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
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Chlorobium_chlorochromatii
-------------------------------------------------------------------
Chlorobium chlorochromatii (epibiont of the phototrophic consortium
"Chlorochromatium aggregatum"), species, green sulfur bacteria
Chlorobium/Pelodictyon group, green sulfur bacteria
Chlorobiaceae, family, green sulfur bacteria
Chlorobiales, order, green sulfur bacteria
Chlorobia, class, green sulfur bacteria
Bacteroidetes/Chlorobi group, superphylum, eubacteria
Chlorobium, genus, green sulfur bacteria
Chlorobi, phylum, green sulfur bacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2585010
# phrap: 2524936
# db:
altered.
2554973 +/- 30037
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 30139
Number of reads with percent X's >= 20%: 239 = 0.5%
Number of reads with percent X's >= 50%: 149 = 0.3%
Number of reads with percent X's >= 80%: 23 = 0.1%
Total reads in project: 45546
Total bp X'd : 1912745
reads >= 20% >= 50% >= 80% screened
Nr with L09136 10831 181 103 11
Nr with pCC1Fos 817 0 0 0
Nr with pMCL200_JGI_XZX+XZK 18491 58 46 12
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 288
Number of reads with percent X's >= 20%: 0 = 0.0%
Number of reads with percent X's >= 50%: 0 = 0.0%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 659
Total bp X'd : 14491
reads >= 20% >= 50% >= 80% screened
Nr with L09136 8 0 0 0
Nr with pCC1Fos 184 0 0 0
Nr with pMCL200_JGI_XZX+XZK 96 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 13678987
C = 11216545
G = 11084020
T = 13138240
N = 191393
X = 1912745
GC fraction = 0.44
Total = 51221930
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436101_fasta.screen.contigs
-------------------------------------------------------------------
A 726053
C 590143
G 558944
T 716285
N 509
fraction GC = 0.44
total bases = 2591934
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 ACFH reads.list > grep.reads.list.ACFH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACFH 4 500
-------------------------------------------------------------------
#Found 11099 total values totalling 39874502.0000. <3592.621137 +/- 7487.168494>
#Range: [ 1051 - 343119 ]
#Most likely bin: [ 2500 - 3000 ] 3364 counts
#Median bin: [ 3000 - 3500 ] 3169 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1000 - 1500 : [ 76 0.01 0.01 ]
|X 1500 - 2000 : [ 117 0.01 0.02 ]
|XXXXX 2000 - 2500 : [ 429 0.04 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 3364 0.30 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3169 0.29 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2215 0.20 0.84 ]
|XXXXXXXXXXXXXXX 4000 - 4500 : [ 1295 0.12 0.96 ]
|XXXXX 4500 - 5000 : [ 385 0.03 1.00 ]
| 5000 - 5500 : [ 10 0.00 1.00 ]
| 5500 - 6000 : [ 2 0.00 1.00 ]
| 6000 - 6500 : [ 1 0.00 1.00 ]
#...
| 8500 - 9000 : [ 1 0.00 1.00 ]
| 9000 - 9500 : [ 1 0.00 1.00 ]
| 9500 - 10000 : [ 3 0.00 1.00 ]
#...
| 13000 - 13500 : [ 1 0.00 1.00 ]
#...
| 27000 - 27500 : [ 1 0.00 1.00 ]
#...
| 30000 - 30500 : [ 5 0.00 1.00 ]
| 30500 - 31000 : [ 2 0.00 1.00 ]
| 31000 - 31500 : [ 2 0.00 1.00 ]
#...
| 32500 - 33000 : [ 1 0.00 1.00 ]
#...
| 45000 - 45500 : [ 1 0.00 1.00 ]
#...
| 64000 - 64500 : [ 1 0.00 1.00 ]
#...
| 71500 - 72000 : [ 2 0.00 1.00 ]
| 72000 - 72500 : [ 2 0.00 1.00 ]
#...
| 82000 - 82500 : [ 1 0.00 1.00 ]
| 82500 - 83000 : [ 1 0.00 1.00 ]
#...
| 105500 - 106000 : [ 1 0.00 1.00 ]
#...
| 168000 - 168500 : [ 1 0.00 1.00 ]
#...
| 170000 - 170500 : [ 1 0.00 1.00 ]
#...
| 175500 - 176000 : [ 1 0.00 1.00 ]
#...
| 194000 - 194500 : [ 1 0.00 1.00 ]
#...
| 210000 - 210500 : [ 1 0.00 1.00 ]
#...
| 231000 - 231500 : [ 1 0.00 1.00 ]
#...
| 234500 - 235000 : [ 1 0.00 1.00 ]
#...
| 255000 - 255500 : [ 1 0.00 1.00 ]
#...
| 341000 - 341500 : [ 1 0.00 1.00 ]
#...
| 343000 - 343500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACFI reads.list > grep.reads.list.ACFI
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACFI 4 500
-------------------------------------------------------------------
#Found 8131 total values totalling 49714994.0000. <6114.253351 +/- 2481.051580>
#Range: [ 146 - 147939 ]
#Most likely bin: [ 5500 - 6000 ] 3102 counts
#Median bin: [ 5500 - 6000 ] 3102 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 6 0.00 0.00 ]
#...
| 1000 - 1500 : [ 3 0.00 0.00 ]
| 1500 - 2000 : [ 5 0.00 0.00 ]
| 2000 - 2500 : [ 3 0.00 0.00 ]
| 2500 - 3000 : [ 6 0.00 0.00 ]
| 3000 - 3500 : [ 4 0.00 0.00 ]
| 3500 - 4000 : [ 7 0.00 0.00 ]
| 4000 - 4500 : [ 7 0.00 0.01 ]
|X 4500 - 5000 : [ 42 0.01 0.01 ]
|XXXXXXXXXXXXX 5000 - 5500 : [ 1008 0.12 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 3102 0.38 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2538 0.31 0.83 ]
|XXXXXXXXXXXXXXX 6500 - 7000 : [ 1186 0.15 0.97 ]
|XX 7000 - 7500 : [ 181 0.02 1.00 ]
| 7500 - 8000 : [ 4 0.00 1.00 ]
| 8000 - 8500 : [ 1 0.00 1.00 ]
#...
| 9000 - 9500 : [ 1 0.00 1.00 ]
#...
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 13500 - 14000 : [ 1 0.00 1.00 ]
#...
| 23000 - 23500 : [ 1 0.00 1.00 ]
#...
| 32500 - 33000 : [ 2 0.00 1.00 ]
| 33000 - 33500 : [ 4 0.00 1.00 ]
| 33500 - 34000 : [ 12 0.00 1.00 ]
| 34000 - 34500 : [ 3 0.00 1.00 ]
#...
| 60500 - 61000 : [ 1 0.00 1.00 ]
#...
| 96500 - 97000 : [ 1 0.00 1.00 ]
#...
| 147500 - 148000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACFK reads.list > grep.reads.list.ACFK
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACFK 4 500
-------------------------------------------------------------------
#Found 544 total values totalling 19860034.0000. <36507.415441 +/- 4749.854652>
#Range: [ 20571 - 68389 ]
#Most likely bin: [ 37000 - 37500 ] 41 counts
#Median bin: [ 36000 - 36500 ] 36 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 20500 - 21000 : [ 1 0.00 0.00 ]
#...
|X 21500 - 22000 : [ 1 0.00 0.00 ]
#...
|XXXX 24500 - 25000 : [ 4 0.01 0.01 ]
|X 25000 - 25500 : [ 1 0.00 0.01 ]
|X 25500 - 26000 : [ 1 0.00 0.01 ]
|XX 26000 - 26500 : [ 2 0.00 0.02 ]
#...
|XX 27000 - 27500 : [ 2 0.00 0.02 ]
|X 27500 - 28000 : [ 1 0.00 0.02 ]
|X 28000 - 28500 : [ 1 0.00 0.03 ]
|XX 28500 - 29000 : [ 2 0.00 0.03 ]
|XXXXX 29000 - 29500 : [ 5 0.01 0.04 ]
|XX 29500 - 30000 : [ 2 0.00 0.04 ]
|XXXX 30000 - 30500 : [ 4 0.01 0.05 ]
|XXXXX 30500 - 31000 : [ 5 0.01 0.06 ]
|XXXXXXXX 31000 - 31500 : [ 8 0.01 0.07 ]
|XXXXXXXXX 31500 - 32000 : [ 9 0.02 0.09 ]
|XXXXXXXXXXXX 32000 - 32500 : [ 12 0.02 0.11 ]
|XXXXXXXXXXXXXX 32500 - 33000 : [ 14 0.03 0.14 ]
|XXXXXXXXXXXXXXX 33000 - 33500 : [ 15 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 27 0.05 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 23 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 38 0.07 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 40 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 35 0.06 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 36 0.07 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 33 0.06 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 41 0.08 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 29 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 21 0.04 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 28 0.05 0.81 ]
|XXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 22 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 20 0.04 0.89 ]
|XXXXXXXXXXX 40000 - 40500 : [ 11 0.02 0.91 ]
|XXXXXXX 40500 - 41000 : [ 7 0.01 0.92 ]
|XXXXXXXXXX 41000 - 41500 : [ 10 0.02 0.94 ]
|XXXXXXX 41500 - 42000 : [ 7 0.01 0.95 ]
|XX 42000 - 42500 : [ 2 0.00 0.96 ]
|XXXXX 42500 - 43000 : [ 5 0.01 0.97 ]
|XXXXXX 43000 - 43500 : [ 6 0.01 0.98 ]
#...
|XXX 44000 - 44500 : [ 3 0.01 0.98 ]
|X 44500 - 45000 : [ 1 0.00 0.98 ]
|X 45000 - 45500 : [ 1 0.00 0.99 ]
|X 45500 - 46000 : [ 1 0.00 0.99 ]
#...
|X 60500 - 61000 : [ 1 0.00 0.99 ]
#...
|X 63000 - 63500 : [ 1 0.00 0.99 ]
|X 63500 - 64000 : [ 1 0.00 0.99 ]
#...
|X 66000 - 66500 : [ 1 0.00 0.99 ]
#...
|X 67000 - 67500 : [ 1 0.00 1.00 ]
#...
|XX 68000 - 68500 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# ACFI 5873 +- 1586 (n=4062)
# ACFK 35932 +- 4048 (n=252)
# ACFH 3199 +- 1149 (n=5617)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436101_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
ACFH 25632 -1 -1 98 696 24699 100 710 100 715
ACFI 21888 -1 -1 98 738 18770 99 668 100 724
ACFK 3840 -1 -1 95 674 2077 99 683 100 690
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
ACFH 12377 100 720 100 735 12322 100 699 100 696
ACFI 9656 99 664 100 729 9114 99 672 100 719
ACFK 1031 98 671 100 664 1046 99 695 100 716
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436101_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 45546 22559 90.96 cumulative total @@
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 3436101_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 45546 total values totalling 31318148.0000. <687.615773 +/- 126.260911>
#Range: [ 15 - 931 ]
#Most likely bin: [ 700 - 750 ] 13580 counts
#Median bin: [ 700 - 750 ] 13580 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 64 0.00 0.00 ]
|X 50 - 100 : [ 198 0.00 0.01 ]
|X 100 - 150 : [ 237 0.01 0.01 ]
|X 150 - 200 : [ 251 0.01 0.02 ]
|X 200 - 250 : [ 251 0.01 0.02 ]
|X 250 - 300 : [ 287 0.01 0.03 ]
|X 300 - 350 : [ 365 0.01 0.04 ]
|X 350 - 400 : [ 395 0.01 0.04 ]
|X 400 - 450 : [ 497 0.01 0.06 ]
|XX 450 - 500 : [ 654 0.01 0.07 ]
|XXX 500 - 550 : [ 980 0.02 0.09 ]
|XXXXX 550 - 600 : [ 1762 0.04 0.13 ]
|XXXXXXXXXXX 600 - 650 : [ 3803 0.08 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 8635 0.19 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 13580 0.30 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 9631 0.21 0.91 ]
|XXXXXXXXXX 800 - 850 : [ 3511 0.08 0.99 ]
|X 850 - 900 : [ 438 0.01 1.00 ]
| 900 - 950 : [ 7 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AKBN
trimt JAZZ trim 15 readlength histogram for ACFH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACFH 3436101_fasta.screen.trimQ15.SaF > reads.trim15.ACFH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACFH.rl 2 50
-------------------------------------------------------------------
#Found 24699 total values totalling 17454516.0000. <706.689178 +/- 116.853842>
#Range: [ 19 - 931 ]
#Most likely bin: [ 700 - 750 ] 6408 counts
#Median bin: [ 700 - 750 ] 6408 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 32 0.00 0.00 ]
| 50 - 100 : [ 78 0.00 0.00 ]
|X 100 - 150 : [ 86 0.00 0.01 ]
|X 150 - 200 : [ 91 0.00 0.01 ]
|X 200 - 250 : [ 83 0.00 0.01 ]
|X 250 - 300 : [ 131 0.01 0.02 ]
|X 300 - 350 : [ 143 0.01 0.03 ]
|X 350 - 400 : [ 122 0.00 0.03 ]
|X 400 - 450 : [ 158 0.01 0.04 ]
|XX 450 - 500 : [ 285 0.01 0.05 ]
|XXX 500 - 550 : [ 486 0.02 0.07 ]
|XXXXXX 550 - 600 : [ 946 0.04 0.11 ]
|XXXXXXXXXXXX 600 - 650 : [ 1932 0.08 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3959 0.16 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6408 0.26 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6277 0.25 0.86 ]
|XXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3062 0.12 0.98 ]
|XXX 850 - 900 : [ 413 0.02 1.00 ]
| 900 - 950 : [ 7 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACFI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACFI 3436101_fasta.screen.trimQ15.SaF > reads.trim15.ACFI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACFI.rl 2 50
-------------------------------------------------------------------
#Found 18770 total values totalling 12463135.0000. <663.992275 +/- 129.990027>
#Range: [ 15 - 851 ]
#Most likely bin: [ 700 - 750 ] 6752 counts
#Median bin: [ 700 - 750 ] 6752 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 26 0.00 0.00 ]
|X 50 - 100 : [ 96 0.01 0.01 ]
|X 100 - 150 : [ 126 0.01 0.01 ]
|X 150 - 200 : [ 140 0.01 0.02 ]
|X 200 - 250 : [ 153 0.01 0.03 ]
|X 250 - 300 : [ 141 0.01 0.04 ]
|X 300 - 350 : [ 205 0.01 0.05 ]
|X 350 - 400 : [ 251 0.01 0.06 ]
|XX 400 - 450 : [ 313 0.02 0.08 ]
|XX 450 - 500 : [ 333 0.02 0.10 ]
|XX 500 - 550 : [ 422 0.02 0.12 ]
|XXXX 550 - 600 : [ 705 0.04 0.16 ]
|XXXXXXXXXX 600 - 650 : [ 1669 0.09 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4358 0.23 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6752 0.36 0.84 ]
|XXXXXXXXXXXXXXXXX 750 - 800 : [ 2908 0.15 0.99 ]
|X 800 - 850 : [ 171 0.01 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACFK
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACFK 3436101_fasta.screen.trimQ15.SaF > reads.trim15.ACFK.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACFK.rl 2 50
-------------------------------------------------------------------
#Found 2077 total values totalling 1400497.0000. <674.288397 +/- 157.972277>
#Range: [ 31 - 885 ]
#Most likely bin: [ 750 - 800 ] 446 counts
#Median bin: [ 700 - 750 ] 420 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 6 0.00 0.00 ]
|XX 50 - 100 : [ 24 0.01 0.01 ]
|XX 100 - 150 : [ 25 0.01 0.03 ]
|XX 150 - 200 : [ 20 0.01 0.04 ]
|X 200 - 250 : [ 15 0.01 0.04 ]
|X 250 - 300 : [ 15 0.01 0.05 ]
|XX 300 - 350 : [ 17 0.01 0.06 ]
|XX 350 - 400 : [ 22 0.01 0.07 ]
|XX 400 - 450 : [ 26 0.01 0.08 ]
|XXX 450 - 500 : [ 36 0.02 0.10 ]
|XXXXXX 500 - 550 : [ 72 0.03 0.13 ]
|XXXXXXXXXX 550 - 600 : [ 111 0.05 0.19 ]
|XXXXXXXXXXXXXXXXXX 600 - 650 : [ 202 0.10 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 318 0.15 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 420 0.20 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 446 0.21 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 278 0.13 0.99 ]
|XX 850 - 900 : [ 24 0.01 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436101
-------------------------------------------------------------------
ACFH.000001.000100 pUC18.fa.4 pEpiFos5.fa.4 LRS.fasta
ACFH.000101.000200 pUC18.fa.4 pEpiFos5.fa.4 LRS.fasta
ACFI.000001.000100 pMCL200.fa.4 LRS.fasta
ACFI.000101.000200 pMCL200.fa.4 LRS.fasta
ACFK.000001.000100 pCC1Fos.fa.4 LRS.fasta
ACFH.000001.000100 pUC18.fa.4 pEpiFos5.fa.4 LRS.fasta
ACFH.000101.000200 pUC18.fa.4 pEpiFos5.fa.4 LRS.fasta
ACFI.000001.000100 pMCL200.fa.4 LRS.fasta
ACFI.000101.000200 pMCL200.fa.4 LRS.fasta
ACFK.000001.000100 pCC1Fos.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436101_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436101_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 45475 total values totalling 20286.4605. <0.446101 +/- 0.056031>
#Range: [ 0.1366 - 0.803 ]
#Most likely bin: [ 0.465 - 0.47 ] 2207 counts
#Median bin: [ 0.45 - 0.455 ] 1991 counts
| 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 ]
#...
| 0.18 - 0.185 : [ 2 0.00 0.00 ]
| 0.185 - 0.19 : [ 1 0.00 0.00 ]
| 0.19 - 0.195 : [ 1 0.00 0.00 ]
#...
| 0.2 - 0.205 : [ 1 0.00 0.00 ]
| 0.205 - 0.21 : [ 1 0.00 0.00 ]
| 0.21 - 0.215 : [ 2 0.00 0.00 ]
| 0.215 - 0.22 : [ 2 0.00 0.00 ]
| 0.22 - 0.225 : [ 2 0.00 0.00 ]
| 0.225 - 0.23 : [ 1 0.00 0.00 ]
| 0.23 - 0.235 : [ 2 0.00 0.00 ]
| 0.235 - 0.24 : [ 4 0.00 0.00 ]
| 0.24 - 0.245 : [ 4 0.00 0.00 ]
| 0.245 - 0.25 : [ 12 0.00 0.00 ]
| 0.25 - 0.255 : [ 24 0.00 0.00 ]
| 0.255 - 0.26 : [ 24 0.00 0.00 ]
| 0.26 - 0.265 : [ 26 0.00 0.00 ]
| 0.265 - 0.27 : [ 18 0.00 0.00 ]
|X 0.27 - 0.275 : [ 36 0.00 0.00 ]
|X 0.275 - 0.28 : [ 50 0.00 0.00 ]
|X 0.28 - 0.285 : [ 59 0.00 0.01 ]
|X 0.285 - 0.29 : [ 65 0.00 0.01 ]
|XX 0.29 - 0.295 : [ 90 0.00 0.01 ]
|XX 0.295 - 0.3 : [ 126 0.00 0.01 ]
|XX 0.3 - 0.305 : [ 137 0.00 0.02 ]
|XXX 0.305 - 0.31 : [ 138 0.00 0.02 ]
|XXX 0.31 - 0.315 : [ 169 0.00 0.02 ]
|XXXX 0.315 - 0.32 : [ 224 0.00 0.03 ]
|XXXX 0.32 - 0.325 : [ 218 0.00 0.03 ]
|XXXX 0.325 - 0.33 : [ 194 0.00 0.04 ]
|XXXXX 0.33 - 0.335 : [ 258 0.01 0.04 ]
|XXXX 0.335 - 0.34 : [ 217 0.00 0.05 ]
|XXXXX 0.34 - 0.345 : [ 254 0.01 0.05 ]
|XXXXX 0.345 - 0.35 : [ 276 0.01 0.06 ]
|XXXXX 0.35 - 0.355 : [ 294 0.01 0.06 ]
|XXXXXXX 0.355 - 0.36 : [ 394 0.01 0.07 ]
|XXXXXXX 0.36 - 0.365 : [ 381 0.01 0.08 ]
|XXXXXXXX 0.365 - 0.37 : [ 414 0.01 0.09 ]
|XXXXXXXX 0.37 - 0.375 : [ 424 0.01 0.10 ]
|XXXXXXXXXX 0.375 - 0.38 : [ 547 0.01 0.11 ]
|XXXXXXXXXXXX 0.38 - 0.385 : [ 638 0.01 0.13 ]
|XXXXXXXXXXXXX 0.385 - 0.39 : [ 696 0.02 0.14 ]
|XXXXXXXXXXXXXX 0.39 - 0.395 : [ 750 0.02 0.16 ]
|XXXXXXXXXXXXXX 0.395 - 0.4 : [ 777 0.02 0.17 ]
|XXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 951 0.02 0.20 ]
|XXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 1049 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 1135 0.02 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 1214 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 1230 0.03 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 1421 0.03 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 1479 0.03 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 1608 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 1793 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 1860 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 1991 0.04 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 2097 0.05 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 2106 0.05 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 2207 0.05 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 2041 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 1912 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 1785 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1608 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1413 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1189 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1218 0.03 0.91 ]
|XXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 926 0.02 0.93 ]
|XXXXXXXXXXXXX 0.51 - 0.515 : [ 732 0.02 0.94 ]
|XXXXXXXXXX 0.515 - 0.52 : [ 574 0.01 0.96 ]
|XXXXXXXX 0.52 - 0.525 : [ 430 0.01 0.97 ]
|XXXXX 0.525 - 0.53 : [ 297 0.01 0.97 ]
|XXXX 0.53 - 0.535 : [ 204 0.00 0.98 ]
|XX 0.535 - 0.54 : [ 135 0.00 0.98 ]
|XX 0.54 - 0.545 : [ 99 0.00 0.98 ]
|X 0.545 - 0.55 : [ 65 0.00 0.98 ]
|X 0.55 - 0.555 : [ 62 0.00 0.98 ]
|X 0.555 - 0.56 : [ 37 0.00 0.99 ]
|X 0.56 - 0.565 : [ 36 0.00 0.99 ]
| 0.565 - 0.57 : [ 23 0.00 0.99 ]
| 0.57 - 0.575 : [ 20 0.00 0.99 ]
| 0.575 - 0.58 : [ 19 0.00 0.99 ]
| 0.58 - 0.585 : [ 10 0.00 0.99 ]
| 0.585 - 0.59 : [ 14 0.00 0.99 ]
| 0.59 - 0.595 : [ 13 0.00 0.99 ]
| 0.595 - 0.6 : [ 13 0.00 0.99 ]
| 0.6 - 0.605 : [ 20 0.00 0.99 ]
| 0.605 - 0.61 : [ 16 0.00 0.99 ]
| 0.61 - 0.615 : [ 17 0.00 0.99 ]
| 0.615 - 0.62 : [ 19 0.00 0.99 ]
| 0.62 - 0.625 : [ 26 0.00 0.99 ]
| 0.625 - 0.63 : [ 27 0.00 0.99 ]
|X 0.63 - 0.635 : [ 31 0.00 0.99 ]
|X 0.635 - 0.64 : [ 29 0.00 0.99 ]
| 0.64 - 0.645 : [ 18 0.00 0.99 ]
| 0.645 - 0.65 : [ 23 0.00 0.99 ]
|X 0.65 - 0.655 : [ 30 0.00 0.99 ]
| 0.655 - 0.66 : [ 27 0.00 1.00 ]
| 0.66 - 0.665 : [ 26 0.00 1.00 ]
|X 0.665 - 0.67 : [ 30 0.00 1.00 ]
| 0.67 - 0.675 : [ 23 0.00 1.00 ]
| 0.675 - 0.68 : [ 18 0.00 1.00 ]
| 0.68 - 0.685 : [ 19 0.00 1.00 ]
| 0.685 - 0.69 : [ 18 0.00 1.00 ]
| 0.69 - 0.695 : [ 12 0.00 1.00 ]
| 0.695 - 0.7 : [ 9 0.00 1.00 ]
| 0.7 - 0.705 : [ 9 0.00 1.00 ]
| 0.705 - 0.71 : [ 12 0.00 1.00 ]
| 0.71 - 0.715 : [ 8 0.00 1.00 ]
| 0.715 - 0.72 : [ 4 0.00 1.00 ]
| 0.72 - 0.725 : [ 9 0.00 1.00 ]
| 0.725 - 0.73 : [ 7 0.00 1.00 ]
| 0.73 - 0.735 : [ 2 0.00 1.00 ]
| 0.735 - 0.74 : [ 4 0.00 1.00 ]
| 0.74 - 0.745 : [ 2 0.00 1.00 ]
| 0.745 - 0.75 : [ 3 0.00 1.00 ]
#...
| 0.765 - 0.77 : [ 1 0.00 1.00 ]
| 0.77 - 0.775 : [ 1 0.00 1.00 ]
#...
| 0.78 - 0.785 : [ 1 0.00 1.00 ]
| 0.785 - 0.79 : [ 1 0.00 1.00 ]
#...
| 0.8 - 0.805 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 11. 6 reads; 1476 bp (untrimmed), 1372 (trimmed).
Contig 12. 13 reads; 1380 bp (untrimmed), 1380 (trimmed).
Contig 13. 13 reads; 154 bp (untrimmed), 154 (trimmed).
Contig 14. 19 reads; 3433 bp (untrimmed), 3226 (trimmed).
Contig 15. 19 reads; 146 bp (untrimmed), 146 (trimmed).
Contig 16. 32 reads; 4114 bp (untrimmed), 3847 (trimmed).
Contig 17. 47 reads; 8683 bp (untrimmed), 8231 (trimmed).
Contig 18. 54 reads; 4177 bp (untrimmed), 3809 (trimmed).
Contig 19. 219 reads; 15814 bp (untrimmed), 15581 (trimmed).
Contig 20. 276 reads; 23974 bp (untrimmed), 23485 (trimmed).
Contig 21. 296 reads; 22815 bp (untrimmed), 22717 (trimmed).
Contig 22. 408 reads; 24693 bp (untrimmed), 24693 (trimmed).
Contig 23. 451 reads; 27478 bp (untrimmed), 27015 (trimmed).
Contig 24. 497 reads; 32517 bp (untrimmed), 32512 (trimmed).
Contig 25. 574 reads; 43203 bp (untrimmed), 43097 (trimmed).
Contig 26. 785 reads; 51812 bp (untrimmed), 51776 (trimmed).
Contig 27. 944 reads; 55006 bp (untrimmed), 55006 (trimmed).
Contig 28. 1151 reads; 64410 bp (untrimmed), 64410 (trimmed).
Contig 29. 1297 reads; 69175 bp (untrimmed), 69142 (trimmed).
Contig 30. 1743 reads; 107651 bp (untrimmed), 107626 (trimmed).
Contig 31. 2462 reads; 127264 bp (untrimmed), 127246 (trimmed).
Contig 32. 2888 reads; 165306 bp (untrimmed), 165306 (trimmed).
Contig 33. 3811 reads; 236793 bp (untrimmed), 236793 (trimmed).
Contig 34. 4215 reads; 250153 bp (untrimmed), 250153 (trimmed).
Contig 35. 4467 reads; 262812 bp (untrimmed), 262781 (trimmed).
Contig 36. 7995 reads; 440157 bp (untrimmed), 439736 (trimmed).
Contig 37. 10168 reads; 534041 bp (untrimmed), 534041 (trimmed).
--------------------------------------------------------------
Totals 44887 reads; 2591934 bp (untrimmed), 2585010 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2590322 bases = 16.22 +- 5.99 = 0.19 +- 5.09
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 33 total values totalling 350.4200. <10.618788 +/- 5.847640>
#Range: [ 1.28 - 18.28 ]
#Most likely bin: [ 15.5 - 16 ] 4 counts
#Median bin: [ 12.5 - 13 ] 1 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 3 0.09 0.09 ]
|XXXXXXXXXX 1.5 - 2 : [ 1 0.03 0.12 ]
|XXXXXXXXXX 2 - 2.5 : [ 1 0.03 0.15 ]
|XXXXXXXXXX 2.5 - 3 : [ 1 0.03 0.18 ]
#...
|XXXXXXXXXX 3.5 - 4 : [ 1 0.03 0.21 ]
|XXXXXXXXXX 4 - 4.5 : [ 1 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 2 0.06 0.30 ]
|XXXXXXXXXX 5 - 5.5 : [ 1 0.03 0.33 ]
#...
|XXXXXXXXXX 7.5 - 8 : [ 1 0.03 0.36 ]
#...
|XXXXXXXXXX 8.5 - 9 : [ 1 0.03 0.39 ]
#...
|XXXXXXXXXX 10.5 - 11 : [ 1 0.03 0.42 ]
#...
|XXXXXXXXXX 11.5 - 12 : [ 1 0.03 0.45 ]
|XXXXXXXXXX 12 - 12.5 : [ 1 0.03 0.48 ]
|XXXXXXXXXX 12.5 - 13 : [ 1 0.03 0.52 ]
|XXXXXXXXXX 13 - 13.5 : [ 1 0.03 0.55 ]
|XXXXXXXXXX 13.5 - 14 : [ 1 0.03 0.58 ]
|XXXXXXXXXX 14 - 14.5 : [ 1 0.03 0.61 ]
|XXXXXXXXXX 14.5 - 15 : [ 1 0.03 0.64 ]
|XXXXXXXXXXXXXXXXXXXX 15 - 15.5 : [ 2 0.06 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15.5 - 16 : [ 4 0.12 0.82 ]
|XXXXXXXXXX 16 - 16.5 : [ 1 0.03 0.85 ]
|XXXXXXXXXX 16.5 - 17 : [ 1 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXX 17 - 17.5 : [ 2 0.06 0.94 ]
|XXXXXXXXXX 17.5 - 18 : [ 1 0.03 0.97 ]
|XXXXXXXXXX 18 - 18.5 : [ 1 0.03 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 23 total values totalling 317.4700. <13.803043 +/- 3.680944>
#Range: [ 4.82 - 18.28 ]
#Most likely bin: [ 15.5 - 16 ] 4 counts
#Median bin: [ 15 - 15.5 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 2 0.09 0.09 ]
#...
|XXXXXXXXXX 7.5 - 8 : [ 1 0.04 0.13 ]
#...
|XXXXXXXXXX 10.5 - 11 : [ 1 0.04 0.17 ]
#...
|XXXXXXXXXX 11.5 - 12 : [ 1 0.04 0.22 ]
|XXXXXXXXXX 12 - 12.5 : [ 1 0.04 0.26 ]
|XXXXXXXXXX 12.5 - 13 : [ 1 0.04 0.30 ]
|XXXXXXXXXX 13 - 13.5 : [ 1 0.04 0.35 ]
|XXXXXXXXXX 13.5 - 14 : [ 1 0.04 0.39 ]
|XXXXXXXXXX 14 - 14.5 : [ 1 0.04 0.43 ]
|XXXXXXXXXX 14.5 - 15 : [ 1 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXX 15 - 15.5 : [ 2 0.09 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15.5 - 16 : [ 4 0.17 0.74 ]
|XXXXXXXXXX 16 - 16.5 : [ 1 0.04 0.78 ]
|XXXXXXXXXX 16.5 - 17 : [ 1 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXX 17 - 17.5 : [ 2 0.09 0.91 ]
|XXXXXXXXXX 17.5 - 18 : [ 1 0.04 0.96 ]
|XXXXXXXXXX 18 - 18.5 : [ 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 2 2 reads 1649 bases = 1.28 +- 0.45 = -0.01 +- 0.85
Contig 4 3 reads 1108 bases = 1.45 +- 0.81 = -0.49 +- 0.92
Contig 5 3 reads 1626 bases = 1.48 +- 0.50 = 1.02 +- 0.69
Contig 6 4 reads 2172 bases = 1.93 +- 0.61 = 0.87 +- 1.36
Contig 8 5 reads 1841 bases = 2.25 +- 0.63 = 2.25 +- 0.63
Contig 3 3 reads 1091 bases = 2.78 +- 0.44 = 2.78 +- 0.44
Contig 11 6 reads 1476 bases = 3.83 +- 1.68 = 1.19 +- 0.99
Contig 9 6 reads 1386 bases = 4.26 +- 1.98 = -0.25 +- 0.69
Contig 14 19 reads 3433 bases = 4.82 +- 3.37 = 4.82 +- 3.37
Contig 17 47 reads 8683 bases = 4.82 +- 2.06 = 0.21 +- 3.95
Contig 10 6 reads 1112 bases = 5.00 +- 1.32 = 5.00 +- 1.32
Contig 16 32 reads 4114 bases = 7.61 +- 2.94 = 2.83 +- 3.58
Contig 12 13 reads 1380 bases = 8.69 +- 3.26 = 1.82 +- 1.26
Contig 20 276 reads 23974 bases = 10.93 +- 4.93 = 0.48 +- 4.16
Contig 18 54 reads 4177 bases = 11.54 +- 14.95 = 11.54 +- 14.95
Contig 21 296 reads 22815 bases = 12.14 +- 3.67 = 0.65 +- 5.89
Contig 25 574 reads 43203 bases = 12.55 +- 4.73 = -0.16 +- 4.37
Contig 19 219 reads 15814 bases = 13.27 +- 5.13 = 0.66 +- 4.52
Contig 26 785 reads 51812 bases = 13.96 +- 5.62 = 0.34 +- 4.76
Contig 24 497 reads 32517 bases = 14.36 +- 4.31 = -0.06 +- 5.38
Contig 20 276 reads 23974 bases = 10.93 +- 4.93 = 0.48 +- 4.16
Contig 18 54 reads 4177 bases = 11.54 +- 14.95 = 11.54 +- 14.95
Contig 21 296 reads 22815 bases = 12.14 +- 3.67 = 0.65 +- 5.89
Contig 25 574 reads 43203 bases = 12.55 +- 4.73 = -0.16 +- 4.37
Contig 19 219 reads 15814 bases = 13.27 +- 5.13 = 0.66 +- 4.52
Contig 26 785 reads 51812 bases = 13.96 +- 5.62 = 0.34 +- 4.76
Contig 24 497 reads 32517 bases = 14.36 +- 4.31 = -0.06 +- 5.38
Contig 23 451 reads 27478 bases = 14.80 +- 7.23 = -0.09 +- 4.88
Contig 33 3811 reads 236793 bases = 15.05 +- 5.33 = -0.01 +- 4.68
Contig 30 1743 reads 107651 bases = 15.06 +- 5.22 = 0.22 +- 4.74
Contig 22 408 reads 24693 bases = 15.53 +- 4.16 = 0.57 +- 4.20
Contig 27 944 reads 55006 bases = 15.79 +- 6.44 = 0.27 +- 5.26
Contig 34 4215 reads 250153 bases = 15.83 +- 5.27 = -0.01 +- 5.10
Contig 35 4467 reads 262812 bases = 15.90 +- 5.00 = 0.24 +- 4.92
Contig 32 2888 reads 165306 bases = 16.44 +- 5.17 = 0.23 +- 4.85
Contig 28 1151 reads 64410 bases = 16.56 +- 4.68 = 0.48 +- 4.39
Contig 36 7995 reads 440157 bases = 17.04 +- 5.51 = 0.07 +- 5.06
Contig 29 1297 reads 69175 bases = 17.31 +- 5.61 = 0.04 +- 5.00
Contig 37 10168 reads 534041 bases = 17.88 +- 5.85 = 0.14 +- 5.43
Contig 31 2462 reads 127264 bases = 18.28 +- 9.16 = 0.53 +- 5.50
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 840
HQ Discrepant reads = 34
Chimeric reads = 55
Suspect alignments = 129
-------------------------------------------------------------------
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/microbe4/3436101/edit_dir.18Nov03.QD