################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 3634476 Genus_species: Pelodictyon luteolum DSMZ 273(T) Taxid: 1100 Genome size: 3000 Libraries: AHYH, AHYG, AHYF ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 3634476 ------------------------------------------------------------------- ID=3634476 ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 2348335 # phrap: 2243885 # db: 3000000 2530740 +/- 334545 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length AHYF.5-44 100 97.62 729.64 AHYG.5-108 136 95.03 657.24 AHYH.5-19 32 90.20 504.69 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s AHYH 24 12 89.06 483.00 12 89.58 492.83 AHYG 136 68 95.28 653.50 68 94.77 660.99 AHYF 100 50 97.84 731.40 50 97.41 727.88 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634476_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 3634476_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634476.out /home/copeland/scripts/librariesInfoTxt.sh 3634476 phrap.out > librariesInfo.txt ################################################################### Library vector screening AHYF.000001.000100 screen.out.1 3634476_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634476_fasta.screen /usr/local/sequences/LRS.fasta AHYG.000001.000100 screen.out.1 3634476_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634476_fasta.screen /usr/local/sequences/LRS.fasta AHYG.000101.000200 screen.out.1 3634476_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634476_fasta.screen /usr/local/sequences/LRS.fasta AHYH.000001.000100 screen.out.1 3634476_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634476_fasta.screen /usr/local/sequences/LRS.fasta AHYF.000001.000100 screen.out.1 3634476_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634476_fasta.screen /usr/local/sequences/LRS.fasta AHYG.000001.000100 screen.out.1 3634476_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634476_fasta.screen /usr/local/sequences/LRS.fasta AHYG.000101.000200 screen.out.1 3634476_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634476_fasta.screen /usr/local/sequences/LRS.fasta AHYH.000001.000100 screen.out.1 3634476_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634476_fasta.screen /usr/local/sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 3634476_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 34097 total values totalling 22039412.0000. <646.373933 +/- 175.859856> #Range: [ 22 - 933 ] #Most likely bin: [ 750 - 800 ] 6521 counts #Median bin: [ 700 - 750 ] 6037 counts |X 0 - 50 : [ 84 0.00 0.00 ] |XX 50 - 100 : [ 307 0.01 0.01 ] |XXX 100 - 150 : [ 439 0.01 0.02 ] |XXX 150 - 200 : [ 423 0.01 0.04 ] |XXX 200 - 250 : [ 486 0.01 0.05 ] |XXXX 250 - 300 : [ 611 0.02 0.07 ] |XXXX 300 - 350 : [ 697 0.02 0.09 ] |XXXXX 350 - 400 : [ 734 0.02 0.11 ] |XXXXXX 400 - 450 : [ 900 0.03 0.14 ] |XXXXXX 450 - 500 : [ 1028 0.03 0.17 ] |XXXXXXXXX 500 - 550 : [ 1467 0.04 0.21 ] |XXXXXXXXXXXXX 550 - 600 : [ 2116 0.06 0.27 ] |XXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3099 0.09 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4585 0.13 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6037 0.18 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6521 0.19 0.87 ] |XXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3837 0.11 0.98 ] |XXXX 850 - 900 : [ 704 0.02 1.00 ] | 900 - 950 : [ 22 0.00 1.00 ] JAZZ trim 15 readlength histogram for AHYF Command: /usr/xpg4/bin/grep AHYF 3634476_fasta.screen.screen.ids > reads.trim15.AHYF.