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: 12-12-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634499 4500 50422 Shewanella sp.
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Shewanella_sp.
-------------------------------------------------------------------
Shewanellaceae, family, g-proteobacteria
Alteromonadales, order, g-proteobacteria
Shewanella sp., species, g-proteobacteria
Shewanella, genus, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4543111
# phrap: 4244822
# db:
altered.
4500000
4429311 +/- 131635
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 15285
Number of reads with percent X's >= 20%: 512 = 0.8%
Number of reads with percent X's >= 50%: 216 = 0.3%
Number of reads with percent X's >= 80%: 21 = 0.0%
Total reads in project: 63751
Total bp X'd : 782204
reads >= 20% >= 50% >= 80% screened
Nr with L09136 13713 264 99 12
Nr with pCC1Fos 1161 2 1 0
Nr with pMCL200_JGI_XZX+XZK 411 246 116 9
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 13978919
C = 16159640
G = 16122147
T = 13551441
N = 259681
X = 782204
GC fraction = 0.53
Total = 60854032
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634499_fasta.screen.contigs
-------------------------------------------------------------------
A 1074905
C 1260353
G 1191072
T 1038140
N 838
fraction GC = 0.54
total bases = 4565308
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 AICA reads.list > grep.reads.list.AICA
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICA 4 500
-------------------------------------------------------------------
#Found 13507 total values totalling 43753398.0000. <3239.312801 +/- 2756.807784>
#Range: [ 451 - 310225 ]
#Most likely bin: [ 3000 - 3500 ] 7033 counts
#Median bin: [ 3000 - 3500 ] 7033 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
| 500 - 1000 : [ 19 0.00 0.00 ]
|X 1000 - 1500 : [ 218 0.02 0.02 ]
|XX 1500 - 2000 : [ 355 0.03 0.04 ]
|XXXX 2000 - 2500 : [ 647 0.05 0.09 ]
|XXXXXXXXX 2500 - 3000 : [ 1533 0.11 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 7033 0.52 0.73 ]
|XXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3313 0.25 0.97 ]
|XX 4000 - 4500 : [ 385 0.03 1.00 ]
#...
| 29000 - 29500 : [ 1 0.00 1.00 ]
#...
| 65500 - 66000 : [ 1 0.00 1.00 ]
#...
| 310000 - 310500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICB reads.list > grep.reads.list.AICB
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICB 4 500
-------------------------------------------------------------------
#Found 11040 total values totalling 68213883.0000. <6178.793750 +/- 1853.046441>
#Range: [ 642 - 96115 ]
#Most likely bin: [ 6000 - 6500 ] 2782 counts
#Median bin: [ 6000 - 6500 ] 2782 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 19 0.00 0.00 ]
|XX 1000 - 1500 : [ 131 0.01 0.01 ]
|XX 1500 - 2000 : [ 120 0.01 0.02 ]
|XX 2000 - 2500 : [ 137 0.01 0.04 ]
|XX 2500 - 3000 : [ 121 0.01 0.05 ]
|XX 3000 - 3500 : [ 114 0.01 0.06 ]
|XX 3500 - 4000 : [ 109 0.01 0.07 ]
|XXX 4000 - 4500 : [ 180 0.02 0.08 ]
|XXXX 4500 - 5000 : [ 252 0.02 0.11 ]
|XXXXXXX 5000 - 5500 : [ 500 0.05 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1810 0.16 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2782 0.25 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2356 0.21 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1687 0.15 0.93 ]
|XXXXXXXXXX 7500 - 8000 : [ 678 0.06 1.00 ]
|X 8000 - 8500 : [ 39 0.00 1.00 ]
#...
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 28000 - 28500 : [ 1 0.00 1.00 ]
#...
| 70500 - 71000 : [ 1 0.00 1.00 ]
#...
| 93000 - 93500 : [ 1 0.00 1.00 ]
#...
| 96000 - 96500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICC reads.list > grep.reads.list.AICC
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICC 4 500
-------------------------------------------------------------------
#Found 1093 total values totalling 41860892.0000. <38299.077768 +/- 3915.672003>
#Range: [ 24746 - 47425 ]
#Most likely bin: [ 38000 - 38500 ] 64 counts
#Median bin: [ 38000 - 38500 ] 64 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 24500 - 25000 : [ 1 0.00 0.00 ]
#...
|X 26500 - 27000 : [ 2 0.00 0.00 ]
#...
