SECTION I Assembly QD Report ################################################################### Phrap Assembly QC Date: 12-09-2005 ------------------------------------------------------------------- SECTION II Project Information Summary ################################################################### Project information from 'PROJECTS' db ------------------------------------------------------------------- # Project GenusSpecies TaxID Size(KBases) 4001426 Acidovorax 1683 NULL 4600 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: 4857790 # phrap: 4183992 # db: 4600000 4547260 +/- 277593 SECTION V Read Accounting And Quality ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #lanes Q20 Pass Rate Q20 Avg Read Len BHFI.9-12 28416 98.20 776.22 BHFN.9-44 26112 96.47 723.36 BHFO.5-44 10752 95.11 590.94 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s BHFI 236 118 98.24 774.76 118 98.16 777.68 BHFN 272 136 96.49 723.18 136 96.45 723.54 BHFO 112 56 95.18 587.52 56 95.03 594.36 BHFP 0 0 0.00 0.00 0 0.00 0.00 BHFS 0 0 0.00 0.00 0 0.00 0.00 BHFT 0 0 0.00 0.00 0 0.00 0.00 SAUT 0 0 0.00 0.00 0 0.00 0.00 SAUU 0 0 0.00 0.00 0 0.00 0.00 SAUW 0 0 0.00 0.00 0 0.00 0.00 SBAO 0 0 0.00 0.00 0 0.00 0.00 SCCF 2 1 100.00 775.00 1 98.96 788.00 ################################################################### reads2plates summary ------------------------------------------------------------------- plate(s) reads clones N/plate avg% LIBRARY @ 148 28391 14200 95.95 99.94 BHFI @ 56 10752 5376 96.00 100.00 BHFO @ 136 26112 13056 96.00 100.00 BHFN @ ] 65255 32632 95.98 cumulative total@@ LIBRARY PLATE ID COUNT [ BHFI 148 BHFO 56 BHFN 136 ] for 340 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 4001426_fasta.screen.trimQ15.SaF 4 50 #Found 65255 total values totalling 45869913.0000. <702.933308 +/- 224.138444> #Range: [ 0 - 989 ] #Most likely bin: [ 800 - 850 ] 19176 counts #Median bin: [ 750 - 800 ] 14241 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXX 0 - 50 : [ 3194 0.05 0.05 ] |X 50 - 100 : [ 667 0.01 0.06 ] |X 100 - 150 : [ 423 0.01 0.07 ] |X 150 - 200 : [ 472 0.01 0.07 ] |X 200 - 250 : [ 557 0.01 0.08 ] |XX 250 - 300 : [ 732 0.01 0.09 ] |XX 300 - 350 : [ 726 0.01 0.10 ] |X 350 - 400 : [ 662 0.01 0.11 ] |X 400 - 450 : [ 641 0.01 0.12 ] |X 450 - 500 : [ 699 0.01 0.13 ] |XX 500 - 550 : [ 871 0.01 0.15 ] |XXX 550 - 600 : [ 1268 0.02 0.17 ] |XXXX 600 - 650 : [ 1948 0.03 0.20 ] |XXXXXXX 650 - 700 : [ 3246 0.05 0.25 ] |XXXXXXXXXXXXXX 700 - 750 : [ 6628 0.10 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 14241 0.22 0.57 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 19176 0.29 0.86 ] |XXXXXXXXXXXXXXXXX 850 - 900 : [ 8318 0.13 0.99 ] |XX 900 - 950 : [ 765 0.01 1.00 ] | 950 - 1000 : [ 21 0.00 1.00 ] trimt JAZZ trim 15 readlength histogram for BHFP trimt JAZZ trim 15 readlength histogram for BHFS trimt JAZZ trim 15 readlength histogram for BHFT trimt JAZZ trim 15 readlength histogram for SAUT trimt JAZZ trim 15 readlength histogram for SAUU trimt JAZZ trim 15 readlength histogram for SAUW trimt JAZZ trim 15 readlength histogram for BHFI Command: /usr/xpg4/bin/grep BHFI 4001426_fasta.screen.trimQ15.SaF > reads.trim15.BHFI.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.BHFI.rl 2 50 #Found 28391 total values totalling 21041361.0000. <741.127857 +/- 199.345636> #Range: [ 0 - 989 ] #Most likely bin: [ 800 - 850 ] 9682 counts #Median bin: [ 800 - 850 ] 9682 counts #Histogram Bins Count Fraction Cum_Fraction |XXXX 0 - 50 : [ 1017 0.04 0.04 ] |X 50 - 100 : [ 176 0.01 0.04 ] |X 100 - 150 : [ 146 0.01 0.05 ] |X 150 - 200 : [ 173 0.01 0.05 ] |X 200 - 250 : [ 190 0.01 0.06 ] |X 250 - 300 : [ 192 0.01 0.07 ] |X 300 - 350 : [ 200 0.01 0.07 ] |X 350 - 400 : [ 189 0.01 0.08 ] |X 400 - 450 : [ 199 0.01 0.09 ] |X 450 - 500 : [ 225 0.01 0.10 ] |X 500 - 550 : [ 238 0.01 0.10 ] |X 550 - 600 : [ 331 0.01 0.12 ] |XX 600 - 650 : [ 476 0.02 0.13 ] |XXXX 650 - 700 : [ 853 0.03 0.16 ] |XXXXXXXXXX 700 - 750 : [ 2308 0.08 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6442 0.23 0.47 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 9682 0.34 0.81 ] |XXXXXXXXXXXXXXXXXXX 850 - 900 : [ 4697 0.17 0.98 ] |XXX 900 - 950 : [ 637 0.02 1.00 ] | 950 - 1000 : [ 20 0.00 1.00 ] trimt JAZZ trim 15 readlength histogram for BHFN Command: /usr/xpg4/bin/grep BHFN 4001426_fasta.screen.trimQ15.SaF > reads.trim15.BHFN.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.BHFN.rl 2 50 #Found 26112 total values totalling 18933293.0000. <725.080155 +/- 205.848538> #Range: [ 0 - 950 ] #Most likely bin: [ 800 - 850 ] 8580 counts #Median bin: [ 750 - 800 ] 6194 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXX 0 - 50 : [ 1231 0.05 0.05 ] |X 50 - 100 : [ 120 0.00 0.05 ] |X 100 - 150 : [ 117 0.00 0.06 ] |X 150 - 200 : [ 123 0.00 0.06 ] |X 200 - 250 : [ 146 0.01 0.07 ] |X 250 - 300 : [ 116 0.00 0.07 ] |X 300 - 350 : [ 160 0.01 0.08 ] |X 350 - 400 : [ 161 0.01 0.08 ] |X 400 - 450 : [ 203 0.01 0.09 ] |X 450 - 500 : [ 206 0.01 0.10 ] |X 500 - 550 : [ 280 0.01 0.11 ] |XX 550 - 600 : [ 396 0.02 0.12 ] |XXX 600 - 650 : [ 650 0.02 0.15 ] |XXXXX 650 - 700 : [ 1133 0.04 0.19 ] |XXXXXXXXXXXXX 700 - 750 : [ 2720 0.10 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6194 0.24 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 8580 0.33 0.86 ] |XXXXXXXXXXXXXXXX 850 - 900 : [ 3450 0.13 1.00 ] |X 900 - 950 : [ 125 0.00 1.00 ] | 950 - 1000 : [ 1 0.00 1.00 ] trimt JAZZ trim 15 readlength histogram for BHFO Command: /usr/xpg4/bin/grep BHFO 4001426_fasta.screen.trimQ15.SaF > reads.trim15.BHFO.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.BHFO.rl 2 50 #Found 10752 total values totalling 5895259.0000. <548.294178 +/- 260.968855> #Range: [ 0 - 925 ] #Most likely bin: [ 750 - 800 ] 1605 counts #Median bin: [ 650 - 700 ] 1260 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 946 0.09 0.09 ] |XXXXXXXXX 50 - 100 : [ 371 0.03 0.12 ] |XXXX 100 - 150 : [ 160 0.01 0.14 ] |XXXX 150 - 200 : [ 176 0.02 0.15 ] |XXXXXX 200 - 250 : [ 221 0.02 0.17 ] |XXXXXXXXXXX 250 - 300 : [ 424 0.04 0.21 ] |XXXXXXXXX 300 - 350 : [ 366 0.03 0.25 ] |XXXXXXXX 350 - 400 : [ 312 0.03 0.28 ] |XXXXXX 400 - 450 : [ 239 0.02 0.30 ] |XXXXXXX 450 - 500 : [ 268 0.02 0.32 ] |XXXXXXXXX 500 - 550 : [ 353 0.03 0.36 ] |XXXXXXXXXXXXX 550 - 600 : [ 541 0.05 0.41 ] |XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 822 0.08 0.48 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1260 0.12 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1600 0.15 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1605 0.15 0.90 ] |XXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 914 0.09 0.98 ] |XXXX 850 - 900 : [ 171 0.02 1.00 ] | 900 - 950 : [ 3 0.00 1.00 ] trimt JAZZ trim 15 readlength histogram for SBAO trimt JAZZ trim 15 readlength histogram for SCCF SECTION VI Assembly Parameters ################################################################### Assembly parameters ------------------------------------------------------------------- phrap version SPS - 4.18 SUN Solaris 7,8 Score matrix /psf/QC/Applications/pphrap/matrix/score_matrix A C G T N X A 1 -2 -2 -2 0 0 C -2 1 -2 -2 0 0 G -2 -2 1 -2 0 0 T -2 -2 -2 1 0 0 N 0 0 0 0 0 0 X 0 0 0 0 0 0 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 SECTION VII Library Screening ################################################################### Library vector screening ------------------------------------------------------------------- BHFI.000001.000100 pUC18.fa pUC18.fa LRS.fasta BHFI.000101.000200 pUC18.fa pUC18.fa LRS.fasta BHFN.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta BHFN.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta BHFO.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta BHFI.000001.000100 pUC18.fa pUC18.fa LRS.fasta BHFI.000101.000200 pUC18.fa pUC18.fa LRS.fasta BHFN.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta BHFN.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta BHFO.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta SECTION VIII GC Content ################################################################### GC content histogram: ------------------------------------------------------------------- Command: /bin/nawk '{print $5+$6}' GC.4001426_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 # GC.4001426_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 62222 total values totalling 40208.4330. <0.646209 +/- 0.070799> #Range: [ 0 - 1 ] #Most likely bin: [ 0.67 - 0.675 ] 2602 counts #Median bin: [ 0.655 - 0.66 ] 2564 counts #Entropy = 5.5911 bits | 0 - 0.005 : [ 2 3.21e-05 3.21e-05 2 ] #... | 0.07 - 0.075 : [ 1 1.61e-05 4.82e-05 3 ] #... | 0.11 - 0.115 : [ 1 1.61e-05 6.43e-05 4 ] #... | 0.165 - 0.17 : [ 1 1.61e-05 8.04e-05 5 ] | 0.17 - 0.175 : [ 1 1.61e-05 9.64e-05 6 ] #... | 0.185 - 0.19 : [ 2 3.21e-05 1.29e-04 8 ] | 0.19 - 0.195 : [ 1 1.61e-05 1.45e-04 9 ] | 0.195 - 0.2 : [ 2 3.21e-05 1.77e-04 11 ] #... | 0.205 - 0.21 : [ 1 1.61e-05 1.93e-04 12 ] | 0.21 - 0.215 : [ 2 3.21e-05 2.25e-04 14 ] | 0.215 - 0.22 : [ 1 1.61e-05 2.41e-04 15 ] | 0.22 - 0.225 : [ 2 3.21e-05 2.73e-04 17 ] #... | 0.23 - 0.235 : [ 2 3.21e-05 3.05e-04 19 ] | 0.235 - 0.24 : [ 3 4.82e-05 3.54e-04 22 ] | 0.24 - 0.245 : [ 9 1.45e-04 4.98e-04 31 ] | 0.245 - 0.25 : [ 4 6.43e-05 5.63e-04 35 ] | 0.25 - 0.255 : [ 5 8.04e-05 6.43e-04 40 ] | 0.255 - 0.26 : [ 3 4.82e-05 6.91e-04 43 ] | 0.26 - 0.265 : [ 12 1.93e-04 8.84e-04 55 ] | 0.265 - 0.27 : [ 8 1.29e-04 1.01e-03 63 ] | 0.27 - 0.275 : [ 8 1.29e-04 1.14e-03 71 ] | 0.275 - 0.28 : [ 10 1.61e-04 1.30e-03 81 ] | 0.28 - 0.285 : [ 17 2.73e-04 1.58e-03 98 ] | 0.285 - 0.29 : [ 14 2.25e-04 1.80e-03 112 ] | 0.29 - 0.295 : [ 10 1.61e-04 1.96e-03 122 ] | 0.295 - 0.3 : [ 17 2.73e-04 2.23e-03 139 ] | 0.3 - 0.305 : [ 16 2.57e-04 2.49e-03 155 ] | 0.305 - 0.31 : [ 26 4.18e-04 2.91e-03 181 ] | 0.31 - 0.315 : [ 26 4.18e-04 3.33e-03 207 ] | 0.315 - 0.32 : [ 21 3.38e-04 3.66e-03 228 ] | 0.32 - 0.325 : [ 23 3.70e-04 4.03e-03 251 ] | 0.325 - 0.33 : [ 28 4.50e-04 4.48e-03 279 ] | 0.33 - 0.335 : [ 31 4.98e-04 4.98e-03 310 ] |X 0.335 - 0.34 : [ 35 5.63e-04 5.54e-03 345 ] |X 0.34 - 0.345 : [ 44 7.07e-04 6.25e-03 389 ] |X 0.345 - 0.35 : [ 39 6.27e-04 6.88e-03 428 ] |X 0.35 - 0.355 : [ 41 6.59e-04 7.54e-03 469 ] |X 0.355 - 0.36 : [ 46 7.39e-04 8.28e-03 515 ] |X 0.36 - 0.365 : [ 42 6.75e-04 8.95e-03 557 ] |X 0.365 - 0.37 : [ 53 8.52e-04 9.80e-03 610 ] |X 0.37 - 0.375 : [ 62 9.96e-04 1.08e-02 672 ] |X 0.375 - 0.38 : [ 73 1.17e-03 1.20e-02 745 ] |X 0.38 - 0.385 : [ 63 1.01e-03 1.30e-02 808 ] |X 0.385 - 0.39 : [ 62 9.96e-04 1.40e-02 870 ] |X 0.39 - 0.395 : [ 61 9.80e-04 1.50e-02 931 ] |X 0.395 - 0.4 : [ 54 8.68e-04 1.58e-02 985 ] |X 0.4 - 0.405 : [ 75 1.21e-03 1.70e-02 1060 ] |X 0.405 - 0.41 : [ 72 1.16e-03 1.82e-02 1132 ] |X 0.41 - 0.415 : [ 63 1.01e-03 1.92e-02 1195 ] |X 0.415 - 0.42 : [ 83 1.33e-03 2.05e-02 1278 ] |X 0.42 - 0.425 : [ 81 1.30e-03 2.18e-02 1359 ] |X 0.425 - 0.43 : [ 90 1.45e-03 2.33e-02 1449 ] |X 0.43 - 0.435 : [ 65 1.04e-03 2.43e-02 1514 ] |X 0.435 - 0.44 : [ 73 1.17e-03 2.55e-02 1587 ] |X 0.44 - 0.445 : [ 92 1.48e-03 2.70e-02 1679 ] |X 0.445 - 0.45 : [ 95 1.53e-03 2.85e-02 1774 ] |X 0.45 - 0.455 : [ 82 1.32e-03 2.98e-02 1856 ] |XX 0.455 - 0.46 : [ 101 1.62e-03 3.15e-02 1957 ] |X 0.46 - 0.465 : [ 80 1.29e-03 3.27e-02 2037 ] |X 0.465 - 0.47 : [ 88 1.41e-03 3.42e-02 2125 ] |X 0.47 - 0.475 : [ 90 1.45e-03 3.56e-02 2215 ] |X 0.475 - 0.48 : [ 92 1.48e-03 3.71e-02 2307 ] |X 0.48 - 0.485 : [ 84 1.35e-03 3.84e-02 2391 ] |X 0.485 - 0.49 : [ 92 1.48e-03 3.99e-02 2483 ] |X 0.49 - 0.495 : [ 88 1.41e-03 4.13e-02 2571 ] |X 0.495 - 0.5 : [ 97 1.56e-03 4.29e-02 2668 ] |XX 0.5 - 0.505 : [ 119 1.91e-03 4.48e-02 2787 ] |XX 0.505 - 0.51 : [ 119 1.91e-03 4.67e-02 2906 ] |XX 0.51 - 0.515 : [ 135 2.17e-03 4.89e-02 3041 ] |XXX 0.515 - 0.52 : [ 164 2.64e-03 5.15e-02 3205 ] |XXX 0.52 - 0.525 : [ 174 2.80e-03 5.43e-02 3379 ] |XXX 0.525 - 0.53 : [ 189 3.04e-03 5.73e-02 3568 ] |XXXX 0.53 - 0.535 : [ 231 3.71e-03 6.11e-02 3799 ] |XXX 0.535 - 0.54 : [ 216 3.47e-03 6.45e-02 4015 ] |XXX 0.54 - 0.545 : [ 214 3.44e-03 6.80e-02 4229 ] |XXXXX 0.545 - 0.55 : [ 302 4.85e-03 7.28e-02 4531 ] |XXXXX 0.55 - 0.555 : [ 313 5.03e-03 7.79e-02 4844 ] |XXXXX 0.555 - 0.56 : [ 357 5.74e-03 8.36e-02 5201 ] |XXXXXX 0.56 - 0.565 : [ 422 6.78e-03 9.04e-02 5623 ] |XXXXXXX 0.565 - 0.57 : [ 432 6.94e-03 9.73e-02 6055 ] |XXXXXXXX 0.57 - 0.575 : [ 517 8.31e-03 1.06e-01 6572 ] |XXXXXXXXXX 0.575 - 0.58 : [ 649 1.04e-02 1.16e-01 7221 ] |XXXXXXXXXXXX 0.58 - 0.585 : [ 766 1.23e-02 1.28e-01 7987 ] |XXXXXXXXXXXX 0.585 - 0.59 : [ 775 1.25e-02 1.41e-01 8762 ] |XXXXXXXXXXXXX 0.59 - 0.595 : [ 868 1.40e-02 1.55e-01 9630 ] |XXXXXXXXXXXXXXX 0.595 - 0.6 : [ 962 1.55e-02 1.70e-01 10592 ] |XXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1132 1.82e-02 1.88e-01 11724 ] |XXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1110 1.78e-02 2.06e-01 12834 ] |XXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1278 2.05e-02 2.27e-01 14112 ] |XXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1356 2.18e-02 2.49e-01 15468 ] |XXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1441 2.32e-02 2.72e-01 16909 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 1638 2.63e-02 2.98e-01 18547 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 1808 2.91e-02 3.27e-01 20355 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 2009 3.23e-02 3.59e-01 22364 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 2169 3.49e-02 3.94e-01 24533 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 2290 3.68e-02 4.31e-01 26823 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 2353 3.78e-02 4.69e-01 29176 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 2564 4.12e-02 5.10e-01 31740 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 2578 4.14e-02 5.52e-01 34318 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 2531 4.07e-02 5.92e-01 36849 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 2602 4.18e-02 6.34e-01 39451 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 2547 4.09e-02 6.75e-01 41998 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 2471 3.97e-02 7.15e-01 44469 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 2419 3.89e-02 7.54e-01 46888 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 2258 3.63e-02 7.90e-01 49146 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 2010 3.23e-02 8.22e-01 51156 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 1939 3.12e-02 8.53e-01 53095 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 1630 2.62e-02 8.80e-01 54725 ] |XXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 1445 2.32e-02 9.03e-01 56170 ] |XXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 1208 1.94e-02 9.22e-01 57378 ] |XXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 1051 1.69e-02 9.39e-01 58429 ] |XXXXXXXXXXXXXX 0.725 - 0.73 : [ 890 1.43e-02 9.53e-01 59319 ] |XXXXXXXXXX 0.73 - 0.735 : [ 683 1.10e-02 9.64e-01 60002 ] |XXXXXXXX 0.735 - 0.74 : [ 537 8.63e-03 9.73e-01 60539 ] |XXXXXX 0.74 - 0.745 : [ 399 6.41e-03 9.79e-01 60938 ] |XXXX 0.745 - 0.75 : [ 270 