SECTION I Assembly QD Report ################################################################### Phrap Assembly QC Date: 01-10-2006 ------------------------------------------------------------------- SECTION II Project Information Summary ################################################################### Project information from 'PROJECTS' db ------------------------------------------------------------------- # Project GenusSpecies TaxID Size(KBases) 4001428 Acidovorax 1684 NULL 2300 SECTION III Taxonomic Data Acquired From NCBI ################################################################### Taxonomy summary ------------------------------------------------------------------- Command: /home/copeland/scripts/tax2tree.sh Acidovorax Comamonadaceae, family, b-proteobacteria Burkholderiales, order, b-proteobacteria Betaproteobacteria, class, b-proteobacteria Acidovorax, genus, b-proteobacteria Proteobacteria (purple bacteria), phylum, proteobacteria Bacteria (eubacteria), superkingdom, eubacteria cellular organisms root SECTION IV Estimated Genome Sizes ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 5586745 # phrap: 5213981 # db: 2300000 4366908 +/- 1469426 SECTION V Read Accounting And Quality ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #lanes Q20 Pass Rate Q20 Avg Read Len BHGA.5-16 26880 98.73 751.43 BHGB.9-132 26880 97.40 720.31 BHGC.5-32 5376 96.76 540.07 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s BHGA 220 110 98.83 753.29 110 98.63 749.56 BHGB 280 140 97.27 716.14 140 97.52 724.48 BHGC 56 28 96.99 534.29 28 96.54 545.86 BHGF 0 0 0.00 0.00 0 0.00 0.00 BHGG 0 0 0.00 0.00 0 0.00 0.00 BHGH 0 0 0.00 0.00 0 0.00 0.00 SAWA 0 0 0.00 0.00 0 0.00 0.00 SAWB 0 0 0.00 0.00 0 0.00 0.00 SAWC 0 0 0.00 0.00 0 0.00 0.00 SBAN 0 0 0.00 0.00 0 0.00 0.00 SCCC 2 1 98.96 826.00 1 98.96 824.00 ################################################################### reads2plates summary ------------------------------------------------------------------- plate(s) reads clones N/plate avg% LIBRARY @ 28 5094 2624 93.71 97.62 BHGC @ 140 26043 13191 94.22 98.15 BHGA @ 140 25833 13107 93.62 97.52 BHGB @ ] 56970 28922 93.90 cumulative total@@ LIBRARY PLATE ID COUNT [ BHGA 140 BHGC 28 BHGB 140 ] for 308 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. ################################################################### trimt JAZZ trim 15 readlength histogram: ------------------------------------------------------------------- Command: /home/copeland/scripts/histogram2.pl 4001428_fasta.screen.trimQ15.SaF 4 50 #Found 56970 total values totalling 41247909.0000. <724.028594 +/- 156.078470> #Range: [ 18 - 988 ] #Most likely bin: [ 750 - 800 ] 14690 counts #Median bin: [ 750 - 800 ] 14690 counts #Histogram Bins Count Fraction Cum_Fraction |X 0 - 50 : [ 187 0.00 0.00 ] |X 50 - 100 : [ 337 0.01 0.01 ] |X 100 - 150 : [ 327 0.01 0.01 ] |X 150 - 200 : [ 348 0.01 0.02 ] |X 200 - 250 : [ 469 0.01 0.03 ] |XX 250 - 300 : [ 594 0.01 0.04 ] |X 300 - 350 : [ 547 0.01 0.05 ] |XX 350 - 400 : [ 597 0.01 0.06 ] |XX 400 - 450 : [ 697 0.01 0.07 ] |XX 450 - 500 : [ 899 0.02 0.09 ] |XXX 500 - 550 : [ 1214 0.02 0.11 ] |XXXXX 550 - 600 : [ 1659 0.03 0.14 ] |XXXXXX 600 - 650 : [ 2365 0.04 0.18 ] |XXXXXXXXXXX 650 - 700 : [ 4210 0.07 0.25 ] |XXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7981 0.14 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 14690 0.26 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 14522 0.25 0.91 ] |XXXXXXXXXXXXXX 850 - 900 : [ 4995 0.09 0.99 ] |X 900 - 950 : [ 319 0.01 1.00 ] | 950 - 1000 : [ 13 0.00 1.00 ] trimt JAZZ trim 15 readlength histogram for BHGF trimt JAZZ trim 15 readlength histogram for BHGG trimt JAZZ trim 15 readlength histogram for BHGH trimt JAZZ trim 15 readlength histogram for SAWA trimt JAZZ trim 15 readlength histogram for SAWB trimt JAZZ trim 15 readlength histogram for SAWC trimt JAZZ trim 15 readlength histogram for BHGA Command: /usr/xpg4/bin/grep BHGA 4001428_fasta.screen.trimQ15.SaF > reads.trim15.BHGA.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.BHGA.rl 2 50 #Found 26043 total values totalling 19192757.0000. <736.964136 +/- 145.420156> #Range: [ 18 - 988 ] #Most likely bin: [ 800 - 850 ] 6689 counts #Median bin: [ 750 - 800 ] 6226 counts #Histogram Bins Count Fraction Cum_Fraction | 0 - 50 : [ 53 0.00 0.00 ] |X 50 - 100 : [ 134 0.01 0.01 ] |X 100 - 150 : [ 140 0.01 0.01 ] |X 150 - 200 : [ 158 0.01 0.02 ] |X 200 - 250 : [ 192 0.01 0.03 ] |X 250 - 300 : [ 171 0.01 0.03 ] |X 300 - 350 : [ 204 0.01 0.04 ] |X 350 - 400 : [ 200 0.01 0.05 ] |X 400 - 450 : [ 231 0.01 0.06 ] |XX 450 - 500 : [ 271 0.01 0.07 ] |XX 500 - 550 : [ 375 0.01 0.08 ] |XXX 550 - 600 : [ 584 0.02 0.10 ] |XXXXXX 600 - 650 : [ 1064 0.04 0.15 ] |XXXXXXXXXXXXXX 650 - 700 : [ 2269 0.09 0.23 ] |XXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3966 0.15 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6226 0.24 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6689 0.26 0.88 ] |XXXXXXXXXXXXXXXXX 850 - 900 : [ 2853 0.11 0.99 ] |X 900 - 950 : [ 250 0.01 1.00 ] | 950 - 1000 : [ 13 0.00 1.00 ] trimt JAZZ trim 15 readlength histogram for BHGB Command: /usr/xpg4/bin/grep BHGB 4001428_fasta.screen.trimQ15.SaF > reads.trim15.BHGB.