|X 28500 - 29000 : [ 2 0.00 0.00 ]
|X 29000 - 29500 : [ 2 0.00 0.01 ]
|XX 29500 - 30000 : [ 4 0.00 0.01 ]
|XX 30000 - 30500 : [ 4 0.00 0.01 ]
|XXXX 30500 - 31000 : [ 7 0.01 0.02 ]
|XXXXXX 31000 - 31500 : [ 10 0.01 0.03 ]
|XXXXXXXXX 31500 - 32000 : [ 14 0.01 0.04 ]
|XXXXXXXXXXXXXXXX 32000 - 32500 : [ 26 0.02 0.07 ]
|XXXXXXXXXXXXX 32500 - 33000 : [ 21 0.02 0.09 ]
|XXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 31 0.03 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 35 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 39 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 53 0.05 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 43 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 49 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 48 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 37 0.03 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 49 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 33 0.03 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 64 0.06 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 40 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 59 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 40 0.04 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 37 0.03 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 50 0.05 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 52 0.05 0.78 ]
|XXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 30 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 34 0.03 0.84 ]
|XXXXXXXXXXXXXXXX 42500 - 43000 : [ 25 0.02 0.86 ]
|XXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 32 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 29 0.03 0.92 ]
|XXXXXXXXXXXX 44000 - 44500 : [ 20 0.02 0.94 ]
|XXXXXXXXXXXXXX 44500 - 45000 : [ 23 0.02 0.96 ]
|XXXXXXXXX 45000 - 45500 : [ 15 0.01 0.97 ]
|XXXXXXXXXXX 45500 - 46000 : [ 17 0.02 0.99 ]
|XXXXX 46000 - 46500 : [ 8 0.01 0.99 ]
|XXXX 46500 - 47000 : [ 6 0.01 1.00 ]
|X 47000 - 47500 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AICC 38195 +- 3811 (n=549)
# AICA 3081 +- 606 (n=6934)
# AICB 5966 +- 1463 (n=5703)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634499_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
AICA 34656 -1 -1 92 656 31193 99 691 100 699
AICB 34944 -1 -1 91 627 28321 97 613 100 620
AICC 4608 -1 -1 94 573 4237 96 602 100 619
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AICA 15756 99 688 100 705 15437 99 694 100 693
AICB 13349 96 597 100 601 14972 99 627 100 637
AICC 2154 98 625 100 639 2083 95 577 100 599
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634499_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
24 4237 2212 92.17 96.01 AICC @
180 31193 16535 91.86 95.69 AICA @
176 28321 15370 87.33 90.97 AICB @
] 63751 34117 89.78 cumulative total@@
LIBRARY PLATE ID COUNT [ AICC 24 AICA 180 AICB 176 ] for 380 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 3634499_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 63751 total values totalling 40769881.0000. <639.517513 +/- 196.737086>
#Range: [ 17 - 915 ]
#Most likely bin: [ 750 - 800 ] 12958 counts
#Median bin: [ 700 - 750 ] 9832 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 264 0.00 0.00 ]
|XXX 50 - 100 : [ 976 0.02 0.02 ]
|XXXX 100 - 150 : [ 1141 0.02 0.04 ]
|XXXX 150 - 200 : [ 1135 0.02 0.06 ]
|XXXX 200 - 250 : [ 1211 0.02 0.07 ]
|XXXX 250 - 300 : [ 1337 0.02 0.10 ]
|XXXX 300 - 350 : [ 1432 0.02 0.12 ]
|XXXXX 350 - 400 : [ 1469 0.02 0.14 ]
|XXXXX 400 - 450 : [ 1640 0.03 0.17 ]
|XXXXXX 450 - 500 : [ 1930 0.03 0.20 ]
|XXXXXXX 500 - 550 : [ 2410 0.04 0.23 ]
|XXXXXXXXXXX 550 - 600 : [ 3408 0.05 0.29 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 4908 0.08 0.36 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 6929 0.11 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 9832 0.15 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 12958 0.20 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 9190 0.14 0.98 ]
|XXXXX 850 - 900 : [ 1562 0.02 1.00 ]
| 900 - 950 : [ 19 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICA
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICA 3634499_fasta.screen.trimQ15.SaF > reads.trim15.AICA.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICA.rl 2 50
-------------------------------------------------------------------
#Found 31193 total values totalling 21347315.0000. <684.362357 +/- 177.305369>
#Range: [ 24 - 915 ]
#Most likely bin: [ 750 - 800 ] 7552 counts
#Median bin: [ 700 - 750 ] 4924 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 57 0.00 0.00 ]
|X 50 - 100 : [ 281 0.01 0.01 ]
|XX 100 - 150 : [ 386 0.01 0.02 ]
|XX 150 - 200 : [ 391 0.01 0.04 ]
|XX 200 - 250 : [ 466 0.01 0.05 ]
|XX 250 - 300 : [ 468 0.02 0.07 ]
|XXX 300 - 350 : [ 496 0.02 0.08 ]
|XXX 350 - 400 : [ 496 0.02 0.10 ]
|XXX 400 - 450 : [ 557 0.02 0.12 ]
|XXX 450 - 500 : [ 625 0.02 0.14 ]
|XXXX 500 - 550 : [ 771 0.02 0.16 ]
|XXXXXX 550 - 600 : [ 1156 0.04 0.20 ]
|XXXXXXXXXX 600 - 650 : [ 1845 0.06 0.26 ]
|XXXXXXXXXXXXXXXX 650 - 700 : [ 2986 0.10 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4924 0.16 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 7552 0.24 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6434 0.21 0.96 ]
|XXXXXXX 850 - 900 : [ 1285 0.04 1.00 ]
| 900 - 950 : [ 17 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICB
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICB 3634499_fasta.screen.trimQ15.SaF > reads.trim15.AICB.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICB.rl 2 50
-------------------------------------------------------------------
#Found 28321 total values totalling 16960754.0000. <598.875534 +/- 205.804202>
#Range: [ 21 - 909 ]
#Most likely bin: [ 750 - 800 ] 4881 counts
#Median bin: [ 650 - 700 ] 3206 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 155 0.01 0.01 ]
|XXXXX 50 - 100 : [ 586 0.02 0.03 ]
|XXXXXX 100 - 150 : [ 683 0.02 0.05 ]
|XXXXXX 150 - 200 : [ 690 0.02 0.07 ]
|XXXXXX 200 - 250 : [ 673 0.02 0.10 ]
|XXXXXX 250 - 300 : [ 695 0.02 0.12 ]
|XXXXXX 300 - 350 : [ 753 0.03 0.15 ]
|XXXXXXX 350 - 400 : [ 867 0.03 0.18 ]
|XXXXXXXX 400 - 450 : [ 984 0.03 0.21 ]
|XXXXXXXXX 450 - 500 : [ 1158 0.04 0.26 ]
|XXXXXXXXXXXX 500 - 550 : [ 1415 0.05 0.31 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 1939 0.07 0.37 ]
|XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2561 0.09 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3206 0.11 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4167 0.15 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4881 0.17 0.90 ]
|XXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2635 0.09 0.99 ]
|XX 850 - 900 : [ 271 0.01 1.00 ]
| 900 - 950 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICC
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICC 3634499_fasta.screen.trimQ15.SaF > reads.trim15.AICC.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICC.rl 2 50
-------------------------------------------------------------------
#Found 4237 total values totalling 2461812.0000. <581.027142 +/- 196.343873>
#Range: [ 17 - 897 ]
#Most likely bin: [ 700 - 750 ] 741 counts
#Median bin: [ 650 - 700 ] 737 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 0 - 50 : [ 52 0.01 0.01 ]
|XXXXXX 50 - 100 : [ 109 0.03 0.04 ]
|XXXX 100 - 150 : [ 72 0.02 0.05 ]
|XXX 150 - 200 : [ 54 0.01 0.07 ]
|XXXX 200 - 250 : [ 72 0.02 0.08 ]
|XXXXXXXXX 250 - 300 : [ 174 0.04 0.13 ]
|XXXXXXXXXX 300 - 350 : [ 183 0.04 0.17 ]
|XXXXXX 350 - 400 : [ 106 0.03 0.19 ]
|XXXXX 400 - 450 : [ 99 0.02 0.22 ]
|XXXXXXXX 450 - 500 : [ 147 0.03 0.25 ]
|XXXXXXXXXXXX 500 - 550 : [ 224 0.05 0.30 ]
|XXXXXXXXXXXXXXXXX 550 - 600 : [ 313 0.07 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 502 0.12 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 737 0.17 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 741 0.17 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 525 0.12 0.97 ]
|XXXXXXX 800 - 850 : [ 121 0.03 1.00 ]
| 850 - 900 : [ 6 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ASYF
trimt JAZZ trim 15 readlength histogram for ASWW
trimt JAZZ trim 15 readlength histogram for BBBI
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634499
-------------------------------------------------------------------
AICA.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AICA.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AICB.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AICB.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AICC.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
ASWW.002001.002100
AICA.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AICA.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AICB.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AICB.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AICC.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
ASWW.002001.002100
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634499_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634499_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 63431 total values totalling 34218.4116. <0.539459 +/- 0.058501>
#Range: [ 0.0455 - 0.84 ]
#Most likely bin: [ 0.57 - 0.575 ] 2865 counts
#Median bin: [ 0.55 - 0.555 ] 2494 counts
| 0.045 - 0.05 : [ 1 0.00 0.00 ]
#...
| 0.145 - 0.15 : [ 1 0.00 0.00 ]
#...
