################################################################### Phrap Assembly QC Date: 10-14-2005 ################################################################### Project information from 'PROJECTS' db ------------------------------------------------------------------- # Project GenusSpecies TaxID Size(KBases) 4001319 Pythium coloratum 1587 60 ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 4001319 ------------------------------------------------------------------- ID=4001319 Pythiales, order, oomycetes stramenopiles (heterokonts), eukaryotes Pythium, genus, oomycetes Pythiaceae, family, oomycetes Oomycetes, oomycetes cellular organisms Eukaryota (eucaryotes), superkingdom, eukaryotes root ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 58257 # phrap: 50623 # db: 60000 56293 +/- 4072 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Q20 Pass Rate Q20 Avg Read Len BGSZ.5-8 2 90.36 728.00 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s SUFN 0 0 0.00 0.00 0 0.00 0.00 BGSZ 2 1 89.06 720.00 1 91.67 736.00 ################################################################### Assembly parameters command_line: /usr/local/bin/assemble.SCR -J -F pUC18.fa -B 4 Fri Oct 14 10:28:44 PDT 2005 /usr/local/bin/determineReadTypes.perl > determineReadTypes.log 2>&1 Fri Oct 14 10:28:45 PDT 2005 /usr/local/bin/phd2fasta -id ../phd_dir -os 4001319_fasta -oq 4001319_fasta.qual Fri Oct 14 10:28:46 PDT 2005 cp 4001319_fasta 4001319_fasta.screen; echo 1 Fri Oct 14 10:28:46 PDT 2005 /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 4001319_fasta.screen /usr/local/sequences/LRS.fasta -minmatch 20 -minscore 50 -M /psf/QC/Applications/pphrap/matrix/score_matrix.2 -screen > screen.out.std Fri Oct 14 10:28:48 PDT 2005 /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 4001319_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa -minmatch 12 -minscore 18 -M /psf/QC/Applications/pphrap/matrix/score_matrix.2 -screen > screen.out.1 Fri Oct 14 10:28:51 PDT 2005 /usr/local/bin/SaF_dir/trim/trimt -x 4001319_fasta.screen 15 Fri Oct 14 10:28:52 PDT 2005 /usr/local/src/assembly/pphrap/pphrap.SUN3.57 4001319_fasta.screen -new_ace -minmatch 30 -maxmatch 55 -minscore 55 -revise_greedy -max_subclone_size 50000 -vector_bound 20 > phrap.out Fri Oct 14 10:29:03 PDT 2005 reads2plates 4001319_fasta.screen > 4001319_fasta.screen.r2p Fri Oct 14 10:29:04 PDT 2005 /usr/local/bin/plates2contigs -BRIEF > plates2contigs.dat & Fri Oct 14 10:29:04 PDT 2005 /usr/local/bin/plates2contigs -BRIEF -384 > plates2contigs.384 & Fri Oct 14 10:29:04 PDT 2005 /usr/local/bin/plates2contigs -BRIEF -384 -F > plates2contigs.F & Fri Oct 14 10:29:04 PDT 2005 /usr/local/bin/plates2contigs -BRIEF -384 -R > plates2contigs.R & Fri Oct 14 10:29:04 PDT 2005 /usr/local/bin/plates2contigs -BRIEF -384 % > plates2contigs.% & Fri Oct 14 10:29:07 PDT 2005 reads2plates -384 4001319_fasta.screen.singlets -reads > 4001319_fasta.screen.singlets.r2p Fri Oct 14 10:29:07 PDT 2005 agrep -f 4001319_fasta.screen.singlets.reads 4001319_fasta.screen.trimQ15.SaF > 4001319_fasta.screen.singlets.trimQ15.i & Fri Oct 14 10:29:08 PDT 2005 cat 4001319_fasta.screen.singlets | /usr/production/bin/perl /home/copeland/scripts/rlFilter.pl > singlets.rl; /home/jchapman/perlscripts/histogram2.pl singlets.rl 2 50 > singlets.rl.hist Fri Oct 14 10:29:11 PDT 2005 /home/copeland/scripts/megablast.sh 4001319_fasta.screen.contigs /home/copeland/BLAST/JGIContaminants Fri Oct 14 10:29:13 PDT 2005 /home/copeland/scripts/megablast.sh 4001319_fasta.screen.contigs /home/copeland/BLAST/JGIVectors Fri Oct 14 10:29:15 PDT 2005 /usr/production/bin/perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.4001319.out Fri Oct 14 10:29:15 PDT 2005 /home/copeland/scripts/librariesInfoTxt.sh 4001319 phrap.out > librariesInfo.txt Fri Oct 14 10:29:16 PDT 2005 ################################################################### Library vector screening ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.4001319_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.4001319_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 587 total values totalling 172.0787. <0.293149 +/- 0.145461> #Range: [ 0 - 0.6818 ] #Most likely bin: [ 0.17 - 0.175 ] 20 counts #Median bin: [ 0.24 - 0.245 ] 12 counts #Entropy = 6.2694 bits |XXXX 0 - 0.005 : [ 2 3.41e-03 3.41e-03 2 ] #... |XX 0.025 - 0.03 : [ 1 1.70e-03 5.11e-03 3 ] #... |XX 0.07 - 0.075 : [ 1 1.70e-03 6.81e-03 4 ] #... |XXXXXX 0.095 - 0.1 : [ 3 5.11e-03 1.19e-02 7 ] |XX 0.1 - 0.105 : [ 1 1.70e-03 1.36e-02 8 ] #... |XXXX 0.11 - 0.115 : [ 2 3.41e-03 1.70e-02 10 ] |XX 0.115 - 0.12 : [ 1 1.70e-03 1.87e-02 11 ] |XX 0.12 - 0.125 : [ 1 1.70e-03 2.04e-02 12 ] |XXXXXXXX 0.125 - 0.13 : [ 4 6.81e-03 2.73e-02 16 ] |XXXXXXXXXXXXXXXXXX 0.13 - 0.135 : [ 9 1.53e-02 4.26e-02 25 ] |XXXXXXXXXXXXXX 0.135 - 0.14 : [ 7 1.19e-02 5.45e-02 32 ] |XXXXXXXXXXXXXXXXXXXX 0.14 - 0.145 : [ 10 1.70e-02 7.16e-02 42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.145 - 0.15 : [ 15 2.56e-02 9.71e-02 57 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.15 - 0.155 : [ 14 2.39e-02 1.21e-01 71 ] |XXXXXXXXXXXXXXXX 0.155 - 0.16 : [ 8 1.36e-02 1.35e-01 79 ] |XXXXXXXXXXXXXXXX 0.16 - 0.165 : [ 8 1.36e-02 1.48e-01 87 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.165 - 0.17 : [ 17 2.90e-02 1.77e-01 104 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.17 - 0.175 : [ 20 3.41e-02 2.11e-01 124 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.175 - 0.18 : [ 15 2.56e-02 2.37e-01 139 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.18 - 0.185 : [ 13 2.21e-02 2.59e-01 152 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.185 - 0.19 : [ 13 2.21e-02 2.81e-01 165 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.19 - 0.195 : [ 15 2.56e-02 3.07e-01 180 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.195 - 0.2 : [ 12 2.04e-02 3.27e-01 192 ] |XXXXXXXXXXXXXXXXXX 0.2 - 0.205 : [ 9 1.53e-02 3.42e-01 201 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.205 - 0.21 : [ 12 2.04e-02 3.63e-01 213 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.21 - 0.215 : [ 13 2.21e-02 3.85e-01 226 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.215 - 0.22 : [ 14 2.39e-02 4.09e-01 240 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.22 - 0.225 : [ 17 2.90e-02 4.38e-01 257 ] |XXXXXXXXXXXXXXXXXX 0.225 - 0.23 : [ 9 1.53e-02 4.53e-01 266 ] |XXXXXXXXXXXXXXXXXX 0.23 - 0.235 : [ 9 1.53e-02 4.68e-01 275 ] |XXXXXXXXXXXXXXXXXXXX 0.235 - 0.24 : [ 10 1.70e-02 4.86e-01 285 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.24 - 0.245 : [ 12 2.04e-02 5.06e-01 297 ] |XXXXXXXXXXXXXXXXXX 0.245 - 0.25 : [ 9 1.53e-02 5.21e-01 306 ] |XXXXXXXXXXXXXXXXXXXX 0.25 - 0.255 : [ 10 1.70e-02 5.38e-01 316 ] |XXXXXXXXXX 0.255 - 0.26 : [ 5 8.52e-03 5.47e-01 321 ] |XXXXXXXXXXXXXXXXXXXX 0.26 - 0.265 : [ 10 1.70e-02 5.64e-01 331 ] |XXXXXX 0.265 - 0.27 : [ 3 5.11e-03 5.69e-01 334 ] |XXXXXXXXXXXXXXXXXXXX 0.27 - 0.275 : [ 10 1.70e-02 5.86e-01 344 ] |XXXXXXXXXXXXXXXXXXXXXX 0.275 - 0.28 : [ 11 1.87e-02 6.05e-01 355 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.28 - 0.285 : [ 13 2.21e-02 6.27e-01 368 ] |XXXXXXXXXXXXXX 0.285 - 0.29 : [ 7 1.19e-02 6.39e-01 375 ] |XXXXXX 0.29 - 0.295 : [ 3 5.11e-03 6.44e-01 378 ] |XXXXXXXXXXXX 0.295 - 0.3 : [ 6 1.02e-02 6.54e-01 384 ] |XXXXXXXXXX 0.3 - 0.305 : [ 5 8.52e-03 6.63e-01 389 ] |XXXXXXXXXXXX 0.305 - 0.31 : [ 6 1.02e-02 6.73e-01 395 ] |XXXXXXXX 0.31 - 0.315 : [ 4 6.81e-03 6.80e-01 399 ] |XXXXXXXXXX 0.315 - 0.32 : [ 5 8.52e-03 6.88e-01 404 ] |XXXXXXXXXXXXXX 0.32 - 0.325 : [ 7 1.19e-02 7.00e-01 411 ] #... |XXXXXXXXXX 0.33 - 0.335 : [ 5 8.52e-03 7.09e-01 416 ] |XXXXXXXXXXXXXX 0.335 - 0.34 : [ 7 1.19e-02 7.21e-01 423 ] |XXXXXX 0.34 - 0.345 : [ 3 5.11e-03 7.26e-01 426 ] |XXXX 0.345 - 0.35 : [ 2 3.41e-03 7.29e-01 428 ] |XXXXXX 0.35 - 0.355 : [ 3 5.11e-03 7.34e-01 431 ] |XXXXXXXXXXXX 0.355 - 0.36 : [ 6 1.02e-02 7.44e-01 437 ] |XXXXXXXX 0.36 - 0.365 : [ 4 6.81e-03 7.51e-01 441 ] |XXXXXXXX 0.365 - 0.37 : [ 4 6.81e-03 7.58e-01 445 ] |XXXXXX 0.37 - 0.375 : [ 3 5.11e-03 7.63e-01 448 ] |XXXXXXXXXXXX 0.375 - 0.38 : [ 6 1.02e-02 7.73e-01 454 ] |XX 0.38 - 0.385 : [ 1 1.70e-03 7.75e-01 455 ] |XXXX 0.385 - 0.39 : [ 2 3.41e-03 7.79e-01 457 ] |XXXXXXXXXXXXXX 0.39 - 0.395 : [ 7 1.19e-02 7.90e-01 464 ] |XX 0.395 - 0.4 : [ 1 1.70e-03 7.92e-01 465 ] |XXXX 0.4 - 0.405 : [ 2 3.41e-03 7.96e-01 467 ] |XXXXXX 0.405 - 0.41 : [ 3 5.11e-03 8.01e-01 470 ] |XX 0.41 - 0.415 : [ 1 1.70e-03 8.02e-01 471 ] |XXXX 0.415 - 0.42 : [ 2 3.41e-03 8.06e-01 473 ] #... |XX 0.43 - 0.435 : [ 1 1.70e-03 8.07e-01 474 ] #... |XXXX 0.44 - 0.445 : [ 2 3.41e-03 8.11e-01 476 ] #... |XX 0.45 - 0.455 : [ 1 1.70e-03 8.13e-01 477 ] #... |XXXXXXXXXX 0.46 - 0.465 : [ 5 8.52e-03 8.21e-01 482 ] |XX 0.465 - 0.47 : [ 1 1.70e-03 8.23e-01 483 ] #... |XX 0.475 - 0.48 : [ 1 1.70e-03 8.25e-01 484 ] |XXXX 0.48 - 0.485 : [ 2 3.41e-03 8.28e-01 486 ] |XX 0.485 - 0.49 : [ 1 1.70e-03 8.30e-01 487 ] |XX 0.49 - 0.495 : [ 1 1.70e-03 8.31e-01 488 ] #... |XXXXXXXX 0.5 - 0.505 : [ 4 6.81e-03 8.38e-01 492 ] |XXXXXXXX 0.505 - 0.51 : [ 4 6.81e-03 8.45e-01 496 ] |XXXX 0.51 - 0.515 : [ 2 3.41e-03 8.48e-01 498 ] |XXXX 0.515 - 0.52 : [ 2 3.41e-03 8.52e-01 500 ] |XXXXXX 0.52 - 0.525 : [ 3 5.11e-03 8.57e-01 503 ] |XXXXXXXX 0.525 - 0.53 : [ 4 6.81e-03 8.64e-01 507 ] |XXXXXXXXXX 0.53 - 0.535 : [ 5 8.52e-03 8.72e-01 512 ] |XXXXXX 0.535 - 0.54 : [ 3 5.11e-03 8.77e-01 515 ] |XXXXXXXXXXXXXX 0.54 - 0.545 : [ 7 1.19e-02 8.89e-01 522 ] |XXXXXX 0.545 - 0.55 : [ 3 5.11e-03 8.94e-01 525 ] |XXXXXXXXXX 0.55 - 0.555 : [ 5 8.52e-03 9.03e-01 530 ] |XXXXXXXXXXXXXX 0.555 - 0.56 : [ 7 1.19e-02 9.15e-01 537 ] |XXXXXX 0.56 - 0.565 : [ 3 5.11e-03 9.20e-01 540 ] |XXXXXXXXXX 0.565 - 0.57 : [ 5 8.52e-03 9.28e-01 545 ] |XXXXXX 0.57 - 0.575 : [ 3 5.11e-03 9.34e-01 548 ] |XXXXXX 0.575 - 0.58 : [ 3 5.11e-03 9.39e-01 551 ] |XXXXXXXXXX 0.58 - 0.585 : [ 5 8.52e-03 9.47e-01 556 ] |XXXXXXXXXXXX 0.585 - 0.59 : [ 6 1.02e-02 9.57e-01 562 ] |XXXXXXXX 0.59 - 0.595 : [ 4 6.81e-03 9.64e-01 566 ] |XXXXXXXXXXXX 0.595 - 0.6 : [ 6 1.02e-02 9.74e-01 572 ] |XXXXXXXXXX 0.6 - 0.605 : [ 5 8.52e-03 9.83e-01 577 ] |XXXX 0.605 - 0.61 : [ 2 3.41e-03 9.86e-01 579 ] |XX 0.61 - 0.615 : [ 1 1.70e-03 9.88e-01 580 ] |XX 0.615 - 0.62 : [ 1 1.70e-03 9.90e-01 581 ] #... |XX 0.625 - 0.63 : [ 1 1.70e-03 9.91e-01 582 ] #... |XX 0.64 - 0.645 : [ 1 1.70e-03 9.93e-01 583 ] #... |XX 0.66 - 0.665 : [ 1 1.70e-03 9.95e-01 584 ] |XX 0.665 - 0.67 : [ 1 1.70e-03 9.97e-01 585 ] #... |XX 0.675 - 0.68 : [ 1 1.70e-03 9.98e-01 586 ] |XX 0.68 - 0.685 : [ 1 1.70e-03 1.00e+00 587 ] ################################################################### reads2plates summary plate(s) reads clones N/plate avg% LIBRARY @ 4 767 384 96.00 100.00 BGSZ @ ] 767 384 96.00 cumulative total@@ LIBRARY PLATE ID COUNT [ BGSZ 4 ] for 4 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 = 86 HQ Discrepant reads = 3 Chimeric reads = 3 Suspect alignments = 4 ################################################################### # Contig# Reads Contig Len C O N T I G I N F O R M A T I O N Fri Oct 14 10:29:18 2005 File: phrap.out C O N T I G I N F O R M A T I O N Fri Oct 14 10:29:18 2005 File: phrap.out -------------------------------------------------------------- Contig 1. 2 reads; 149 bp (untrimmed), 149 (trimmed). Contig 2. 2 reads; 202 bp (untrimmed), 202 (trimmed). Contig 3. 2 reads; 99 bp (untrimmed), 99 (trimmed). Contig 4. 2 reads; 97 bp (untrimmed), 97 (trimmed). Contig 5. 2 reads; 1580 bp (untrimmed), 1456 (trimmed). Contig 6. 2 reads; 163 bp (untrimmed), 163 (trimmed). Contig 7. 2 reads; 101 bp (untrimmed), 101 (trimmed). Contig 8. 2 reads; 172 bp (untrimmed), 172 (trimmed). Contig 9. 2 reads; 158 bp (untrimmed), 158 (trimmed). Contig 10. 2 reads; 158 bp (untrimmed), 158 (trimmed). Contig 11. 2 reads; 117 bp (untrimmed), 117 (trimmed). Contig 12. 2 reads; 86 bp (untrimmed), 86 (trimmed). Contig 13. 2 reads; 1649 bp (untrimmed), 1515 (trimmed). Contig 14. 2 reads; 1147 bp (untrimmed), 671 (trimmed). Contig 15. 3 reads; 2328 bp (untrimmed), 2203 (trimmed). Contig 16. 4 reads; 1311 bp (untrimmed), 1246 (trimmed). Contig 17. 11 reads; 2280 bp (untrimmed), 2246 (trimmed). Contig 18. 25 reads; 3723 bp (untrimmed), 3568 (trimmed). Contig 19. 163 reads; 17058 bp (untrimmed), 16874 (trimmed). Contig 20. 274 reads; 27102 bp (untrimmed), 26976 (trimmed). -------------------------------------------------------------- Totals 508 reads; 59680 bp (untrimmed), 58257 (trimmed). ################################################################### Histogram of Good Contig Trimmed Length (>=2000 bp & >=10 reads) ------------------------------------------------------------------- Command: contig | grep '^Contig' | hist - 8 2000 3 10 10000000 8 2000 10000000 #Found 4 total values totalling 49664.0000. <12416.000000 +/- 10168.374600> #Range: [ 2246 - 26976 ] #Most likely bin: [ 2000 - 4000 ] 2 counts #Median bin: [ 2000 - 4000 ] 2 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 2 0.50 0.50 ] #... |XXXXXXXXXXXXXXXXXXXX 16000 - 18000 : [ 1 0.25 0.75 ] #... |XXXXXXXXXXXXXXXXXXXX 26000 - 28000 : [ 1 0.25 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 225648 C = 103265 G = 102257 T = 213104 N = 7145 X = 113130 GC fraction = 0.27 Total = 764549 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 4001319_fasta.screen.contigs A 22220 C 7546 G 8273 N 18 T 21623 fraction GC = 0.27 total bases = 59680 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 20 total values totalling 508.0000. <25.400000 +/- 66.921148> #Range: [ 2 - 274 ] #Most likely bin: [ 2 - 3 ] 14 counts #Median bin: [ 2 - 3 ] 14 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 3 : [ 14 0.70 0.70 ] |XXX 3 - 4 : [ 1 0.05 0.75 ] |XXX 4 - 5 : [ 1 0.05 0.80 ] #... |XXX 11 - 12 : [ 1 0.05 0.85 ] #... |XXX 25 - 26 : [ 1 0.05 0.90 ] #... |XXX 163 - 164 : [ 1 0.05 0.95 ] #... |XXX 274 - 275 : [ 1 0.05 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 20 total values totalling 59680.0000. <2984.000000 +/- 6634.594464> #Range: [ 86 - 27102 ] #Most likely bin: [ 0 - 1000 ] 11 counts #Median bin: [ 0 - 1000 ] 11 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 1000 : [ 11 0.55 0.55 ] |XXXXXXXXXXXXXXX 1000 - 2000 : [ 4 0.20 0.75 ] |XXXXXXX 2000 - 3000 : [ 2 0.10 0.85 ] |XXXX 3000 - 4000 : [ 1 0.05 0.90 ] #... |XXXX 17000 - 18000 : [ 1 0.05 0.95 ] #... |XXXX 27000 - 28000 : [ 1 0.05 1.00 ] ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 58178 bases = 7.69 +- 4.25 = 0.16 +- 3.30 m1 = 2.35 m2 = 1.79 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 9 total values totalling 36.8700. <4.096667 +/- 3.084002> #Range: [ 1.18 - 9.33 ] #Most likely bin: [ 1 - 1.5 ] 3 counts #Median bin: [ 2.5 - 3 ] 1 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 3 0.33 0.33 ] |XXXXXXXXXXXXX 1.5 - 2 : [ 1 0.11 0.44 ] #... |XXXXXXXXXXXXX 2.5 - 3 : [ 1 0.11 0.56 ] #... |XXXXXXXXXXXXX 4 - 4.5 : [ 1 0.11 0.67 ] #... |XXXXXXXXXXXXX 6 - 6.5 : [ 1 0.11 0.78 ] #... |XXXXXXXXXXXXX 8.5 - 9 : [ 1 0.11 0.89 ] |XXXXXXXXXXXXX 9 - 9.5 : [ 1 0.11 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 4 total values totalling 28.6800. <7.170000 +/- 1.968540> #Range: [ 4.48 - 9.33 ] #Most likely bin: [ 0 - 0.5 ] 1 counts #Median bin: [ 6 - 6.5 ] 1 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 1 0.25 0.25 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 1 0.25 0.50 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 1 0.25 0.75 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 1 0.25 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 13 2 reads 1649 bases = 1.18 +- 0.39 = 0.08 +- 0.90 m1 = 0.13 m2 = -0.17 Contig 15 3 reads 2328 bases = 1.23 +- 0.42 = 0.45 +- 1.09 m1 = 0.15 m2 = -0.25 Contig 5 2 reads 1580 bases = 1.29 +- 0.45 = 1.29 +- 0.45 m1 = 0.16 m2 = 0.00 Contig 14 2 reads 1147 bases = 1.59 +- 0.49 = 0.12 +- 0.63 m1 = 0.15 m2 = -0.04 Contig 16 4 reads 1311 bases = 2.90 +- 1.24 = -0.07 +- 0.64 m1 = 0.53 m2 = 0.28 Contig 17 11 reads 2280 bases = 4.48 +- 1.71 = 0.29 +- 1.13 m1 = 0.66 m2 = 0.41 Contig 18 25 reads 3723 bases = 6.12 +- 2.76 = 0.47 +- 1.64 m1 = 1.25 m2 = 1.24 Contig 19 163 reads 17058 bases = 8.75 +- 4.71 = 0.12 +- 4.38 m1 = 2.54 m2 = 0.77 Contig 20 274 reads 27102 bases = 9.33 +- 2.76 = 0.05 +- 3.25 m1 = 0.82 m2 = -0.73 Contig 13 2 reads 1649 bases = 1.18 +- 0.39 = 0.08 +- 0.90 m1 = 0.13 m2 = -0.17 Contig 15 3 reads 2328 bases = 1.23 +- 0.42 = 0.45 +- 1.09 m1 = 0.15 m2 = -0.25 Contig 5 2 reads 1580 bases = 1.29 +- 0.45 = 1.29 +- 0.45 m1 = 0.16 m2 = 0.00 Contig 14 2 reads 1147 bases = 1.59 +- 0.49 = 0.12 +- 0.63 m1 = 0.15 m2 = -0.04 Contig 16 4 reads 1311 bases = 2.90 +- 1.24 = -0.07 +- 0.64 m1 = 0.53 m2 = 0.28 Contig 17 11 reads 2280 bases = 4.48 +- 1.71 = 0.29 +- 1.13 m1 = 0.66 m2 = 0.41 Contig 18 25 reads 3723 bases = 6.12 +- 2.76 = 0.47 +- 1.64 m1 = 1.25 m2 = 1.24 Contig 19 163 reads 17058 bases = 8.75 +- 4.71 = 0.12 +- 4.38 m1 = 2.54 m2 = 0.77 Contig 20 274 reads 27102 bases = 9.33 +- 2.76 = 0.05 +- 3.25 m1 = 0.82 m2 = -0.73 ################################################################### Histogram of Assembled Average Insert Sizes Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list ------------------------------------------------------------------- Command: /usr/xpg4/bin/grep BGSZ reads.list > grep.reads.list.BGSZ Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BGSZ 4 500 #Found 205 total values totalling 699730.0000. <3413.317073 +/- 598.928028> #Range: [ 950 - 4245 ] #Most likely bin: [ 3000 - 3500 ] 84 counts #Median bin: [ 3000 - 3500 ] 84 counts #Histogram Bins Count Fraction Cum_Fraction | 500 - 1000 : [ 1 0.00 0.00 ] |XXX 1000 - 1500 : [ 6 0.03 0.03 ] |X 1500 - 2000 : [ 3 0.01 0.05 ] |XXX 2000 - 2500 : [ 6 0.03 0.08 ] |XXX 2500 - 3000 : [ 7 0.03 0.11 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 84 0.41 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 78 0.38 0.90 ] |XXXXXXXXXX 4000 - 4500 : [ 20 0.10 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # BGSZ 3160 +- 773 (n=101) ################################################################### 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. ------------------------------------------------------------------- ################################################################### trimt JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 4001319_fasta.screen.trimQ15.SaF 4 50 ------------------------------------------------------------------- #Found 767 total values totalling 410482.0000. <535.178618 +/- 358.003912> #Range: [ 0 - 983 ] #Most likely bin: [ 0 - 50 ] 185 counts #Median bin: [ 700 - 750 ] 44 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 185 0.24 0.24 ] |XXXXX 50 - 100 : [ 23 0.03 0.27 ] |XX 100 - 150 : [ 11 0.01 0.29 ] |XXX 150 - 200 : [ 12 0.02 0.30 ] |XX 200 - 250 : [ 8 0.01 0.31 ] |X 250 - 300 : [ 5 0.01 0.32 ] |XX 300 - 350 : [ 8 0.01 0.33 ] |XX 350 - 400 : [ 8 0.01 0.34 ] |X 400 - 450 : [ 6 0.01 0.35 ] |XXX 450 - 500 : [ 15 0.02 0.37 ] |XXX 500 - 550 : [ 13 0.02 0.38 ] |XX 550 - 600 : [ 10 0.01 0.40 ] |XXX 600 - 650 : [ 12 0.02 0.41 ] |XXXXXXXXX 650 - 700 : [ 41 0.05 0.47 ] |XXXXXXXXXX 700 - 750 : [ 44 0.06 0.52 ] |XXXXXXXXXXXXXXXXXXX 750 - 800 : [ 89 0.12 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 142 0.19 0.82 ] |XXXXXXXXXXXXXXXXXXXXX 850 - 900 : [ 98 0.13 0.95 ] |XXXXXXX 900 - 950 : [ 31 0.04 0.99 ] |X 950 - 1000 : [ 6 0.01 1.00 ] trimt JAZZ trim 15 readlength histogram for SUFN trimt JAZZ trim 15 readlength histogram for BGSZ Command: /usr/xpg4/bin/grep BGSZ 4001319_fasta.screen.trimQ15.SaF > reads.trim15.BGSZ.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.BGSZ.rl 2 50 #Found 767 total values totalling 410482.0000. <535.178618 +/- 358.003912> #Range: [ 0 - 983 ] #Most likely bin: [ 0 - 50 ] 185 counts #Median bin: [ 700 - 750 ] 44 counts #Histogram Bins Count Fraction Cum_Fraction |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 185 0.24 0.24 ] |XXXXX 50 - 100 : [ 23 0.03 0.27 ] |XX 100 - 150 : [ 11 0.01 0.29 ] |XXX 150 - 200 : [ 12 0.02 0.30 ] |XX 200 - 250 : [ 8 0.01 0.31 ] |X 250 - 300 : [ 5 0.01 0.32 ] |XX 300 - 350 : [ 8 0.01 0.33 ] |XX 350 - 400 : [ 8 0.01 0.34 ] |X 400 - 450 : [ 6 0.01 0.35 ] |XXX 450 - 500 : [ 15 0.02 0.37 ] |XXX 500 - 550 : [ 13 0.02 0.38 ] |XX 550 - 600 : [ 10 0.01 0.40 ] |XXX 600 - 650 : [ 12 0.02 0.41 ] |XXXXXXXXX 650 - 700 : [ 41 0.05 0.47 ] |XXXXXXXXXX 700 - 750 : [ 44 0.06 0.52 ] |XXXXXXXXXXXXXXXXXXX 750 - 800 : [ 89 0.12 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 142 0.19 0.82 ] |XXXXXXXXXXXXXXXXXXXXX 850 - 900 : [ 98 0.13 0.95 ] |XXXXXXX 900 - 950 : [ 31 0.04 0.99 ] |X 950 - 1000 : [ 6 0.01 1.00 ] ################################################################### Ideal Assembly with avg read len of 535.178618 bp, 508 reads, genome size 56293 bp Command: idealAssembly 56293 508 535.178618 ------------------------------------------------------------------- Genome = 56293 bases Nreads = 508 readLength = 535.178618 Depth = 4.83 N_contigs = N_gaps = 4 mean gap size = 110 bases mean contig size = 125 reads (~ 13869 bases) %cover = 99.20 %singlet = 0.03 assembly size = 55826 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 1 contigs containing at least 210 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 ------------------------------------------------------------------- Number of reads with X's: 289 Number of reads with percent X's >= 20%: 123 = 16.0% Number of reads with percent X's >= 50%: 122 = 15.9% Number of reads with percent X's >= 80%: 97 = 12.6% Total reads in project: 767 Total bp X'd : 113130 reads >= 20% >= 50% >= 80% screened Nr with L09136 289 123 122 97 ################################################################### Contam Summary with *.singlets: Command: contam_summary -c -s -g ------------------------------------------------------------------- Number of reads with X's: 122 Number of reads with percent X's >= 20%: 92 = 35.5% Number of reads with percent X's >= 50%: 91 = 35.1% Number of reads with percent X's >= 80%: 86 = 33.2% Total reads in project: 259 Total bp X'd : 83770 reads >= 20% >= 50% >= 80% screened Nr with L09136 122 92 91 86 File generated in /psf/bermuda/draft002/in_progress/projects/4001319/edit_dir.14Oct05.QC