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYF.rl 2 50 #Found 14540 total values totalling 9834787.0000. <676.395254 +/- 167.348777> #Range: [ 22 - 933 ] #Most likely bin: [ 750 - 800 ] 2867 counts #Median bin: [ 700 - 750 ] 2562 counts | 0 - 50 : [ 18 0.00 0.00 ] |X 50 - 100 : [ 94 0.01 0.01 ] |XX 100 - 150 : [ 158 0.01 0.02 ] |XX 150 - 200 : [ 156 0.01 0.03 ] |XXX 200 - 250 : [ 184 0.01 0.04 ] |XX 250 - 300 : [ 162 0.01 0.05 ] |XXX 300 - 350 : [ 212 0.01 0.07 ] |XXXX 350 - 400 : [ 253 0.02 0.09 ] |XXXX 400 - 450 : [ 305 0.02 0.11 ] |XXXXX 450 - 500 : [ 372 0.03 0.13 ] |XXXXXXX 500 - 550 : [ 476 0.03 0.16 ] |XXXXXXXXX 550 - 600 : [ 679 0.05 0.21 ] |XXXXXXXXXXXXXXXX 600 - 650 : [ 1137 0.08 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1860 0.13 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2562 0.18 0.59 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2867 0.20 0.79 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2393 0.16 0.96 ] |XXXXXXXXX 850 - 900 : [ 630 0.04 1.00 ] | 900 - 950 : [ 22 0.00 1.00 ] JAZZ trim 15 readlength histogram for AHYG Command: /usr/xpg4/bin/grep AHYG 3634476_fasta.screen.screen.ids > reads.trim15.AHYG.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYG.rl 2 50 #Found 17250 total values totalling 10945862.0000. <634.542725 +/- 171.219692> #Range: [ 22 - 891 ] #Most likely bin: [ 750 - 800 ] 3449 counts #Median bin: [ 650 - 700 ] 2337 counts | 0 - 50 : [ 39 0.00 0.00 ] |XX 50 - 100 : [ 141 0.01 0.01 ] |XXX 100 - 150 : [ 220 0.01 0.02 ] |XXX 150 - 200 : [ 219 0.01 0.04 ] |XXX 200 - 250 : [ 250 0.01 0.05 ] |XXX 250 - 300 : [ 299 0.02 0.07 ] |XXXX 300 - 350 : [ 334 0.02 0.09 ] |XXXXX 350 - 400 : [ 414 0.02 0.11 ] |XXXXXX 400 - 450 : [ 537 0.03 0.14 ] |XXXXXXX 450 - 500 : [ 587 0.03 0.18 ] |XXXXXXXXXX 500 - 550 : [ 899 0.05 0.23 ] |XXXXXXXXXXXXXXX 550 - 600 : [ 1276 0.07 0.30 ] |XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1721 0.10 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2337 0.14 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3035 0.18 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3449 0.20 0.91 ] |XXXXXXXXXXXXXXXX 800 - 850 : [ 1420 0.08 1.00 ] |X 850 - 900 : [ 73 0.00 1.00 ] JAZZ trim 15 readlength histogram for AHYH Command: /usr/xpg4/bin/grep AHYH 3634476_fasta.screen.screen.ids > reads.trim15.AHYH.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYH.rl 2 50 #Found 2307 total values totalling 1258763.0000. <545.627655 +/- 210.955577> #Range: [ 22 - 860 ] #Most likely bin: [ 700 - 750 ] 440 counts #Median bin: [ 600 - 650 ] 241 counts |XX 0 - 50 : [ 27 0.01 0.01 ] |XXXXXXX 50 - 100 : [ 72 0.03 0.04 ] |XXXXXX 100 - 150 : [ 61 0.03 0.07 ] |XXXX 150 - 200 : [ 48 0.02 0.09 ] |XXXXX 200 - 250 : [ 52 0.02 0.11 ] |XXXXXXXXXXXXXX 250 - 300 : [ 150 0.07 0.18 ] |XXXXXXXXXXXXXX 300 - 350 : [ 151 0.07 0.24 ] |XXXXXX 350 - 400 : [ 67 0.03 0.27 ] |XXXXX 400 - 450 : [ 58 0.03 0.30 ] |XXXXXX 450 - 500 : [ 69 0.03 0.33 ] |XXXXXXXX 500 - 550 : [ 92 0.04 0.37 ] |XXXXXXXXXXXXXXX 550 - 600 : [ 161 0.07 0.44 ] |XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 241 0.10 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 388 0.17 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 440 0.19 0.90 ] |XXXXXXXXXXXXXXXXXXX 750 - 800 : [ 205 0.09 0.99 ] |XX 800 - 850 : [ 24 0.01 1.00 ] | 850 - 900 : [ 1 0.00 1.00 ] ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.3634476_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.3634476_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 34013 total values totalling 19511.8479. <0.573659 +/- 0.044272> #Range: [ 0 - 0.7838 ] #Most likely bin: [ 0.59 - 0.595 ] 1864 counts #Median bin: [ 0.58 - 0.585 ] 1844 counts | 0 - 0.005 : [ 2 0.00 0.00 ] #... | 0.215 - 0.22 : [ 1 0.00 0.00 ] #... | 0.29 - 0.295 : [ 2 0.00 0.00 ] #... | 0.3 - 0.305 : [ 1 0.00 0.00 ] #... | 0.315 - 0.32 : [ 1 0.00 0.00 ] | 0.32 - 0.325 : [ 1 0.00 0.00 ] | 0.325 - 0.33 : [ 1 0.00 0.00 ] #... | 0.34 - 0.345 : [ 2 0.00 0.00 ] | 0.345 - 0.35 : [ 1 0.00 0.00 ] | 0.35 - 0.355 : [ 1 0.00 0.00 ] | 0.355 - 0.36 : [ 2 0.00 0.00 ] | 0.36 - 0.365 : [ 1 0.00 0.00 ] | 0.365 - 0.37 : [ 3 0.00 0.00 ] | 0.37 - 0.375 : [ 6 0.00 0.00 ] | 0.375 - 0.38 : [ 5 0.00 0.00 ] | 0.38 - 0.385 : [ 12 0.00 0.00 ] | 0.385 - 0.39 : [ 10 0.00 0.00 ] | 0.39 - 0.395 : [ 17 0.00 0.00 ] | 0.395 - 0.4 : [ 10 0.00 0.00 ] | 0.4 - 0.405 : [ 23 0.00 0.00 ] | 0.405 - 0.41 : [ 21 0.00 0.00 ] | 0.41 - 0.415 : [ 18 0.00 0.00 ] |X 0.415 - 0.42 : [ 24 0.00 0.00 ] | 0.42 - 0.425 : [ 16 0.00 0.01 ] |X 0.425 - 0.43 : [ 32 0.00 0.01 ] |X 0.43 - 0.435 : [ 26 0.00 0.01 ] |X 0.435 - 0.44 : [ 46 0.00 0.01 ] |X 0.44 - 0.445 : [ 57 0.00 0.01 ] |X 0.445 - 0.45 : [ 59 0.00 0.01 ] |XX 0.45 - 0.455 : [ 74 0.00 0.01 ] |XX 0.455 - 0.46 : [ 82 0.00 0.02 ] |XXX 0.46 - 0.465 : [ 126 0.00 0.02 ] |XXX 0.465 - 0.47 : [ 125 0.00 0.02 ] |XXX 0.47 - 0.475 : [ 161 0.00 0.03 ] |XXXX 0.475 - 0.48 : [ 183 0.01 0.03 ] |XXXXX 0.48 - 0.485 : [ 216 0.01 0.04 ] |XXXXX 0.485 - 0.49 : [ 248 0.01 0.05 ] |XXXXXX 0.49 - 0.495 : [ 275 0.01 0.06 ] |XXXXXXX 0.495 - 0.5 : [ 304 0.01 0.06 ] |XXXXXXXXX 0.5 - 0.505 : [ 429 0.01 0.08 ] |XXXXXXXX 0.505 - 0.51 : [ 394 0.01 0.09 ] |XXXXXXXXXX 0.51 - 0.515 : [ 447 0.01 0.10 ] |XXXXXXXXXXX 0.515 - 0.52 : [ 496 0.01 0.12 ] |XXXXXXXXXXXXX 0.52 - 0.525 : [ 586 0.02 0.13 ] |XXXXXXXXXXXXXX 0.525 - 0.53 : [ 663 0.02 0.15 ] |XXXXXXXXXXXXXX 0.53 - 0.535 : [ 653 0.02 0.17 ] |XXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 753 0.02 0.19 ] |XXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 847 0.02 0.22 ] |XXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 959 0.03 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1095 0.03 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1199 0.04 0.32 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1376 0.04 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1497 0.04 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1650 0.05 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1718 0.05 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1844 0.05 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1791 0.05 0.61 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 1864 0.05 0.66 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 1744 0.05 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1805 0.05 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1581 0.05 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1323 0.04 0.85 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1175 0.03 0.88 ] |XXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 925 0.03 0.91 ] |XXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 725 0.02 0.93 ] |XXXXXXXXXXXXXX 0.63 - 0.635 : [ 636 0.02 0.95 ] |XXXXXXXXXXX 0.635 - 0.64 : [ 500 0.01 0.97 ] |XXXXXXXX 0.64 - 0.645 : [ 362 0.01 0.98 ] |XXXXX 0.645 - 0.65 : [ 247 0.01 0.98 ] |XXXX 0.65 - 0.655 : [ 167 0.00 0.99 ] |XX 0.655 - 0.66 : [ 115 0.00 0.99 ] |XX 0.66 - 0.665 : [ 82 0.00 1.00 ] |X 0.665 - 0.67 : [ 51 0.00 1.00 ] |X 0.67 - 0.675 : [ 32 0.00 1.00 ] | 0.675 - 0.68 : [ 19 0.00 1.00 ] | 0.68 - 0.685 : [ 18 0.00 1.00 ] | 0.685 - 0.69 : [ 11 0.00 1.00 ] | 0.69 - 0.695 : [ 11 0.00 1.00 ] | 0.695 - 0.7 : [ 5 0.00 1.00 ] | 0.7 - 0.705 : [ 5 0.00 1.00 ] | 0.705 - 0.71 : [ 7 0.00 1.00 ] | 0.71 - 0.715 : [ 1 0.00 1.00 ] #... | 0.72 - 0.725 : [ 1 0.00 1.00 ] | 0.725 - 0.73 : [ 1 0.00 1.00 ] | 0.73 - 0.735 : [ 2 0.00 1.00 ] | 0.735 - 0.74 : [ 2 0.00 1.00 ] #... | 0.75 - 0.755 : [ 1 0.00 1.00 ] #... | 0.765 - 0.77 : [ 1 0.00 1.00 ] | 0.77 - 0.775 : [ 1 0.00 1.00 ] #... | 0.78 - 0.785 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones N/plate avg% LIBRARY @ 80 14542 7424 92.80 96.67 AHYF @ 104 17252 8976 86.31 89.90 AHYG @ 15 2307 1317 87.80 91.46 AHYH @ ] 34101 17717 89.03 cumulative total@@ LIBRARY PLATE ID COUNT [ AHYF 80 AHYG 104 AHYH 15 ] for 199 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 = 1 HQ Discrepant reads = 15 Chimeric reads = 184 Suspect alignments = 2955 ################################################################### C O N T I G I N F O R M A T I O N Sun Sep 5 21:15:42 2004 File: /psf/project/microbe3/3634476/edit_dir.06Aug04.QD/phrap.out Contig 3. 1 read; 657 bp (untrimmed), 485 (trimmed). Contig 4. 1 read; 1444 bp (untrimmed), 0 (trimmed). Contig 5. 1 read; 942 bp (untrimmed), 640 (trimmed). Contig 6. 1 read; 1030 bp (untrimmed), 261 (trimmed). Contig 7. 2 reads; 189 bp (untrimmed), 189 (trimmed). Contig 8. 2 reads; 961 bp (untrimmed), 454 (trimmed). Contig 9. 5 reads; 1325 bp (untrimmed), 1285 (trimmed). Contig 10. 18 reads; 3840 bp (untrimmed), 3623 (trimmed). Contig 11. 47 reads; 6371 bp (untrimmed), 6352 (trimmed). Contig 12. 140 reads; 13081 bp (untrimmed), 12835 (trimmed). Contig 13. 297 reads; 22449 bp (untrimmed), 22341 (trimmed). Contig 14. 304 reads; 23769 bp (untrimmed), 23719 (trimmed). Contig 15. 423 reads; 36886 bp (untrimmed), 36875 (trimmed). Contig 16. 453 reads; 36185 bp (untrimmed), 36173 (trimmed). Contig 17. 559 reads; 36516 bp (untrimmed), 36323 (trimmed). Contig 18. 639 reads; 45213 bp (untrimmed), 45086 (trimmed). Contig 19. 705 reads; 49339 bp (untrimmed), 49264 (trimmed). Contig 20. 796 reads; 58947 bp (untrimmed), 58839 (trimmed). Contig 21. 1031 reads; 84218 bp (untrimmed), 83896 (trimmed). Contig 22. 1238 reads; 86308 bp (untrimmed), 86308 (trimmed). Contig 23. 1241 reads; 86014 bp (untrimmed), 85725 (trimmed). Contig 24. 1327 reads; 92944 bp (untrimmed), 92877 (trimmed). Contig 25. 1491 reads; 107458 bp (untrimmed), 107393 (trimmed). Contig 26. 3171 reads; 215412 bp (untrimmed), 215323 (trimmed). Contig 27. 3464 reads; 222838 bp (untrimmed), 222770 (trimmed). Contig 28. 7205 reads; 495016 bp (untrimmed), 494967 (trimmed). Contig 29. 9495 reads; 623594 bp (untrimmed), 623486 (trimmed). -------------------------------------------------------------- Totals 34059 reads; 2355481 bp (untrimmed), 2348335 (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 20 total values totalling 2344175.0000. <117208.750000 +/- 159709.861822> #Range: [ 3623 - 623486 ] #Most likely bin: [ 36000 - 38000 ] 3 counts #Median bin: [ 48000 - 50000 ] 1 counts |XXXXXXXXXXXXX 2000 - 4000 : [ 1 0.05 0.05 ] #... |XXXXXXXXXXXXX 6000 - 8000 : [ 1 0.05 0.10 ] #... |XXXXXXXXXXXXX 12000 - 14000 : [ 1 0.05 0.15 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXX 22000 - 24000 : [ 2 0.10 0.25 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 38000 : [ 3 0.15 0.40 ] #... |XXXXXXXXXXXXX 44000 - 46000 : [ 1 0.05 0.45 ] #... |XXXXXXXXXXXXX 48000 - 50000 : [ 1 0.05 0.50 ] #... |XXXXXXXXXXXXX 58000 - 60000 : [ 1 0.05 0.55 ] #... |XXXXXXXXXXXXX 82000 - 84000 : [ 1 0.05 0.60 ] |XXXXXXXXXXXXX 84000 - 86000 : [ 1 0.05 0.65 ] |XXXXXXXXXXXXX 86000 - 88000 : [ 1 0.05 0.70 ] #... |XXXXXXXXXXXXX 92000 - 94000 : [ 1 0.05 0.75 ] #... |XXXXXXXXXXXXX 106000 - 108000 : [ 1 0.05 0.80 ] #... |XXXXXXXXXXXXX 214000 - 216000 : [ 1 0.05 0.85 ] #... |XXXXXXXXXXXXX 222000 - 224000 : [ 1 0.05 0.90 ] #... |XXXXXXXXXXXXX 494000 - 496000 : [ 1 0.05 0.95 ] #... |XXXXXXXXXXXXX 622000 - 624000 : [ 1 0.05 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 6961221 C = 9126753 G = 9178464 T = 6758524 N = 181855 X = 317810 GC fraction = 0.56 Total = 32524627 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 3634476_fasta.screen.contigs A 517308 C 689279 G 660921 N 203 T 487676 X 94 fraction GC = 0.57 total bases = 2355481 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 2348684 bases = 12.62 +- 4.57 = 0.14 +- 4.24 m1 = 1.66 m2 = 0.73 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 22 total values totalling 229.8200. <10.446364 +/- 3.461082> #Range: [ 1.37 - 13.53 ] #Most likely bin: [ 12.5 - 13 ] 4 counts #Median bin: [ 11.5 - 12 ] 2 counts |XXXXXXXXXX 1 - 1.5 : [ 1 0.05 0.05 ] #... |XXXXXXXXXX 2.5 - 3 : [ 1 0.05 0.09 ] #... |XXXXXXXXXX 4 - 4.5 : [ 1 0.05 0.14 ] #... |XXXXXXXXXX 6 - 6.5 : [ 1 0.05 0.18 ] #... |XXXXXXXXXX 9 - 9.5 : [ 1 0.05 0.23 ] #... |XXXXXXXXXX 10 - 10.5 : [ 1 0.05 0.27 ] |XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 2 0.09 0.36 ] |XXXXXXXXXX 11 - 11.5 : [ 1 0.05 0.41 ] |XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 2 0.09 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 4 0.18 0.68 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.18 0.86 ] |XXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 2 0.09 0.95 ] |XXXXXXXXXX 13.5 - 14 : [ 1 0.05 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 20 total values totalling 225.5200. <11.276000 +/- 2.354760> #Range: [ 4.04 - 13.53 ] #Most likely bin: [ 12.5 - 13 ] 4 counts #Median bin: [ 12 - 12.5 ] 4 counts |XXXXXXXXXX 4 - 4.5 : [ 1 0.05 0.05 ] #... |XXXXXXXXXX 6 - 6.5 : [ 1 0.05 0.10 ] #... |XXXXXXXXXX 9 - 9.5 : [ 1 0.05 0.15 ] #... |XXXXXXXXXX 10 - 10.5 : [ 1 0.05 0.20 ] |XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 2 0.10 0.30 ] |XXXXXXXXXX 11 - 11.5 : [ 1 0.05 0.35 ] |XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 2 0.10 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 4 0.20 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.20 0.85 ] |XXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 2 0.10 0.95 ] |XXXXXXXXXX 13.5 - 14 : [ 1 0.05 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 8 2 reads 961 bases = 1.37 +- 0.48 = -0.63 +- 0.48 m1 = 0.17 m2 = -0.00 Contig 9 5 reads 1325 bases = 2.93 +- 1.14 = 0.42 +- 0.70 m1 = 0.44 m2 = 0.20 Contig 10 18 reads 3840 bases = 4.04 +- 1.84 = 0.24 +- 2.01 m1 = 0.84 m2 = -0.16 Contig 11 47 reads 6371 bases = 6.07 +- 3.08 = 2.71 +- 3.63 m1 = 1.56 m2 = -0.93 Contig 12 140 reads 13081 bases = 9.41 +- 4.20 = 0.32 +- 5.48 m1 = 1.88 m2 = -3.10 Contig 15 423 reads 36886 bases = 10.05 +- 4.14 = 0.22 +- 4.87 m1 = 1.70 m2 = -1.66 Contig 21 1031 reads 84218 bases = 10.64 +- 4.18 = 0.32 +- 4.51 m1 = 1.64 m2 = -0.73 Contig 16 453 reads 36185 bases = 10.74 +- 4.16 = 0.13 +- 4.53 m1 = 1.61 m2 = -0.79 Contig 14 304 reads 23769 bases = 11.02 +- 3.49 = 1.31 +- 4.44 m1 = 1.10 m2 = -1.88 Contig 20 796 reads 58947 bases = 11.59 +- 4.66 = 0.17 +- 4.23 m1 = 1.87 m2 = 0.95 Contig 13 297 reads 22449 bases = 11.87 +- 4.45 = 0.26 +- 4.73 m1 = 1.67 m2 = -0.64 Contig 25 1491 reads 107458 bases = 12.19 +- 4.97 = -0.05 +- 5.14 m1 = 2.03 m2 = -0.43 Contig 22 1238 reads 86308 bases = 12.44 +- 4.24 = 0.07 +- 4.60 m1 = 1.45 m2 = -0.81 Contig 24 1327 reads 92944 bases = 12.45 +- 3.89 = 0.29 +- 4.00 m1 = 1.22 m2 = -0.22 Contig 19 705 reads 49339 bases = 12.46 +- 4.22 = 0.39 +- 4.79 m1 = 1.43 m2 = -1.29 Contig 23 1241 reads 86014 bases = 12.50 +- 4.02 = 0.47 +- 3.75 m1 = 1.29 m2 = 0.52 Contig 18 639 reads 45213 bases = 12.54 +- 4.71 = 0.00 +- 3.71 m1 = 1.77 m2 = 2.12 Contig 28 7205 reads 495016 bases = 12.70 +- 5.05 = -0.00 +- 4.15 m1 = 2.01 m2 = 2.08 Contig 26 3171 reads 215412 bases = 12.77 +- 4.34 = 0.02 +- 4.08 m1 = 1.47 m2 = 0.54 Contig 29 9495 reads 623594 bases = 13.22 +- 4.34 = 0.11 +- 4.02 m1 = 1.42 m2 = 0.66 Contig 10 18 reads 3840 bases = 4.04 +- 1.84 = 0.24 +- 2.01 m1 = 0.84 m2 = -0.16 Contig 11 47 reads 6371 bases = 6.07 +- 3.08 = 2.71 +- 3.63 m1 = 1.56 m2 = -0.93 Contig 12 140 reads 13081 bases = 9.41 +- 4.20 = 0.32 +- 5.48 m1 = 1.88 m2 = -3.10 Contig 15 423 reads 36886 bases = 10.05 +- 4.14 = 0.22 +- 4.87 m1 = 1.70 m2 = -1.66 Contig 21 1031 reads 84218 bases = 10.64 +- 4.18 = 0.32 +- 4.51 m1 = 1.64 m2 = -0.73 Contig 16 453 reads 36185 bases = 10.74 +- 4.16 = 0.13 +- 4.53 m1 = 1.61 m2 = -0.79 Contig 14 304 reads 23769 bases = 11.02 +- 3.49 = 1.31 +- 4.44 m1 = 1.10 m2 = -1.88 Contig 20 796 reads 58947 bases = 11.59 +- 4.66 = 0.17 +- 4.23 m1 = 1.87 m2 = 0.95 Contig 13 297 reads 22449 bases = 11.87 +- 4.45 = 0.26 +- 4.73 m1 = 1.67 m2 = -0.64 Contig 25 1491 reads 107458 bases = 12.19 +- 4.97 = -0.05 +- 5.14 m1 = 2.03 m2 = -0.43 Contig 22 1238 reads 86308 bases = 12.44 +- 4.24 = 0.07 +- 4.60 m1 = 1.45 m2 = -0.81 Contig 24 1327 reads 92944 bases = 12.45 +- 3.89 = 0.29 +- 4.00 m1 = 1.22 m2 = -0.22 Contig 19 705 reads 49339 bases = 12.46 +- 4.22 = 0.39 +- 4.79 m1 = 1.43 m2 = -1.29 Contig 23 1241 reads 86014 bases = 12.50 +- 4.02 = 0.47 +- 3.75 m1 = 1.29 m2 = 0.52 Contig 18 639 reads 45213 bases = 12.54 +- 4.71 = 0.00 +- 3.71 m1 = 1.77 m2 = 2.12 Contig 28 7205 reads 495016 bases = 12.70 +- 5.05 = -0.00 +- 4.15 m1 = 2.01 m2 = 2.08 Contig 26 3171 reads 215412 bases = 12.77 +- 4.34 = 0.02 +- 4.08 m1 = 1.47 m2 = 0.54 Contig 29 9495 reads 623594 bases = 13.22 +- 4.34 = 0.11 +- 4.02 m1 = 1.42 m2 = 0.66 Contig 17 559 reads 36516 bases = 13.29 +- 4.66 = 0.54 +- 4.88 m1 = 1.63 m2 = -0.52 Contig 27 3464 reads 222838 bases = 13.53 +- 4.07 = 0.17 +- 4.29 m1 = 1.22 m2 = -0.47 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 29 total values totalling 34059.0000. <1174.448276 +/- 2155.019219> #Range: [ 1 - 9495 ] #Most likely bin: [ 1 - 2 ] 6 counts #Median bin: [ 423 - 424 ] 1 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 2 : [ 6 0.21 0.21 ] |XXXXXXXXXXXXX 2 - 3 : [ 2 0.07 0.28 ] #... |XXXXXXX 5 - 6 : [ 1 0.03 0.31 ] #... |XXXXXXX 18 - 19 : [ 1 0.03 0.34 ] #... |XXXXXXX 47 - 48 : [ 1 0.03 0.38 ] #... |XXXXXXX 140 - 141 : [ 1 0.03 0.41 ] #... |XXXXXXX 297 - 298 : [ 1 0.03 0.45 ] #... |XXXXXXX 304 - 305 : [ 1 0.03 0.48 ] #... |XXXXXXX 423 - 424 : [ 1 0.03 0.52 ] #... |XXXXXXX 453 - 454 : [ 1 0.03 0.55 ] #... |XXXXXXX 559 - 560 : [ 1 0.03 0.59 ] #... |XXXXXXX 639 - 640 : [ 1 0.03 0.62 ] #... |XXXXXXX 705 - 706 : [ 1 0.03 0.66 ] #... |XXXXXXX 796 - 797 : [ 1 0.03 0.69 ] #... |XXXXXXX 1031 - 1032 : [ 1 0.03 0.72 ] #... |XXXXXXX 1238 - 1239 : [ 1 0.03 0.76 ] #... |XXXXXXX 1241 - 1242 : [ 1 0.03 0.79 ] #... |XXXXXXX 1327 - 1328 : [ 1 0.03 0.83 ] #... |XXXXXXX 1491 - 1492 : [ 1 0.03 0.86 ] #... |XXXXXXX 3171 - 3172 : [ 1 0.03 0.90 ] #... |XXXXXXX 3464 - 3465 : [ 1 0.03 0.93 ] #... |XXXXXXX 7205 - 7206 : [ 1 0.03 0.97 ] #... |XXXXXXX 9495 - 9496 : [ 1 0.03 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 29 total values totalling 2355481.0000. <81223.482759 +/- 143122.511789> #Range: [ 189 - 623594 ] #Most likely bin: [ 1000 - 2000 ] 5 counts #Median bin: [ 36000 - 37000 ] 3 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 1000 : [ 4 0.14 0.14 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 5 0.17 0.31 ] #... |XXXXXXXX 3000 - 4000 : [ 1 0.03 0.34 ] #... |XXXXXXXX 6000 - 7000 : [ 1 0.03 0.38 ] #... |XXXXXXXX 13000 - 14000 : [ 1 0.03 0.41 ] #... |XXXXXXXX 22000 - 23000 : [ 1 0.03 0.45 ] |XXXXXXXX 23000 - 24000 : [ 1 0.03 0.48 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 36000 - 37000 : [ 3 0.10 0.59 ] #... |XXXXXXXX 45000 - 46000 : [ 1 0.03 0.62 ] #... |XXXXXXXX 49000 - 50000 : [ 1 0.03 0.66 ] #... |XXXXXXXX 58000 - 59000 : [ 1 0.03 0.69 ] #... |XXXXXXXX 84000 - 85000 : [ 1 0.03 0.72 ] #... |XXXXXXXXXXXXXXXX 86000 - 87000 : [ 2 0.07 0.79 ] #... |XXXXXXXX 92000 - 93000 : [ 1 0.03 0.83 ] #... |XXXXXXXX 107000 - 108000 : [ 1 0.03 0.86 ] #... |XXXXXXXX 215000 - 216000 : [ 1 0.03 0.90 ] #... |XXXXXXXX 222000 - 223000 : [ 1 0.03 0.93 ] #... |XXXXXXXX 495000 - 496000 : [ 1 0.03 0.97 ] #... |XXXXXXXX 623000 - 624000 : [ 1 0.03 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 AHYF reads.list > grep.reads.list.AHYF Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYF 4 500 #Found 6846 total values totalling 21699436.0000. <3169.651767 +/- 4828.275462> #Range: [ - 348872 ] #Most likely bin: [ 3000 - 3500 ] 4474 counts #Median bin: [ 3000 - 3500 ] 4474 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 3 0.00 0.00 ] | 1000 - 1500 : [ 47 0.01 0.01 ] |X 1500 - 2000 : [ 121 0.02 0.03 ] |X 2000 - 2500 : [ 156 0.02 0.05 ] |XXXXXXXXXXXXXXXXX 2500 - 3000 : [ 1920 0.28 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4474 0.65 0.98 ] |X 3500 - 4000 : [ 111 0.02 1.00 ] | 4000 - 4500 : [ 1 0.00 1.00 ] | 4500 - 5000 : [ 1 0.00 1.00 ] #... | 5500 - 6000 : [ 1 0.00 1.00 ] | 6000 - 6500 : [ 2 0.00 1.00 ] #... | 14500 - 15000 : [ 1 0.00 1.00 ] #... | 28000 - 28500 : [ 1 0.00 1.00 ] #... | 48500 - 49000 : [ 1 0.00 1.00 ] #... | 82500 - 83000 : [ 1 0.00 1.00 ] #... | 83500 - 84000 : [ 1 0.00 1.00 ] #... | 101500 - 102000 : [ 1 0.00 1.00 ] #... | 120000 - 120500 : [ 1 0.00 1.00 ] #... | 348500 - 349000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AHYG reads.list > grep.reads.list.AHYG Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYG 4 500 #Found 7585 total values totalling 54950045.0000. <7244.567568 +/- 12889.836904> #Range: [ - 446815 ] #Most likely bin: [ 6000 - 6500 ] 1581 counts #Median bin: [ 6500 - 7000 ] 1439 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 8 0.00 0.00 ] |X 1000 - 1500 : [ 56 0.01 0.01 ] |XX 1500 - 2000 : [ 68 0.01 0.02 ] |XX 2000 - 2500 : [ 65 0.01 0.03 ] |XX 2500 - 3000 : [ 63 0.01 0.03 ] |X 3000 - 3500 : [ 58 0.01 0.04 ] |XX 3500 - 4000 : [ 89 0.01 0.05 ] |XXX 4000 - 4500 : [ 111 0.01 0.07 ] |XXX 4500 - 5000 : [ 124 0.02 0.08 ] |XXXXX 5000 - 5500 : [ 217 0.03 0.11 ] |XXXXXXXXXXXXXXXX 5500 - 6000 : [ 620 0.08 0.20 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1581 0.21 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1439 0.19 0.59 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1251 0.16 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 919 0.12 0.88 ] |XXXXXXXXXXXXXXXX 8000 - 8500 : [ 644 0.08 0.96 ] |XXXXXX 8500 - 9000 : [ 237 0.03 1.00 ] | 9000 - 9500 : [ 3 0.00 1.00 ] | 9500 - 10000 : [ 2 0.00 1.00 ] | 10000 - 10500 : [ 1 0.00 1.00 ] #... | 11500 - 12000 : [ 2 0.00 1.00 ] #... | 52000 - 52500 : [ 1 0.00 1.00 ] #... | 55000 - 55500 : [ 1 0.00 1.00 ] #... | 56000 - 56500 : [ 1 0.00 1.00 ] #... | 74000 - 74500 : [ 1 0.00 1.00 ] #... | 78000 - 78500 : [ 1 0.00 1.00 ] #... | 90000 - 90500 : [ 1 0.00 1.00 ] | 90500 - 91000 : [ 1 0.00 1.00 ] | 91000 - 91500 : [ 1 0.00 1.00 ] #... | 96500 - 97000 : [ 1 0.00 1.00 ] #... | 98500 - 99000 : [ 1 0.00 1.00 ] #... | 106000 - 106500 : [ 2 0.00 1.00 ] #... | 150500 - 151000 : [ 1 0.00 1.00 ] #... | 172500 - 173000 : [ 1 0.00 1.00 ] #... | 176500 - 177000 : [ 1 0.00 1.00 ] #... | 179000 - 179500 : [ 1 0.00 1.00 ] #... | 230500 - 231000 : [ 1 0.00 1.00 ] #... | 250500 - 251000 : [ 1 0.00 1.00 ] #... | 273000 - 273500 : [ 1 0.00 1.00 ] #... | 278000 - 278500 : [ 1 0.00 1.00 ] #... | 295000 - 295500 : [ 1 0.00 1.00 ] #... | 314500 - 315000 : [ 1 0.00 1.00 ] #... | 324000 - 324500 : [ 1 0.00 1.00 ] #... | 417000 - 417500 : [ 1 0.00 1.00 ] #... | 420500 - 421000 : [ 1 0.00 1.00 ] #... | 446500 - 447000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AHYH reads.list > grep.reads.list.AHYH Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYH 4 500 #Found 707 total values totalling 27775650.0000. <39286.633663 +/- 5765.908246> #Range: [ - 155338 ] #Most likely bin: [ 40000 - 40500 ] 46 counts #Median bin: [ 39000 - 39500 ] 33 counts |X 0 - 500 : [ 1 0.00 0.00 ] #... |X 23500 - 24000 : [ 1 0.00 0.00 ] #... |X 29000 - 29500 : [ 1 0.00 0.00 ] #... |XX 30500 - 31000 : [ 2 0.00 0.01 ] |XXX 31000 - 31500 : [ 3 0.00 0.01 ] |XXX 31500 - 32000 : [ 4 0.01 0.02 ] |XXXXXXXXXXX 32000 - 32500 : [ 13 0.02 0.04 ] |XXXX 32500 - 33000 : [ 5 0.01 0.04 ] |XXXXXXXXXX 33000 - 33500 : [ 12 0.02 0.06 ] |XXXXXXXXXXX 33500 - 34000 : [ 13 0.02 0.08 ] |XXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 23 0.03 0.11 ] |XXXXXXXXXX 34500 - 35000 : [ 11 0.02 0.13 ] |XXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 21 0.03 0.16 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 31 0.04 0.20 ] |XXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 23 0.03 0.23 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 33 0.05 0.28 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 34 0.05 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 35 0.05 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 33 0.05 0.42 ] |XXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 25 0.04 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 33 0.05 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 33 0.05 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 46 0.07 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 36 0.05 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 31 0.04 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 36 0.05 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 35 0.05 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 31 0.04 0.86 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 30 0.04 0.90 ] |XXXXXXXXXXXXXXXXX 43500 - 44000 : [ 20 0.03 0.93 ] |XXXXXXXXXXXXXXXXX 44000 - 44500 : [ 19 0.03 0.95 ] |XXXXXXXXXX 44500 - 45000 : [ 11 0.02 0.97 ] |XXXXXXXX 45000 - 45500 : [ 9 0.01 0.98 ] |XXXXXX 45500 - 46000 : [ 7 0.01 0.99 ] |XXXX 46000 - 46500 : [ 5 0.01 1.00 ] #... |X 155000 - 155500 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # AHYH 39152 +- 3475 (n=360) # AHYG 6521 +- 1455 (n=3836) # AHYF 2939 +- 433 (n=3560) ################################################################### 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 646.373933 bp, 34059 reads, genome size 2530740 bp Command: idealAssembly 2530740 34059 646.373933 ------------------------------------------------------------------- Genome = 2530740 bases Nreads = 34059 readLength = 646.373933 Depth = 8.70 N_contigs = N_gaps = 6 mean gap size = 73 bases mean contig size = 5997 reads (~ 445588 bases) %cover = 99.98 %singlet = 0.00 assembly size = 2530317 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 1 contigs containing at least 10063 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: 3634476 Command line options used were: -c -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 6765 Number of reads with percent X's >= 20%: 145 = 0.4% Number of reads with percent X's >= 50%: 75 = 0.2% Number of reads with percent X's >= 80%: 13 = 0.0% Total nr of reads in project is: 34101 Total nr of X's: 317810 Total nr not found in screened files: 0 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with L09136-pUC18 6143 47 25 7 Nr with pCC1Fos 487 10 1 0 Nr with pMCL200 135 88 49 6 ################################################################### Contam Summary with *.singlets: Command: contam_summary -c -s -g ------------------------------------------------------------------- Contamination Summary for JGI id: 3634476 Command line options used were: -c -g -s WORKING IN LOCAL DIRECTORY Number of reads with X's: 2 Number of reads with percent X's >= 20%: 0 = 0.0% Number of reads with percent X's >= 50%: 0 = 0.0% Number of reads with percent X's >= 80%: 0 = 0.0% Total nr of reads in project is: 42 Total nr of X's: 61 Total nr not found in screened files: 0 Nr of reads screened >= 20% >= 50% >= 80% screened Nr with L09136-pUC18 2 0 0 0 ################################################################### Bad M1 Contigs ------------------------------------------------------------------- ################################################################### Bad M2 Contigs ------------------------------------------------------------------- ################################################################### Ran Plates2contigs: Output Location: Ran in.dir: Output Location: Viewed Contigs with Phrapview: ################################################################### Conclusions: