Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-13-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
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Project Size(KB) TaxID GenusSpecies
3634490 3000 NULL Nitrobacter winogradskyi
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Nitrobacter_winogradskyi
-------------------------------------------------------------------
Bradyrhizobiaceae, family, a-proteobacteria
Alphaproteobacteria, class, a-proteobacteria
Nitrobacter winogradskyi, species, a-proteobacteria
Nitrobacter, genus, a-proteobacteria
Rhizobiales (rhizobacteria), order, a-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3400335
# phrap: 3088371
# db:
altered.
3000000
3162902 +/- 171722
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 7859
Number of reads with percent X's >= 20%: 266 = 0.7%
Number of reads with percent X's >= 50%: 145 = 0.4%
Number of reads with percent X's >= 80%: 21 = 0.1%
Total reads in project: 36849
Total bp X'd : 404034
reads >= 20% >= 50% >= 80% screened
Nr with L09136 6682 47 25 8
Nr with pCC1Fos 899 3 1 0
Nr with pMCL200_JGI_XZX+XZK 278 216 119 13
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 14
Number of reads with percent X's >= 20%: 4 = 9.1%
Number of reads with percent X's >= 50%: 4 = 9.1%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 44
Total bp X'd : 2916
reads >= 20% >= 50% >= 80% screened
Nr with L09136 10 0 0 0
Nr with pMCL200_JGI_XZX+XZK 4 4 4 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 6756507
C = 10746148
G = 10782869
T = 6694250
N = 111323
X = 404034
GC fraction = 0.61
Total = 35495131
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634490_fasta.screen.contigs
-------------------------------------------------------------------
A 649292
C 1058924
G 1054667
T 644193
N 24
fraction GC = 0.62
total bases = 3407100
Libraries and Reads
-------------------------------------------------------------------
Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
-------------------------------------------------------------------
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAO reads.list > grep.reads.list.AIAO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAO 4 500
-------------------------------------------------------------------
#Found 7649 total values totalling 50022663.0000. <6539.765067 +/- 42916.101083>
#Range: [ 879 - 1074153 ]
#Most likely bin: [ 3500 - 4000 ] 3815 counts
#Median bin: [ 3500 - 4000 ] 3815 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 4 0.00 0.00 ]
| 1000 - 1500 : [ 26 0.00 0.00 ]
| 1500 - 2000 : [ 37 0.00 0.01 ]
|X 2000 - 2500 : [ 60 0.01 0.02 ]
|X 2500 - 3000 : [ 138 0.02 0.03 ]
|XXXXXXXXXXXX 3000 - 3500 : [ 1108 0.14 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3815 0.50 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 2291 0.30 0.98 ]
|X 4500 - 5000 : [ 118 0.02 0.99 ]
#...
| 6500 - 7000 : [ 1 0.00 0.99 ]
#...
| 16000 - 16500 : [ 1 0.00 0.99 ]
#...
| 20500 - 21000 : [ 4 0.00 0.99 ]
| 21000 - 21500 : [ 2 0.00 0.99 ]
#...
| 35500 - 36000 : [ 1 0.00 0.99 ]
#...
| 53500 - 54000 : [ 1 0.00 0.99 ]
#...
| 77500 - 78000 : [ 3 0.00 0.99 ]
| 78000 - 78500 : [ 2 0.00 1.00 ]
#...
| 93000 - 93500 : [ 1 0.00 1.00 ]
#...
| 123500 - 124000 : [ 1 0.00 1.00 ]
| 124000 - 124500 : [ 3 0.00 1.00 ]
| 124500 - 125000 : [ 1 0.00 1.00 ]
#...
| 418000 - 418500 : [ 1 0.00 1.00 ]
| 418500 - 419000 : [ 3 0.00 1.00 ]
| 419000 - 419500 : [ 6 0.00 1.00 ]
| 419500 - 420000 : [ 1 0.00 1.00 ]
#...
| 479500 - 480000 : [ 1 0.00 1.00 ]
#...
| 633500 - 634000 : [ 3 0.00 1.00 ]
| 634000 - 634500 : [ 1 0.00 1.00 ]
| 634500 - 635000 : [ 1 0.00 1.00 ]
#...
| 696500 - 697000 : [ 1 0.00 1.00 ]
#...
| 720500 - 721000 : [ 4 0.00 1.00 ]
| 721000 - 721500 : [ 2 0.00 1.00 ]
| 721500 - 722000 : [ 2 0.00 1.00 ]
#...
| 866000 - 866500 : [ 1 0.00 1.00 ]
#...
| 1073000 - 1073500 : [ 1 0.00 1.00 ]
| 1073500 - 1074000 : [ 1 0.00 1.00 ]
| 1074000 - 1074500 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAP reads.list > grep.reads.list.AIAP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAP 4 500
-------------------------------------------------------------------
#Found 5483 total values totalling 70158623.0000. <12795.663505 +/- 54107.093581>
#Range: [ 225 - 1077584 ]
#Most likely bin: [ 8000 - 8500 ] 1217 counts
#Median bin: [ 8000 - 8500 ] 1217 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 2 0.00 0.00 ]
| 500 - 1000 : [ 3 0.00 0.00 ]
|X 1000 - 1500 : [ 31 0.01 0.01 ]
|X 1500 - 2000 : [ 38 0.01 0.01 ]
|X 2000 - 2500 : [ 29 0.01 0.02 ]
|X 2500 - 3000 : [ 32 0.01 0.02 ]
|X 3000 - 3500 : [ 41 0.01 0.03 ]
|X 3500 - 4000 : [ 33 0.01 0.04 ]
|X 4000 - 4500 : [ 29 0.01 0.04 ]
|X 4500 - 5000 : [ 34 0.01 0.05 ]
|X 5000 - 5500 : [ 39 0.01 0.06 ]
|XX 5500 - 6000 : [ 49 0.01 0.07 ]
|XXX 6000 - 6500 : [ 105 0.02 0.08 ]
|XXXXX 6500 - 7000 : [ 142 0.03 0.11 ]
|XXXXXXXXXXXX 7000 - 7500 : [ 367 0.07 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 912 0.17 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1217 0.22 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 1029 0.19 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 752 0.14 0.89 ]
|XXXXXXXXXXXXXXX 9500 - 10000 : [ 444 0.08 0.97 ]
|XXX 10000 - 10500 : [ 89 0.02 0.99 ]
#...
| 11000 - 11500 : [ 1 0.00 0.99 ]
#...
| 23500 - 24000 : [ 2 0.00 0.99 ]
| 24000 - 24500 : [ 2 0.00 0.99 ]
| 24500 - 25000 : [ 2 0.00 0.99 ]
| 25000 - 25500 : [ 4 0.00 0.99 ]
| 25500 - 26000 : [ 2 0.00 0.99 ]
| 26000 - 26500 : [ 2 0.00 0.99 ]
#...
| 35500 - 36000 : [ 1 0.00 0.99 ]
#...
| 82500 - 83000 : [ 1 0.00 0.99 ]
| 83000 - 83500 : [ 1 0.00 0.99 ]
#...
| 127500 - 128000 : [ 1 0.00 0.99 ]
| 128000 - 128500 : [ 2 0.00 0.99 ]
| 128500 - 129000 : [ 5 0.00 0.99 ]
| 129000 - 129500 : [ 1 0.00 0.99 ]
#...
| 230500 - 231000 : [ 1 0.00 0.99 ]
#...
| 294000 - 294500 : [ 1 0.00 0.99 ]
#...
| 356500 - 357000 : [ 1 0.00 0.99 ]
#...
| 421000 - 421500 : [ 1 0.00 0.99 ]
#...
| 422500 - 423000 : [ 1 0.00 0.99 ]
#...
| 424000 - 424500 : [ 3 0.00 0.99 ]
#...
| 425000 - 425500 : [ 1 0.00 0.99 ]
#...
| 599000 - 599500 : [ 1 0.00 0.99 ]
#...
| 625000 - 625500 : [ 1 0.00 0.99 ]
#...
| 636500 - 637000 : [ 1 0.00 1.00 ]
#...
| 638000 - 638500 : [ 3 0.00 1.00 ]
| 638500 - 639000 : [ 2 0.00 1.00 ]
| 639000 - 639500 : [ 1 0.00 1.00 ]
| 639500 - 640000 : [ 2 0.00 1.00 ]
#...
| 723500 - 724000 : [ 1 0.00 1.00 ]
#...
| 724500 - 725000 : [ 3 0.00 1.00 ]
| 725000 - 725500 : [ 3 0.00 1.00 ]
| 725500 - 726000 : [ 2 0.00 1.00 ]
| 726000 - 726500 : [ 5 0.00 1.00 ]
| 726500 - 727000 : [ 3 0.00 1.00 ]
| 727000 - 727500 : [ 1 0.00 1.00 ]
#...
| 1077500 - 1078000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAS reads.list > grep.reads.list.AIAS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAS 4 500
-------------------------------------------------------------------
#Found 438 total values totalling 34616463.0000. <79033.020548 +/- 142434.556495>
#Range: [ 23257 - 880473 ]
#Most likely bin: [ 41500 - 42000 ] 53 counts
#Median bin: [ 42000 - 42500 ] 45 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 23000 - 23500 : [ 1 0.00 0.00 ]
#...
|XX 31500 - 32000 : [ 3 0.01 0.01 ]
#...
|XX 32500 - 33000 : [ 3 0.01 0.02 ]
#...
|XXX 34000 - 34500 : [ 4 0.01 0.03 ]
|XXX 34500 - 35000 : [ 4 0.01 0.03 ]
|X 35000 - 35500 : [ 1 0.00 0.04 ]
|X 35500 - 36000 : [ 1 0.00 0.04 ]
#...
|X 37000 - 37500 : [ 1 0.00 0.04 ]
|XX 37500 - 38000 : [ 2 0.00 0.05 ]
|XX 38000 - 38500 : [ 3 0.01 0.05 ]
|XX 38500 - 39000 : [ 3 0.01 0.06 ]
|XXXXXXXXXXX 39000 - 39500 : [ 14 0.03 0.09 ]
|XXXXXXXXXXXXX 39500 - 40000 : [ 17 0.04 0.13 ]
|XXXXXXXXXXXXXX 40000 - 40500 : [ 18 0.04 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 33 0.08 0.25 ]
|XXXXXXXXXXXXX 41000 - 41500 : [ 17 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 53 0.12 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 45 0.10 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 31 0.07 0.58 ]
|XXXXXXXXXXXXXXX 43000 - 43500 : [ 20 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 27 0.06 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXX 44000 - 44500 : [ 31 0.07 0.76 ]
|XXXXXXXXXXXXXXXXXXX 44500 - 45000 : [ 25 0.06 0.82 ]
|XXXXXXXXXXXXXXXXX 45000 - 45500 : [ 23 0.05 0.87 ]
|XXXXXXXXXXX 45500 - 46000 : [ 14 0.03 0.90 ]
|XXXXX 46000 - 46500 : [ 6 0.01 0.91 ]
|X 46500 - 47000 : [ 1 0.00 0.92 ]
|X 47000 - 47500 : [ 1 0.00 0.92 ]
#...
|X 83500 - 84000 : [ 1 0.00 0.92 ]
#...
|X 92500 - 93000 : [ 1 0.00 0.92 ]
#...
|X 177000 - 177500 : [ 1 0.00 0.92 ]
#...
|X 290000 - 290500 : [ 1 0.00 0.93 ]
#...
|X 306500 - 307000 : [ 1 0.00 0.93 ]
|X 307000 - 307500 : [ 1 0.00 0.93 ]
#...
|X 308000 - 308500 : [ 1 0.00 0.93 ]
|XX 308500 - 309000 : [ 3 0.01 0.94 ]
#...
|XX 309500 - 310000 : [ 3 0.01 0.95 ]
#...
|XX 310500 - 311000 : [ 2 0.00 0.95 ]
|XX 311000 - 311500 : [ 3 0.01 0.96 ]
|XX 311500 - 312000 : [ 2 0.00 0.96 ]
#...
|X 574000 - 574500 : [ 1 0.00 0.97 ]
#...
|XX 671500 - 672000 : [ 2 0.00 0.97 ]
|X 672000 - 672500 : [ 1 0.00 0.97 ]
#...
|X 705500 - 706000 : [ 1 0.00 0.97 ]
#...
|XX 757500 - 758000 : [ 2 0.00 0.98 ]
#...
|X 759500 - 760000 : [ 1 0.00 0.98 ]
#...
|X 775500 - 776000 : [ 1 0.00 0.98 ]
#...
|X 776500 - 777000 : [ 1 0.00 0.99 ]
|XX 777000 - 777500 : [ 2 0.00 0.99 ]
#...
|X 778500 - 779000 : [ 1 0.00 0.99 ]
#...
|X 872500 - 873000 : [ 1 0.00 1.00 ]
#...
|XX 880000 - 880500 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIAO 3721 +- 507 (n=3842)
# AIAS 42078 +- 2588 (n=189)
# AIAP 7891 +- 1800 (n=2621)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634490_fasta.screen.trimQ15.SaF and database (md_run table)
* note J15 is Jazz trimmed length, Q20 is count of Quality 20+ bases
-------------------------------------------------------------------
DB |----J15---| |----Q20---| Fasta |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIAO 19200 -1 -1 97 758 18432 94 780 97 781
AIAP 25344 -1 -1 89 596 22413 72 588 85 593
AIAS 3072 -1 -1 96 624 3072 93 611 96 652
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIAO 9216 94 769 98 780 9216 94 791 96 782
AIAP 12166 69 571 82 576 10247 77 605 87 611
AIAS 1536 93 659 95 673 1536 93 564 96 631
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634490_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
96 17347 8746 91.10 94.90 AIAO @
132 16603 9910 75.08 78.20 AIAP @
16 2899 1494 93.38 97.27 AIAS @
] 36849 20150 82.58 cumulative total@@
LIBRARY PLATE ID COUNT [ AIAO 96 AIAP 132 AIAS 16 ] for 244 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.
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trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3634490_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 43917 total values totalling 24863503.0000. <566.147574 +/- 303.551318>
#Range: [ 0 - 944 ]
#Most likely bin: [ 800 - 850 ] 8065 counts
#Median bin: [ 700 - 750 ] 4590 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 6903 0.16 0.16 ]
|XXX 50 - 100 : [ 615 0.01 0.17 ]
|XXX 100 - 150 : [ 597 0.01 0.18 ]
|XX 150 - 200 : [ 483 0.01 0.20 ]
|XXX 200 - 250 : [ 540 0.01 0.21 ]
|XXXX 250 - 300 : [ 799 0.02 0.23 ]
|XXXX 300 - 350 : [ 798 0.02 0.24 ]
|XXXX 350 - 400 : [ 854 0.02 0.26 ]
|XXXX 400 - 450 : [ 866 0.02 0.28 ]
|XXXXX 450 - 500 : [ 1075 0.02 0.31 ]
|XXXXXX 500 - 550 : [ 1304 0.03 0.34 ]
|XXXXXXXX 550 - 600 : [ 1548 0.04 0.37 ]
|XXXXXXXXX 600 - 650 : [ 1752 0.04 0.41 ]
|XXXXXXXXXXXX 650 - 700 : [ 2520 0.06 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4590 0.10 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 7900 0.18 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 8065 0.18 0.94 ]
|XXXXXXXXXXXXX 850 - 900 : [ 2579 0.06 1.00 ]
|X 900 - 950 : [ 129 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ASKX
trimt JAZZ trim 15 readlength histogram for ASNA
trimt JAZZ trim 15 readlength histogram for ASNB
trimt JAZZ trim 15 readlength histogram for ASNK
trimt JAZZ trim 15 readlength histogram for ASNN
trimt JAZZ trim 15 readlength histogram for ASNO
trimt JAZZ trim 15 readlength histogram for AIAO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAO 3634490_fasta.screen.trimQ15.SaF > reads.trim15.AIAO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAO.rl 2 50
-------------------------------------------------------------------
#Found 18432 total values totalling 13513507.0000. <733.154677 +/- 208.027433>
#Range: [ 0 - 944 ]
#Most likely bin: [ 800 - 850 ] 6204 counts
#Median bin: [ 750 - 800 ] 4917 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 0 - 50 : [ 1056 0.06 0.06 ]
| 50 - 100 : [ 60 0.00 0.06 ]
| 100 - 150 : [ 57 0.00 0.06 ]
| 150 - 200 : [ 53 0.00 0.07 ]
| 200 - 250 : [ 61 0.00 0.07 ]
| 250 - 300 : [ 58 0.00 0.07 ]
| 300 - 350 : [ 50 0.00 0.08 ]
| 350 - 400 : [ 63 0.00 0.08 ]
| 400 - 450 : [ 53 0.00 0.08 ]
| 450 - 500 : [ 61 0.00 0.09 ]
|X 500 - 550 : [ 82 0.00 0.09 ]
|X 550 - 600 : [ 117 0.01 0.10 ]
|X 600 - 650 : [ 219 0.01 0.11 ]
|XXXXX 650 - 700 : [ 731 0.04 0.15 ]
|XXXXXXXXXXXXXX 700 - 750 : [ 2120 0.12 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4917 0.27 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6204 0.34 0.87 ]
|XXXXXXXXXXXXXXX 850 - 900 : [ 2348 0.13 0.99 ]
|X 900 - 950 : [ 122 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAP 3634490_fasta.screen.trimQ15.SaF > reads.trim15.AIAP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAP.rl 2 50
-------------------------------------------------------------------
#Found 22413 total values totalling 9598308.0000. <428.247356 +/- 309.188896>
#Range: [ 0 - 921 ]
#Most likely bin: [ 0 - 50 ] 5680 counts
#Median bin: [ 500 - 550 ] 1120 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 5680 0.25 0.25 ]
|XXXX 50 - 100 : [ 507 0.02 0.28 ]
|XXXX 100 - 150 : [ 509 0.02 0.30 ]
|XXX 150 - 200 : [ 398 0.02 0.32 ]
|XXX 200 - 250 : [ 446 0.02 0.34 ]
|XXXX 250 - 300 : [ 581 0.03 0.36 ]
|XXXX 300 - 350 : [ 548 0.02 0.39 ]
|XXXXX 350 - 400 : [ 666 0.03 0.42 ]
|XXXXX 400 - 450 : [ 719 0.03 0.45 ]
|XXXXXXX 450 - 500 : [ 950 0.04 0.49 ]
|XXXXXXXX 500 - 550 : [ 1120 0.05 0.54 ]
|XXXXXXXXX 550 - 600 : [ 1313 0.06 0.60 ]
|XXXXXXXXX 600 - 650 : [ 1306 0.06 0.66 ]
|XXXXXXXXXX 650 - 700 : [ 1399 0.06 0.72 ]
|XXXXXXXXXXXXX 700 - 750 : [ 1916 0.09 0.81 ]
|XXXXXXXXXXXXXXXXX 750 - 800 : [ 2481 0.11 0.92 ]
|XXXXXXXXXXXX 800 - 850 : [ 1653 0.07 0.99 ]
|XX 850 - 900 : [ 214 0.01 1.00 ]
| 900 - 950 : [ 7 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAS 3634490_fasta.screen.trimQ15.SaF > reads.trim15.AIAS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAS.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 1751688.0000. <570.210938 +/- 232.468549>
#Range: [ 0 - 893 ]
#Most likely bin: [ 700 - 750 ] 554 counts
#Median bin: [ 650 - 700 ] 390 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXX 0 - 50 : [ 167 0.05 0.05 ]
|XXX 50 - 100 : [ 48 0.02 0.07 ]
|XX 100 - 150 : [ 31 0.01 0.08 ]
|XX 150 - 200 : [ 32 0.01 0.09 ]
|XX 200 - 250 : [ 33 0.01 0.10 ]
|XXXXXXXXXXXX 250 - 300 : [ 160 0.05 0.15 ]
|XXXXXXXXXXXXXX 300 - 350 : [ 200 0.07 0.22 ]
|XXXXXXXXX 350 - 400 : [ 125 0.04 0.26 ]
|XXXXXXX 400 - 450 : [ 94 0.03 0.29 ]
|XXXXX 450 - 500 : [ 64 0.02 0.31 ]
|XXXXXXX 500 - 550 : [ 102 0.03 0.34 ]
|XXXXXXXXX 550 - 600 : [ 118 0.04 0.38 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 227 0.07 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 390 0.13 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 554 0.18 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 502 0.16 0.93 ]
|XXXXXXXXXXXXXXX 800 - 850 : [ 208 0.07 0.99 ]
|X 850 - 900 : [ 17 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for APYX
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634490
-------------------------------------------------------------------
AIAO.000001.000100 pUC18.fa LRS.fasta
AIAO.000101.000200 pUC18.fa LRS.fasta
AIAP.000001.000100 pMCL200.fa LRS.fasta
AIAP.000101.000200 pMCL200.fa LRS.fasta
AIAS.000001.000100 pCC1Fos.fa LRS.fasta
AIAO.000001.000100 pUC18.fa LRS.fasta
AIAO.000101.000200 pUC18.fa LRS.fasta
AIAP.000001.000100 pMCL200.fa LRS.fasta
AIAP.000101.000200 pMCL200.fa LRS.fasta
AIAS.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634490_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634490_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 36740 total values totalling 22729.4740. <0.618657 +/- 0.041029>
#Range: [ 0.2667 - 0.871 ]
#Most likely bin: [ 0.63 - 0.635 ] 1990 counts
#Median bin: [ 0.62 - 0.625 ] 1972 counts
| 0.265 - 0.27 : [ 1 0.00 0.00 ]
#...
| 0.305 - 0.31 : [ 1 0.00 0.00 ]
#...
| 0.33 - 0.335 : [ 2 0.00 0.00 ]
| 0.335 - 0.34 : [ 1 0.00 0.00 ]
#...
| 0.365 - 0.37 : [ 2 0.00 0.00 ]
| 0.37 - 0.375 : [ 3 0.00 0.00 ]
| 0.375 - 0.38 : [ 1 0.00 0.00 ]
| 0.38 - 0.385 : [ 2 0.00 0.00 ]
| 0.385 - 0.39 : [ 2 0.00 0.00 ]
| 0.39 - 0.395 : [ 1 0.00 0.00 ]
| 0.395 - 0.4 : [ 1 0.00 0.00 ]
| 0.4 - 0.405 : [ 1 0.00 0.00 ]
| 0.405 - 0.41 : [ 3 0.00 0.00 ]
| 0.41 - 0.415 : [ 2 0.00 0.00 ]
#...
| 0.42 - 0.425 : [ 5 0.00 0.00 ]
| 0.425 - 0.43 : [ 3 0.00 0.00 ]
| 0.43 - 0.435 : [ 4 0.00 0.00 ]
| 0.435 - 0.44 : [ 5 0.00 0.00 ]
| 0.44 - 0.445 : [ 3 0.00 0.00 ]
| 0.445 - 0.45 : [ 6 0.00 0.00 ]
| 0.45 - 0.455 : [ 5 0.00 0.00 ]
| 0.455 - 0.46 : [ 8 0.00 0.00 ]
| 0.46 - 0.465 : [ 5 0.00 0.00 ]
| 0.465 - 0.47 : [ 13 0.00 0.00 ]
| 0.47 - 0.475 : [ 19 0.00 0.00 ]
|X 0.475 - 0.48 : [ 25 0.00 0.00 ]
| 0.48 - 0.485 : [ 22 0.00 0.00 ]
|X 0.485 - 0.49 : [ 27 0.00 0.00 ]
|X 0.49 - 0.495 : [ 31 0.00 0.01 ]
|X 0.495 - 0.5 : [ 40 0.00 0.01 ]
|X 0.5 - 0.505 : [ 74 0.00 0.01 ]
|X 0.505 - 0.51 : [ 55 0.00 0.01 ]
|XX 0.51 - 0.515 : [ 83 0.00 0.01 ]
|XX 0.515 - 0.52 : [ 98 0.00 0.02 ]
|XXX 0.52 - 0.525 : [ 142 0.00 0.02 ]
|XXXX 0.525 - 0.53 : [ 176 0.00 0.02 ]
|XXXX 0.53 - 0.535 : [ 204 0.01 0.03 ]
|XXXXX 0.535 - 0.54 : [ 241 0.01 0.04 ]
|XXXXXX 0.54 - 0.545 : [ 300 0.01 0.04 ]
|XXXXXX 0.545 - 0.55 : [ 322 0.01 0.05 ]
|XXXXXXXXX 0.55 - 0.555 : [ 441 0.01 0.06 ]
|XXXXXXXXXX 0.555 - 0.56 : [ 483 0.01 0.08 ]
|XXXXXXXXXXXX 0.56 - 0.565 : [ 574 0.02 0.09 ]
|XXXXXXXXXXXXX 0.565 - 0.57 : [ 667 0.02 0.11 ]
|XXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 821 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 906 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1027 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1163 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 1319 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 1404 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1581 0.04 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1700 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1848 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1958 0.05 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1972 0.05 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 1904 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 1990 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 1870 0.05 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 1791 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 1606 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 1488 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 1228 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 1055 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 949 0.03 0.92 ]
|XXXXXXXXXXXXXXX 0.67 - 0.675 : [ 732 0.02 0.94 ]
|XXXXXXXXXXXX 0.675 - 0.68 : [ 584 0.02 0.95 ]
|XXXXXXXXX 0.68 - 0.685 : [ 436 0.01 0.96 ]
|XXXXXX 0.685 - 0.69 : [ 298 0.01 0.97 ]
|XXXXX 0.69 - 0.695 : [ 224 0.01 0.98 ]
|XXXX 0.695 - 0.7 : [ 203 0.01 0.98 ]
|XXX 0.7 - 0.705 : [ 137 0.00 0.99 ]
|XX 0.705 - 0.71 : [ 108 0.00 0.99 ]
|XX 0.71 - 0.715 : [ 84 0.00 0.99 ]
|X 0.715 - 0.72 : [ 41 0.00 0.99 ]
|X 0.72 - 0.725 : [ 45 0.00 1.00 ]
|X 0.725 - 0.73 : [ 31 0.00 1.00 ]
|X 0.73 - 0.735 : [ 25 0.00 1.00 ]
| 0.735 - 0.74 : [ 12 0.00 1.00 ]
| 0.74 - 0.745 : [ 23 0.00 1.00 ]
| 0.745 - 0.75 : [ 5 0.00 1.00 ]
| 0.75 - 0.755 : [ 13 0.00 1.00 ]
| 0.755 - 0.76 : [ 9 0.00 1.00 ]
| 0.76 - 0.765 : [ 6 0.00 1.00 ]
| 0.765 - 0.77 : [ 6 0.00 1.00 ]
| 0.77 - 0.775 : [ 7 0.00 1.00 ]
| 0.775 - 0.78 : [ 4 0.00 1.00 ]
| 0.78 - 0.785 : [ 2 0.00 1.00 ]
| 0.785 - 0.79 : [ 2 0.00 1.00 ]
| 0.79 - 0.795 : [ 3 0.00 1.00 ]
| 0.795 - 0.8 : [ 3 0.00 1.00 ]
| 0.8 - 0.805 : [ 2 0.00 1.00 ]
#...
| 0.82 - 0.825 : [ 2 0.00 1.00 ]
| 0.825 - 0.83 : [ 2 0.00 1.00 ]
#...
| 0.835 - 0.84 : [ 1 0.00 1.00 ]
| 0.84 - 0.845 : [ 1 0.00 1.00 ]
| 0.845 - 0.85 : [ 1 0.00 1.00 ]
| 0.85 - 0.855 : [ 1 0.00 1.00 ]
| 0.855 - 0.86 : [ 1 0.00 1.00 ]
| 0.86 - 0.865 : [ 1 0.00 1.00 ]
#...
| 0.87 - 0.875 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 23. 308 reads; 27199 bp (untrimmed), 27173 (trimmed).
Contig 24. 317 reads; 31712 bp (untrimmed), 31597 (trimmed).
Contig 25. 325 reads; 16700 bp (untrimmed), 16682 (trimmed).
Contig 26. 332 reads; 29983 bp (untrimmed), 29964 (trimmed).
Contig 27. 353 reads; 37203 bp (untrimmed), 36880 (trimmed).
Contig 28. 357 reads; 33294 bp (untrimmed), 33214 (trimmed).
Contig 29. 380 reads; 39673 bp (untrimmed), 39349 (trimmed).
Contig 30. 385 reads; 33208 bp (untrimmed), 33182 (trimmed).
Contig 31. 397 reads; 39437 bp (untrimmed), 39213 (trimmed).
Contig 32. 411 reads; 41575 bp (untrimmed), 41572 (trimmed).
Contig 33. 415 reads; 43472 bp (untrimmed), 43289 (trimmed).
Contig 34. 427 reads; 39907 bp (untrimmed), 39506 (trimmed).
Contig 35. 451 reads; 43312 bp (untrimmed), 42639 (trimmed).
Contig 36. 452 reads; 44407 bp (untrimmed), 44381 (trimmed).
Contig 37. 496 reads; 47934 bp (untrimmed), 47905 (trimmed).
Contig 38. 556 reads; 53667 bp (untrimmed), 53375 (trimmed).
Contig 39. 578 reads; 55678 bp (untrimmed), 55628 (trimmed).
Contig 40. 653 reads; 60459 bp (untrimmed), 60279 (trimmed).
Contig 41. 791 reads; 89845 bp (untrimmed), 89765 (trimmed).
Contig 42. 816 reads; 73342 bp (untrimmed), 73182 (trimmed).
Contig 43. 1006 reads; 105271 bp (untrimmed), 104948 (trimmed).
Contig 44. 1205 reads; 100118 bp (untrimmed), 100046 (trimmed).
Contig 45. 1451 reads; 137868 bp (untrimmed), 137747 (trimmed).
Contig 46. 2167 reads; 205725 bp (untrimmed), 205673 (trimmed).
Contig 47. 4967 reads; 437422 bp (untrimmed), 437346 (trimmed).
Contig 48. 6065 reads; 546851 bp (untrimmed), 546842 (trimmed).
Contig 49. 8800 reads; 788585 bp (untrimmed), 788097 (trimmed).
--------------------------------------------------------------
Totals 36805 reads; 3407100 bp (untrimmed), 3400335 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3405994 bases = 9.70 +- 3.98 = 0.09 +- 3.23
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 46 total values totalling 413.0200. <8.978696 +/- 2.582529>
#Range: [ 1.98 - 17.54 ]
#Most likely bin: [ 8.5 - 9 ] 10 counts
#Median bin: [ 9 - 9.5 ] 10 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 1.5 - 2 : [ 1 0.02 0.02 ]
#...
|XXXX 2.5 - 3 : [ 1 0.02 0.04 ]
#...
|XXXX 3.5 - 4 : [ 1 0.02 0.07 ]
#...
|XXXX 4.5 - 5 : [ 1 0.02 0.09 ]
|XXXXXXXX 5 - 5.5 : [ 2 0.04 0.13 ]
#...
|XXXX 7 - 7.5 : [ 1 0.02 0.15 ]
|XXXXXXXX 7.5 - 8 : [ 2 0.04 0.20 ]
|XXXX 8 - 8.5 : [ 1 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 10 0.22 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 10 0.22 0.65 ]
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 5 0.11 0.76 ]
|XXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 5 0.11 0.87 ]
|XXXXXXXX 10.5 - 11 : [ 2 0.04 0.91 ]
|XXXX 11 - 11.5 : [ 1 0.02 0.93 ]
#...
|XXXXXXXX 13.5 - 14 : [ 2 0.04 0.98 ]
#...
|XXXX 17.5 - 18 : [ 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 42 total values totalling 391.1000. <9.311905 +/- 1.971804>
#Range: [ 4.93 - 17.54 ]
#Most likely bin: [ 8.5 - 9 ] 10 counts
#Median bin: [ 9 - 9.5 ] 10 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 4.5 - 5 : [ 1 0.02 0.02 ]
|XXXXXXXX 5 - 5.5 : [ 2 0.05 0.07 ]
#...
|XXXX 7 - 7.5 : [ 1 0.02 0.10 ]
|XXXXXXXX 7.5 - 8 : [ 2 0.05 0.14 ]
|XXXX 8 - 8.5 : [ 1 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 10 0.24 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 10 0.24 0.64 ]
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 5 0.12 0.76 ]
|XXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 5 0.12 0.88 ]
|XXXXXXXX 10.5 - 11 : [ 2 0.05 0.93 ]
|XXXX 11 - 11.5 : [ 1 0.02 0.95 ]
#...
|XXXX 13.5 - 14 : [ 1 0.02 0.98 ]
#...
|XXXX 17.5 - 18 : [ 1 0.02 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 4 4 reads 1730 bases = 1.98 +- 0.93 = 0.16 +- 1.04
Contig 5 4 reads 1220 bases = 2.53 +- 1.17 = 2.53 +- 1.17
Contig 6 5 reads 1225 bases = 3.80 +- 1.42 = 0.74 +- 0.91
Contig 11 54 reads 9743 bases = 4.93 +- 2.20 = 0.90 +- 4.51
Contig 10 50 reads 8481 bases = 5.37 +- 2.26 = 2.09 +- 2.12
Contig 7 18 reads 2962 bases = 5.41 +- 1.98 = 0.32 +- 1.58
Contig 16 161 reads 19077 bases = 7.46 +- 3.04 = 0.19 +- 3.03
Contig 20 206 reads 24166 bases = 7.70 +- 2.65 = 0.24 +- 3.65
Contig 41 791 reads 89845 bases = 7.95 +- 2.95 = 0.06 +- 3.06
Contig 22 259 reads 27485 bases = 8.49 +- 3.18 = 0.29 +- 2.63
Contig 43 1006 reads 105271 bases = 8.55 +- 2.93 = 0.01 +- 3.21
Contig 27 353 reads 37203 bases = 8.59 +- 3.06 = 0.12 +- 3.47
Contig 29 380 reads 39673 bases = 8.63 +- 2.92 = 0.33 +- 2.67
Contig 33 415 reads 43472 bases = 8.70 +- 3.31 = 0.09 +- 3.04
Contig 13 83 reads 8289 bases = 8.80 +- 3.37 = 1.96 +- 3.83
Contig 17 171 reads 17538 bases = 8.80 +- 3.10 = 0.28 +- 2.74
Contig 18 172 reads 17265 bases = 8.83 +- 3.12 = 0.26 +- 2.87
Contig 32 411 reads 41575 bases = 8.84 +- 3.57 = 0.04 +- 2.89
Contig 24 317 reads 31712 bases = 8.88 +- 3.60 = 0.49 +- 3.09
Contig 15 144 reads 14487 bases = 8.89 +- 3.65 = -0.05 +- 2.70
Contig 39 578 reads 55678 bases = 9.31 +- 2.83 = 0.13 +- 3.28
Contig 36 452 reads 44407 bases = 9.32 +- 3.19 = 0.03 +- 3.08
Contig 45 1451 reads 137868 bases = 9.46 +- 3.34 = 0.16 +- 3.21
Contig 46 2167 reads 205725 bases = 9.47 +- 3.49 = 0.05 +- 3.12
Contig 34 427 reads 39907 bases = 9.51 +- 3.27 = 0.05 +- 3.01
Contig 28 357 reads 33294 bases = 9.60 +- 3.29 = 0.07 +- 2.69
Contig 26 332 reads 29983 bases = 9.80 +- 3.35 = -0.05 +- 2.64
Contig 40 653 reads 60459 bases = 9.81 +- 3.12 = 0.15 +- 3.36
Contig 48 6065 reads 546851 bases = 9.96 +- 3.33 = -0.01 +- 3.34
Contig 49 8800 reads 788585 bases = 10.03 +- 3.48 = 0.00 +- 3.29
Contig 42 816 reads 73342 bases = 10.06 +- 3.40 = 0.02 +- 3.46
Contig 47 4967 reads 437422 bases = 10.15 +- 3.90 = 0.15 +- 3.17
Contig 23 308 reads 27199 bases = 10.29 +- 3.20 = 0.22 +- 3.65
Contig 30 385 reads 33208 bases = 10.42 +- 3.50 = 0.16 +- 2.79
Contig 14 85 reads 7179 bases = 10.83 +- 3.93 = 0.79 +- 2.17
Contig 44 1205 reads 100118 bases = 10.88 +- 3.37 = -0.01 +- 3.32
Contig 21 234 reads 19262 bases = 11.09 +- 3.17 = 0.42 +- 3.65
Contig 8 18 reads 1213 bases = 13.61 +- 5.98 = 4.35 +- 2.66
Contig 19 173 reads 11204 bases = 13.85 +- 10.56 = 0.67 +- 5.16
Contig 25 325 reads 16700 bases = 17.54 +- 24.91 = 0.38 +- 4.37
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1266
HQ Discrepant reads = 44
Chimeric reads = 47
Suspect alignments = 186
-------------------------------------------------------------------
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
File generated in /psf/project/finished1/microbe/3634490/edit_dir.12Jul04.QD