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
3634479 2800 2203 Methanospirillum hungatei
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Methanospirillum_hungatei
-------------------------------------------------------------------
Methanomicrobia, class, euryarchaeotes
Methanospirillaceae, family, euryarchaeotes
Euryarchaeota, phylum, euryarchaeotes
Methanospirillum hungatei, species, euryarchaeotes
Methanospirillum, genus, euryarchaeotes
Methanomicrobiales, order, euryarchaeotes
Archaea, superkingdom, archaea
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3516775
# phrap: 3331298
# db:
altered.
2800000
3216024 +/- 303762
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 10308
Number of reads with percent X's >= 20%: 450 = 0.9%
Number of reads with percent X's >= 50%: 216 = 0.4%
Number of reads with percent X's >= 80%: 14 = 0.0%
Total reads in project: 48134
Total bp X'd : 625208
reads >= 20% >= 50% >= 80% screened
Nr with L09136 7404 70 32 3
Nr with pCC1Fos 1505 255 114 1
Nr with pMCL200_JGI_XZX+XZK 1399 125 70 10
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 26
Number of reads with percent X's >= 20%: 3 = 3.8%
Number of reads with percent X's >= 50%: 3 = 3.8%
Number of reads with percent X's >= 80%: 1 = 1.3%
Total reads in project: 78
Total bp X'd : 3049
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3 0 0 0
Nr with pCC1Fos 18 0 0 0
Nr with pMCL200_JGI_XZX+XZK 5 3 3 1
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 12315693
C = 10437493
G = 10429810
T = 12106867
N = 238907
X = 625208
GC fraction = 0.45
Total = 46153978
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634479_fasta.screen.contigs
-------------------------------------------------------------------
A 970944
C 799319
G 794099
T 961079
N 2854
fraction GC = 0.45
total bases = 3528295
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 AHYT reads.list > grep.reads.list.AHYT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYT 4 500
-------------------------------------------------------------------
#Found 7540 total values totalling 28243294.0000. <3745.794960 +/- 10647.798681>
#Range: [ 646 - 497655 ]
#Most likely bin: [ 3000 - 3500 ] 3055 counts
#Median bin: [ 3000 - 3500 ] 3055 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 12 0.00 0.00 ]
|X 1000 - 1500 : [ 47 0.01 0.01 ]
|X 1500 - 2000 : [ 67 0.01 0.02 ]
|XX 2000 - 2500 : [ 172 0.02 0.04 ]
|XXXXXXXXXXXXXXXX 2500 - 3000 : [ 1222 0.16 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3055 0.41 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1979 0.26 0.87 ]
|XXXXXXXXXXXX 4000 - 4500 : [ 908 0.12 0.99 ]
|X 4500 - 5000 : [ 64 0.01 1.00 ]
| 5000 - 5500 : [ 1 0.00 1.00 ]
#...
| 7500 - 8000 : [ 1 0.00 1.00 ]
#...
| 61000 - 61500 : [ 1 0.00 1.00 ]
#...
| 102500 - 103000 : [ 2 0.00 1.00 ]
#...
| 107500 - 108000 : [ 1 0.00 1.00 ]
#...
| 165000 - 165500 : [ 1 0.00 1.00 ]
#...
| 186000 - 186500 : [ 1 0.00 1.00 ]
#...
| 225000 - 225500 : [ 1 0.00 1.00 ]
#...
| 233000 - 233500 : [ 1 0.00 1.00 ]
#...
| 290500 - 291000 : [ 1 0.00 1.00 ]
#...
| 352000 - 352500 : [ 1 0.00 1.00 ]
#...
| 460500 - 461000 : [ 1 0.00 1.00 ]
#...
| 497500 - 498000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYU reads.list > grep.reads.list.AHYU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYU 4 500
-------------------------------------------------------------------
#Found 11165 total values totalling 81552771.0000. <7304.323421 +/- 5357.111700>
#Range: [ 784 - 422406 ]
#Most likely bin: [ 7000 - 7500 ] 2702 counts
#Median bin: [ 7000 - 7500 ] 2702 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 10 0.00 0.00 ]
|X 1000 - 1500 : [ 78 0.01 0.01 ]
|X 1500 - 2000 : [ 75 0.01 0.01 ]
|X 2000 - 2500 : [ 90 0.01 0.02 ]
|X 2500 - 3000 : [ 94 0.01 0.03 ]
|X 3000 - 3500 : [ 91 0.01 0.04 ]
|X 3500 - 4000 : [ 90 0.01 0.05 ]
|X 4000 - 4500 : [ 87 0.01 0.06 ]
|XX 4500 - 5000 : [ 108 0.01 0.06 ]
|XX 5000 - 5500 : [ 151 0.01 0.08 ]
|XXX 5500 - 6000 : [ 225 0.02 0.10 ]
|XXXXXX 6000 - 6500 : [ 376 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1788 0.16 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 2702 0.24 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 2219 0.20 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1828 0.16 0.90 ]
|XXXXXXXXXXXXXXXX 8500 - 9000 : [ 1059 0.09 0.99 ]
|X 9000 - 9500 : [ 91 0.01 1.00 ]
#...
| 25000 - 25500 : [ 1 0.00 1.00 ]
#...
| 364000 - 364500 : [ 1 0.00 1.00 ]
#...
| 422000 - 422500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYW reads.list > grep.reads.list.AHYW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYW 4 500
-------------------------------------------------------------------
#Found 1039 total values totalling 38080742.0000. <36651.339750 +/- 5043.270386>
#Range: [ 682 - 133710 ]
#Most likely bin: [ 35500 - 36000 ] 70 counts
#Median bin: [ 36000 - 36500 ] 60 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 500 - 1000 : [ 3 0.00 0.00 ]
#...
|X 24500 - 25000 : [ 1 0.00 0.00 ]
|X 25000 - 25500 : [ 1 0.00 0.00 ]
#...
|X 26000 - 26500 : [ 2 0.00 0.01 ]
#...
|X 27000 - 27500 : [ 2 0.00 0.01 ]
|X 27500 - 28000 : [ 1 0.00 0.01 ]
|XX 28000 - 28500 : [ 3 0.00 0.01 ]
|XX 28500 - 29000 : [ 4 0.00 0.02 ]
|XXX 29000 - 29500 : [ 5 0.00 0.02 ]
|XXXXX 29500 - 30000 : [ 9 0.01 0.03 ]
|XXXXXXX 30000 - 30500 : [ 12 0.01 0.04 ]
|XXXXX 30500 - 31000 : [ 8 0.01 0.05 ]
|XXXXXXX 31000 - 31500 : [ 13 0.01 0.06 ]
|XXXXXXXXXXXXX 31500 - 32000 : [ 23 0.02 0.08 ]
|XXXXXXXXXXX 32000 - 32500 : [ 19 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 31 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 45 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 51 0.05 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 56 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 62 0.06 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 54 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 70 0.07 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 60 0.06 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 63 0.06 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 49 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 55 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 41 0.04 0.72 ]
|XXXXXXXXXXXXXXXXX 38500 - 39000 : [ 30 0.03 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 38 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 31 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 43 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 35 0.03 0.89 ]
|XXXXXXXXXX 41000 - 41500 : [ 17 0.02 0.90 ]
|XXXXXXXXXXXXX 41500 - 42000 : [ 23 0.02 0.92 ]
|XXXXXXXXXX 42000 - 42500 : [ 17 0.02 0.94 ]
|XXXXX 42500 - 43000 : [ 8 0.01 0.95 ]
|XXXXXXXXX 43000 - 43500 : [ 16 0.02 0.96 ]
|XXXX 43500 - 44000 : [ 7 0.01 0.97 ]
|XXXXXX 44000 - 44500 : [ 10 0.01 0.98 ]
|XXXXX 44500 - 45000 : [ 9 0.01 0.99 ]
|XX 45000 - 45500 : [ 4 0.00 0.99 ]
|XX 45500 - 46000 : [ 4 0.00 1.00 ]
#...
|X 46500 - 47000 : [ 2 0.00 1.00 ]
#...
|X 47500 - 48000 : [ 1 0.00 1.00 ]
#...
|X 133500 - 134000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHYT 3238 +- 600 (n=3599)
# AHYW 36241 +- 5094 (n=479)
# AHYU 7121 +- 1450 (n=5547)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634479_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
AHYT 19968 -1 -1 95 667 19671 88 599 91 611
AHYU 29184 94 777 98 721 29119 90 706 96 706
AHYW 6144 89 579 78 394 6144 59 539 79 494
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHYT 9872 89 605 92 620 9799 87 593 91 601
AHYU 14556 89 709 95 707 14563 92 704 97 705
AHYW 3072 57 545 75 497 3072 61 532 83 492
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634479_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
100 17618 9282 92.82 96.69 AHYT @
152 26465 13669 89.93 93.67 AHYU @
32 4051 2233 69.78 72.69 AHYW @
] 48134 25184 88.68 cumulative total@@
LIBRARY PLATE ID COUNT [ AHYT 100 AHYU 152 AHYW 32 ] for 284 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 3634479_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 54934 total values totalling 31093411.0000. <566.013962 +/- 273.850157>
#Range: [ 0 - 929 ]
#Most likely bin: [ 750 - 800 ] 9369 counts
#Median bin: [ 650 - 700 ] 5536 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 6572 0.12 0.12 ]
|XXXX 50 - 100 : [ 1035 0.02 0.14 ]
|XXX 100 - 150 : [ 747 0.01 0.15 ]
|XXX 150 - 200 : [ 752 0.01 0.17 ]
|XXXX 200 - 250 : [ 821 0.01 0.18 ]
|XXXX 250 - 300 : [ 887 0.02 0.20 ]
|XXXXX 300 - 350 : [ 1061 0.02 0.22 ]
|XXXXX 350 - 400 : [ 1119 0.02 0.24 ]
|XXXXX 400 - 450 : [ 1286 0.02 0.26 ]
|XXXXXXX 450 - 500 : [ 1548 0.03 0.29 ]
|XXXXXXXX 500 - 550 : [ 1891 0.03 0.32 ]
|XXXXXXXXXXX 550 - 600 : [ 2563 0.05 0.37 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 3727 0.07 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5536 0.10 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7964 0.14 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 9369 0.17 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6694 0.12 0.98 ]
|XXXXXX 850 - 900 : [ 1340 0.02 1.00 ]
| 900 - 950 : [ 22 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYT 3634479_fasta.screen.trimQ15.SaF > reads.trim15.AHYT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYT.rl 2 50
-------------------------------------------------------------------
#Found 19671 total values totalling 10440215.0000. <530.741447 +/- 252.824315>
#Range: [ 0 - 901 ]
#Most likely bin: [ 700 - 750 ] 2514 counts
#Median bin: [ 600 - 650 ] 1969 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1938 0.10 0.10 ]
|XXXXXX 50 - 100 : [ 370 0.02 0.12 ]
|XXXXXX 100 - 150 : [ 370 0.02 0.14 ]
|XXXXXX 150 - 200 : [ 406 0.02 0.16 ]
|XXXXXX 200 - 250 : [ 405 0.02 0.18 ]
|XXXXXXX 250 - 300 : [ 449 0.02 0.20 ]
|XXXXXXXX 300 - 350 : [ 513 0.03 0.23 ]
|XXXXXXXXX 350 - 400 : [ 542 0.03 0.25 ]
|XXXXXXXXXXXX 400 - 450 : [ 734 0.04 0.29 ]
|XXXXXXXXXXXXXXX 450 - 500 : [ 927 0.05 0.34 ]
|XXXXXXXXXXXXXXXXX 500 - 550 : [ 1092 0.06 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1418 0.07 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1969 0.10 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2418 0.12 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2514 0.13 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2091 0.11 0.92 ]
|XXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1279 0.07 0.99 ]
|XXXX 850 - 900 : [ 234 0.01 1.00 ]
| 900 - 950 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYU 3634479_fasta.screen.trimQ15.SaF > reads.trim15.AHYU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYU.rl 2 50
-------------------------------------------------------------------
#Found 29119 total values totalling 18631627.0000. <639.844328 +/- 247.309459>
#Range: [ 0 - 929 ]
#Most likely bin: [ 750 - 800 ] 6875 counts
#Median bin: [ 700 - 750 ] 4863 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 0 - 50 : [ 2526 0.09 0.09 ]
|XX 50 - 100 : [ 258 0.01 0.10 ]
|X 100 - 150 : [ 201 0.01 0.10 ]
|X 150 - 200 : [ 217 0.01 0.11 ]
|X 200 - 250 : [ 241 0.01 0.12 ]
|X 250 - 300 : [ 248 0.01 0.13 ]
|XX 300 - 350 : [ 302 0.01 0.14 ]
|XX 350 - 400 : [ 335 0.01 0.15 ]
|XX 400 - 450 : [ 396 0.01 0.16 ]
|XXX 450 - 500 : [ 532 0.02 0.18 ]
|XXXX 500 - 550 : [ 695 0.02 0.20 ]
|XXXXXX 550 - 600 : [ 976 0.03 0.24 ]
|XXXXXXXX 600 - 650 : [ 1426 0.05 0.29 ]
|XXXXXXXXXXXXXXX 650 - 700 : [ 2594 0.09 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4863 0.17 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6875 0.24 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5312 0.18 0.96 ]
|XXXXXX 850 - 900 : [ 1102 0.04 1.00 ]
| 900 - 950 : [ 20 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYW 3634479_fasta.screen.trimQ15.SaF > reads.trim15.AHYW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYW.rl 2 50
-------------------------------------------------------------------
#Found 6144 total values totalling 2021569.0000. <329.031413 +/- 300.042428>
#Range: [ 0 - 889 ]
#Most likely bin: [ 0 - 50 ] 2108 counts
#Median bin: [ 250 - 300 ] 190 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2108 0.34 0.34 ]
|XXXXXXXX 50 - 100 : [ 407 0.07 0.41 ]
|XXX 100 - 150 : [ 176 0.03 0.44 ]
|XX 150 - 200 : [ 129 0.02 0.46 ]
|XXX 200 - 250 : [ 175 0.03 0.49 ]
|XXXX 250 - 300 : [ 190 0.03 0.52 ]
|XXXXX 300 - 350 : [ 246 0.04 0.56 ]
|XXXXX 350 - 400 : [ 242 0.04 0.60 ]
|XXX 400 - 450 : [ 156 0.03 0.62 ]
|XX 450 - 500 : [ 89 0.01 0.64 ]
|XX 500 - 550 : [ 104 0.02 0.65 ]
|XXX 550 - 600 : [ 169 0.03 0.68 ]
|XXXXXX 600 - 650 : [ 332 0.05 0.74 ]
|XXXXXXXXXX 650 - 700 : [ 524 0.09 0.82 ]
|XXXXXXXXXXX 700 - 750 : [ 587 0.10 0.92 ]
|XXXXXXXX 750 - 800 : [ 403 0.07 0.98 ]
|XX 800 - 850 : [ 103 0.02 1.00 ]
| 850 - 900 : [ 4 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634479
-------------------------------------------------------------------
AHYT.000001.000100 pUC18.fa LRS.fasta
AHYT.000101.000200 pUC18.fa LRS.fasta
AHYU.000001.000100 pMCL200.fa LRS.fasta
AHYU.000101.000200 pMCL200.fa LRS.fasta
AHYW.000001.000100 pCC1Fos.fa LRS.fasta
AHYT.000001.000100 pUC18.fa LRS.fasta
AHYT.000101.000200 pUC18.fa LRS.fasta
AHYU.000001.000100 pMCL200.fa LRS.fasta
AHYU.000101.000200 pMCL200.fa LRS.fasta
AHYW.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634479_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634479_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 47902 total values totalling 21802.6791. <0.455152 +/- 0.056542>
#Range: [ 0.1351 - 1 ]
#Most likely bin: [ 0.465 - 0.47 ] 1906 counts
#Median bin: [ 0.46 - 0.465 ] 1798 counts
#Entropy = 5.4908 bits
| 0.135 - 0.14 : [ 1 0.00 0.00 ]
| 0.14 - 0.145 : [ 1 0.00 0.00 ]
#...
| 0.155 - 0.16 : [ 1 0.00 0.00 ]
#...
| 0.175 - 0.18 : [ 1 0.00 0.00 ]
| 0.18 - 0.185 : [ 2 0.00 0.00 ]
#...
| 0.19 - 0.195 : [ 3 0.00 0.00 ]
| 0.195 - 0.2 : [ 1 0.00 0.00 ]
| 0.2 - 0.205 : [ 1 0.00 0.00 ]
| 0.205 - 0.21 : [ 2 0.00 0.00 ]
| 0.21 - 0.215 : [ 1 0.00 0.00 ]
| 0.215 - 0.22 : [ 1 0.00 0.00 ]
| 0.22 - 0.225 : [ 1 0.00 0.00 ]
| 0.225 - 0.23 : [ 5 0.00 0.00 ]
| 0.23 - 0.235 : [ 5 0.00 0.00 ]
| 0.235 - 0.24 : [ 6 0.00 0.00 ]
| 0.24 - 0.245 : [ 7 0.00 0.00 ]
| 0.245 - 0.25 : [ 7 0.00 0.00 ]
| 0.25 - 0.255 : [ 16 0.00 0.00 ]
| 0.255 - 0.26 : [ 20 0.00 0.00 ]
|X 0.26 - 0.265 : [ 32 0.00 0.00 ]
|X 0.265 - 0.27 : [ 48 0.00 0.00 ]
|X 0.27 - 0.275 : [ 35 0.00 0.00 ]
|X 0.275 - 0.28 : [ 36 0.00 0.00 ]
|X 0.28 - 0.285 : [ 47 0.00 0.01 ]
|X 0.285 - 0.29 : [ 54 0.00 0.01 ]
|XX 0.29 - 0.295 : [ 78 0.00 0.01 ]
|X 0.295 - 0.3 : [ 53 0.00 0.01 ]
|XX 0.3 - 0.305 : [ 80 0.00 0.01 ]
|XX 0.305 - 0.31 : [ 99 0.00 0.01 ]
|XX 0.31 - 0.315 : [ 95 0.00 0.02 ]
|XXX 0.315 - 0.32 : [ 120 0.00 0.02 ]
|XXX 0.32 - 0.325 : [ 125 0.00 0.02 ]
|XXXX 0.325 - 0.33 : [ 179 0.00 0.02 ]
|XXXXX 0.33 - 0.335 : [ 219 0.00 0.03 ]
|XXXXX 0.335 - 0.34 : [ 239 0.00 0.03 ]
|XXXXXX 0.34 - 0.345 : [ 284 0.01 0.04 ]
|XXXXXXX 0.345 - 0.35 : [ 354 0.01 0.05 ]
|XXXXXXXX 0.35 - 0.355 : [ 380 0.01 0.06 ]
|XXXXXXXXX 0.355 - 0.36 : [ 408 0.01 0.06 ]
|XXXXXXXXX 0.36 - 0.365 : [ 447 0.01 0.07 ]
|XXXXXXXXXX 0.365 - 0.37 : [ 493 0.01 0.08 ]
|XXXXXXXXXX 0.37 - 0.375 : [ 497 0.01 0.09 ]
|XXXXXXXXXXXX 0.375 - 0.38 : [ 572 0.01 0.11 ]
|XXXXXXXXXXXX 0.38 - 0.385 : [ 568 0.01 0.12 ]
|XXXXXXXXXXXXXX 0.385 - 0.39 : [ 653 0.01 0.13 ]
|XXXXXXXXXXXXXX 0.39 - 0.395 : [ 652 0.01 0.14 ]
|XXXXXXXXXXXXXXX 0.395 - 0.4 : [ 734 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 961 0.02 0.18 ]
|XXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 966 0.02 0.20 ]
|XXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 945 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 1047 0.02 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 1146 0.02 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 1204 0.03 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 1321 0.03 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 1390 0.03 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 1552 0.03 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 1614 0.03 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 1703 0.04 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 1706 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 1798 0.04 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 1906 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 1826 0.04 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 1888 0.04 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 1832 0.04 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1762 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1776 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1490 0.03 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1783 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1386 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1328 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1229 0.03 0.90 ]
|XXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 960 0.02 0.92 ]
|XXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 786 0.02 0.94 ]
|XXXXXXXXXXXXX 0.53 - 0.535 : [ 633 0.01 0.95 ]
|XXXXXXXXXXX 0.535 - 0.54 : [ 532 0.01 0.96 ]
|XXXXXXXXXX 0.54 - 0.545 : [ 461 0.01 0.97 ]
|XXXXXXX 0.545 - 0.55 : [ 327 0.01 0.98 ]
|XXXXX 0.55 - 0.555 : [ 227 0.00 0.98 ]
|XXX 0.555 - 0.56 : [ 162 0.00 0.99 ]
|XX 0.56 - 0.565 : [ 110 0.00 0.99 ]
|X 0.565 - 0.57 : [ 71 0.00 0.99 ]
|X 0.57 - 0.575 : [ 68 0.00 0.99 ]
|X 0.575 - 0.58 : [ 61 0.00 0.99 ]
|X 0.58 - 0.585 : [ 65 0.00 1.00 ]
|X 0.585 - 0.59 : [ 27 0.00 1.00 ]
| 0.59 - 0.595 : [ 23 0.00 1.00 ]
| 0.595 - 0.6 : [ 12 0.00 1.00 ]
|X 0.6 - 0.605 : [ 26 0.00 1.00 ]
| 0.605 - 0.61 : [ 17 0.00 1.00 ]
| 0.61 - 0.615 : [ 9 0.00 1.00 ]
| 0.615 - 0.62 : [ 7 0.00 1.00 ]
| 0.62 - 0.625 : [ 7 0.00 1.00 ]
| 0.625 - 0.63 : [ 12 0.00 1.00 ]
| 0.63 - 0.635 : [ 7 0.00 1.00 ]
| 0.635 - 0.64 : [ 10 0.00 1.00 ]
| 0.64 - 0.645 : [ 10 0.00 1.00 ]
| 0.645 - 0.65 : [ 5 0.00 1.00 ]
| 0.65 - 0.655 : [ 3 0.00 1.00 ]
| 0.655 - 0.66 : [ 9 0.00 1.00 ]
| 0.66 - 0.665 : [ 1 0.00 1.00 ]
| 0.665 - 0.67 : [ 3 0.00 1.00 ]
| 0.67 - 0.675 : [ 2 0.00 1.00 ]
| 0.675 - 0.68 : [ 3 0.00 1.00 ]
| 0.68 - 0.685 : [ 2 0.00 1.00 ]
| 0.685 - 0.69 : [ 5 0.00 1.00 ]
| 0.69 - 0.695 : [ 1 0.00 1.00 ]
#...
| 0.7 - 0.705 : [ 4 0.00 1.00 ]
| 0.705 - 0.71 : [ 1 0.00 1.00 ]
| 0.71 - 0.715 : [ 2 0.00 1.00 ]
| 0.715 - 0.72 : [ 1 0.00 1.00 ]
| 0.72 - 0.725 : [ 2 0.00 1.00 ]
| 0.725 - 0.73 : [ 2 0.00 1.00 ]
#...
| 0.735 - 0.74 : [ 1 0.00 1.00 ]
#...
| 0.75 - 0.755 : [ 1 0.00 1.00 ]
#...
| 0.77 - 0.775 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 48. 207 reads; 17194 bp (untrimmed), 17137 (trimmed).
Contig 49. 228 reads; 22791 bp (untrimmed), 22426 (trimmed).
Contig 50. 346 reads; 26496 bp (untrimmed), 26105 (trimmed).
Contig 51. 354 reads; 32134 bp (untrimmed), 32062 (trimmed).
Contig 52. 441 reads; 30386 bp (untrimmed), 30199 (trimmed).
Contig 53. 503 reads; 41137 bp (untrimmed), 40997 (trimmed).
Contig 54. 527 reads; 50506 bp (untrimmed), 50437 (trimmed).
Contig 55. 578 reads; 47962 bp (untrimmed), 47767 (trimmed).
Contig 56. 700 reads; 47818 bp (untrimmed), 47776 (trimmed).
Contig 57. 709 reads; 50188 bp (untrimmed), 50146 (trimmed).
Contig 58. 759 reads; 69286 bp (untrimmed), 69218 (trimmed).
Contig 59. 845 reads; 39308 bp (untrimmed), 39287 (trimmed).
Contig 60. 929 reads; 83009 bp (untrimmed), 82960 (trimmed).
Contig 61. 1044 reads; 77119 bp (untrimmed), 76739 (trimmed).
Contig 62. 1050 reads; 74568 bp (untrimmed), 74413 (trimmed).
Contig 63. 1062 reads; 90230 bp (untrimmed), 90068 (trimmed).
Contig 64. 1227 reads; 86867 bp (untrimmed), 86844 (trimmed).
Contig 65. 1423 reads; 105030 bp (untrimmed), 104958 (trimmed).
Contig 66. 1452 reads; 94828 bp (untrimmed), 94714 (trimmed).
Contig 67. 1719 reads; 98317 bp (untrimmed), 98209 (trimmed).
Contig 68. 1753 reads; 154511 bp (untrimmed), 154048 (trimmed).
Contig 69. 1945 reads; 133267 bp (untrimmed), 133007 (trimmed).
Contig 70. 2089 reads; 192145 bp (untrimmed), 192027 (trimmed).
Contig 71. 2194 reads; 158039 bp (untrimmed), 157812 (trimmed).
Contig 72. 2801 reads; 250008 bp (untrimmed), 249944 (trimmed).
Contig 73. 9282 reads; 615122 bp (untrimmed), 614811 (trimmed).
Contig 74. 10514 reads; 721039 bp (untrimmed), 720867 (trimmed).
--------------------------------------------------------------
Totals 48056 reads; 3528295 bp (untrimmed), 3516775 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3520088 bases = 11.88 +- 5.31 = 0.13 +- 3.75
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 57 total values totalling 573.1700. <10.055614 +/- 7.233813>
#Range: [ 1.14 - 46.81 ]
#Most likely bin: [ 9 - 9.5 ] 7 counts
#Median bin: [ 9.5 - 10 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 1 - 1.5 : [ 1 0.02 0.02 ]
|XXXXXXXXXXXXXXXXX 1.5 - 2 : [ 3 0.05 0.07 ]
|XXXXXXXXXXX 2 - 2.5 : [ 2 0.04 0.11 ]
|XXXXXXXXXXX 2.5 - 3 : [ 2 0.04 0.14 ]
|XXXXXX 3 - 3.5 : [ 1 0.02 0.16 ]
|XXXXXXXXXXX 3.5 - 4 : [ 2 0.04 0.19 ]
#...
|XXXXXXXXXXX 4.5 - 5 : [ 2 0.04 0.23 ]
|XXXXXXXXXXX 5 - 5.5 : [ 2 0.04 0.26 ]
#...
|XXXXXX 8 - 8.5 : [ 1 0.02 0.28 ]
|XXXXXXXXXXXXXXXXX 8.5 - 9 : [ 3 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 7 0.12 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 6 0.11 0.56 ]
|XXXXXXXXXXX 10 - 10.5 : [ 2 0.04 0.60 ]
|XXXXXXXXXXXXXXXXX 10.5 - 11 : [ 3 0.05 0.65 ]
|XXXXXX 11 - 11.5 : [ 1 0.02 0.67 ]
|XXXXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.05 0.72 ]
|XXXXXXXXXXXXXXXXX 12 - 12.5 : [ 3 0.05 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 7 0.12 0.89 ]
|XXXXXXXXXXX 13 - 13.5 : [ 2 0.04 0.93 ]
#...
|XXXXXX 15 - 15.5 : [ 1 0.02 0.95 ]
#...
|XXXXXX 16 - 16.5 : [ 1 0.02 0.96 ]
#...
|XXXXXX 37 - 37.5 : [ 1 0.02 0.98 ]
#...
|XXXXXX 46.5 - 47 : [ 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 38 total values totalling 412.4400. <10.853684 +/- 1.903261>
#Range: [ 5.33 - 15.42 ]
#Most likely bin: [ 12.5 - 13 ] 7 counts
#Median bin: [ 10.5 - 11 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 5 - 5.5 : [ 1 0.03 0.03 ]
#...
|XXXXXX 8 - 8.5 : [ 1 0.03 0.05 ]
|XXXXXXXXXXX 8.5 - 9 : [ 2 0.05 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 7 0.18 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 5 0.13 0.42 ]
|XXXXXXXXXXX 10 - 10.5 : [ 2 0.05 0.47 ]
|XXXXXXXXXXXXXXXXX 10.5 - 11 : [ 3 0.08 0.55 ]
|XXXXXX 11 - 11.5 : [ 1 0.03 0.58 ]
|XXXXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.08 0.66 ]
|XXXXXXXXXXXXXXXXX 12 - 12.5 : [ 3 0.08 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 7 0.18 0.92 ]
|XXXXXXXXXXX 13 - 13.5 : [ 2 0.05 0.97 ]
#...
|XXXXXX 15 - 15.5 : [ 1 0.03 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 6 2 reads 556 bases = 1.14 +- 0.35 = 1.14 +- 0.35
Contig 11 3 reads 781 bases = 1.74 +- 0.94 = 0.95 +- 0.21
Contig 7 2 reads 650 bases = 1.76 +- 0.42 = 1.76 +- 0.42
Contig 30 18 reads 678 bases = 1.98 +- 0.91 = -1.93 +- 0.96
Contig 17 4 reads 575 bases = 2.44 +- 0.83 = -0.04 +- 0.26
Contig 18 4 reads 564 bases = 2.46 +- 0.90 = 0.08 +- 0.28
Contig 19 4 reads 510 bases = 2.64 +- 0.99 = -0.06 +- 0.33
Contig 14 3 reads 927 bases = 2.94 +- 0.26 = 2.94 +- 0.26
Contig 23 6 reads 662 bases = 3.47 +- 1.41 = -0.05 +- 0.35
Contig 29 13 reads 680 bases = 3.76 +- 0.95 = -3.73 +- 1.02
Contig 25 9 reads 728 bases = 3.99 +- 1.33 = 0.89 +- 0.85
Contig 27 9 reads 1691 bases = 4.51 +- 2.06 = 1.47 +- 1.57
Contig 28 11 reads 1793 bases = 4.81 +- 3.00 = 0.80 +- 2.60
Contig 24 9 reads 1505 bases = 5.18 +- 2.37 = 0.83 +- 3.04
Contig 31 20 reads 3408 bases = 5.33 +- 2.26 = 0.40 +- 2.48
Contig 36 34 reads 3626 bases = 8.35 +- 4.06 = 2.13 +- 1.92
Contig 46 168 reads 17633 bases = 8.50 +- 2.88 = 0.45 +- 3.91
Contig 37 39 reads 681 bases = 8.54 +- 2.62 = -8.45 +- 2.85
Contig 49 228 reads 22791 bases = 8.93 +- 3.30 = 1.24 +- 3.54
Contig 43 102 reads 10166 bases = 9.04 +- 3.11 = 0.55 +- 3.24
Contig 45 164 reads 13173 bases = 11.22 +- 3.50 = 0.22 +- 3.32
Contig 50 346 reads 26496 bases = 11.56 +- 3.96 = 0.33 +- 3.73
Contig 61 1044 reads 77119 bases = 11.86 +- 4.78 = -0.03 +- 4.12
Contig 65 1423 reads 105030 bases = 11.98 +- 4.25 = 0.20 +- 3.58
Contig 71 2194 reads 158039 bases = 12.18 +- 4.22 = 0.03 +- 3.74
Contig 59 845 reads 39308 bases = 12.34 +- 3.96 = 0.54 +- 3.95
Contig 64 1227 reads 86867 bases = 12.44 +- 3.75 = 0.04 +- 3.57
Contig 57 709 reads 50188 bases = 12.50 +- 3.90 = 0.22 +- 3.71
Contig 62 1050 reads 74568 bases = 12.52 +- 3.88 = 0.21 +- 3.80
Contig 56 700 reads 47818 bases = 12.79 +- 3.44 = 0.29 +- 3.40
Contig 74 10514 reads 721039 bases = 12.80 +- 4.87 = 0.05 +- 3.98
Contig 52 441 reads 30386 bases = 12.88 +- 3.59 = 0.31 +- 3.71
Contig 69 1945 reads 133267 bases = 12.88 +- 4.80 = 0.03 +- 3.69
Contig 38 41 reads 2779 bases = 12.98 +- 4.97 = 0.20 +- 2.45
Contig 73 9282 reads 615122 bases = 13.25 +- 8.12 = 0.02 +- 3.83
Contig 66 1452 reads 94828 bases = 13.29 +- 3.49 = 0.41 +- 3.53
Contig 67 1719 reads 98317 bases = 15.42 +- 3.86 = 0.08 +- 3.91
Contig 35 34 reads 1842 bases = 16.02 +- 9.06 = 0.22 +- 3.49
Contig 40 56 reads 876 bases = 37.00 +- 21.56 = 37.00 +- 21.56
Contig 42 71 reads 629 bases = 46.81 +- 9.25 = 46.75 +- 9.24
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 513
HQ Discrepant reads = 44
Chimeric reads = 113
Suspect alignments = 843
-------------------------------------------------------------------
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/finished2/microbe/3634479/edit_dir.11Nov04.QD