- 927 (n=5972) ################################################################### 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 636.385968 bp, 66399 reads, genome size 3255300 bp Command: idealAssembly 3255300 66399 636.385968 ------------------------------------------------------------------- Genome = 3255300 bases Nreads = 66399 readLength = 636.385968 Depth = 12.98 N_contigs = N_gaps = 0 mean gap size = 48 bases mean contig size = 433866 reads (~ 21270859 bases) %cover = 100.00 %singlet = 0.00 assembly size = 3255292 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 0 contigs containing at least 728027 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: 3634605 Command line options used were: -c -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 12397 Number of reads with percent X's >= 20%: 662 = 1.0% Number of reads with percent X's >= 50%: 453 = 0.7% Number of reads with percent X's >= 80%: 21 = 0.0% Total nr of reads in project is: 66447 Total nr of X's: 813831 Total nr not found in screened files: 0 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with L09136-pUC18 11585 560 416 19 Nr with pCC1Fos 654 49 7 0 Nr with pMCL200 158 53 30 2 ################################################################### Contam Summary with *.singlets: Command: contam_summary -c -s -g ------------------------------------------------------------------- Contamination Summary for JGI id: 3634605 Command line options used were: -c -g -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 15 Number of reads with percent X's >= 20%: 3 = 6.2% Number of reads with percent X's >= 50%: 2 = 4.2% Number of reads with percent X's >= 80%: 0 = 0.0% Total nr of reads in project is: 48 Total nr of X's: 1889 Total nr not found in screened files: 0 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with L09136-pUC18 8 2 1 0 Nr with pCC1Fos 6 0 0 0 Nr with pMCL200 1 1 1 0 ################################################################### Bad M1 Contigs ------------------------------------------------------------------- ################################################################### Bad M2 Contigs ------------------------------------------------------------------- ################################################################### Ran Plates2contigs: Output Location: Ran in.dir: Output Location: Viewed Contigs with Phrapview: ################################################################### Conclusions: