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
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634489 3000 912 Nitrobacter hamburgensis
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Nitrobacter_hamburgensis
-------------------------------------------------------------------
Bradyrhizobiaceae, family, a-proteobacteria
Alphaproteobacteria, class, a-proteobacteria
Nitrobacter hamburgensis, 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: 5002643
# phrap: 4749602
# db:
altered.
3000000
4250748 +/- 890425
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 12401
Number of reads with percent X's >= 20%: 320 = 0.5%
Number of reads with percent X's >= 50%: 152 = 0.3%
Number of reads with percent X's >= 80%: 14 = 0.0%
Total reads in project: 58565
Total bp X'd : 604570
reads >= 20% >= 50% >= 80% screened
Nr with L09136 11506 163 87 12
Nr with pCC1Fos 691 32 12 0
Nr with pMCL200_JGI_XZX+XZK 204 125 53 2
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 4
Number of reads with percent X's >= 20%: 1 = 4.0%
Number of reads with percent X's >= 50%: 1 = 4.0%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 25
Total bp X'd : 880
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3 0 0 0
Nr with pMCL200_JGI_XZX+XZK 1 1 1 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 10777424
C = 16230029
G = 16506416
T = 10327458
N = 299909
X = 604570
GC fraction = 0.60
Total = 54745806
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634489_fasta.screen.contigs
-------------------------------------------------------------------
A 961012
C 1546035
G 1539948
T 963851
N 687
fraction GC = 0.62
total bases = 5011533
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 AIAI reads.list > grep.reads.list.AIAI
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAI 4 500
-------------------------------------------------------------------
#Found 10836 total values totalling 48050627.0000. <4434.350960 +/- 23986.549930>
#Range: [ 699 - 911214 ]
#Most likely bin: [ 3000 - 3500 ] 4351 counts
#Median bin: [ 3500 - 4000 ] 4033 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 14 0.00 0.00 ]
|X 1000 - 1500 : [ 61 0.01 0.01 ]
|X 1500 - 2000 : [ 72 0.01 0.01 ]
|X 2000 - 2500 : [ 89 0.01 0.02 ]
|XXXXXXX 2500 - 3000 : [ 711 0.07 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4351 0.40 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 4033 0.37 0.86 ]
|XXXXXXXXXXXXX 4000 - 4500 : [ 1468 0.14 1.00 ]
| 4500 - 5000 : [ 3 0.00 1.00 ]
#...
| 5500 - 6000 : [ 4 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
#...
| 28000 - 28500 : [ 1 0.00 1.00 ]
#...
| 29000 - 29500 : [ 1 0.00 1.00 ]
#...
| 41500 - 42000 : [ 1 0.00 1.00 ]
#...
| 42500 - 43000 : [ 1 0.00 1.00 ]
#...
| 53500 - 54000 : [ 1 0.00 1.00 ]
| 54000 - 54500 : [ 1 0.00 1.00 ]
#...
| 55000 - 55500 : [ 1 0.00 1.00 ]
#...
| 83500 - 84000 : [ 1 0.00 1.00 ]
#...
| 101500 - 102000 : [ 1 0.00 1.00 ]
#...
| 130500 - 131000 : [ 1 0.00 1.00 ]
#...
| 138500 - 139000 : [ 1 0.00 1.00 ]
#...
| 140500 - 141000 : [ 1 0.00 1.00 ]
#...
| 156500 - 157000 : [ 1 0.00 1.00 ]
#...
| 204500 - 205000 : [ 1 0.00 1.00 ]
#...
| 248500 - 249000 : [ 1 0.00 1.00 ]
#...
| 266000 - 266500 : [ 1 0.00 1.00 ]
#...
| 306000 - 306500 : [ 1 0.00 1.00 ]
#...
| 388500 - 389000 : [ 1 0.00 1.00 ]
#...
| 446000 - 446500 : [ 1 0.00 1.00 ]
#...
| 453500 - 454000 : [ 1 0.00 1.00 ]
#...
| 476500 - 477000 : [ 1 0.00 1.00 ]
#...
| 531500 - 532000 : [ 1 0.00 1.00 ]
#...
| 736500 - 737000 : [ 1 0.00 1.00 ]
#...
| 744000 - 744500 : [ 1 0.00 1.00 ]
#...
| 761000 - 761500 : [ 1 0.00 1.00 ]
#...
| 879500 - 880000 : [ 1 0.00 1.00 ]
#...
| 886000 - 886500 : [ 1 0.00 1.00 ]
#...
| 894000 - 894500 : [ 1 0.00 1.00 ]
#...
| 911000 - 911500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAK reads.list > grep.reads.list.AIAK
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAK 4 500
-------------------------------------------------------------------
#Found 11016 total values totalling 83473622.0000. <7577.489288 +/- 21391.352111>
#Range: [ 770 - 740887 ]
#Most likely bin: [ 6500 - 7000 ] 3676 counts
#Median bin: [ 7000 - 7500 ] 2967 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 12 0.00 0.00 ]
|X 1000 - 1500 : [ 57 0.01 0.01 ]
|X 1500 - 2000 : [ 51 0.00 0.01 ]
|X 2000 - 2500 : [ 76 0.01 0.02 ]
|X 2500 - 3000 : [ 67 0.01 0.02 ]
|X 3000 - 3500 : [ 73 0.01 0.03 ]
|X 3500 - 4000 : [ 69 0.01 0.04 ]
|X 4000 - 4500 : [ 55 0.00 0.04 ]
|X 4500 - 5000 : [ 74 0.01 0.05 ]
|X 5000 - 5500 : [ 89 0.01 0.06 ]
|XX 5500 - 6000 : [ 154 0.01 0.07 ]
|XXXXXXXXXX 6000 - 6500 : [ 942 0.09 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 3676 0.33 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 2967 0.27 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 2153 0.20 0.95 ]
|XXXXX 8000 - 8500 : [ 476 0.04 1.00 ]
| 8500 - 9000 : [ 1 0.00 1.00 ]
| 9000 - 9500 : [ 4 0.00 1.00 ]
| 9500 - 10000 : [ 3 0.00 1.00 ]
| 10000 - 10500 : [ 1 0.00 1.00 ]
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
#...
| 52000 - 52500 : [ 2 0.00 1.00 ]
#...
| 156500 - 157000 : [ 1 0.00 1.00 ]
#...
| 408500 - 409000 : [ 1 0.00 1.00 ]
#...
| 493000 - 493500 : [ 1 0.00 1.00 ]
#...
| 562500 - 563000 : [ 1 0.00 1.00 ]
#...
| 739000 - 739500 : [ 2 0.00 1.00 ]
| 739500 - 740000 : [ 2 0.00 1.00 ]
| 740000 - 740500 : [ 3 0.00 1.00 ]
| 740500 - 741000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAN reads.list > grep.reads.list.AIAN
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAN 4 500
-------------------------------------------------------------------
#Found 543 total values totalling 21210862.0000. <39062.360958 +/- 5082.226307>
#Range: [ 107 - 76243 ]
#Most likely bin: [ 39000 - 39500 ] 32 counts
#Median bin: [ 39000 - 39500 ] 32 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 0 - 500 : [ 3 0.01 0.01 ]
#...
|X 29500 - 30000 : [ 1 0.00 0.01 ]
#...
|XXXXXX 31000 - 31500 : [ 5 0.01 0.02 ]
|XXXX 31500 - 32000 : [ 3 0.01 0.02 ]
|XXXXXXXXXXX 32000 - 32500 : [ 9 0.02 0.04 ]
|XXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 14 0.03 0.06 ]
|XXXXXXXXXXXXXXX 33000 - 33500 : [ 12 0.02 0.09 ]
|XXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 15 0.03 0.11 ]
|XXXXXXXXXXX 34000 - 34500 : [ 9 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 20 0.04 0.17 ]
|XXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 14 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 16 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 25 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 23 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 27 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 24 0.04 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 19 0.03 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 25 0.05 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 32 0.06 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 21 0.04 0.58 ]
|XXXXXXXXXXXX 40000 - 40500 : [ 10 0.02 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 27 0.05 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 21 0.04 0.69 ]
|XXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 17 0.03 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 25 0.05 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 18 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 20 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 19 0.03 0.87 ]
|XXXXXXXXXXX 44000 - 44500 : [ 9 0.02 0.89 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 44500 - 45000 : [ 21 0.04 0.93 ]
|XXXXXXXXXXXXXXXXXX 45000 - 45500 : [ 14 0.03 0.95 ]
|XXXXXXXXXXXXXXX 45500 - 46000 : [ 12 0.02 0.98 ]
|XXXXXXXXX 46000 - 46500 : [ 7 0.01 0.99 ]
|XX 46500 - 47000 : [ 2 0.00 0.99 ]
|X 47000 - 47500 : [ 1 0.00 0.99 ]
|XX 47500 - 48000 : [ 2 0.00 1.00 ]
#...
|X 76000 - 76500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIAK 6778 +- 1160 (n=5553)
# AIAN 38979 +- 4502 (n=283)
# AIAI 3393 +- 1018 (n=5644)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634489_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
AIAI 29184 -1 -1 98 724 29133 95 678 97 685
AIAK 34560 -1 -1 93 668 34198 81 619 89 619
AIAN 3072 -1 -1 85 475 3072 76 570 85 555
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIAI 13799 95 668 97 681 15334 95 687 97 689
AIAK 16673 77 605 87 602 17525 84 632 91 634
AIAN 1536 75 563 83 554 1536 78 577 88 556
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634489_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
144 27855 13425 93.23 97.11 AIAI @
176 28240 14953 84.96 88.50 AIAK @
16 2470 1348 84.25 87.76 AIAN @
] 58565 29726 88.47 cumulative total@@
LIBRARY PLATE ID COUNT [ AIAI 144 AIAK 176 AIAN 16 ] for 336 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 3634489_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 66403 total values totalling 37423981.0000. <563.588708 +/- 268.720667>
#Range: [ 0 - 994 ]
#Most likely bin: [ 750 - 800 ] 9673 counts
#Median bin: [ 650 - 700 ] 7586 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 7465 0.11 0.11 ]
|XXXXX 50 - 100 : [ 1168 0.02 0.13 ]
|XXXX 100 - 150 : [ 1050 0.02 0.15 ]
|XXXX 150 - 200 : [ 932 0.01 0.16 ]
|XXXXX 200 - 250 : [ 1108 0.02 0.18 ]
|XXXXX 250 - 300 : [ 1192 0.02 0.19 ]
|XXXXX 300 - 350 : [ 1143 0.02 0.21 ]
|XXXXX 350 - 400 : [ 1299 0.02 0.23 ]
|XXXXXX 400 - 450 : [ 1428 0.02 0.25 ]
|XXXXXXXX 450 - 500 : [ 1894 0.03 0.28 ]
|XXXXXXXXXXX 500 - 550 : [ 2551 0.04 0.32 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 3803 0.06 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 5765 0.09 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 7586 0.11 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8948 0.13 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 9673 0.15 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7517 0.11 0.97 ]
|XXXXXXX 850 - 900 : [ 1704 0.03 1.00 ]
|X 900 - 950 : [ 164 0.00 1.00 ]
| 950 - 1000 : [ 13 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAI 3634489_fasta.screen.trimQ15.SaF > reads.trim15.AIAI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAI.rl 2 50
-------------------------------------------------------------------
#Found 29133 total values totalling 18828021.0000. <646.278138 +/- 203.433363>
#Range: [ 0 - 994 ]
#Most likely bin: [ 700 - 750 ] 5617 counts
#Median bin: [ 700 - 750 ] 5617 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXX 0 - 50 : [ 1160 0.04 0.04 ]
|XX 50 - 100 : [ 248 0.01 0.05 ]
|XX 100 - 150 : [ 248 0.01 0.06 ]
|XX 150 - 200 : [ 270 0.01 0.07 ]
|XX 200 - 250 : [ 303 0.01 0.08 ]
|XXX 250 - 300 : [ 360 0.01 0.09 ]
|XX 300 - 350 : [ 320 0.01 0.10 ]
|XXX 350 - 400 : [ 418 0.01 0.11 ]
|XXXX 400 - 450 : [ 508 0.02 0.13 ]
|XXXX 450 - 500 : [ 629 0.02 0.15 ]
|XXXXXX 500 - 550 : [ 911 0.03 0.18 ]
|XXXXXXXXXX 550 - 600 : [ 1469 0.05 0.23 ]
|XXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2661 0.09 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4269 0.15 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5617 0.19 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5015 0.17 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3546 0.12 0.96 ]
|XXXXXXX 850 - 900 : [ 1010 0.03 0.99 ]
|X 900 - 950 : [ 158 0.01 1.00 ]
| 950 - 1000 : [ 13 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAK
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAK 3634489_fasta.screen.trimQ15.SaF > reads.trim15.AIAK.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAK.rl 2 50
-------------------------------------------------------------------
#Found 34198 total values totalling 17238284.0000. <504.072870 +/- 294.771844>
#Range: [ 0 - 911 ]
#Most likely bin: [ 0 - 50 ] 5728 counts
#Median bin: [ 600 - 650 ] 2841 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 5728 0.17 0.17 ]
|XXXXX 50 - 100 : [ 775 0.02 0.19 ]
|XXXXX 100 - 150 : [ 727 0.02 0.21 ]
|XXXX 150 - 200 : [ 606 0.02 0.23 ]
|XXXXX 200 - 250 : [ 729 0.02 0.25 ]
|XXXXX 250 - 300 : [ 673 0.02 0.27 ]
|XXXXX 300 - 350 : [ 737 0.02 0.29 ]
|XXXXXX 350 - 400 : [ 811 0.02 0.32 ]
|XXXXXX 400 - 450 : [ 860 0.03 0.34 ]
|XXXXXXXX 450 - 500 : [ 1166 0.03 0.37 ]
|XXXXXXXXXX 500 - 550 : [ 1491 0.04 0.42 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 2132 0.06 0.48 ]
|XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2841 0.08 0.56 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2995 0.09 0.65 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2991 0.09 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4370 0.13 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3871 0.11 0.98 ]
|XXXXX 850 - 900 : [ 689 0.02 1.00 ]
| 900 - 950 : [ 6 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAN
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAN 3634489_fasta.screen.trimQ15.SaF > reads.trim15.AIAN.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAN.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 1357676.0000. <441.951823 +/- 286.454899>
#Range: [ 0 - 883 ]
#Most likely bin: [ 0 - 50 ] 577 counts
#Median bin: [ 500 - 550 ] 149 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 577 0.19 0.19 ]
|XXXXXXXXXX 50 - 100 : [ 145 0.05 0.24 ]
|XXXXX 100 - 150 : [ 75 0.02 0.26 ]
|XXXX 150 - 200 : [ 56 0.02 0.28 ]
|XXXXX 200 - 250 : [ 76 0.02 0.30 ]
|XXXXXXXXXXX 250 - 300 : [ 159 0.05 0.35 ]
|XXXXXX 300 - 350 : [ 86 0.03 0.38 ]
|XXXXX 350 - 400 : [ 70 0.02 0.40 ]
|XXXX 400 - 450 : [ 60 0.02 0.42 ]
|XXXXXXX 450 - 500 : [ 99 0.03 0.46 ]
|XXXXXXXXXX 500 - 550 : [ 149 0.05 0.51 ]
|XXXXXXXXXXXXXX 550 - 600 : [ 202 0.07 0.57 ]
|XXXXXXXXXXXXXXXXXX 600 - 650 : [ 263 0.09 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 322 0.10 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 340 0.11 0.87 ]
|XXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 288 0.09 0.97 ]
|XXXXXXX 800 - 850 : [ 100 0.03 1.00 ]
| 850 - 900 : [ 5 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATTP
trimt JAZZ trim 15 readlength histogram for ATTS
trimt JAZZ trim 15 readlength histogram for ATTT
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634489
-------------------------------------------------------------------
AIAI.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIAI.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIAK.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIAK.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AIAN.000001.000100 pCC1Fos.fa LRS.fasta
AIAI.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIAI.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIAK.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIAK.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AIAN.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634489_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634489_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 58383 total values totalling 35840.4793. <0.613886 +/- 0.043929>
#Range: [ 0.3096 - 0.913 ]
#Most likely bin: [ 0.63 - 0.635 ] 2756 counts
#Median bin: [ 0.615 - 0.62 ] 2609 counts
| 0.305 - 0.31 : [ 1 0.00 0.00 ]
#...
| 0.315 - 0.32 : [ 1 0.00 0.00 ]
#...
| 0.325 - 0.33 : [ 2 0.00 0.00 ]
| 0.33 - 0.335 : [ 1 0.00 0.00 ]
#...
| 0.34 - 0.345 : [ 1 0.00 0.00 ]
#...
| 0.35 - 0.355 : [ 1 0.00 0.00 ]
| 0.355 - 0.36 : [ 2 0.00 0.00 ]
| 0.36 - 0.365 : [ 3 0.00 0.00 ]
| 0.365 - 0.37 : [ 2 0.00 0.00 ]
| 0.37 - 0.375 : [ 1 0.00 0.00 ]
| 0.375 - 0.38 : [ 2 0.00 0.00 ]
| 0.38 - 0.385 : [ 3 0.00 0.00 ]
| 0.385 - 0.39 : [ 3 0.00 0.00 ]
| 0.39 - 0.395 : [ 4 0.00 0.00 ]
#...
| 0.4 - 0.405 : [ 4 0.00 0.00 ]
| 0.405 - 0.41 : [ 5 0.00 0.00 ]
| 0.41 - 0.415 : [ 8 0.00 0.00 ]
| 0.415 - 0.42 : [ 6 0.00 0.00 ]
| 0.42 - 0.425 : [ 8 0.00 0.00 ]
| 0.425 - 0.43 : [ 7 0.00 0.00 ]
| 0.43 - 0.435 : [ 13 0.00 0.00 ]
| 0.435 - 0.44 : [ 10 0.00 0.00 ]
| 0.44 - 0.445 : [ 18 0.00 0.00 ]
| 0.445 - 0.45 : [ 17 0.00 0.00 ]
| 0.45 - 0.455 : [ 18 0.00 0.00 ]
| 0.455 - 0.46 : [ 14 0.00 0.00 ]
| 0.46 - 0.465 : [ 18 0.00 0.00 ]
| 0.465 - 0.47 : [ 22 0.00 0.00 ]
| 0.47 - 0.475 : [ 32 0.00 0.00 ]
|X 0.475 - 0.48 : [ 40 0.00 0.00 ]
|X 0.48 - 0.485 : [ 65 0.00 0.01 ]
|X 0.485 - 0.49 : [ 67 0.00 0.01 ]
|X 0.49 - 0.495 : [ 82 0.00 0.01 ]
|X 0.495 - 0.5 : [ 75 0.00 0.01 ]
|XX 0.5 - 0.505 : [ 158 0.00 0.01 ]
|XX 0.505 - 0.51 : [ 132 0.00 0.01 ]
|XXX 0.51 - 0.515 : [ 199 0.00 0.02 ]
|XXXX 0.515 - 0.52 : [ 257 0.00 0.02 ]
|XXXX 0.52 - 0.525 : [ 309 0.01 0.03 ]
|XXXXX 0.525 - 0.53 : [ 364 0.01 0.03 ]
|XXXXXX 0.53 - 0.535 : [ 439 0.01 0.04 ]
|XXXXXXXX 0.535 - 0.54 : [ 538 0.01 0.05 ]
|XXXXXXXXX 0.54 - 0.545 : [ 649 0.01 0.06 ]
|XXXXXXXXXXX 0.545 - 0.55 : [ 776 0.01 0.07 ]
|XXXXXXXXXXXXX 0.55 - 0.555 : [ 886 0.02 0.09 ]
|XXXXXXXXXXXXXX 0.555 - 0.56 : [ 992 0.02 0.11 ]
|XXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1184 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1371 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1544 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1810 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1993 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 2143 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 2156 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 2229 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 2562 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 2479 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 2665 0.05 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 2609 0.04 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 2637 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 2720 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 2756 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 2619 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 2531 0.04 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 2326 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 2130 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 1898 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 1542 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 1342 0.02 0.92 ]
|XXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 1133 0.02 0.94 ]
|XXXXXXXXXXXXX 0.675 - 0.68 : [ 887 0.02 0.95 ]
|XXXXXXXXXX 0.68 - 0.685 : [ 671 0.01 0.96 ]
|XXXXXXXX 0.685 - 0.69 : [ 519 0.01 0.97 ]
|XXXXXX 0.69 - 0.695 : [ 379 0.01 0.98 ]
|XXXXX 0.695 - 0.7 : [ 314 0.01 0.98 ]
|XXXX 0.7 - 0.705 : [ 263 0.00 0.99 ]
|XXX 0.705 - 0.71 : [ 186 0.00 0.99 ]
|XX 0.71 - 0.715 : [ 132 0.00 0.99 ]
|X 0.715 - 0.72 : [ 81 0.00 0.99 ]
|X 0.72 - 0.725 : [ 68 0.00 1.00 ]
|X 0.725 - 0.73 : [ 62 0.00 1.00 ]
| 0.73 - 0.735 : [ 34 0.00 1.00 ]
| 0.735 - 0.74 : [ 33 0.00 1.00 ]
| 0.74 - 0.745 : [ 31 0.00 1.00 ]
| 0.745 - 0.75 : [ 15 0.00 1.00 ]
| 0.75 - 0.755 : [ 18 0.00 1.00 ]
| 0.755 - 0.76 : [ 6 0.00 1.00 ]
| 0.76 - 0.765 : [ 12 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 : [ 5 0.00 1.00 ]
| 0.78 - 0.785 : [ 2 0.00 1.00 ]
| 0.785 - 0.79 : [ 4 0.00 1.00 ]
| 0.79 - 0.795 : [ 1 0.00 1.00 ]
| 0.795 - 0.8 : [ 1 0.00 1.00 ]
| 0.8 - 0.805 : [ 6 0.00 1.00 ]
| 0.805 - 0.81 : [ 2 0.00 1.00 ]
| 0.81 - 0.815 : [ 1 0.00 1.00 ]
#...
| 0.84 - 0.845 : [ 1 0.00 1.00 ]
#...
| 0.895 - 0.9 : [ 1 0.00 1.00 ]
#...
| 0.91 - 0.915 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 41. 443 reads; 47465 bp (untrimmed), 47034 (trimmed).
Contig 42. 471 reads; 58636 bp (untrimmed), 58495 (trimmed).
Contig 43. 498 reads; 42392 bp (untrimmed), 42103 (trimmed).
Contig 44. 501 reads; 42324 bp (untrimmed), 42105 (trimmed).
Contig 45. 512 reads; 46895 bp (untrimmed), 46701 (trimmed).
Contig 46. 548 reads; 49069 bp (untrimmed), 48875 (trimmed).
Contig 47. 631 reads; 62318 bp (untrimmed), 62297 (trimmed).
Contig 48. 658 reads; 55824 bp (untrimmed), 55824 (trimmed).
Contig 49. 683 reads; 59804 bp (untrimmed), 59774 (trimmed).
Contig 50. 706 reads; 66689 bp (untrimmed), 66668 (trimmed).
Contig 51. 716 reads; 67592 bp (untrimmed), 67324 (trimmed).
Contig 52. 731 reads; 75673 bp (untrimmed), 75620 (trimmed).
Contig 53. 1003 reads; 91344 bp (untrimmed), 91295 (trimmed).
Contig 54. 1312 reads; 111703 bp (untrimmed), 111670 (trimmed).
Contig 55. 1340 reads; 114645 bp (untrimmed), 114640 (trimmed).
Contig 56. 1352 reads; 114115 bp (untrimmed), 114045 (trimmed).
Contig 57. 1371 reads; 109894 bp (untrimmed), 109799 (trimmed).
Contig 58. 1708 reads; 141401 bp (untrimmed), 141342 (trimmed).
Contig 59. 1780 reads; 151166 bp (untrimmed), 151145 (trimmed).
Contig 60. 1801 reads; 146375 bp (untrimmed), 146359 (trimmed).
Contig 61. 1937 reads; 147581 bp (untrimmed), 147291 (trimmed).
Contig 62. 2363 reads; 215560 bp (untrimmed), 215529 (trimmed).
Contig 63. 2758 reads; 223920 bp (untrimmed), 223909 (trimmed).
Contig 64. 2937 reads; 242918 bp (untrimmed), 242829 (trimmed).
Contig 65. 3534 reads; 297685 bp (untrimmed), 297680 (trimmed).
Contig 66. 3828 reads; 309034 bp (untrimmed), 308898 (trimmed).
Contig 67. 16855 reads; 1387873 bp (untrimmed), 1387696 (trimmed).
--------------------------------------------------------------
Totals 58540 reads; 5011533 bp (untrimmed), 5002643 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 5009592 bases = 9.92 +- 3.75 = 0.11 +- 3.34
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 63 total values totalling 533.3800. <8.466349 +/- 2.768850>
#Range: [ 2.13 - 17.87 ]
#Most likely bin: [ 10 - 10.5 ] 14 counts
#Median bin: [ 9 - 9.5 ] 7 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 2 - 2.5 : [ 4 0.06 0.06 ]
|XXXXXX 2.5 - 3 : [ 2 0.03 0.10 ]
|XXX 3 - 3.5 : [ 1 0.02 0.11 ]
#...
|XXX 4.5 - 5 : [ 1 0.02 0.13 ]
#...
|XXXXXX 5.5 - 6 : [ 2 0.03 0.16 ]
|XXX 6 - 6.5 : [ 1 0.02 0.17 ]
|XXXXXXXXX 6.5 - 7 : [ 3 0.05 0.22 ]
|XXXXXX 7 - 7.5 : [ 2 0.03 0.25 ]
|XXXXXXXXX 7.5 - 8 : [ 3 0.05 0.30 ]
|XXXXXXXXXXX 8 - 8.5 : [ 4 0.06 0.37 ]
|XXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 7 0.11 0.48 ]
|XXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 7 0.11 0.59 ]
|XXXXXXXXXXXXXX 9.5 - 10 : [ 5 0.08 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 14 0.22 0.89 ]
|XXXXXX 10.5 - 11 : [ 2 0.03 0.92 ]
|XXXXXXXXX 11 - 11.5 : [ 3 0.05 0.97 ]
|XXX 11.5 - 12 : [ 1 0.02 0.98 ]
#...
|XXX 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 52 total values totalling 488.3900. <9.392115 +/- 1.898049>
#Range: [ 3.14 - 17.87 ]
#Most likely bin: [ 10 - 10.5 ] 14 counts
#Median bin: [ 9 - 9.5 ] 7 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 3 - 3.5 : [ 1 0.02 0.02 ]
#...
|XXX 5.5 - 6 : [ 1 0.02 0.04 ]
#...
|XXXXXX 6.5 - 7 : [ 2 0.04 0.08 ]
|XXX 7 - 7.5 : [ 1 0.02 0.10 ]
|XXXXXXXXX 7.5 - 8 : [ 3 0.06 0.15 ]
|XXXXXXXXXXX 8 - 8.5 : [ 4 0.08 0.23 ]
|XXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 7 0.13 0.37 ]
|XXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 7 0.13 0.50 ]
|XXXXXXXXXXXXXX 9.5 - 10 : [ 5 0.10 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 14 0.27 0.87 ]
|XXXXXX 10.5 - 11 : [ 2 0.04 0.90 ]
|XXXXXXXXX 11 - 11.5 : [ 3 0.06 0.96 ]
|XXX 11.5 - 12 : [ 1 0.02 0.98 ]
#...
|XXX 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 5 3 reads 1209 bases = 2.13 +- 0.67 = 1.02 +- 0.73
Contig 16 22 reads 898 bases = 2.17 +- 4.76 = 1.48 +- 1.99
Contig 6 3 reads 1171 bases = 2.25 +- 0.88 = 2.25 +- 0.88
Contig 7 3 reads 1085 bases = 2.49 +- 0.82 = 2.49 +- 0.82
Contig 8 7 reads 2267 bases = 2.72 +- 1.33 = 2.72 +- 1.33
Contig 10 8 reads 2628 bases = 2.87 +- 1.74 = 0.79 +- 2.37
Contig 12 10 reads 2619 bases = 3.14 +- 1.40 = 0.99 +- 1.00
Contig 9 8 reads 1439 bases = 4.51 +- 2.05 = 1.91 +- 0.82
Contig 18 25 reads 3732 bases = 5.88 +- 3.23 = 0.17 +- 1.52
Contig 13 11 reads 1664 bases = 5.98 +- 1.96 = 5.98 +- 1.96
Contig 14 12 reads 1361 bases = 6.08 +- 2.23 = 0.59 +- 1.53
Contig 35 346 reads 43835 bases = 6.62 +- 2.74 = 0.41 +- 2.96
Contig 11 10 reads 819 bases = 6.64 +- 4.00 = 6.64 +- 4.00
Contig 42 471 reads 58636 bases = 6.86 +- 2.85 = 0.13 +- 2.81
Contig 15 15 reads 1424 bases = 7.15 +- 6.17 = 7.15 +- 6.17
Contig 32 323 reads 39548 bases = 7.15 +- 2.40 = 0.27 +- 2.92
Contig 21 112 reads 12017 bases = 7.73 +- 2.55 = 0.06 +- 3.99
Contig 41 443 reads 47465 bases = 7.78 +- 2.96 = 0.03 +- 2.71
Contig 38 392 reads 42761 bases = 7.88 +- 3.22 = 0.01 +- 2.75
Contig 52 731 reads 75673 bases = 8.15 +- 2.61 = 0.18 +- 3.21
Contig 55 1340 reads 114645 bases = 10.02 +- 3.47 = 0.07 +- 3.68
Contig 65 3534 reads 297685 bases = 10.02 +- 3.48 = 0.09 +- 3.30
Contig 48 658 reads 55824 bases = 10.05 +- 3.77 = 0.31 +- 3.31
Contig 44 501 reads 42324 bases = 10.08 +- 3.83 = -0.05 +- 3.07
Contig 40 427 reads 35957 bases = 10.09 +- 3.43 = 0.10 +- 3.17
Contig 56 1352 reads 114115 bases = 10.15 +- 3.54 = 0.15 +- 3.18
Contig 58 1708 reads 141401 bases = 10.23 +- 3.48 = 0.05 +- 3.30
Contig 27 203 reads 16294 bases = 10.28 +- 6.83 = 0.09 +- 3.12
Contig 29 217 reads 18148 bases = 10.30 +- 4.62 = 0.56 +- 3.25
Contig 64 2937 reads 242918 bases = 10.31 +- 5.23 = 0.12 +- 3.27
Contig 67 16855 reads 1387873 bases = 10.32 +- 3.52 = 0.01 +- 3.48
Contig 63 2758 reads 223920 bases = 10.44 +- 3.50 = 0.01 +- 3.34
Contig 60 1801 reads 146375 bases = 10.48 +- 3.53 = 0.17 +- 3.48
Contig 57 1371 reads 109894 bases = 10.57 +- 3.59 = 0.05 +- 3.47
Contig 66 3828 reads 309034 bases = 10.59 +- 3.45 = 0.02 +- 3.33
Contig 36 347 reads 26531 bases = 11.11 +- 4.31 = 0.47 +- 3.04
Contig 61 1937 reads 147581 bases = 11.13 +- 4.95 = 0.19 +- 3.39
Contig 39 403 reads 30440 bases = 11.23 +- 3.38 = 0.53 +- 3.80
Contig 34 326 reads 23356 bases = 11.85 +- 4.28 = 0.50 +- 3.36
Contig 19 68 reads 3161 bases = 17.87 +- 10.89 = 2.70 +- 2.40
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 707
HQ Discrepant reads = 50
Chimeric reads = 192
Suspect alignments = 312
-------------------------------------------------------------------
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/microbe5/3634489/edit_dir.10Aug04.QD