4.34e-03 9.84e-01 61208 ] |XXXX 0.75 - 0.755 : [ 269 4.32e-03 9.88e-01 61477 ] |XXX 0.755 - 0.76 : [ 167 2.68e-03 9.91e-01 61644 ] |XX 0.76 - 0.765 : [ 119 1.91e-03 9.93e-01 61763 ] |X 0.765 - 0.77 : [ 97 1.56e-03 9.94e-01 61860 ] |X 0.77 - 0.775 : [ 58 9.32e-04 9.95e-01 61918 ] |X 0.775 - 0.78 : [ 50 8.04e-04 9.96e-01 61968 ] |X 0.78 - 0.785 : [ 36 5.79e-04 9.96e-01 62004 ] |X 0.785 - 0.79 : [ 36 5.79e-04 9.97e-01 62040 ] |X 0.79 - 0.795 : [ 33 5.30e-04 9.98e-01 62073 ] | 0.795 - 0.8 : [ 17 2.73e-04 9.98e-01 62090 ] | 0.8 - 0.805 : [ 14 2.25e-04 9.98e-01 62104 ] | 0.805 - 0.81 : [ 13 2.09e-04 9.98e-01 62117 ] | 0.81 - 0.815 : [ 6 9.64e-05 9.98e-01 62123 ] | 0.815 - 0.82 : [ 7 1.13e-04 9.99e-01 62130 ] | 0.82 - 0.825 : [ 11 1.77e-04 9.99e-01 62141 ] | 0.825 - 0.83 : [ 10 1.61e-04 9.99e-01 62151 ] | 0.83 - 0.835 : [ 8 1.29e-04 9.99e-01 62159 ] | 0.835 - 0.84 : [ 4 6.43e-05 9.99e-01 62163 ] | 0.84 - 0.845 : [ 12 1.93e-04 9.99e-01 62175 ] | 0.845 - 0.85 : [ 7 1.13e-04 9.99e-01 62182 ] | 0.85 - 0.855 : [ 5 8.04e-05 9.99e-01 62187 ] | 0.855 - 0.86 : [ 1 1.61e-05 9.99e-01 62188 ] | 0.86 - 0.865 : [ 3 4.82e-05 1.00e+00 62191 ] | 0.865 - 0.87 : [ 5 8.04e-05 1.00e+00 62196 ] | 0.87 - 0.875 : [ 1 1.61e-05 1.00e+00 62197 ] | 0.875 - 0.88 : [ 4 6.43e-05 1.00e+00 62201 ] | 0.88 - 0.885 : [ 1 1.61e-05 1.00e+00 62202 ] | 0.885 - 0.89 : [ 3 4.82e-05 1.00e+00 62205 ] | 0.89 - 0.895 : [ 1 1.61e-05 1.00e+00 62206 ] | 0.895 - 0.9 : [ 1 1.61e-05 1.00e+00 62207 ] | 0.9 - 0.905 : [ 3 4.82e-05 1.00e+00 62210 ] | 0.905 - 0.91 : [ 3 4.82e-05 1.00e+00 62213 ] | 0.91 - 0.915 : [ 1 1.61e-05 1.00e+00 62214 ] | 0.915 - 0.92 : [ 2 3.21e-05 1.00e+00 62216 ] | 0.92 - 0.925 : [ 1 1.61e-05 1.00e+00 62217 ] | 0.925 - 0.93 : [ 2 3.21e-05 1.00e+00 62219 ] | 0.93 - 0.935 : [ 1 1.61e-05 1.00e+00 62220 ] #... | 0.955 - 0.96 : [ 1 1.61e-05 1.00e+00 62221 ] #... | 1 - 1.005 : [ 1 1.61e-05 1.00e+00 62222 ] SECTION IX Plate Summary SECTION X Phrap Assembly Summary ################################################################### Reads in assembly summary ------------------------------------------------------------------- Small Inserts = 273 HQ Discrepant reads = 55 Chimeric reads = 38 Suspect alignments = 382 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 Thu Dec 8 14:48:05 2005 File: phrap.out Contig 447. 756 reads; 74184 bp (untrimmed), 74117 (trimmed). Contig 448. 780 reads; 58880 bp (untrimmed), 58754 (trimmed). Contig 449. 786 reads; 70354 bp (untrimmed), 70161 (trimmed). Contig 450. 796 reads; 77266 bp (untrimmed), 77221 (trimmed). Contig 451. 800 reads; 81265 bp (untrimmed), 81242 (trimmed). Contig 452. 801 reads; 76861 bp (untrimmed), 76806 (trimmed). Contig 453. 835 reads; 54321 bp (untrimmed), 54229 (trimmed). Contig 454. 878 reads; 75036 bp (untrimmed), 74897 (trimmed). Contig 455. 897 reads; 70938 bp (untrimmed), 70863 (trimmed). Contig 456. 979 reads; 84115 bp (untrimmed), 83916 (trimmed). Contig 457. 1008 reads; 98002 bp (untrimmed), 97869 (trimmed). Contig 458. 1164 reads; 57695 bp (untrimmed), 57354 (trimmed). Contig 459. 1182 reads; 110176 bp (untrimmed), 110108 (trimmed). Contig 460. 1317 reads; 116342 bp (untrimmed), 116274 (trimmed). Contig 461. 1393 reads; 117966 bp (untrimmed), 117929 (trimmed). Contig 462. 1449 reads; 128882 bp (untrimmed), 128832 (trimmed). Contig 463. 1481 reads; 50118 bp (untrimmed), 49673 (trimmed). Contig 464. 1516 reads; 136190 bp (untrimmed), 136084 (trimmed). Contig 465. 1522 reads; 137668 bp (untrimmed), 137141 (trimmed). Contig 466. 1529 reads; 141364 bp (untrimmed), 140999 (trimmed). Contig 467. 1933 reads; 168343 bp (untrimmed), 168235 (trimmed). Contig 468. 2040 reads; 208780 bp (untrimmed), 208666 (trimmed). Contig 469. 2074 reads; 204356 bp (untrimmed), 204298 (trimmed). Contig 470. 2123 reads; 193175 bp (untrimmed), 193082 (trimmed). Contig 471. 2248 reads; 179131 bp (untrimmed), 179064 (trimmed). Contig 472. 2434 reads; 261492 bp (untrimmed), 261446 (trimmed). Contig 473. 4241 reads; 365580 bp (untrimmed), 365338 (trimmed). -------------------------------------------------------------- Totals 52328 reads; 4958006 bp (untrimmed), 4857790 (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 65 total values totalling 4530385.0000. <69698.230769 +/- 67552.486592> #Range: [ 3008 - 365338 ] #Most likely bin: [ 36000 - 38000 ] 4 counts #Median bin: [ 50000 - 52000 ] 2 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 3 0.05 0.05 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 6000 : [ 3 0.05 0.09 ] #... |XXXXXXXXXX 8000 - 10000 : [ 1 0.02 0.11 ] |XXXXXXXXXX 10000 - 12000 : [ 1 0.02 0.12 ] |XXXXXXXXXX 12000 - 14000 : [ 1 0.02 0.14 ] |XXXXXXXXXXXXXXXXXXXX 14000 - 16000 : [ 2 0.03 0.17 ] |XXXXXXXXXX 16000 - 18000 : [ 1 0.02 0.18 ] #... |XXXXXXXXXXXXXXXXXXXX 20000 - 22000 : [ 2 0.03 0.22 ] |XXXXXXXXXXXXXXXXXXXX 22000 - 24000 : [ 2 0.03 0.25 ] #... |XXXXXXXXXX 26000 - 28000 : [ 1 0.02 0.26 ] |XXXXXXXXXXXXXXXXXXXX 28000 - 30000 : [ 2 0.03 0.29 ] #... |XXXXXXXXXX 32000 - 34000 : [ 1 0.02 0.31 ] |XXXXXXXXXXXXXXXXXXXX 34000 - 36000 : [ 2 0.03 0.34 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 38000 : [ 4 0.06 0.40 ] |XXXXXXXXXX 38000 - 40000 : [ 1 0.02 0.42 ] |XXXXXXXXXX 40000 - 42000 : [ 1 0.02 0.43 ] |XXXXXXXXXX 42000 - 44000 : [ 1 0.02 0.45 ] |XXXXXXXXXXXXXXXXXXXX 44000 - 46000 : [ 2 0.03 0.48 ] #... |XXXXXXXXXX 48000 - 50000 : [ 1 0.02 0.49 ] |XXXXXXXXXXXXXXXXXXXX 50000 - 52000 : [ 2 0.03 0.52 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 54000 - 56000 : [ 3 0.05 0.57 ] |XXXXXXXXXXXXXXXXXXXX 56000 - 58000 : [ 2 0.03 0.60 ] |XXXXXXXXXX 58000 - 60000 : [ 1 0.02 0.62 ] |XXXXXXXXXX 60000 - 62000 : [ 1 0.02 0.63 ] |XXXXXXXXXX 62000 - 64000 : [ 1 0.02 0.65 ] #... |XXXXXXXXXXXXXXXXXXXX 70000 - 72000 : [ 2 0.03 0.68 ] #... |XXXXXXXXXXXXXXXXXXXX 74000 - 76000 : [ 2 0.03 0.71 ] |XXXXXXXXXXXXXXXXXXXX 76000 - 78000 : [ 2 0.03 0.74 ] #... |XXXXXXXXXX 80000 - 82000 : [ 1 0.02 0.75 ] |XXXXXXXXXX 82000 - 84000 : [ 1 0.02 0.77 ] #... |XXXXXXXXXX 96000 - 98000 : [ 1 0.02 0.78 ] #... |XXXXXXXXXX 110000 - 112000 : [ 1 0.02 0.80 ] #... |XXXXXXXXXXXXXXXXXXXX 116000 - 118000 : [ 2 0.03 0.83 ] #... |XXXXXXXXXX 128000 - 130000 : [ 1 0.02 0.85 ] #... |XXXXXXXXXXXXXXXXXXXX 136000 - 138000 : [ 2 0.03 0.88 ] #... |XXXXXXXXXX 140000 - 142000 : [ 1 0.02 0.89 ] #... |XXXXXXXXXX 168000 - 170000 : [ 1 0.02 0.91 ] #... |XXXXXXXXXX 178000 - 180000 : [ 1 0.02 0.92 ] #... |XXXXXXXXXX 192000 - 194000 : [ 1 0.02 0.94 ] #... |XXXXXXXXXX 204000 - 206000 : [ 1 0.02 0.95 ] #... |XXXXXXXXXX 208000 - 210000 : [ 1 0.02 0.97 ] #... |XXXXXXXXXX 260000 - 262000 : [ 1 0.02 0.98 ] #... |XXXXXXXXXX 364000 - 366000 : [ 1 0.02 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 11777140 C = 20446924 G = 20181350 T = 11902693 N = 468661 X = 920374 GC fraction = 0.62 Total = 65697142 ################################################################### Base Count for contigs: ------------------------------------------------------------------- A 848806 C 1617199 G 1611981 T 846112 N 33908 fraction GC = 0.65 total bases = 4958006 SECTION XIII Depth ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 4646661 bases = 10.38 +- 5.57 = 0.02 +- 3.63 m1 = 2.99 m2 = 4.47 ################################################################### Histogram of All Contig Depth Values: ------------------------------------------------------------------- Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 #Found 148 total values totalling 1009.4300. <6.820473 +/- 8.775302> #Range: [ 1.05 - 75.79 ] #Most likely bin: [ 1 - 1.5 ] 39 counts #Median bin: [ 2.5 - 3 ] 1 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 39 0.26 0.26 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 33 0.22 0.49 ] |X 2 - 2.5 : [ 1 0.01 0.49 ] |X 2.5 - 3 : [ 1 0.01 0.50 ] #... |XX 3.5 - 4 : [ 2 0.01 0.51 ] |X 4 - 4.5 : [ 1 0.01 0.52 ] |X 4.5 - 5 : [ 1 0.01 0.53 ] |X 5 - 5.5 : [ 1 0.01 0.53 ] #... |XX 6 - 6.5 : [ 2 0.01 0.55 ] |X 6.5 - 7 : [ 1 0.01 0.55 ] |X 7 - 7.5 : [ 1 0.01 0.56 ] |X 7.5 - 8 : [ 1 0.01 0.57 ] |X 8 - 8.5 : [ 1 0.01 0.57 ] |XXXXXX 8.5 - 9 : [ 6 0.04 0.61 ] |XXXXXXX 9 - 9.5 : [ 7 0.05 0.66 ] |XXXXXXXXX 9.5 - 10 : [ 9 0.06 0.72 ] |XXXXXXXXXXXXXXXX 10 - 10.5 : [ 16 0.11 0.83 ] |XXXXXXXX 10.5 - 11 : [ 8 0.05 0.89 ] |X 11 - 11.5 : [ 1 0.01 0.89 ] |XXXXX 11.5 - 12 : [ 5 0.03 0.93 ] |XX 12 - 12.5 : [ 2 0.01 0.94 ] #... |XX 14 - 14.5 : [ 2 0.01 0.95 ] #... |X 18.5 - 19 : [ 1 0.01 0.96 ] #... |X 21 - 21.5 : [ 1 0.01 0.97 ] #... |X 24.5 - 25 : [ 1 0.01 0.97 ] #... |X 27.5 - 28 : [ 1 0.01 0.98 ] #... |X 36.5 - 37 : [ 1 0.01 0.99 ] #... |X 48.5 - 49 : [ 1 0.01 0.99 ] #... |X 75.5 - 76 : [ 1 0.01 1.00 ] Histogram of Major Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000 #Found 65 total values totalling 741.3600. <11.405538 +/- 5.879733> #Range: [ 4.27 - 48.52 ] #Most likely bin: [ 10 - 10.5 ] 16 counts #Median bin: [ 10 - 10.5 ] 16 counts #Histogram Bins Count Fraction Cum_Fraction |XX 4 - 4.5 : [ 1 0.02 0.02 ] #... |XX 6 - 6.5 : [ 1 0.02 0.03 ] #... |XX 7 - 7.5 : [ 1 0.02 0.05 ] |XX 7.5 - 8 : [ 1 0.02 0.06 ] |XX 8 - 8.5 : [ 1 0.02 0.08 ] |XXXXXXXXXXXXXXX 8.5 - 9 : [ 6 0.09 0.17 ] |XXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 7 0.11 0.28 ] |XXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 9 0.14 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 16 0.25 0.66 ] |XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 8 0.12 0.78 ] |XX 11 - 11.5 : [ 1 0.02 0.80 ] |XXXXXXXXXX 11.5 - 12 : [ 4 0.06 0.86 ] |XXXXX 12 - 12.5 : [ 2 0.03 0.89 ] #... |XXXXX 14 - 14.5 : [ 2 0.03 0.92 ] #... |XX 18.5 - 19 : [ 1 0.02 0.94 ] #... |XX 21 - 21.5 : [ 1 0.02 0.95 ] #... |XX 24.5 - 25 : [ 1 0.02 0.97 ] #... |XX 27.5 - 28 : [ 1 0.02 0.98 ] #... |XX 48.5 - 49 : [ 1 0.02 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 351 2 reads 1542 bases = 1.05 +- 0.21 = -0.24 +- 0.95 m1 = 0.04 m2 = -0.21 Contig 338 2 reads 1860 bases = 1.06 +- 0.25 = -0.06 +- 0.97 m1 = 0.06 m2 = -0.22 Contig 349 2 reads 1602 bases = 1.06 +- 0.23 = 0.19 +- 0.95 m1 = 0.05 m2 = -0.21 Contig 350 2 reads 1934 bases = 1.06 +- 0.24 = 0.00 +- 0.97 m1 = 0.06 m2 = -0.22 Contig 365 2 reads 1767 bases = 1.08 +- 0.27 = 1.08 +- 0.27 m1 = 0.07 m2 = 0.00 Contig 341 2 reads 1825 bases = 1.09 +- 0.28 = 1.09 +- 0.28 m1 = 0.07 m2 = 0.00 Contig 363 2 reads 1860 bases = 1.09 +- 0.28 = 1.09 +- 0.28 m1 = 0.07 m2 = 0.00 Contig 316 2 reads 1643 bases = 1.10 +- 0.31 = 0.06 +- 0.94 m1 = 0.08 m2 = -0.20 Contig 319 2 reads 1750 bases = 1.10 +- 0.30 = -0.08 +- 0.95 m1 = 0.08 m2 = -0.20 Contig 370 2 reads 1769 bases = 1.10 +- 0.30 = -0.03 +- 0.95 m1 = 0.08 m2 = -0.20 Contig 340 2 reads 1774 bases = 1.11 +- 0.31 = 1.11 +- 0.31 m1 = 0.09 m2 = 0.00 Contig 360 2 reads 1781 bases = 1.11 +- 0.31 = 1.11 +- 0.31 m1 = 0.09 m2 = 0.00 Contig 374 2 reads 1635 bases = 1.13 +- 0.34 = 0.00 +- 0.93 m1 = 0.10 m2 = -0.19 Contig 377 2 reads 1628 bases = 1.14 +- 0.35 = 0.00 +- 0.93 m1 = 0.11 m2 = -0.19 Contig 385 2 reads 1745 bases = 1.15 +- 0.36 = 1.15 +- 0.36 m1 = 0.11 m2 = 0.00 Contig 354 2 reads 1250 bases = 1.16 +- 0.36 = 1.16 +- 0.36 m1 = 0.11 m2 = 0.00 Contig 352 2 reads 1475 bases = 1.17 +- 0.37 = 1.17 +- 0.37 m1 = 0.12 m2 = 0.00 Contig 314 2 reads 1208 bases = 1.18 +- 0.38 = 1.18 +- 0.38 m1 = 0.12 m2 = 0.00 Contig 320 2 reads 1629 bases = 1.19 +- 0.40 = 1.19 +- 0.40 m1 = 0.13 m2 = 0.00 Contig 323 2 reads 1647 bases = 1.19 +- 0.39 = 1.19 +- 0.39 m1 = 0.13 m2 = 0.00 Contig 421 252 reads 21969 bases = 10.85 +- 3.59 = 0.44 +- 3.52 m1 = 1.19 m2 = 0.12 Contig 461 1393 reads 117966 bases = 10.85 +- 3.63 = 0.13 +- 3.53 m1 = 1.21 m2 = 0.18 Contig 454 878 reads 75036 bases = 10.86 +- 4.95 = -0.04 +- 3.59 m1 = 2.26 m2 = 2.91 Contig 426 341 reads 29167 bases = 11.08 +- 4.49 = 0.33 +- 3.49 m1 = 1.82 m2 = 2.01 Contig 406 17 reads 1292 bases = 11.60 +- 5.38 = 3.67 +- 1.24 m1 = 2.49 m2 = 6.84 Contig 471 2248 reads 179131 bases = 11.73 +- 5.23 = 0.08 +- 3.84 m1 = 2.33 m2 = 3.15 Contig 427 366 reads 29597 bases = 11.75 +- 3.18 = 0.40 +- 3.98 m1 = 0.86 m2 = -1.42 Contig 455 897 reads 70938 bases = 11.86 +- 6.93 = -0.04 +- 4.12 m1 = 4.05 m2 = 7.78 Contig 437 438 reads 34620 bases = 11.95 +- 10.98 = 0.63 +- 3.76 m1 = 10.09 m2 = 26.61 Contig 424 306 reads 22708 bases = 12.17 +- 5.02 = -0.02 +- 4.16 m1 = 2.07 m2 = 1.98 Contig 448 780 reads 58880 bases = 12.30 +- 3.61 = 0.15 +- 4.10 m1 = 1.06 m2 = -0.95 Contig 453 835 reads 54321 bases = 14.12 +- 10.39 = 0.33 +- 4.20 m1 = 7.64 m2 = 22.58 Contig 419 223 reads 14467 bases = 14.38 +- 5.68 = -2.02 +- 7.63 m1 = 2.24 m2 = -6.49 Contig 458 1164 reads 57695 bases = 18.97 +- 9.31 = -0.57 +- 5.71 m1 = 4.57 m2 = 13.52 Contig 418 220 reads 9515 bases = 21.45 +- 13.59 = -2.47 +- 4.99 m1 = 8.61 m2 = 39.97 Contig 425 333 reads 12496 bases = 24.74 +- 10.86 = -4.72 +- 6.12 m1 = 4.77 m2 = 20.12 Contig 463 1481 reads 50118 bases = 27.81 +- 9.67 = -0.85 +- 7.46 m1 = 3.36 m2 = 9.47 Contig 412 67 reads 1717 bases = 36.72 +- 27.40 = 5.25 +- 4.07 m1 = 20.45 m2 = 183.61 Contig 415 158 reads 3081 bases = 48.52 +- 42.42 = 7.98 +- 8.97 m1 = 37.09 m2 = 429.78 Contig 414 157 reads 1947 bases = 75.79 +- 48.94 = 29.46 +- 21.20 m1 = 31.60 m2 = 486.43 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 473 total values totalling 52328.0000. <110.630021 +/- 387.150937> #Range: [ 1 - 4241 ] #Most likely bin: [ 1 - 2 ] 310 counts #Median bin: [ 1 - 2 ] 310 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 2 : [ 310 0.66 0.66 ] |XXXXXXXXXXX 2 - 3 : [ 84 0.18 0.83 ] | 3 - 4 : [ 3 0.01 0.84 ] | 4 - 5 : [ 2 0.00 0.84 ] #... | 6 - 7 : [ 1 0.00 0.85 ] #... | 8 - 9 : [ 2 0.00 0.85 ] | 9 - 10 : [ 1 0.00 0.85 ] #... | 11 - 12 : [ 1 0.00 0.85 ] #... | 14 - 15 : [ 1 0.00 0.86 ] #... | 17 - 18 : [ 1 0.00 0.86 ] #... | 23 - 24 : [ 1 0.00 0.86 ] #... | 28 - 29 : [ 1 0.00 0.86 ] | 29 - 30 : [ 1 0.00 0.86 ] #... | 43 - 44 : [ 1 0.00 0.87 ] #... | 48 - 49 : [ 1 0.00 0.87 ] #... | 67 - 68 : [ 1 0.00 0.87 ] #... | 109 - 110 : [ 1 0.00 0.87 ] #... | 157 - 158 : [ 1 0.00 0.88 ] | 158 - 159 : [ 1 0.00 0.88 ] #... | 168 - 169 : [ 1 0.00 0.88 ] #... | 171 - 172 : [ 1 0.00 0.88 ] #... | 220 - 221 : [ 1 0.00 0.88 ] #... | 223 - 224 : [ 1 0.00 0.89 ] #... | 238 - 239 : [ 1 0.00 0.89 ] #... | 252 - 253 : [ 1 0.00 0.89 ] #... | 259 - 260 : [ 1 0.00 0.89 ] #... | 261 - 262 : [ 1 0.00 0.89 ] #... | 306 - 307 : [ 1 0.00 0.90 ] #... | 333 - 334 : [ 1 0.00 0.90 ] #... | 341 - 342 : [ 1 0.00 0.90 ] #... | 366 - 367 : [ 1 0.00 0.90 ] #... | 368 - 369 : [ 1 0.00 0.90 ] #... | 370 - 371 : [ 1 0.00 0.91 ] #... | 372 - 373 : [ 1 0.00 0.91 ] #... | 384 - 385 : [ 1 0.00 0.91 ] #... | 388 - 389 : [ 1 0.00 0.91 ] #... | 396 - 397 : [ 1 0.00 0.92 ] #... | 402 - 403 : [ 1 0.00 0.92 ] #... | 415 - 416 : [ 1 0.00 0.92 ] #... | 433 - 434 : [ 1 0.00 0.92 ] #... | 438 - 439 : [ 1 0.00 0.92 ] #... | 447 - 448 : [ 1 0.00 0.93 ] #... | 488 - 489 : [ 1 0.00 0.93 ] #... | 510 - 511 : [ 1 0.00 0.93 ] #... | 543 - 544 : [ 1 0.00 0.93 ] #... | 548 - 549 : [ 1 0.00 0.93 ] #... | 564 - 565 : [ 1 0.00 0.94 ] #... | 606 - 607 : [ 1 0.00 0.94 ] #... | 609 - 610 : [ 1 0.00 0.94 ] #... | 717 - 718 : [ 1 0.00 0.94 ] #... | 756 - 757 : [ 1 0.00 0.95 ] #... | 780 - 781 : [ 1 0.00 0.95 ] #... | 786 - 787 : [ 1 0.00 0.95 ] #... | 796 - 797 : [ 1 0.00 0.95 ] #... | 800 - 801 : [ 1 0.00 0.95 ] | 801 - 802 : [ 1 0.00 0.96 ] #... | 835 - 836 : [ 1 0.00 0.96 ] #... | 878 - 879 : [ 1 0.00 0.96 ] #... | 897 - 898 : [ 1 0.00 0.96 ] #... | 979 - 980 : [ 1 0.00 0.96 ] #... | 1008 - 1009 : [ 1 0.00 0.97 ] #... | 1164 - 1165 : [ 1 0.00 0.97 ] #... | 1182 - 1183 : [ 1 0.00 0.97 ] #... | 1317 - 1318 : [ 1 0.00 0.97 ] #... | 1393 - 1394 : [ 1 0.00 0.97 ] #... | 1449 - 1450 : [ 1 0.00 0.98 ] #... | 1481 - 1482 : [ 1 0.00 0.98 ] #... | 1516 - 1517 : [ 1 0.00 0.98 ] #... | 1522 - 1523 : [ 1 0.00 0.98 ] #... | 1529 - 1530 : [ 1 0.00 0.99 ] #... | 1933 - 1934 : [ 1 0.00 0.99 ] #... | 2040 - 2041 : [ 1 0.00 0.99 ] #... | 2074 - 2075 : [ 1 0.00 0.99 ] #... | 2123 - 2124 : [ 1 0.00 0.99 ] #... | 2248 - 2249 : [ 1 0.00 1.00 ] #... | 2434 - 2435 : [ 1 0.00 1.00 ] #... | 4241 - 4242 : [ 1 0.00 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 473 total values totalling 4958006.0000. <10482.042283 +/- 34472.624976> #Range: [ 128 - 365580 ] #Most likely bin: [ 1000 - 2000 ] 206 counts #Median bin: [ 1000 - 2000 ] 206 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 1000 : [ 202 0.43 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 206 0.44 0.86 ] #... | 3000 - 4000 : [ 2 0.00 0.87 ] |X 4000 - 5000 : [ 3 0.01 0.87 ] | 5000 - 6000 : [ 1 0.00 0.88 ] #... | 9000 - 10000 : [ 1 0.00 0.88 ] | 10000 - 11000 : [ 1 0.00 0.88 ] #... | 12000 - 13000 : [ 1 0.00 0.88 ] #... | 14000 - 15000 : [ 1 0.00 0.88 ] | 15000 - 16000 : [ 1 0.00 0.89 ] #... | 17000 - 18000 : [ 1 0.00 0.89 ] #... | 21000 - 22000 : [ 1 0.00 0.89 ] | 22000 - 23000 : [ 2 0.00 0.89 ] | 23000 - 24000 : [ 1 0.00 0.90 ] #... | 28000 - 29000 : [ 1 0.00 0.90 ] | 29000 - 30000 : [ 2 0.00 0.90 ] #... | 32000 - 33000 : [ 1 0.00 0.90 ] #... | 34000 - 35000 : [ 2 0.00 0.91 ] #... | 36000 - 37000 : [ 1 0.00 0.91 ] |X 37000 - 38000 : [ 3 0.01 0.92 ] #... | 39000 - 40000 : [ 1 0.00 0.92 ] | 40000 - 41000 : [ 1 0.00 0.92 ] #... | 43000 - 44000 : [ 1 0.00 0.92 ] #... | 45000 - 46000 : [ 2 0.00 0.93 ] #... |X 50000 - 51000 : [ 3 0.01 0.93 ] #... | 54000 - 55000 : [ 1 0.00 0.94 ] | 55000 - 56000 : [ 2 0.00 0.94 ] | 56000 - 57000 : [ 1 0.00 0.94 ] | 57000 - 58000 : [ 1 0.00 0.95 ] | 58000 - 59000 : [ 1 0.00 0.95 ] #... | 60000 - 61000 : [ 1 0.00 0.95 ] #... | 63000 - 64000 : [ 1 0.00 0.95 ] #... | 70000 - 71000 : [ 2 0.00 0.96 ] #... | 74000 - 75000 : [ 1 0.00 0.96 ] | 75000 - 76000 : [ 1 0.00 0.96 ] | 76000 - 77000 : [ 1 0.00 0.96 ] | 77000 - 78000 : [ 1 0.00 0.96 ] #... | 81000 - 82000 : [ 1 0.00 0.97 ] #... | 84000 - 85000 : [ 1 0.00 0.97 ] #... | 98000 - 99000 : [ 1 0.00 0.97 ] #... | 110000 - 111000 : [ 1 0.00 0.97 ] #... | 116000 - 117000 : [ 1 0.00 0.97 ] | 117000 - 118000 : [ 1 0.00 0.98 ] #... | 128000 - 129000 : [ 1 0.00 0.98 ] #... | 136000 - 137000 : [ 1 0.00 0.98 ] | 137000 - 138000 : [ 1 0.00 0.98 ] #... | 141000 - 142000 : [ 1 0.00 0.99 ] #... | 168000 - 169000 : [ 1 0.00 0.99 ] #... | 179000 - 180000 : [ 1 0.00 0.99 ] #... | 193000 - 194000 : [ 1 0.00 0.99 ] #... | 204000 - 205000 : [ 1 0.00 0.99 ] #... | 208000 - 209000 : [ 1 0.00 1.00 ] #... | 261000 - 262000 : [ 1 0.00 1.00 ] #... | 365000 - 366000 : [ 1 0.00 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 BHFI reads.list > grep.reads.list.BHFI Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BHFI 4 500 #Found 7133 total values totalling 19933006.0000. <2794.477219 +/- 3395.458216> #Range: [ 1041 - 185921 ] #Most likely bin: [ 2500 - 3000 ] 3681 counts #Median bin: [ 2500 - 3000 ] 3681 counts #Histogram Bins Count Fraction Cum_Fraction | 1000 - 1500 : [ 17 0.00 0.00 ] |X 1500 - 2000 : [ 73 0.01 0.01 ] |XXXXXXXXXXXXXXXXXXXX 2000 - 2500 : [ 1801 0.25 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 3681 0.52 0.78 ] |XXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1557 0.22 1.00 ] #... | 29500 - 30000 : [ 1 0.00 1.00 ] #... | 156000 - 156500 : [ 1 0.00 1.00 ] | 156500 - 157000 : [ 1 0.00 1.00 ] #... | 185500 - 186000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep BHFN reads.list > grep.reads.list.BHFN Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BHFN 4 500 #Found 9310 total values totalling 57936565.0000. <6223.046724 +/- 4457.043801> #Range: [ 1118 - 255226 ] #Most likely bin: [ 5500 - 6000 ] 2809 counts #Median bin: [ 6000 - 6500 ] 2793 counts #Histogram Bins Count Fraction Cum_Fraction | 1000 - 1500 : [ 2 0.00 0.00 ] | 1500 - 2000 : [ 4 0.00 0.00 ] | 2000 - 2500 : [ 6 0.00 0.00 ] | 2500 - 3000 : [ 17 0.00 0.00 ] | 3000 - 3500 : [ 13 0.00 0.00 ] | 3500 - 4000 : [ 12 0.00 0.01 ] | 4000 - 4500 : [ 9 0.00 0.01 ] | 4500 - 5000 : [ 33 0.00 0.01 ] |XXXXXXXXXXXXXXXX 5000 - 5500 : [ 1146 0.12 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 2809 0.30 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2793 0.30 0.74 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1975 0.21 0.95 ] |XXXXXXX 7000 - 7500 : [ 476 0.05 1.00 ] | 7500 - 8000 : [ 2 0.00 1.00 ] | 8000 - 8500 : [ 1 0.00 1.00 ] | 8500 - 9000 : [ 1 0.00 1.00 ] #... | 12500 - 13000 : [ 1 0.00 1.00 ] #... | 26500 - 27000 : [ 1 0.00 1.00 ] #... | 32500 - 33000 : [ 1 0.00 1.00 ] #... | 38000 - 38500 : [ 1 0.00 1.00 ] #... | 45500 - 46000 : [ 1 0.00 1.00 ] #... | 69500 - 70000 : [ 1 0.00 1.00 ] #... | 159500 - 160000 : [ 1 0.00 1.00 ] #... | 160500 - 161000 : [ 2 0.00 1.00 ] #... | 207500 - 208000 : [ 1 0.00 1.00 ] #... | 255000 - 255500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep BHFO reads.list > grep.reads.list.BHFO Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BHFO 4 500 #Found 1892 total values totalling 69687081.0000. <36832.495243 +/- 3861.145048> #Range: [ 24774 - 53856 ] #Most likely bin: [ 34500 - 35000 ] 101 counts #Median bin: [ 36500 - 37000 ] 72 counts #Histogram Bins Count Fraction Cum_Fraction |X 24500 - 25000 : [ 3 0.00 0.00 ] |X 25000 - 25500 : [ 2 0.00 0.00 ] | 25500 - 26000 : [ 1 0.00 0.00 ] | 26000 - 26500 : [ 1 0.00 0.00 ] #... | 27000 - 27500 : [ 1 0.00 0.00 ] |XX 27500 - 28000 : [ 4 0.00 0.01 ] |XXX 28000 - 28500 : [ 8 0.00 0.01 ] |XX 28500 - 29000 : [ 6 0.00 0.01 ] |XXX 29000 - 29500 : [ 8 0.00 0.02 ] |XXXXXXX 29500 - 30000 : [ 18 0.01 0.03 ] |XXXXXX 30000 - 30500 : [ 14 0.01 0.03 ] |XXXXXXXX 30500 - 31000 : [ 21 0.01 0.05 ] |XXXXXXXXXXXXX 31000 - 31500 : [ 33 0.02 0.06 ] |XXXXXXXXXXXXXXXXXXXXX 31500 - 32000 : [ 52 0.03 0.09 ] |XXXXXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 60 0.03 0.12 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 78 0.04 0.16 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 89 0.05 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 83 0.04 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 86 0.05 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 101 0.05 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 97 0.05 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 81 0.04 0.45 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 94 0.05 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 72 0.04 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 71 0.04 0.57 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 84 0.04 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 80 0.04 0.66 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 75 0.04 0.70 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 90 0.05 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 75 0.04 0.79 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 64 0.03 0.82 ] |XXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 47 0.02 0.85 ] |XXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 50 0.03 0.87 ] |XXXXXXXXXXXXXXXXX 41500 - 42000 : [ 43 0.02 0.89 ] |XXXXXXXXXXXXXXX 42000 - 42500 : [ 38 0.02 0.91 ] |XXXXXXXXXXXXXXX 42500 - 43000 : [ 38 0.02 0.93 ] |XXXXXXXXXXXXX 43000 - 43500 : [ 32 0.02 0.95 ] |XXXXXXXXXXXX 43500 - 44000 : [ 31 0.02 0.97 ] |XXXXXXX 44000 - 44500 : [ 17 0.01 0.98 ] |XXXXXX 44500 - 45000 : [ 14 0.01 0.98 ] |XXXXX 45000 - 45500 : [ 12 0.01 0.99 ] |XXXX 45500 - 46000 : [ 10 0.01 1.00 ] |XX 46000 - 46500 : [ 5 0.00 1.00 ] #... | 47000 - 47500 : [ 1 0.00 1.00 ] #... | 52500 - 53000 : [ 1 0.00 1.00 ] #... | 53500 - 54000 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes: ------------------------------------------------------------------- Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out # BHFI 2592 +- 6320 (n=7179) # BHFO 34050 +- 17139 (n=1954) # BHFN 6018 +- 7484 (n=9329) 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 702.933308 bp, 52328 reads, genome size 4547260 bp ------------------------------------------------------------------- Command: idealAssembly 4547260 52328 702.933308 Genome = 4547260 bases Nreads = 52328 readLength = 702.933308 Depth = 8.09 N_contigs = N_gaps = 16 mean gap size = 86 bases mean contig size = 3259 reads (~ 283174 bases) %cover = 99.97 %singlet = 0.00 assembly size = 4545861 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 3 contigs containing at least 5468 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: 16890 Number of reads with percent X's >= 20%: 61 = 0.1% Number of reads with percent X's >= 50%: 34 = 0.1% Number of reads with percent X's >= 80%: 9 = 0.0% Total reads in project: 61717 Total bp X'd : 633060 reads >= 20% >= 50% >= 80% screened Nr with L09136 12422 41 30 8 Nr with pCC1Fos 4427 10 0 0 Nr with pMCL200_JGI_XZX+XZK 41 10 4 1 ################################################################### Contam Summary with *.singlets: ------------------------------------------------------------------- Command: contam_summary -c -s -g Number of reads with X's: 5333 Number of reads with percent X's >= 20%: 255 = 2.0% Number of reads with percent X's >= 50%: 231 = 1.8% Number of reads with percent X's >= 80%: 197 = 1.5% Total reads in project: 12927 Total bp X'd : 386617 reads >= 20% >= 50% >= 80% screened Nr with L09136 4970 84 80 76 Nr with pCC1Fos 208 23 12 4 Nr with pMCL200_JGI_XZX+XZK 155 148 139 117 File generated in /psf/project/microbe5/4001426/edit_dir.08Dec05.QD