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.BHGB.rl 2 50 #Found 25833 total values totalling 19335073.0000. <748.464096 +/- 135.281871> #Range: [ 21 - 949 ] #Most likely bin: [ 750 - 800 ] 8189 counts #Median bin: [ 750 - 800 ] 8189 counts #Histogram Bins Count Fraction Cum_Fraction | 0 - 50 : [ 42 0.00 0.00 ] |X 50 - 100 : [ 116 0.00 0.01 ] |X 100 - 150 : [ 123 0.00 0.01 ] |X 150 - 200 : [ 131 0.01 0.02 ] |X 200 - 250 : [ 167 0.01 0.02 ] |X 250 - 300 : [ 175 0.01 0.03 ] |X 300 - 350 : [ 164 0.01 0.04 ] |X 350 - 400 : [ 195 0.01 0.04 ] |X 400 - 450 : [ 213 0.01 0.05 ] |X 450 - 500 : [ 225 0.01 0.06 ] |X 500 - 550 : [ 291 0.01 0.07 ] |XX 550 - 600 : [ 379 0.01 0.09 ] |XXX 600 - 650 : [ 616 0.02 0.11 ] |XXXXXX 650 - 700 : [ 1267 0.05 0.16 ] |XXXXXXXXXXXXXXXXX 700 - 750 : [ 3556 0.14 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8189 0.32 0.61 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7778 0.30 0.91 ] |XXXXXXXXXX 850 - 900 : [ 2137 0.08 1.00 ] | 900 - 950 : [ 69 0.00 1.00 ] trimt JAZZ trim 15 readlength histogram for BHGC Command: /usr/xpg4/bin/grep BHGC 4001428_fasta.screen.trimQ15.SaF > reads.trim15.BHGC.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.BHGC.rl 2 50 #Found 5094 total values totalling 2720079.0000. <533.977032 +/- 177.523303> #Range: [ 19 - 871 ] #Most likely bin: [ 550 - 600 ] 696 counts #Median bin: [ 550 - 600 ] 696 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXX 0 - 50 : [ 92 0.02 0.02 ] |XXXXX 50 - 100 : [ 87 0.02 0.04 ] |XXXX 100 - 150 : [ 64 0.01 0.05 ] |XXX 150 - 200 : [ 59 0.01 0.06 ] |XXXXXX 200 - 250 : [ 110 0.02 0.08 ] |XXXXXXXXXXXXXX 250 - 300 : [ 248 0.05 0.13 ] |XXXXXXXXXX 300 - 350 : [ 179 0.04 0.16 ] |XXXXXXXXXXXX 350 - 400 : [ 202 0.04 0.20 ] |XXXXXXXXXXXXXXX 400 - 450 : [ 253 0.05 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXX 450 - 500 : [ 403 0.08 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 548 0.11 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 696 0.14 0.58 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 685 0.13 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 674 0.13 0.84 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 459 0.09 0.93 ] |XXXXXXXXXXXXXXXX 750 - 800 : [ 275 0.05 0.99 ] |XXX 800 - 850 : [ 55 0.01 1.00 ] | 850 - 900 : [ 5 0.00 1.00 ] trimt JAZZ trim 15 readlength histogram for SBAN trimt JAZZ trim 15 readlength histogram for SCCC SECTION VI Assembly Parameters ################################################################### Assembly parameters ------------------------------------------------------------------- phrap version SPS - 3.57 SUN/Ultra-2/3 Equivalent to Phil Green's version 0.990329 Score matrix (set by value of penalty: -2) A C G T N X A 1 -2 -2 -2 0 -3 C -2 1 -2 -2 0 -3 G -2 -2 1 -2 0 -3 T -2 -2 -2 1 0 -3 N 0 0 0 0 0 0 X -3 -3 -3 -3 0 -3 gap_init: -4 gap_ext: -3 ins_gap_ext: -3 del_gap_ext: -3 Using complexity-adjusted scores. Assumed background frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000 minmatch: 30 maxmatch: 55 max_group_size: 20 minscore: 55 bandwidth: 14 indexwordsize: 10 vector_bound: 20 word_raw: 0 trim_penalty: -2 trim_score: 20 trim_qual: 13 maxgap: 30 repeat_stringency: 0.950000 qual_show: 20 confirm_length: 8 confirm_trim: 1 confirm_penalty: -5 confirm_score: 30 node_seg: 8 node_space: 4 forcelevel: 0 bypasslevel: 1 max_subclone_size: 50000 SECTION VII Library Screening ################################################################### Library vector screening ------------------------------------------------------------------- BHGA.000001.000100 pUC18.fa pUC18.fa LRS.fasta BHGA.000101.000200 pUC18.fa pUC18.fa LRS.fasta BHGB.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta BHGB.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta BHGC.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta BHGA.000001.000100 pUC18.fa pUC18.fa LRS.fasta BHGA.000101.000200 pUC18.fa pUC18.fa LRS.fasta BHGB.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta BHGB.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta BHGC.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta SECTION VIII GC Content ################################################################### GC content histogram: ------------------------------------------------------------------- Command: /bin/nawk '{print $5+$6}' GC.4001428_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 # GC.4001428_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 56815 total values totalling 36881.0695. <0.649143 +/- 0.051153> #Range: [ 0.12 - 0.9334 ] #Most likely bin: [ 0.665 - 0.67 ] 2842 counts #Median bin: [ 0.655 - 0.66 ] 2600 counts #Entropy = 5.2976 bits | 0.12 - 0.125 : [ 1 1.76e-05 1.76e-05 1 ] #... | 0.205 - 0.21 : [ 1 1.76e-05 3.52e-05 2 ] #... | 0.215 - 0.22 : [ 1 1.76e-05 5.28e-05 3 ] | 0.22 - 0.225 : [ 2 3.52e-05 8.80e-05 5 ] #... | 0.235 - 0.24 : [ 1 1.76e-05 1.06e-04 6 ] #... | 0.245 - 0.25 : [ 2 3.52e-05 1.41e-04 8 ] | 0.25 - 0.255 : [ 1 1.76e-05 1.58e-04 9 ] #... | 0.265 - 0.27 : [ 1 1.76e-05 1.76e-04 10 ] | 0.27 - 0.275 : [ 2 3.52e-05 2.11e-04 12 ] | 0.275 - 0.28 : [ 1 1.76e-05 2.29e-04 13 ] #... | 0.285 - 0.29 : [ 2 3.52e-05 2.64e-04 15 ] #... | 0.295 - 0.3 : [ 1 1.76e-05 2.82e-04 16 ] | 0.3 - 0.305 : [ 1 1.76e-05 2.99e-04 17 ] | 0.305 - 0.31 : [ 1 1.76e-05 3.17e-04 18 ] #... | 0.32 - 0.325 : [ 1 1.76e-05 3.34e-04 19 ] | 0.325 - 0.33 : [ 1 1.76e-05 3.52e-04 20 ] | 0.33 - 0.335 : [ 2 3.52e-05 3.87e-04 22 ] #... | 0.34 - 0.345 : [ 1 1.76e-05 4.05e-04 23 ] | 0.345 - 0.35 : [ 2 3.52e-05 4.40e-04 25 ] | 0.35 - 0.355 : [ 1 1.76e-05 4.58e-04 26 ] | 0.355 - 0.36 : [ 2 3.52e-05 4.93e-04 28 ] | 0.36 - 0.365 : [ 2 3.52e-05 5.28e-04 30 ] | 0.365 - 0.37 : [ 2 3.52e-05 5.63e-04 32 ] #... | 0.375 - 0.38 : [ 1 1.76e-05 5.81e-04 33 ] | 0.38 - 0.385 : [ 2 3.52e-05 6.16e-04 35 ] | 0.385 - 0.39 : [ 1 1.76e-05 6.34e-04 36 ] | 0.39 - 0.395 : [ 4 7.04e-05 7.04e-04 40 ] #... | 0.4 - 0.405 : [ 7 1.23e-04 8.27e-04 47 ] | 0.405 - 0.41 : [ 7 1.23e-04 9.50e-04 54 ] | 0.41 - 0.415 : [ 7 1.23e-04 1.07e-03 61 ] | 0.415 - 0.42 : [ 12 2.11e-04 1.28e-03 73 ] | 0.42 - 0.425 : [ 7 1.23e-04 1.41e-03 80 ] | 0.425 - 0.43 : [ 14 2.46e-04 1.65e-03 94 ] | 0.43 - 0.435 : [ 13 2.29e-04 1.88e-03 107 ] | 0.435 - 0.44 : [ 19 3.34e-04 2.22e-03 126 ] | 0.44 - 0.445 : [ 24 4.22e-04 2.64e-03 150 ] | 0.445 - 0.45 : [ 26 4.58e-04 3.10e-03 176 ] | 0.45 - 0.455 : [ 24 4.22e-04 3.52e-03 200 ] | 0.455 - 0.46 : [ 24 4.22e-04 3.94e-03 224 ] | 0.46 - 0.465 : [ 35 6.16e-04 4.56e-03 259 ] |X 0.465 - 0.47 : [ 37 6.51e-04 5.21e-03 296 ] |X 0.47 - 0.475 : [ 38 6.69e-04 5.88e-03 334 ] |X 0.475 - 0.48 : [ 40 7.04e-04 6.58e-03 374 ] |X 0.48 - 0.485 : [ 55 9.68e-04 7.55e-03 429 ] |X 0.485 - 0.49 : [ 53 9.33e-04 8.48e-03 482 ] |X 0.49 - 0.495 : [ 59 1.04e-03 9.52e-03 541 ] |X 0.495 - 0.5 : [ 45 7.92e-04 1.03e-02 586 ] |X 0.5 - 0.505 : [ 92 1.62e-03 1.19e-02 678 ] |XX 0.505 - 0.51 : [ 123 2.16e-03 1.41e-02 801 ] |XX 0.51 - 0.515 : [ 135 2.38e-03 1.65e-02 936 ] |XX 0.515 - 0.52 : [ 144 2.53e-03 1.90e-02 1080 ] |XXX 0.52 - 0.525 : [ 187 3.29e-03 2.23e-02 1267 ] |XXX 0.525 - 0.53 : [ 218 3.84e-03 2.61e-02 1485 ] |XXXX 0.53 - 0.535 : [ 249 4.38e-03 3.05e-02 1734 ] |XXXX 0.535 - 0.54 : [ 271 4.77e-03 3.53e-02 2005 ] |XXXX 0.54 - 0.545 : [ 267 4.70e-03 4.00e-02 2272 ] |XXXX 0.545 - 0.55 : [ 311 5.47e-03 4.55e-02 2583 ] |XXXXX 0.55 - 0.555 : [ 344 6.05e-03 5.15e-02 2927 ] |XXXXXX 0.555 - 0.56 : [ 391 6.88e-03 5.84e-02 3318 ] |XXXXXX 0.56 - 0.565 : [ 440 7.74e-03 6.61e-02 3758 ] |XXXXXXX 0.565 - 0.57 : [ 512 9.01e-03 7.52e-02 4270 ] |XXXXXXX 0.57 - 0.575 : [ 526 9.26e-03 8.44e-02 4796 ] |XXXXXXXXX 0.575 - 0.58 : [ 631 1.11e-02 9.55e-02 5427 ] |XXXXXXXXX 0.58 - 0.585 : [ 665 1.17e-02 1.07e-01 6092 ] |XXXXXXXXXX 0.585 - 0.59 : [ 741 1.30e-02 1.20e-01 6833 ] |XXXXXXXXXXX 0.59 - 0.595 : [ 812 1.43e-02 1.35e-01 7645 ] |XXXXXXXXXXXXX 0.595 - 0.6 : [ 904 1.59e-02 1.50e-01 8549 ] |XXXXXXXXXXXXXX 0.6 - 0.605 : [ 983 1.73e-02 1.68e-01 9532 ] |XXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1114 1.96e-02 1.87e-01 10646 ] |XXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1268 2.23e-02 2.10e-01 11914 ] |XXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1354 2.38e-02 2.34e-01 13268 ] |XXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1606 2.83e-02 2.62e-01 14874 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 1681 2.96e-02 2.91e-01 16555 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 1866 3.28e-02 3.24e-01 18421 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 2000 3.52e-02 3.59e-01 20421 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 2170 3.82e-02 3.98e-01 22591 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 2318 4.08e-02 4.38e-01 24909 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 2524 4.44e-02 4.83e-01 27433 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 2600 4.58e-02 5.29e-01 30033 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 2711 4.77e-02 5.76e-01 32744 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 2842 5.00e-02 6.26e-01 35586 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 2733 4.81e-02 6.74e-01 38319 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 2631 4.63e-02 7.21e-01 40950 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 2558 4.50e-02 7.66e-01 43508 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 2197 3.87e-02 8.04e-01 45705 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 2062 3.63e-02 8.41e-01 47767 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 1838 3.24e-02 8.73e-01 49605 ] |XXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 1531 2.69e-02 9.00e-01 51136 ] |XXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 1250 2.20e-02 9.22e-01 52386 ] |XXXXXXXXXXXXXXX 0.71 - 0.715 : [ 1077 1.90e-02 9.41e-01 53463 ] |XXXXXXXXXXXX 0.715 - 0.72 : [ 869 1.53e-02 9.56e-01 54332 ] |XXXXXXXXX 0.72 - 0.725 : [ 665 1.17e-02 9.68e-01 54997 ] |XXXXXXX 0.725 - 0.73 : [ 494 8.69e-03 9.77e-01 55491 ] |XXXXX 0.73 - 0.735 : [ 379 6.67e-03 9.83e-01 55870 ] |XXXX 0.735 - 0.74 : [ 281 4.95e-03 9.88e-01 56151 ] |XXX 0.74 - 0.745 : [ 200 3.52e-03 9.92e-01 56351 ] |XX 0.745 - 0.75 : [ 122 2.15e-03 9.94e-01 56473 ] |X 0.75 - 0.755 : [ 93 1.64e-03 9.96e-01 56566 ] |X 0.755 - 0.76 : [ 57 1.00e-03 9.97e-01 56623 ] | 0.76 - 0.765 : [ 35 6.16e-04 9.97e-01 56658 ] | 0.765 - 0.77 : [ 31 5.46e-04 9.98e-01 56689 ] | 0.77 - 0.775 : [ 20 3.52e-04 9.98e-01 56709 ] | 0.775 - 0.78 : [ 17 2.99e-04 9.98e-01 56726 ] | 0.78 - 0.785 : [ 15 2.64e-04 9.99e-01 56741 ] | 0.785 - 0.79 : [ 13 2.29e-04 9.99e-01 56754 ] | 0.79 - 0.795 : [ 8 1.41e-04 9.99e-01 56762 ] #... | 0.8 - 0.805 : [ 11 1.94e-04 9.99e-01 56773 ] #... | 0.81 - 0.815 : [ 5 8.80e-05 9.99e-01 56778 ] | 0.815 - 0.82 : [ 8 1.41e-04 9.99e-01 56786 ] | 0.82 - 0.825 : [ 6 1.06e-04 1.00e+00 56792 ] | 0.825 - 0.83 : [ 3 5.28e-05 1.00e+00 56795 ] #... | 0.835 - 0.84 : [ 1 1.76e-05 1.00e+00 56796 ] #... | 0.845 - 0.85 : [ 3 5.28e-05 1.00e+00 56799 ] | 0.85 - 0.855 : [ 3 5.28e-05 1.00e+00 56802 ] #... | 0.86 - 0.865 : [ 1 1.76e-05 1.00e+00 56803 ] | 0.865 - 0.87 : [ 1 1.76e-05 1.00e+00 56804 ] #... | 0.875 - 0.88 : [ 2 3.52e-05 1.00e+00 56806 ] | 0.88 - 0.885 : [ 1 1.76e-05 1.00e+00 56807 ] | 0.885 - 0.89 : [ 1 1.76e-05 1.00e+00 56808 ] #... | 0.9 - 0.905 : [ 3 5.28e-05 1.00e+00 56811 ] #... | 0.91 - 0.915 : [ 1 1.76e-05 1.00e+00 56812 ] #... | 0.925 - 0.93 : [ 1 1.76e-05 1.00e+00 56813 ] | 0.93 - 0.935 : [ 2 3.52e-05 1.00e+00 56815 ] SECTION IX Plate Summary SECTION X Phrap Assembly Summary ################################################################### Reads in assembly summary ------------------------------------------------------------------- Small Inserts = 205 HQ Discrepant reads = 50 Chimeric reads = 43 Suspect alignments = 242 SECTION XI Contig Information ################################################################### # Contig# Reads Contig Len C O N T I G I N F O R M A T I O N Tue Jan 10 11:24:52 2006 File: phrap.out Contig 38. 536 reads; 50153 bp (untrimmed), 50131 (trimmed). Contig 39. 576 reads; 57073 bp (untrimmed), 56973 (trimmed). Contig 40. 579 reads; 66869 bp (untrimmed), 66838 (trimmed). Contig 41. 645 reads; 69867 bp (untrimmed), 69842 (trimmed). Contig 42. 662 reads; 64645 bp (untrimmed), 63960 (trimmed). Contig 43. 663 reads; 67799 bp (untrimmed), 67755 (trimmed). Contig 44. 741 reads; 80383 bp (untrimmed), 80323 (trimmed). Contig 45. 747 reads; 76837 bp (untrimmed), 76758 (trimmed). Contig 46. 796 reads; 85729 bp (untrimmed), 85690 (trimmed). Contig 47. 984 reads; 32170 bp (untrimmed), 32149 (trimmed). Contig 48. 1124 reads; 104440 bp (untrimmed), 104181 (trimmed). Contig 49. 1181 reads; 106102 bp (untrimmed), 105768 (trimmed). Contig 50. 1474 reads; 144623 bp (untrimmed), 144549 (trimmed). Contig 51. 1653 reads; 168874 bp (untrimmed), 168454 (trimmed). Contig 52. 1690 reads; 184653 bp (untrimmed), 183994 (trimmed). Contig 53. 1831 reads; 202968 bp (untrimmed), 202912 (trimmed). Contig 54. 1858 reads; 197967 bp (untrimmed), 197944 (trimmed). Contig 55. 1976 reads; 183875 bp (untrimmed), 183843 (trimmed). Contig 56. 1980 reads; 178149 bp (untrimmed), 177393 (trimmed). Contig 57. 2049 reads; 204597 bp (untrimmed), 204466 (trimmed). Contig 58. 2340 reads; 227370 bp (untrimmed), 227350 (trimmed). Contig 59. 2342 reads; 236815 bp (untrimmed), 236804 (trimmed). Contig 60. 2547 reads; 255082 bp (untrimmed), 254784 (trimmed). Contig 61. 2733 reads; 229461 bp (untrimmed), 229412 (trimmed). Contig 62. 2973 reads; 295333 bp (untrimmed), 294910 (trimmed). Contig 63. 3493 reads; 340915 bp (untrimmed), 340834 (trimmed). Contig 64. 10543 reads; 1028779 bp (untrimmed), 1028750 (trimmed). -------------------------------------------------------------- Totals 56781 reads; 5597859 bp (untrimmed), 5586745 (trimmed). SECTION XII Histogram Of Major Contigs Trimmed Length ################################################################### Histogram of Good Contig Trimmed Length (>=2000 bp & >=10 reads) ------------------------------------------------------------------- Command: contig | grep '^Contig' | hist - 8 2000 3 10 10000000 8 2000 10000000 #Found 56 total values totalling 5575698.0000. <99566.035714 +/- 151711.772195> #Range: [ 2752 - 1028750 ] #Most likely bin: [ 4000 - 6000 ] 4 counts #Median bin: [ 46000 - 48000 ] 1 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXX 2000 - 4000 : [ 1 0.02 0.02 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 6000 : [ 4 0.07 0.09 ] |XXXXXXXXXXXXXXXXXXXX 6000 - 8000 : [ 2 0.04 0.12 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 10000 : [ 3 0.05 0.18 ] #... |XXXXXXXXXXXXXXXXXXXX 12000 - 14000 : [ 2 0.04 0.21 ] #... |XXXXXXXXXX 16000 - 18000 : [ 1 0.02 0.23 ] #... |XXXXXXXXXXXXXXXXXXXX 20000 - 22000 : [ 2 0.04 0.27 ] |XXXXXXXXXX 22000 - 24000 : [ 1 0.02 0.29 ] |XXXXXXXXXX 24000 - 26000 : [ 1 0.02 0.30 ] |XXXXXXXXXX 26000 - 28000 : [ 1 0.02 0.32 ] |XXXXXXXXXXXXXXXXXXXX 28000 - 30000 : [ 2 0.04 0.36 ] |XXXXXXXXXXXXXXXXXXXX 30000 - 32000 : [ 2 0.04 0.39 ] |XXXXXXXXXX 32000 - 34000 : [ 1 0.02 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 36000 : [ 3 0.05 0.46 ] #... |XXXXXXXXXX 40000 - 42000 : [ 1 0.02 0.48 ] #... |XXXXXXXXXX 46000 - 48000 : [ 1 0.02 0.50 ] |XXXXXXXXXX 48000 - 50000 : [ 1 0.02 0.52 ] |XXXXXXXXXX 50000 - 52000 : [ 1 0.02 0.54 ] |XXXXXXXXXX 52000 - 54000 : [ 1 0.02 0.55 ] #... |XXXXXXXXXX 56000 - 58000 : [ 1 0.02 0.57 ] #... |XXXXXXXXXX 62000 - 64000 : [ 1 0.02 0.59 ] #... |XXXXXXXXXXXXXXXXXXXX 66000 - 68000 : [ 2 0.04 0.62 ] |XXXXXXXXXX 68000 - 70000 : [ 1 0.02 0.64 ] #... |XXXXXXXXXX 76000 - 78000 : [ 1 0.02 0.66 ] #... |XXXXXXXXXX 80000 - 82000 : [ 1 0.02 0.68 ] #... |XXXXXXXXXX 84000 - 86000 : [ 1 0.02 0.70 ] #... |XXXXXXXXXXXXXXXXXXXX 104000 - 106000 : [ 2 0.04 0.73 ] #... |XXXXXXXXXX 144000 - 146000 : [ 1 0.02 0.75 ] #... |XXXXXXXXXX 168000 - 170000 : [ 1 0.02 0.77 ] #... |XXXXXXXXXX 176000 - 178000 : [ 1 0.02 0.79 ] #... |XXXXXXXXXXXXXXXXXXXX 182000 - 184000 : [ 2 0.04 0.82 ] #... |XXXXXXXXXX 196000 - 198000 : [ 1 0.02 0.84 ] #... |XXXXXXXXXX 202000 - 204000 : [ 1 0.02 0.86 ] |XXXXXXXXXX 204000 - 206000 : [ 1 0.02 0.88 ] #... |XXXXXXXXXX 226000 - 228000 : [ 1 0.02 0.89 ] |XXXXXXXXXX 228000 - 230000 : [ 1 0.02 0.91 ] #... |XXXXXXXXXX 236000 - 238000 : [ 1 0.02 0.93 ] #... |XXXXXXXXXX 254000 - 256000 : [ 1 0.02 0.95 ] #... |XXXXXXXXXX 294000 - 296000 : [ 1 0.02 0.96 ] #... |XXXXXXXXXX 340000 - 342000 : [ 1 0.02 0.98 ] #... |XXXXXXXXXX 1028000 - 1030000 : [ 1 0.02 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 10015886 C = 17880719 G = 17868863 T = 10063181 N = 353368 X = 494269 GC fraction = 0.63 Total = 56676286 ################################################################### Base Count for contigs: ------------------------------------------------------------------- A 971412 C 1823068 G 1827465 T 975768 N 146 fraction GC = 0.65 total bases = 5597859 SECTION XIII Depth ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 5597859 bases = 9.44 +- 3.80 = 0.13 +- 3.34 m1 = 1.53 m2 = 0.82 ################################################################### Histogram of All Contig Depth Values: ------------------------------------------------------------------- Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 #Found 64 total values totalling 554.5900. <8.665469 +/- 3.348362> #Range: [ 2.07 - 29.01 ] #Most likely bin: [ 9 - 9.5 ] 14 counts #Median bin: [ 8.5 - 9 ] 10 counts #Histogram Bins Count Fraction Cum_Fraction |XXX 2 - 2.5 : [ 1 0.02 0.02 ] |XXXXXX 2.5 - 3 : [ 2 0.03 0.05 ] |XXX 3 - 3.5 : [ 1 0.02 0.06 ] |XXXXXX 3.5 - 4 : [ 2 0.03 0.09 ] |XXX 4 - 4.5 : [ 1 0.02 0.11 ] #... |XXXXXX 6 - 6.5 : [ 2 0.03 0.14 ] |XXX 6.5 - 7 : [ 1 0.02 0.16 ] |XXXXXX 7 - 7.5 : [ 2 0.03 0.19 ] |XXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 8 0.12 0.31 ] |XXXXXXXXXXX 8 - 8.5 : [ 4 0.06 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 10 0.16 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 14 0.22 0.75 ] |XXXXXXXXXXXXXXXXX 9.5 - 10 : [ 6 0.09 0.84 ] |XXXXXXXXXXXXXXXXX 10 - 10.5 : [ 6 0.09 0.94 ] |XXX 10.5 - 11 : [ 1 0.02 0.95 ] |XXX 11 - 11.5 : [ 1 0.02 0.97 ] #... |XXX 14 - 14.5 : [ 1 0.02 0.98 ] #... |XXX 29 - 29.5 : [ 1 0.02 1.00 ] Histogram of Major Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000 #Found 57 total values totalling 527.7100. <9.258070 +/- 2.995981> #Range: [ 3.73 - 29.01 ] #Most likely bin: [ 9 - 9.5 ] 14 counts #Median bin: [ 9 - 9.5 ] 14 counts #Histogram Bins Count Fraction Cum_Fraction |XXX 3.5 - 4 : [ 1 0.02 0.02 ] #... |XXXXXX 6 - 6.5 : [ 2 0.04 0.05 ] |XXX 6.5 - 7 : [ 1 0.02 0.07 ] |XXXXXX 7 - 7.5 : [ 2 0.04 0.11 ] |XXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 7 0.12 0.23 ] |XXXXXXXXXXX 8 - 8.5 : [ 4 0.07 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 10 0.18 0.47 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 14 0.25 0.72 ] |XXXXXXXXXXXXXXXXX 9.5 - 10 : [ 6 0.11 0.82 ] |XXXXXXXXXXXXXXXXX 10 - 10.5 : [ 6 0.11 0.93 ] |XXX 10.5 - 11 : [ 1 0.02 0.95 ] |XXX 11 - 11.5 : [ 1 0.02 0.96 ] #... |XXX 14 - 14.5 : [ 1 0.02 0.98 ] #... |XXX 29 - 29.5 : [ 1 0.02 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 1 3 reads 785 bases = 2.07 +- 0.72 = 2.07 +- 0.72 m1 = 0.25 m2 = 0.00 Contig 2 3 reads 1119 bases = 2.53 +- 0.77 = 2.53 +- 0.77 m1 = 0.23 m2 = 0.00 Contig 3 6 reads 2211 bases = 2.65 +- 0.76 = 2.65 +- 0.76 m1 = 0.22 m2 = 0.00 Contig 4 6 reads 1447 bases = 3.46 +- 1.38 = 2.34 +- 1.07 m1 = 0.55 m2 = 0.19 Contig 7 11 reads 2554 bases = 3.73 +- 2.44 = 0.20 +- 1.83 m1 = 1.60 m2 = 0.65 Contig 6 9 reads 1441 bases = 3.90 +- 2.51 = 3.90 +- 2.51 m1 = 1.61 m2 = 0.00 Contig 5 7 reads 1426 bases = 4.41 +- 2.18 = 0.73 +- 1.10 m1 = 1.08 m2 = 0.89 Contig 10 29 reads 4346 bases = 6.31 +- 2.36 = 2.78 +- 3.21 m1 = 0.88 m2 = -1.18 Contig 9 25 reads 3518 bases = 6.39 +- 3.92 = 1.59 +- 3.25 m1 = 2.40 m2 = 1.19 Contig 19 101 reads 13176 bases = 6.78 +- 2.35 = 0.03 +- 3.34 m1 = 0.81 m2 = -1.40 Contig 16 74 reads 9616 bases = 7.29 +- 2.78 = 1.52 +- 4.28 m1 = 1.06 m2 = -2.66 Contig 12 61 reads 7509 bases = 7.43 +- 2.25 = 0.60 +- 2.74 m1 = 0.68 m2 = -0.60 Contig 26 247 reads 30330 bases = 7.60 +- 3.33 = 0.42 +- 2.87 m1 = 1.46 m2 = 0.71 Contig 17 77 reads 9306 bases = 7.65 +- 3.20 = 0.19 +- 1.92 m1 = 1.34 m2 = 1.63 Contig 18 83 reads 9716 bases = 7.68 +- 3.40 = 0.15 +- 2.11 m1 = 1.50 m2 = 1.77 Contig 20 117 reads 13791 bases = 7.82 +- 3.25 = 0.36 +- 3.09 m1 = 1.35 m2 = 0.24 Contig 8 14 reads 1735 bases = 7.86 +- 4.71 = 3.36 +- 2.13 m1 = 2.83 m2 = 4.42 Contig 28 253 reads 29681 bases = 7.90 +- 3.86 = 0.29 +- 2.88 m1 = 1.88 m2 = 1.64 Contig 24 219 reads 25074 bases = 7.93 +- 2.42 = 0.48 +- 3.75 m1 = 0.74 m2 = -2.06 Contig 29 292 reads 34733 bases = 7.93 +- 3.30 = 0.43 +- 3.43 m1 = 1.38 m2 = -0.21 Contig 39 576 reads 57073 bases = 9.45 +- 3.48 = 0.50 +- 2.77 m1 = 1.28 m2 = 1.10 Contig 42 662 reads 64645 bases = 9.46 +- 3.05 = 0.06 +- 2.81 m1 = 0.98 m2 = 0.35 Contig 50 1474 reads 144623 bases = 9.48 +- 3.32 = 0.01 +- 3.59 m1 = 1.16 m2 = -0.46 Contig 58 2340 reads 227370 bases = 9.48 +- 3.38 = 0.10 +- 3.27 m1 = 1.21 m2 = 0.19 Contig 64 10543 reads 1028779 bases = 9.50 +- 3.51 = 0.03 +- 3.33 m1 = 1.29 m2 = 0.31 Contig 63 3493 reads 340915 bases = 9.52 +- 3.12 = 0.10 +- 3.15 m1 = 1.02 m2 = -0.05 Contig 31 327 reads 31975 bases = 9.67 +- 3.27 = 0.05 +- 3.63 m1 = 1.10 m2 = -0.63 Contig 30 302 reads 28455 bases = 9.74 +- 3.58 = 0.27 +- 2.32 m1 = 1.32 m2 = 1.85 Contig 14 65 reads 6186 bases = 9.97 +- 4.63 = 0.49 +- 3.63 m1 = 2.15 m2 = 2.07 Contig 48 1124 reads 104440 bases = 9.98 +- 3.50 = 0.18 +- 3.53 m1 = 1.23 m2 = -0.05 Contig 38 536 reads 50153 bases = 10.00 +- 3.58 = 0.49 +- 3.73 m1 = 1.28 m2 = -0.29 Contig 55 1976 reads 183875 bases = 10.03 +- 3.64 = 0.03 +- 3.34 m1 = 1.32 m2 = 0.52 Contig 56 1980 reads 178149 bases = 10.30 +- 3.50 = 0.19 +- 3.41 m1 = 1.19 m2 = 0.17 Contig 49 1181 reads 106102 bases = 10.34 +- 4.07 = -0.04 +- 3.45 m1 = 1.60 m2 = 1.17 Contig 13 64 reads 5449 bases = 10.41 +- 5.97 = 1.47 +- 4.26 m1 = 3.42 m2 = 4.37 Contig 11 56 reads 5026 bases = 10.46 +- 4.84 = 0.40 +- 2.32 m1 = 2.24 m2 = 4.52 Contig 21 199 reads 17633 bases = 10.69 +- 3.83 = 0.38 +- 3.76 m1 = 1.37 m2 = 0.14 Contig 61 2733 reads 229461 bases = 11.05 +- 3.58 = 0.07 +- 3.77 m1 = 1.16 m2 = -0.35 Contig 15 68 reads 4512 bases = 14.20 +- 5.93 = 2.46 +- 3.34 m1 = 2.48 m2 = 6.01 Contig 47 984 reads 32170 bases = 29.01 +- 9.31 = 1.10 +- 6.07 m1 = 2.99 m2 = 12.46 SECTION XIV Histograms Of Number Of Reads Per Contig And Lengths Of Contigs ################################################################### Histogram of Number of Reads per Contig: ------------------------------------------------------------------- Command: hist contig.grep 3 1 #Found 64 total values totalling 56781.0000. <887.203125 +/- 1493.386098> #Range: [ 3 - 10543 ] #Most likely bin: [ 6 - 7 ] 2 counts #Median bin: [ 331 - 332 ] 1 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 4 : [ 2 0.03 0.03 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 7 : [ 2 0.03 0.06 ] |XXXXXXXXXXXXXXXXXXXX 7 - 8 : [ 1 0.02 0.08 ] #... |XXXXXXXXXXXXXXXXXXXX 9 - 10 : [ 1 0.02 0.09 ] #... |XXXXXXXXXXXXXXXXXXXX 11 - 12 : [ 1 0.02 0.11 ] #... |XXXXXXXXXXXXXXXXXXXX 14 - 15 : [ 1 0.02 0.12 ] #... |XXXXXXXXXXXXXXXXXXXX 25 - 26 : [ 1 0.02 0.14 ] #... |XXXXXXXXXXXXXXXXXXXX 29 - 30 : [ 1 0.02 0.16 ] #... |XXXXXXXXXXXXXXXXXXXX 56 - 57 : [ 1 0.02 0.17 ] #... |XXXXXXXXXXXXXXXXXXXX 61 - 62 : [ 1 0.02 0.19 ] #... |XXXXXXXXXXXXXXXXXXXX 64 - 65 : [ 1 0.02 0.20 ] |XXXXXXXXXXXXXXXXXXXX 65 - 66 : [ 1 0.02 0.22 ] #... |XXXXXXXXXXXXXXXXXXXX 68 - 69 : [ 1 0.02 0.23 ] #... |XXXXXXXXXXXXXXXXXXXX 74 - 75 : [ 1 0.02 0.25 ] #... |XXXXXXXXXXXXXXXXXXXX 77 - 78 : [ 1 0.02 0.27 ] #... |XXXXXXXXXXXXXXXXXXXX 83 - 84 : [ 1 0.02 0.28 ] #... |XXXXXXXXXXXXXXXXXXXX 101 - 102 : [ 1 0.02 0.30 ] #... |XXXXXXXXXXXXXXXXXXXX 117 - 118 : [ 1 0.02 0.31 ] #... |XXXXXXXXXXXXXXXXXXXX 199 - 200 : [ 1 0.02 0.33 ] |XXXXXXXXXXXXXXXXXXXX 200 - 201 : [ 1 0.02 0.34 ] #... |XXXXXXXXXXXXXXXXXXXX 209 - 210 : [ 1 0.02 0.36 ] #... |XXXXXXXXXXXXXXXXXXXX 219 - 220 : [ 1 0.02 0.38 ] #... |XXXXXXXXXXXXXXXXXXXX 227 - 228 : [ 1 0.02 0.39 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 247 - 248 : [ 2 0.03 0.42 ] #... |XXXXXXXXXXXXXXXXXXXX 253 - 254 : [ 1 0.02 0.44 ] #... |XXXXXXXXXXXXXXXXXXXX 292 - 293 : [ 1 0.02 0.45 ] #... |XXXXXXXXXXXXXXXXXXXX 302 - 303 : [ 1 0.02 0.47 ] #... |XXXXXXXXXXXXXXXXXXXX 327 - 328 : [ 1 0.02 0.48 ] #... |XXXXXXXXXXXXXXXXXXXX 331 - 332 : [ 1 0.02 0.50 ] #... |XXXXXXXXXXXXXXXXXXXX 359 - 360 : [ 1 0.02 0.52 ] |XXXXXXXXXXXXXXXXXXXX 360 - 361 : [ 1 0.02 0.53 ] #... |XXXXXXXXXXXXXXXXXXXX 447 - 448 : [ 1 0.02 0.55 ] #... |XXXXXXXXXXXXXXXXXXXX 457 - 458 : [ 1 0.02 0.56 ] #... |XXXXXXXXXXXXXXXXXXXX 510 - 511 : [ 1 0.02 0.58 ] #... |XXXXXXXXXXXXXXXXXXXX 536 - 537 : [ 1 0.02 0.59 ] #... |XXXXXXXXXXXXXXXXXXXX 576 - 577 : [ 1 0.02 0.61 ] #... |XXXXXXXXXXXXXXXXXXXX 579 - 580 : [ 1 0.02 0.62 ] #... |XXXXXXXXXXXXXXXXXXXX 645 - 646 : [ 1 0.02 0.64 ] #... |XXXXXXXXXXXXXXXXXXXX 662 - 663 : [ 1 0.02 0.66 ] |XXXXXXXXXXXXXXXXXXXX 663 - 664 : [ 1 0.02 0.67 ] #... |XXXXXXXXXXXXXXXXXXXX 741 - 742 : [ 1 0.02 0.69 ] #... |XXXXXXXXXXXXXXXXXXXX 747 - 748 : [ 1 0.02 0.70 ] #... |XXXXXXXXXXXXXXXXXXXX 796 - 797 : [ 1 0.02 0.72 ] #... |XXXXXXXXXXXXXXXXXXXX 984 - 985 : [ 1 0.02 0.73 ] #... |XXXXXXXXXXXXXXXXXXXX 1124 - 1125 : [ 1 0.02 0.75 ] #... |XXXXXXXXXXXXXXXXXXXX 1181 - 1182 : [ 1 0.02 0.77 ] #... |XXXXXXXXXXXXXXXXXXXX 1474 - 1475 : [ 1 0.02 0.78 ] #... |XXXXXXXXXXXXXXXXXXXX 1653 - 1654 : [ 1 0.02 0.80 ] #... |XXXXXXXXXXXXXXXXXXXX 1690 - 1691 : [ 1 0.02 0.81 ] #... |XXXXXXXXXXXXXXXXXXXX 1831 - 1832 : [ 1 0.02 0.83 ] #... |XXXXXXXXXXXXXXXXXXXX 1858 - 1859 : [ 1 0.02 0.84 ] #... |XXXXXXXXXXXXXXXXXXXX 1976 - 1977 : [ 1 0.02 0.86 ] #... |XXXXXXXXXXXXXXXXXXXX 1980 - 1981 : [ 1 0.02 0.88 ] #... |XXXXXXXXXXXXXXXXXXXX 2049 - 2050 : [ 1 0.02 0.89 ] #... |XXXXXXXXXXXXXXXXXXXX 2340 - 2341 : [ 1 0.02 0.91 ] #... |XXXXXXXXXXXXXXXXXXXX 2342 - 2343 : [ 1 0.02 0.92 ] #... |XXXXXXXXXXXXXXXXXXXX 2547 - 2548 : [ 1 0.02 0.94 ] #... |XXXXXXXXXXXXXXXXXXXX 2733 - 2734 : [ 1 0.02 0.95 ] #... |XXXXXXXXXXXXXXXXXXXX 2973 - 2974 : [ 1 0.02 0.97 ] #... |XXXXXXXXXXXXXXXXXXXX 3493 - 3494 : [ 1 0.02 0.98 ] #... |XXXXXXXXXXXXXXXXXXXX 10543 - 10544 : [ 1 0.02 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 64 total values totalling 5597859.0000. <87466.546875 +/- 145574.481410> #Range: [ 785 - 1028779 ] #Most likely bin: [ 1000 - 2000 ] 5 counts #Median bin: [ 34000 - 35000 ] 1 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXX 0 - 1000 : [ 1 0.02 0.02 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 5 0.08 0.09 ] |XXXXXXXXXXXXXXXX 2000 - 3000 : [ 2 0.03 0.12 ] |XXXXXXXX 3000 - 4000 : [ 1 0.02 0.14 ] |XXXXXXXXXXXXXXXX 4000 - 5000 : [ 2 0.03 0.17 ] |XXXXXXXXXXXXXXXX 5000 - 6000 : [ 2 0.03 0.20 ] |XXXXXXXX 6000 - 7000 : [ 1 0.02 0.22 ] |XXXXXXXX 7000 - 8000 : [ 1 0.02 0.23 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 9000 - 10000 : [ 3 0.05 0.28 ] #... |XXXXXXXXXXXXXXXX 13000 - 14000 : [ 2 0.03 0.31 ] #... |XXXXXXXX 17000 - 18000 : [ 1 0.02 0.33 ] #... |XXXXXXXX 20000 - 21000 : [ 1 0.02 0.34 ] |XXXXXXXX 21000 - 22000 : [ 1 0.02 0.36 ] |XXXXXXXX 22000 - 23000 : [ 1 0.02 0.38 ] #... |XXXXXXXX 25000 - 26000 : [ 1 0.02 0.39 ] #... |XXXXXXXX 27000 - 28000 : [ 1 0.02 0.41 ] |XXXXXXXX 28000 - 29000 : [ 1 0.02 0.42 ] |XXXXXXXX 29000 - 30000 : [ 1 0.02 0.44 ] |XXXXXXXX 30000 - 31000 : [ 1 0.02 0.45 ] |XXXXXXXX 31000 - 32000 : [ 1 0.02 0.47 ] |XXXXXXXX 32000 - 33000 : [ 1 0.02 0.48 ] #... |XXXXXXXX 34000 - 35000 : [ 1 0.02 0.50 ] |XXXXXXXX 35000 - 36000 : [ 1 0.02 0.52 ] |XXXXXXXX 36000 - 37000 : [ 1 0.02 0.53 ] #... |XXXXXXXX 41000 - 42000 : [ 1 0.02 0.55 ] #... |XXXXXXXX 47000 - 48000 : [ 1 0.02 0.56 ] |XXXXXXXX 48000 - 49000 : [ 1 0.02 0.58 ] #... |XXXXXXXX 50000 - 51000 : [ 1 0.02 0.59 ] #... |XXXXXXXX 52000 - 53000 : [ 1 0.02 0.61 ] #... |XXXXXXXX 57000 - 58000 : [ 1 0.02 0.62 ] #... |XXXXXXXX 64000 - 65000 : [ 1 0.02 0.64 ] #... |XXXXXXXX 66000 - 67000 : [ 1 0.02 0.66 ] |XXXXXXXX 67000 - 68000 : [ 1 0.02 0.67 ] #... |XXXXXXXX 69000 - 70000 : [ 1 0.02 0.69 ] #... |XXXXXXXX 76000 - 77000 : [ 1 0.02 0.70 ] #... |XXXXXXXX 80000 - 81000 : [ 1 0.02 0.72 ] #... |XXXXXXXX 85000 - 86000 : [ 1 0.02 0.73 ] #... |XXXXXXXX 104000 - 105000 : [ 1 0.02 0.75 ] #... |XXXXXXXX 106000 - 107000 : [ 1 0.02 0.77 ] #... |XXXXXXXX 144000 - 145000 : [ 1 0.02 0.78 ] #... |XXXXXXXX 168000 - 169000 : [ 1 0.02 0.80 ] #... |XXXXXXXX 178000 - 179000 : [ 1 0.02 0.81 ] #... |XXXXXXXX 183000 - 184000 : [ 1 0.02 0.83 ] |XXXXXXXX 184000 - 185000 : [ 1 0.02 0.84 ] #... |XXXXXXXX 197000 - 198000 : [ 1 0.02 0.86 ] #... |XXXXXXXX 202000 - 203000 : [ 1 0.02 0.88 ] #... |XXXXXXXX 204000 - 205000 : [ 1 0.02 0.89 ] #... |XXXXXXXX 227000 - 228000 : [ 1 0.02 0.91 ] #... |XXXXXXXX 229000 - 230000 : [ 1 0.02 0.92 ] #... |XXXXXXXX 236000 - 237000 : [ 1 0.02 0.94 ] #... |XXXXXXXX 255000 - 256000 : [ 1 0.02 0.95 ] #... |XXXXXXXX 295000 - 296000 : [ 1 0.02 0.97 ] #... |XXXXXXXX 340000 - 341000 : [ 1 0.02 0.98 ] #... |XXXXXXXX 1028000 - 1029000 : [ 1 0.02 1.00 ] SECTION XV Assembled Average Insert Sizes ################################################################### Histogram of Assembled Average Insert Sizes: ------------------------------------------------------------------- Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list Command: /usr/xpg4/bin/grep BHGA reads.list > grep.reads.list.BHGA Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BHGA 4 500 #Found 9432 total values totalling 39727925.0000. <4212.036154 +/- 22141.462535> #Range: [ 1047 - 890868 ] #Most likely bin: [ 3000 - 3500 ] 5872 counts #Median bin: [ 3000 - 3500 ] 5872 counts #Histogram Bins Count Fraction Cum_Fraction | 1000 - 1500 : [ 21 0.00 0.00 ] | 1500 - 2000 : [ 26 0.00 0.00 ] | 2000 - 2500 : [ 11 0.00 0.01 ] |XXXXXXXXXXXXXXX 2500 - 3000 : [ 2233 0.24 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 5872 0.62 0.87 ] |XXXXXXXX 3500 - 4000 : [ 1222 0.13 1.00 ] #... | 4500 - 5000 : [ 1 0.00 1.00 ] | 5000 - 5500 : [ 1 0.00 1.00 ] #... | 9000 - 9500 : [ 1 0.00 1.00 ] #... | 10500 - 11000 : [ 1 0.00 1.00 ] #... | 13500 - 14000 : [ 1 0.00 1.00 ] #... | 16000 - 16500 : [ 1 0.00 1.00 ] #... | 29000 - 29500 : [ 1 0.00 1.00 ] | 29500 - 30000 : [ 2 0.00 1.00 ] | 30000 - 30500 : [ 1 0.00 1.00 ] #... | 32500 - 33000 : [ 1 0.00 1.00 ] #... | 33500 - 34000 : [ 1 0.00 1.00 ] #... | 35500 - 36000 : [ 1 0.00 1.00 ] #... | 42000 - 42500 : [ 2 0.00 1.00 ] #... | 48000 - 48500 : [ 1 0.00 1.00 ] | 48500 - 49000 : [ 1 0.00 1.00 ] #... | 50000 - 50500 : [ 1 0.00 1.00 ] #... | 66500 - 67000 : [ 1 0.00 1.00 ] #... | 74500 - 75000 : [ 1 0.00 1.00 ] #... | 79000 - 79500 : [ 1 0.00 1.00 ] #... | 91500 - 92000 : [ 1 0.00 1.00 ] | 92000 - 92500 : [ 1 0.00 1.00 ] #... | 97000 - 97500 : [ 1 0.00 1.00 ] | 97500 - 98000 : [ 1 0.00 1.00 ] #... | 112000 - 112500 : [ 1 0.00 1.00 ] #... | 127500 - 128000 : [ 1 0.00 1.00 ] #... | 144000 - 144500 : [ 1 0.00 1.00 ] #... | 150000 - 150500 : [ 1 0.00 1.00 ] #... | 165000 - 165500 : [ 1 0.00 1.00 ] #... | 190000 - 190500 : [ 1 0.00 1.00 ] #... | 195000 - 195500 : [ 1 0.00 1.00 ] #... | 230000 - 230500 : [ 1 0.00 1.00 ] #... | 253000 - 253500 : [ 1 0.00 1.00 ] #... | 268000 - 268500 : [ 1 0.00 1.00 ] #... | 285000 - 285500 : [ 1 0.00 1.00 ] #... | 322500 - 323000 : [ 1 0.00 1.00 ] #... | 354500 - 355000 : [ 1 0.00 1.00 ] #... | 471000 - 471500 : [ 1 0.00 1.00 ] #... | 494500 - 495000 : [ 1 0.00 1.00 ] #... | 514500 - 515000 : [ 1 0.00 1.00 ] #... | 621500 - 622000 : [ 1 0.00 1.00 ] #... | 634000 - 634500 : [ 1 0.00 1.00 ] #... | 652000 - 652500 : [ 1 0.00 1.00 ] #... | 754000 - 754500 : [ 1 0.00 1.00 ] #... | 800000 - 800500 : [ 1 0.00 1.00 ] #... | 890500 - 891000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep BHGB reads.list > grep.reads.list.BHGB Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BHGB 4 500 #Found 10248 total values totalling 95239270.0000. <9293.449454 +/- 13116.265466> #Range: [ 1361 - 608126 ] #Most likely bin: [ 8000 - 8500 ] 2317 counts #Median bin: [ 8500 - 9000 ] 2310 counts #Histogram Bins Count Fraction Cum_Fraction | 1000 - 1500 : [ 3 0.00 0.00 ] | 1500 - 2000 : [ 2 0.00 0.00 ] | 2000 - 2500 : [ 8 0.00 0.00 ] | 2500 - 3000 : [ 10 0.00 0.00 ] | 3000 - 3500 : [ 14 0.00 0.00 ] | 3500 - 4000 : [ 17 0.00 0.01 ] | 4000 - 4500 : [ 7 0.00 0.01 ] | 4500 - 5000 : [ 17 0.00 0.01 ] | 5000 - 5500 : [ 12 0.00 0.01 ] | 5500 - 6000 : [ 12 0.00 0.01 ] | 6000 - 6500 : [ 28 0.00 0.01 ] |X 6500 - 7000 : [ 58 0.01 0.02 ] |XXXXX 7000 - 7500 : [ 263 0.03 0.04 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1713 0.17 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 2317 0.23 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 2310 0.23 0.66 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 2156 0.21 0.87 ] |XXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 1083 0.11 0.98 ] |XXX 10000 - 10500 : [ 167 0.02 1.00 ] | 10500 - 11000 : [ 3 0.00 1.00 ] #... | 14000 - 14500 : [ 1 0.00 1.00 ] #... | 34000 - 34500 : [ 1 0.00 1.00 ] #... | 42000 - 42500 : [ 1 0.00 1.00 ] #... | 76500 - 77000 : [ 1 0.00 1.00 ] #... | 87500 - 88000 : [ 1 0.00 1.00 ] #... | 95500 - 96000 : [ 3 0.00 1.00 ] | 96000 - 96500 : [ 8 0.00 1.00 ] | 96500 - 97000 : [ 6 0.00 1.00 ] | 97000 - 97500 : [ 2 0.00 1.00 ] | 97500 - 98000 : [ 7 0.00 1.00 ] #... | 109000 - 109500 : [ 1 0.00 1.00 ] #... | 112500 - 113000 : [ 1 0.00 1.00 ] #... | 126000 - 126500 : [ 1 0.00 1.00 ] #... | 167500 - 168000 : [ 1 0.00 1.00 ] #... | 178000 - 178500 : [ 1 0.00 1.00 ] #... | 232000 - 232500 : [ 1 0.00 1.00 ] #... | 258000 - 258500 : [ 1 0.00 1.00 ] #... | 263000 - 263500 : [ 1 0.00 1.00 ] #... | 265500 - 266000 : [ 1 0.00 1.00 ] #... | 274500 - 275000 : [ 1 0.00 1.00 ] #... | 276000 - 276500 : [ 1 0.00 1.00 ] #... | 281000 - 281500 : [ 1 0.00 1.00 ] #... | 333500 - 334000 : [ 1 0.00 1.00 ] #... | 396500 - 397000 : [ 1 0.00 1.00 ] #... | 416000 - 416500 : [ 1 0.00 1.00 ] #... | 471000 - 471500 : [ 1 0.00 1.00 ] #... | 608000 - 608500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep BHGC reads.list > grep.reads.list.BHGC Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BHGC 4 500 #Found 1417 total values totalling 54701434.0000. <38603.693719 +/- 7719.438130> #Range: [ 20751 - 131547 ] #Most likely bin: [ 34500 - 35000 ] 70 counts #Median bin: [ 37500 - 38000 ] 65 counts #Histogram Bins Count Fraction Cum_Fraction |X 20500 - 21000 : [ 1 0.00 0.00 ] |X 21000 - 21500 : [ 1 0.00 0.00 ] #... |X 22000 - 22500 : [ 1 0.00 0.00 ] #... |X 25000 - 25500 : [ 1 0.00 0.00 ] #... |X 26000 - 26500 : [ 2 0.00 0.00 ] #... |X 27000 - 27500 : [ 1 0.00 0.00 ] |X 27500 - 28000 : [ 1 0.00 0.01 ] #... |X 28500 - 29000 : [ 2 0.00 0.01 ] |XX 29000 - 29500 : [ 3 0.00 0.01 ] |XXXXXXXX 29500 - 30000 : [ 14 0.01 0.02 ] |XXX 30000 - 30500 : [ 6 0.00 0.02 ] |XXXXXX 30500 - 31000 : [ 11 0.01 0.03 ] |XXXXXXXXXX 31000 - 31500 : [ 17 0.01 0.04 ] |XXXXXXXXXXXXXX 31500 - 32000 : [ 25 0.02 0.06 ] |XXXXXXXXXXXXXXX 32000 - 32500 : [ 26 0.02 0.08 ] |XXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 33 0.02 0.10 ] |XXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 37 0.03 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 55 0.04 0.17 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 45 0.03 0.20 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 70 0.05 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 58 0.04 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 58 0.04 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 54 0.04 0.37 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 67 0.05 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 68 0.05 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 65 0.05 0.51 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 61 0.04 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 63 0.04 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 61 0.04 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 43 0.03 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 57 0.04 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 47 0.03 0.74 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 44 0.03 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 48 0.03 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 41 0.03 0.84 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 53 0.04 0.88 ] |XXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 35 0.02 0.90 ] |XXXXXXXXXXXXXXX 43500 - 44000 : [ 27 0.02 0.92 ] |XXXXXXXXXXXX 44000 - 44500 : [ 21 0.01 0.93 ] |XXXXXXXXXXX 44500 - 45000 : [ 20 0.01 0.95 ] |XXXXXXXXXX 45000 - 45500 : [ 18 0.01 0.96 ] |XXXXXXX 45500 - 46000 : [ 13 0.01 0.97 ] |XXXXXXXXXX 46000 - 46500 : [ 17 0.01 0.98 ] |XXX 46500 - 47000 : [ 6 0.00 0.99 ] #... |X 54000 - 54500 : [ 1 0.00 0.99 ] #... |X 56000 - 56500 : [ 1 0.00 0.99 ] #... |X 57500 - 58000 : [ 1 0.00 0.99 ] #... |X 58500 - 59000 : [ 1 0.00 0.99 ] #... |X 62000 - 62500 : [ 1 0.00 0.99 ] |X 62500 - 63000 : [ 1 0.00 0.99 ] #... |X 65000 - 65500 : [ 1 0.00 0.99 ] |X 65500 - 66000 : [ 2 0.00 0.99 ] |X 66000 - 66500 : [ 1 0.00 0.99 ] |X 66500 - 67000 : [ 1 0.00 0.99 ] |X 67000 - 67500 : [ 1 0.00 0.99 ] |X 67500 - 68000 : [ 1 0.00 1.00 ] #... |X 119500 - 120000 : [ 1 0.00 1.00 ] #... |X 123000 - 123500 : [ 1 0.00 1.00 ] |X 123500 - 124000 : [ 1 0.00 1.00 ] #... |X 124500 - 125000 : [ 1 0.00 1.00 ] #... |X 128500 - 129000 : [ 1 0.00 1.00 ] |X 129000 - 129500 : [ 1 0.00 1.00 ] #... |X 131500 - 132000 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes: ------------------------------------------------------------------- Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out # BHGC 38053 +- 4104 (n=718) # BHGA 3145 +- 1273 (n=4653) # BHGB 8550 +- 1052 (n=5054) SECTION XVI Comparison Of Actual And Theoretical Assembly ################################################################### 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 724.028594 bp, 56781 reads, genome size 4366908 bp ------------------------------------------------------------------- Command: idealAssembly 4366908 56781 724.028594 Genome = 4366908 bases Nreads = 56781 readLength = 724.028594 Depth = 9.41 N_contigs = N_gaps = 5 mean gap size = 76 bases mean contig size = 12262 reads (~ 943014 bases) %cover = 99.99 %singlet = 0.00 assembly size = 4366552 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 1 contigs containing at least 20575 reads each SECTION XVII Everything Else * 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 Number of reads with X's: 13059 Number of reads with percent X's >= 20%: 74 = 0.1% Number of reads with percent X's >= 50%: 49 = 0.1% Number of reads with percent X's >= 80%: 8 = 0.0% Total reads in project: 56970 Total bp X'd : 494269 reads >= 20% >= 50% >= 80% screened Nr with L09136 10550 69 48 8 Nr with pCC1Fos 2451 0 0 0 Nr with pMCL200_JGI_XZX+XZK 58 5 1 0 ################################################################### Contam Summary with *.singlets: ------------------------------------------------------------------- Command: contam_summary -c -s -g Number of reads with X's: 54 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 reads in project: 189 Total bp X'd : 2123 reads >= 20% >= 50% >= 80% screened Nr with L09136 11 0 0 0 Nr with pCC1Fos 43 0 0 0 File generated in /psf/project/microbe5/4001428/edit_dir.09Jan06.QD