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
3634495 3200 117207 Sphingopyxis alaskensis
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Sphingopyxis_alaskensis
-------------------------------------------------------------------
Sphingomonadales, order, a-proteobacteria
Sphingopyxis, genus, a-proteobacteria
Sphingopyxis alaskensis, species, a-proteobacteria
Sphingomonadaceae, family, a-proteobacteria
Alphaproteobacteria, class, a-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3371435
# phrap: 3169170
# db:
altered.
3200000
3246868 +/- 88976
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 11076
Number of reads with percent X's >= 20%: 1515 = 3.1%
Number of reads with percent X's >= 50%: 1254 = 2.6%
Number of reads with percent X's >= 80%: 996 = 2.0%
Total reads in project: 49119
Total bp X'd : 1480533
reads >= 20% >= 50% >= 80% screened
Nr with L09136 8559 250 188 128
Nr with LRS 115 115 114 113
Nr with pCC1Fos 1143 8 5 1
Nr with pMCL200_JGI_XZX+XZK 1259 1142 947 754
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 999
Number of reads with percent X's >= 20%: 901 = 36.5%
Number of reads with percent X's >= 50%: 857 = 34.7%
Number of reads with percent X's >= 80%: 792 = 32.1%
Total reads in project: 2467
Total bp X'd : 780030
reads >= 20% >= 50% >= 80% screened
Nr with L09136 185 120 115 111
Nr with LRS 115 115 114 113
Nr with pCC1Fos 20 5 3 1
Nr with pMCL200_JGI_XZX+XZK 679 661 625 567
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Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 7998578
C = 14570053
G = 14285696
T = 8198040
N = 381722
X = 1481534
GC fraction = 0.62
Total = 46915623
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634495_fasta.screen.contigs
-------------------------------------------------------------------
A 590794
C 1118765
G 1096393
T 579911
N 90
fraction GC = 0.65
total bases = 3385953
Libraries and Reads
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Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
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-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBI reads.list > grep.reads.list.AIBI
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBI 4 500
-------------------------------------------------------------------
#Found 8659 total values totalling 30830446.0000. <3560.508835 +/- 7685.240395>
#Range: [ 903 - 276515 ]
#Most likely bin: [ 3000 - 3500 ] 3522 counts
#Median bin: [ 3000 - 3500 ] 3522 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 8 0.00 0.00 ]
|X 1000 - 1500 : [ 86 0.01 0.01 ]
|XX 1500 - 2000 : [ 135 0.02 0.03 ]
|XXX 2000 - 2500 : [ 239 0.03 0.05 ]
|XXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 1990 0.23 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3522 0.41 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2149 0.25 0.94 ]
|XXXXXX 4000 - 4500 : [ 509 0.06 1.00 ]
| 4500 - 5000 : [ 1 0.00 1.00 ]
#...
| 15500 - 16000 : [ 1 0.00 1.00 ]
#...
| 19500 - 20000 : [ 1 0.00 1.00 ]
#...
| 34000 - 34500 : [ 1 0.00 1.00 ]
#...
| 40500 - 41000 : [ 1 0.00 1.00 ]
#...
| 56000 - 56500 : [ 1 0.00 1.00 ]
#...
| 60000 - 60500 : [ 1 0.00 1.00 ]
#...
| 64500 - 65000 : [ 1 0.00 1.00 ]
#...
| 72000 - 72500 : [ 1 0.00 1.00 ]
#...
| 83500 - 84000 : [ 1 0.00 1.00 ]
#...
| 88500 - 89000 : [ 1 0.00 1.00 ]
#...
| 151000 - 151500 : [ 1 0.00 1.00 ]
#...
| 221000 - 221500 : [ 3 0.00 1.00 ]
| 221500 - 222000 : [ 2 0.00 1.00 ]
| 222000 - 222500 : [ 2 0.00 1.00 ]
| 222500 - 223000 : [ 1 0.00 1.00 ]
#...
| 276500 - 277000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBK reads.list > grep.reads.list.AIBK
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBK 4 500
-------------------------------------------------------------------
#Found 10103 total values totalling 69159391.0000. <6845.431159 +/- 9813.161445>
#Range: [ 716 - 378119 ]
#Most likely bin: [ 6500 - 7000 ] 2778 counts
#Median bin: [ 6500 - 7000 ] 2778 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 5 0.00 0.00 ]
|X 1000 - 1500 : [ 93 0.01 0.01 ]
|XX 1500 - 2000 : [ 113 0.01 0.02 ]
|XX 2000 - 2500 : [ 121 0.01 0.03 ]
|XX 2500 - 3000 : [ 114 0.01 0.04 ]
|XX 3000 - 3500 : [ 118 0.01 0.06 ]
|XX 3500 - 4000 : [ 106 0.01 0.07 ]
|X 4000 - 4500 : [ 102 0.01 0.08 ]
|XXX 4500 - 5000 : [ 176 0.02 0.09 ]
|XXXXX 5000 - 5500 : [ 314 0.03 0.12 ]
|XXXXXXX 5500 - 6000 : [ 480 0.05 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2350 0.23 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2778 0.27 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1851 0.18 0.86 ]
|XXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1164 0.12 0.98 ]
|XXX 8000 - 8500 : [ 185 0.02 1.00 ]
| 8500 - 9000 : [ 6 0.00 1.00 ]
| 9000 - 9500 : [ 1 0.00 1.00 ]
| 9500 - 10000 : [ 1 0.00 1.00 ]
#...
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
#...
| 23000 - 23500 : [ 1 0.00 1.00 ]
#...
| 28000 - 28500 : [ 1 0.00 1.00 ]
#...
| 45500 - 46000 : [ 1 0.00 1.00 ]
#...
| 49500 - 50000 : [ 1 0.00 1.00 ]
#...
| 76500 - 77000 : [ 1 0.00 1.00 ]
#...
| 108000 - 108500 : [ 1 0.00 1.00 ]
#...
| 109500 - 110000 : [ 1 0.00 1.00 ]
#...
| 140000 - 140500 : [ 1 0.00 1.00 ]
#...
| 201500 - 202000 : [ 1 0.00 1.00 ]
#...
| 224000 - 224500 : [ 1 0.00 1.00 ]
| 224500 - 225000 : [ 7 0.00 1.00 ]
| 225000 - 225500 : [ 1 0.00 1.00 ]
| 225500 - 226000 : [ 1 0.00 1.00 ]
#...
| 226500 - 227000 : [ 1 0.00 1.00 ]
#...
| 304000 - 304500 : [ 1 0.00 1.00 ]
#...
| 352000 - 352500 : [ 1 0.00 1.00 ]
#...
| 378000 - 378500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBN reads.list > grep.reads.list.AIBN
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBN 4 500
-------------------------------------------------------------------
#Found 1132 total values totalling 44615492.0000. <39412.978799 +/- 19999.591419>
#Range: [ 25312 - 263196 ]
#Most likely bin: [ 34000 - 34500 ] 62 counts
#Median bin: [ 37000 - 37500 ] 47 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 25000 - 25500 : [ 1 0.00 0.00 ]
#...
|X 26000 - 26500 : [ 1 0.00 0.00 ]
#...
|XX 27500 - 28000 : [ 3 0.00 0.00 ]
#...
|X 28500 - 29000 : [ 2 0.00 0.01 ]
|X 29000 - 29500 : [ 2 0.00 0.01 ]
|XX 29500 - 30000 : [ 3 0.00 0.01 ]
|XXXXX 30000 - 30500 : [ 8 0.01 0.02 ]
|XXXXXXX 30500 - 31000 : [ 11 0.01 0.03 ]
|XXXXXXXXXXXXXX 31000 - 31500 : [ 22 0.02 0.05 ]
|XXXXXXX 31500 - 32000 : [ 11 0.01 0.06 ]
|XXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 33 0.03 0.09 ]
|XXXXXXXXXXXXXX 32500 - 33000 : [ 21 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 39 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 44 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 62 0.05 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 45 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 55 0.05 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 56 0.05 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 51 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 54 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 47 0.04 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 43 0.04 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 46 0.04 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 54 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 35 0.03 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 42 0.04 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 48 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 45 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 40 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 32 0.03 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 34 0.03 0.87 ]
|XXXXXXXXXXXXXXX 42500 - 43000 : [ 24 0.02 0.90 ]
|XXXXXXXXXXXXXXXX 43000 - 43500 : [ 25 0.02 0.92 ]
|XXXXXXXXXXXXXX 43500 - 44000 : [ 22 0.02 0.94 ]
|XXXXXXXXXX 44000 - 44500 : [ 15 0.01 0.95 ]
|XXXXXXXX 44500 - 45000 : [ 13 0.01 0.96 ]
|XXXXXXXXXX 45000 - 45500 : [ 15 0.01 0.98 ]
|XXXXX 45500 - 46000 : [ 7 0.01 0.98 ]
|XXX 46000 - 46500 : [ 5 0.00 0.99 ]
|X 46500 - 47000 : [ 2 0.00 0.99 ]
|X 47000 - 47500 : [ 2 0.00 0.99 ]
|X 47500 - 48000 : [ 1 0.00 0.99 ]
|X 48000 - 48500 : [ 2 0.00 0.99 ]
#...
|X 255000 - 255500 : [ 1 0.00 0.99 ]
#...
|X 256000 - 256500 : [ 1 0.00 0.99 ]
|X 256500 - 257000 : [ 1 0.00 0.99 ]
#...
|X 258000 - 258500 : [ 2 0.00 1.00 ]
|X 258500 - 259000 : [ 1 0.00 1.00 ]
#...
|X 260000 - 260500 : [ 1 0.00 1.00 ]
|X 260500 - 261000 : [ 1 0.00 1.00 ]
#...
|X 263000 - 263500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIBI 3148 +- 604 (n=4338)
# AIBN 37551 +- 3952 (n=548)
# AIBK 6248 +- 1552 (n=5174)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634495_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
AIBI 19968 -1 -1 99 730 19968 97 740 99 740
AIBK 25344 -1 -1 97 682 25311 92 692 97 688
AIBN 3840 -1 -1 92 545 3840 87 540 92 591
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIBI 9984 97 729 99 740 9984 97 750 98 741
AIBK 12665 92 704 97 700 12646 91 679 96 676
AIBN 1920 87 541 92 582 1920 87 540 92 600
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634495_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
20 3840 1920 96.00 100.00 AIBN @
104 19968 9984 96.00 100.00 AIBI @
132 25311 12669 95.98 99.98 AIBK @
] 49119 24573 95.99 cumulative total@@
LIBRARY PLATE ID COUNT [ AIBN 20 AIBI 104 AIBK 132 ] for 256 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 3634495_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 49119 total values totalling 32195086.0000. <655.450762 +/- 226.735585>
#Range: [ 0 - 932 ]
#Most likely bin: [ 750 - 800 ] 10746 counts
#Median bin: [ 700 - 750 ] 7603 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 0 - 50 : [ 2689 0.05 0.05 ]
|XX 50 - 100 : [ 586 0.01 0.07 ]
|X 100 - 150 : [ 340 0.01 0.07 ]
|X 150 - 200 : [ 376 0.01 0.08 ]
|XX 200 - 250 : [ 442 0.01 0.09 ]
|XXX 250 - 300 : [ 782 0.02 0.11 ]
|XXX 300 - 350 : [ 711 0.01 0.12 ]
|XXX 350 - 400 : [ 722 0.01 0.14 ]
|XXX 400 - 450 : [ 833 0.02 0.15 ]
|XXX 450 - 500 : [ 931 0.02 0.17 ]
|XXXX 500 - 550 : [ 1105 0.02 0.19 ]
|XXXXXX 550 - 600 : [ 1621 0.03 0.23 ]
|XXXXXXXXXXX 600 - 650 : [ 2840 0.06 0.28 ]
|XXXXXXXXXXXXXXXXX 650 - 700 : [ 4545 0.09 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7603 0.15 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 10746 0.22 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 9765 0.20 0.95 ]
|XXXXXXXXX 850 - 900 : [ 2420 0.05 1.00 ]
| 900 - 950 : [ 62 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBI 3634495_fasta.screen.trimQ15.SaF > reads.trim15.AIBI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBI.rl 2 50
-------------------------------------------------------------------
#Found 19968 total values totalling 14292894.0000. <715.789964 +/- 184.982822>
#Range: [ 0 - 932 ]
#Most likely bin: [ 800 - 850 ] 5774 counts
#Median bin: [ 750 - 800 ] 5190 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 0 - 50 : [ 531 0.03 0.03 ]
|X 50 - 100 : [ 135 0.01 0.03 ]
|X 100 - 150 : [ 111 0.01 0.04 ]
|X 150 - 200 : [ 110 0.01 0.04 ]
|X 200 - 250 : [ 130 0.01 0.05 ]
|X 250 - 300 : [ 142 0.01 0.06 ]
|X 300 - 350 : [ 177 0.01 0.07 ]
|X 350 - 400 : [ 171 0.01 0.08 ]
|XX 400 - 450 : [ 254 0.01 0.09 ]
|XX 450 - 500 : [ 223 0.01 0.10 ]
|XX 500 - 550 : [ 280 0.01 0.11 ]
|XXX 550 - 600 : [ 418 0.02 0.13 ]
|XXXXX 600 - 650 : [ 770 0.04 0.17 ]
|XXXXXXXXX 650 - 700 : [ 1327 0.07 0.24 ]
|XXXXXXXXXXXXXXXXXX 700 - 750 : [ 2652 0.13 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5190 0.26 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5774 0.29 0.92 ]
|XXXXXXXXXXX 850 - 900 : [ 1519 0.08 1.00 ]
| 900 - 950 : [ 54 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBK
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBK 3634495_fasta.screen.trimQ15.SaF > reads.trim15.AIBK.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBK.rl 2 50
-------------------------------------------------------------------
#Found 25311 total values totalling 16089186.0000. <635.659832 +/- 234.178575>
#Range: [ 0 - 917 ]
#Most likely bin: [ 750 - 800 ] 5236 counts
#Median bin: [ 700 - 750 ] 4533 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXX 0 - 50 : [ 1736 0.07 0.07 ]
|XXX 50 - 100 : [ 368 0.01 0.08 ]
|X 100 - 150 : [ 173 0.01 0.09 ]
|XX 150 - 200 : [ 204 0.01 0.10 ]
|XX 200 - 250 : [ 223 0.01 0.11 ]
|XX 250 - 300 : [ 241 0.01 0.12 ]
|XX 300 - 350 : [ 308 0.01 0.13 ]
|XXX 350 - 400 : [ 351 0.01 0.14 ]
|XXX 400 - 450 : [ 430 0.02 0.16 ]
|XXXX 450 - 500 : [ 573 0.02 0.18 ]
|XXXXX 500 - 550 : [ 677 0.03 0.21 ]
|XXXXXXXX 550 - 600 : [ 994 0.04 0.25 ]
|XXXXXXXXXXXXX 600 - 650 : [ 1724 0.07 0.32 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2767 0.11 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4533 0.18 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5236 0.21 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3874 0.15 0.96 ]
|XXXXXXX 850 - 900 : [ 891 0.04 1.00 ]
| 900 - 950 : [ 8 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBN
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBN 3634495_fasta.screen.trimQ15.SaF > reads.trim15.AIBN.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBN.rl 2 50
-------------------------------------------------------------------
#Found 3840 total values totalling 1813006.0000. <472.136979 +/- 251.134889>
#Range: [ 0 - 886 ]
#Most likely bin: [ 650 - 700 ] 451 counts
#Median bin: [ 500 - 550 ] 148 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 422 0.11 0.11 ]
|XXXXXXX 50 - 100 : [ 83 0.02 0.13 ]
|XXXXX 100 - 150 : [ 56 0.01 0.15 ]
|XXXXX 150 - 200 : [ 62 0.02 0.16 ]
|XXXXXXXX 200 - 250 : [ 89 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 399 0.10 0.29 ]
|XXXXXXXXXXXXXXXXXXXX 300 - 350 : [ 226 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXX 350 - 400 : [ 200 0.05 0.40 ]
|XXXXXXXXXXXXX 400 - 450 : [ 149 0.04 0.44 ]
|XXXXXXXXXXXX 450 - 500 : [ 135 0.04 0.47 ]
|XXXXXXXXXXXXX 500 - 550 : [ 148 0.04 0.51 ]
|XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 209 0.05 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 346 0.09 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 451 0.12 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 418 0.11 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 320 0.08 0.97 ]
|XXXXXXXXXX 800 - 850 : [ 117 0.03 1.00 ]
|X 850 - 900 : [ 10 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AZOZ
trimt JAZZ trim 15 readlength histogram for AZPA
trimt JAZZ trim 15 readlength histogram for AZPB
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634495
-------------------------------------------------------------------
AIBI.000001.000100 pUC18.fa LRS.fasta
AIBI.000101.000200 pUC18.fa LRS.fasta
AIBK.000001.000100 pMCL200.fa LRS.fasta
AIBK.000101.000200 pMCL200.fa LRS.fasta
AIBN.000001.000100 pCC1Fos.fa LRS.fasta
AIBI.000001.000100 pUC18.fa LRS.fasta
AIBI.000101.000200 pUC18.fa LRS.fasta
AIBK.000001.000100 pMCL200.fa LRS.fasta
AIBK.000101.000200 pMCL200.fa LRS.fasta
AIBN.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634495_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634495_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 46467 total values totalling 30342.8475. <0.652998 +/- 0.039972>
#Range: [ 0 - 0.9032 ]
#Most likely bin: [ 0.65 - 0.655 ] 2758 counts
#Median bin: [ 0.65 - 0.655 ] 2758 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.275 - 0.28 : [ 1 0.00 0.00 ]
#...
| 0.315 - 0.32 : [ 1 0.00 0.00 ]
#...
| 0.33 - 0.335 : [ 1 0.00 0.00 ]
#...
| 0.36 - 0.365 : [ 1 0.00 0.00 ]
#...
| 0.37 - 0.375 : [ 2 0.00 0.00 ]
#...
| 0.38 - 0.385 : [ 3 0.00 0.00 ]
#...
| 0.39 - 0.395 : [ 1 0.00 0.00 ]
| 0.395 - 0.4 : [ 2 0.00 0.00 ]
| 0.4 - 0.405 : [ 1 0.00 0.00 ]
| 0.405 - 0.41 : [ 3 0.00 0.00 ]
#...
| 0.415 - 0.42 : [ 2 0.00 0.00 ]
| 0.42 - 0.425 : [ 2 0.00 0.00 ]
| 0.425 - 0.43 : [ 2 0.00 0.00 ]
| 0.43 - 0.435 : [ 1 0.00 0.00 ]
| 0.435 - 0.44 : [ 1 0.00 0.00 ]
| 0.44 - 0.445 : [ 2 0.00 0.00 ]
| 0.445 - 0.45 : [ 2 0.00 0.00 ]
| 0.45 - 0.455 : [ 15 0.00 0.00 ]
| 0.455 - 0.46 : [ 22 0.00 0.00 ]
| 0.46 - 0.465 : [ 15 0.00 0.00 ]
| 0.465 - 0.47 : [ 7 0.00 0.00 ]
| 0.47 - 0.475 : [ 12 0.00 0.00 ]
| 0.475 - 0.48 : [ 4 0.00 0.00 ]
| 0.48 - 0.485 : [ 20 0.00 0.00 ]
| 0.485 - 0.49 : [ 19 0.00 0.00 ]
|X 0.49 - 0.495 : [ 37 0.00 0.00 ]
| 0.495 - 0.5 : [ 11 0.00 0.00 ]
| 0.5 - 0.505 : [ 34 0.00 0.00 ]
|X 0.505 - 0.51 : [ 39 0.00 0.01 ]
| 0.51 - 0.515 : [ 29 0.00 0.01 ]
|X 0.515 - 0.52 : [ 45 0.00 0.01 ]
|X 0.52 - 0.525 : [ 52 0.00 0.01 ]
|X 0.525 - 0.53 : [ 39 0.00 0.01 ]
|X 0.53 - 0.535 : [ 53 0.00 0.01 ]
|X 0.535 - 0.54 : [ 59 0.00 0.01 ]
|X 0.54 - 0.545 : [ 76 0.00 0.01 ]
|X 0.545 - 0.55 : [ 89 0.00 0.02 ]
|X 0.55 - 0.555 : [ 102 0.00 0.02 ]
|X 0.555 - 0.56 : [ 95 0.00 0.02 ]
|XX 0.56 - 0.565 : [ 150 0.00 0.02 ]
|XX 0.565 - 0.57 : [ 160 0.00 0.03 ]
|XXX 0.57 - 0.575 : [ 207 0.00 0.03 ]
|XXX 0.575 - 0.58 : [ 240 0.01 0.04 ]
|XXXX 0.58 - 0.585 : [ 299 0.01 0.04 ]
|XXXXXX 0.585 - 0.59 : [ 413 0.01 0.05 ]
|XXXXXXXX 0.59 - 0.595 : [ 519 0.01 0.06 ]
|XXXXXXXXX 0.595 - 0.6 : [ 618 0.01 0.08 ]
|XXXXXXXXXXXX 0.6 - 0.605 : [ 834 0.02 0.09 ]
|XXXXXXXXXXXXXX 0.605 - 0.61 : [ 989 0.02 0.11 ]
|XXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1186 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1309 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1521 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 1798 0.04 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 2068 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 2243 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 2583 0.06 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 2546 0.05 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 2758 0.06 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 2702 0.06 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 2613 0.06 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 2429 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 2459 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 2179 0.05 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 2008 0.04 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 1766 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 1465 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 1220 0.03 0.91 ]
|XXXXXXXXXXXXXX 0.7 - 0.705 : [ 990 0.02 0.93 ]
|XXXXXXXXXXXX 0.705 - 0.71 : [ 795 0.02 0.95 ]
|XXXXXXXX 0.71 - 0.715 : [ 585 0.01 0.96 ]
|XXXXXX 0.715 - 0.72 : [ 435 0.01 0.97 ]
|XXXXX 0.72 - 0.725 : [ 353 0.01 0.98 ]
|XXXX 0.725 - 0.73 : [ 290 0.01 0.98 ]
|XXX 0.73 - 0.735 : [ 178 0.00 0.99 ]
|XX 0.735 - 0.74 : [ 148 0.00 0.99 ]
|XX 0.74 - 0.745 : [ 108 0.00 0.99 ]
|X 0.745 - 0.75 : [ 66 0.00 0.99 ]
|X 0.75 - 0.755 : [ 63 0.00 0.99 ]
|X 0.755 - 0.76 : [ 48 0.00 1.00 ]
|X 0.76 - 0.765 : [ 44 0.00 1.00 ]
| 0.765 - 0.77 : [ 30 0.00 1.00 ]
| 0.77 - 0.775 : [ 22 0.00 1.00 ]
| 0.775 - 0.78 : [ 21 0.00 1.00 ]
| 0.78 - 0.785 : [ 15 0.00 1.00 ]
| 0.785 - 0.79 : [ 13 0.00 1.00 ]
| 0.79 - 0.795 : [ 6 0.00 1.00 ]
| 0.795 - 0.8 : [ 11 0.00 1.00 ]
| 0.8 - 0.805 : [ 12 0.00 1.00 ]
| 0.805 - 0.81 : [ 7 0.00 1.00 ]
| 0.81 - 0.815 : [ 5 0.00 1.00 ]
| 0.815 - 0.82 : [ 4 0.00 1.00 ]
| 0.82 - 0.825 : [ 3 0.00 1.00 ]
| 0.825 - 0.83 : [ 3 0.00 1.00 ]
| 0.83 - 0.835 : [ 3 0.00 1.00 ]
| 0.835 - 0.84 : [ 2 0.00 1.00 ]
#...
| 0.845 - 0.85 : [ 3 0.00 1.00 ]
| 0.85 - 0.855 : [ 2 0.00 1.00 ]
#...
| 0.86 - 0.865 : [ 3 0.00 1.00 ]
| 0.865 - 0.87 : [ 3 0.00 1.00 ]
#...
| 0.875 - 0.88 : [ 2 0.00 1.00 ]
| 0.88 - 0.885 : [ 2 0.00 1.00 ]
| 0.885 - 0.89 : [ 3 0.00 1.00 ]
| 0.89 - 0.895 : [ 2 0.00 1.00 ]
#...
| 0.9 - 0.905 : [ 2 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 31. 83 reads; 6599 bp (untrimmed), 5549 (trimmed).
Contig 32. 111 reads; 7887 bp (untrimmed), 7866 (trimmed).
Contig 33. 191 reads; 13094 bp (untrimmed), 13037 (trimmed).
Contig 34. 194 reads; 17189 bp (untrimmed), 16308 (trimmed).
Contig 35. 239 reads; 20453 bp (untrimmed), 19914 (trimmed).
Contig 36. 286 reads; 24164 bp (untrimmed), 23925 (trimmed).
Contig 37. 476 reads; 29078 bp (untrimmed), 28052 (trimmed).
Contig 38. 534 reads; 31525 bp (untrimmed), 30839 (trimmed).
Contig 39. 565 reads; 43033 bp (untrimmed), 42358 (trimmed).
Contig 40. 863 reads; 63260 bp (untrimmed), 62486 (trimmed).
Contig 41. 896 reads; 60507 bp (untrimmed), 60484 (trimmed).
Contig 42. 926 reads; 60340 bp (untrimmed), 59304 (trimmed).
Contig 43. 1091 reads; 89064 bp (untrimmed), 88991 (trimmed).
Contig 44. 1268 reads; 108308 bp (untrimmed), 108266 (trimmed).
Contig 45. 1294 reads; 86530 bp (untrimmed), 86388 (trimmed).
Contig 46. 1532 reads; 118009 bp (untrimmed), 117739 (trimmed).
Contig 47. 1653 reads; 116407 bp (untrimmed), 116374 (trimmed).
Contig 48. 1674 reads; 115423 bp (untrimmed), 114731 (trimmed).
Contig 49. 1971 reads; 145404 bp (untrimmed), 145360 (trimmed).
Contig 50. 2174 reads; 157144 bp (untrimmed), 156196 (trimmed).
Contig 51. 2204 reads; 141534 bp (untrimmed), 141391 (trimmed).
Contig 52. 2210 reads; 159446 bp (untrimmed), 159074 (trimmed).
Contig 53. 2597 reads; 211802 bp (untrimmed), 211679 (trimmed).
Contig 54. 3502 reads; 223136 bp (untrimmed), 222777 (trimmed).
Contig 55. 4294 reads; 327362 bp (untrimmed), 327326 (trimmed).
Contig 56. 5263 reads; 393658 bp (untrimmed), 392867 (trimmed).
Contig 57. 8404 reads; 578924 bp (untrimmed), 578859 (trimmed).
--------------------------------------------------------------
Totals 46652 reads; 3385953 bp (untrimmed), 3371435 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3380174 bases = 11.86 +- 4.07 = 0.10 +- 3.62
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 44 total values totalling 357.1300. <8.116591 +/- 4.777926>
#Range: [ 1.10 - 13.93 ]
#Most likely bin: [ 1.5 - 2 ] 7 counts
#Median bin: [ 10 - 10.5 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXX 1 - 1.5 : [ 3 0.07 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 7 0.16 0.23 ]
|XXXXXXXXXXX 2 - 2.5 : [ 2 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 4 0.09 0.36 ]
#...
|XXXXXX 9.5 - 10 : [ 1 0.02 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 6 0.14 0.52 ]
|XXXXXXXXXXX 10.5 - 11 : [ 2 0.05 0.57 ]
|XXXXXXXXXXXXXXXXX 11 - 11.5 : [ 3 0.07 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 5 0.11 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 4 0.09 0.84 ]
|XXXXXXXXXXXXXXXXX 12.5 - 13 : [ 3 0.07 0.91 ]
|XXXXXXXXXXXXXXXXX 13 - 13.5 : [ 3 0.07 0.98 ]
|XXXXXX 13.5 - 14 : [ 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 28 total values totalling 326.3600. <11.655714 +/- 1.137194>
#Range: [ 9.56 - 13.93 ]
#Most likely bin: [ 10 - 10.5 ] 6 counts
#Median bin: [ 11.5 - 12 ] 5 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 9.5 - 10 : [ 1 0.04 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 6 0.21 0.25 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 2 0.07 0.32 ]
|XXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 3 0.11 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 5 0.18 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 4 0.14 0.75 ]
|XXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 3 0.11 0.86 ]
|XXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 3 0.11 0.96 ]
|XXXXXXX 13.5 - 14 : [ 1 0.04 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 21 2 reads 1591 bases = 1.10 +- 0.31 = -0.01 +- 0.95
Contig 20 2 reads 1672 bases = 1.21 +- 0.41 = -0.04 +- 0.89
Contig 10 2 reads 1381 bases = 1.35 +- 0.48 = -0.03 +- 0.80
Contig 15 2 reads 1072 bases = 1.50 +- 0.50 = 1.50 +- 0.50
Contig 16 2 reads 1143 bases = 1.61 +- 0.49 = 1.61 +- 0.49
Contig 9 2 reads 620 bases = 1.74 +- 0.44 = -0.12 +- 0.49
Contig 14 2 reads 957 bases = 1.84 +- 0.37 = 1.84 +- 0.37
Contig 7 2 reads 802 bases = 1.87 +- 0.34 = 1.87 +- 0.34
Contig 17 2 reads 809 bases = 1.96 +- 0.20 = 1.96 +- 0.20
Contig 23 3 reads 1328 bases = 1.98 +- 0.80 = 0.61 +- 1.22
Contig 24 5 reads 2170 bases = 2.04 +- 0.62 = 1.25 +- 0.76
Contig 28 9 reads 3800 bases = 2.17 +- 0.74 = 1.25 +- 1.00
Contig 26 6 reads 2156 bases = 2.52 +- 1.27 = 0.88 +- 0.70
Contig 29 9 reads 2670 bases = 2.52 +- 1.25 = 0.68 +- 1.02
Contig 25 5 reads 1762 bases = 2.58 +- 1.37 = 1.54 +- 0.87
Contig 22 3 reads 966 bases = 2.78 +- 0.63 = 1.00 +- 0.05
Contig 34 194 reads 17189 bases = 9.56 +- 3.67 = 0.36 +- 3.84
Contig 35 239 reads 20453 bases = 10.05 +- 4.42 = 0.33 +- 3.28
Contig 36 286 reads 24164 bases = 10.18 +- 3.70 = 0.29 +- 2.59
Contig 44 1268 reads 108308 bases = 10.23 +- 3.31 = 0.01 +- 3.17
Contig 39 565 reads 43033 bases = 10.98 +- 3.79 = 0.74 +- 3.65
Contig 32 111 reads 7887 bases = 11.40 +- 4.81 = 1.27 +- 5.04
Contig 46 1532 reads 118009 bases = 11.41 +- 3.65 = 0.11 +- 3.31
Contig 55 4294 reads 327362 bases = 11.43 +- 3.80 = 0.14 +- 3.47
Contig 56 5263 reads 393658 bases = 11.55 +- 3.70 = 0.07 +- 3.73
Contig 49 1971 reads 145404 bases = 11.63 +- 3.47 = -0.00 +- 3.40
Contig 40 863 reads 63260 bases = 11.76 +- 3.81 = -0.03 +- 3.55
Contig 52 2210 reads 159446 bases = 11.90 +- 3.52 = -0.04 +- 3.60
Contig 50 2174 reads 157144 bases = 11.99 +- 4.15 = 0.05 +- 3.58
Contig 38 534 reads 31525 bases = 12.04 +- 4.54 = 0.18 +- 4.07
Contig 33 191 reads 13094 bases = 12.13 +- 5.42 = 1.01 +- 3.57
Contig 48 1674 reads 115423 bases = 12.19 +- 4.07 = 0.32 +- 3.60
Contig 47 1653 reads 116407 bases = 12.39 +- 3.61 = -0.02 +- 3.68
Contig 57 8404 reads 578924 bases = 12.52 +- 4.10 = 0.08 +- 3.71
Contig 41 896 reads 60507 bases = 12.65 +- 3.54 = 0.02 +- 4.02
Contig 45 1294 reads 86530 bases = 12.91 +- 4.23 = 0.01 +- 3.77
Contig 51 2204 reads 141534 bases = 13.19 +- 4.50 = 0.05 +- 4.04
Contig 42 926 reads 60340 bases = 13.28 +- 4.30 = 0.02 +- 3.74
Contig 54 3502 reads 223136 bases = 13.43 +- 4.11 = 0.05 +- 3.89
Contig 37 476 reads 29078 bases = 13.93 +- 5.31 = 0.51 +- 4.07
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 531
HQ Discrepant reads = 25
Chimeric reads = 113
Suspect alignments = 308
-------------------------------------------------------------------
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/microbe3/3634495/edit_dir.09Jun04.QD