| 0.18 - 0.185 : [ 1 0.00 0.00 ]
#...
| 0.205 - 0.21 : [ 1 0.00 0.00 ]
#...
| 0.215 - 0.22 : [ 2 0.00 0.00 ]
| 0.22 - 0.225 : [ 1 0.00 0.00 ]
| 0.225 - 0.23 : [ 1 0.00 0.00 ]
| 0.23 - 0.235 : [ 1 0.00 0.00 ]
#...
| 0.24 - 0.245 : [ 4 0.00 0.00 ]
| 0.245 - 0.25 : [ 3 0.00 0.00 ]
| 0.25 - 0.255 : [ 4 0.00 0.00 ]
| 0.255 - 0.26 : [ 5 0.00 0.00 ]
| 0.26 - 0.265 : [ 2 0.00 0.00 ]
| 0.265 - 0.27 : [ 4 0.00 0.00 ]
| 0.27 - 0.275 : [ 4 0.00 0.00 ]
| 0.275 - 0.28 : [ 1 0.00 0.00 ]
| 0.28 - 0.285 : [ 2 0.00 0.00 ]
| 0.285 - 0.29 : [ 3 0.00 0.00 ]
| 0.29 - 0.295 : [ 6 0.00 0.00 ]
| 0.295 - 0.3 : [ 12 0.00 0.00 ]
| 0.3 - 0.305 : [ 13 0.00 0.00 ]
| 0.305 - 0.31 : [ 19 0.00 0.00 ]
| 0.31 - 0.315 : [ 20 0.00 0.00 ]
| 0.315 - 0.32 : [ 15 0.00 0.00 ]
| 0.32 - 0.325 : [ 22 0.00 0.00 ]
| 0.325 - 0.33 : [ 30 0.00 0.00 ]
|X 0.33 - 0.335 : [ 59 0.00 0.00 ]
|X 0.335 - 0.34 : [ 43 0.00 0.00 ]
|X 0.34 - 0.345 : [ 66 0.00 0.01 ]
|X 0.345 - 0.35 : [ 71 0.00 0.01 ]
|X 0.35 - 0.355 : [ 65 0.00 0.01 ]
|X 0.355 - 0.36 : [ 83 0.00 0.01 ]
|X 0.36 - 0.365 : [ 87 0.00 0.01 ]
|XX 0.365 - 0.37 : [ 113 0.00 0.01 ]
|XX 0.37 - 0.375 : [ 152 0.00 0.01 ]
|XX 0.375 - 0.38 : [ 150 0.00 0.02 ]
|XX 0.38 - 0.385 : [ 153 0.00 0.02 ]
|XX 0.385 - 0.39 : [ 170 0.00 0.02 ]
|XXX 0.39 - 0.395 : [ 189 0.00 0.02 ]
|XXX 0.395 - 0.4 : [ 189 0.00 0.03 ]
|XXXX 0.4 - 0.405 : [ 267 0.00 0.03 ]
|XXXX 0.405 - 0.41 : [ 265 0.00 0.04 ]
|XXXX 0.41 - 0.415 : [ 307 0.00 0.04 ]
|XXXX 0.415 - 0.42 : [ 299 0.00 0.05 ]
|XXXXX 0.42 - 0.425 : [ 359 0.01 0.05 ]
|XXXXX 0.425 - 0.43 : [ 373 0.01 0.06 ]
|XXXXX 0.43 - 0.435 : [ 391 0.01 0.06 ]
|XXXXXX 0.435 - 0.44 : [ 404 0.01 0.07 ]
|XXXXXXX 0.44 - 0.445 : [ 477 0.01 0.08 ]
|XXXXXXX 0.445 - 0.45 : [ 481 0.01 0.08 ]
|XXXXXXXX 0.45 - 0.455 : [ 567 0.01 0.09 ]
|XXXXXXXX 0.455 - 0.46 : [ 571 0.01 0.10 ]
|XXXXXXXXX 0.46 - 0.465 : [ 658 0.01 0.11 ]
|XXXXXXXXX 0.465 - 0.47 : [ 666 0.01 0.12 ]
|XXXXXXXXXX 0.47 - 0.475 : [ 744 0.01 0.14 ]
|XXXXXXXXXXX 0.475 - 0.48 : [ 778 0.01 0.15 ]
|XXXXXXXXXXXXX 0.48 - 0.485 : [ 957 0.02 0.16 ]
|XXXXXXXXXXXXX 0.485 - 0.49 : [ 933 0.01 0.18 ]
|XXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1051 0.02 0.19 ]
|XXXXXXXXXXXXXX 0.495 - 0.5 : [ 991 0.02 0.21 ]
|XXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1411 0.02 0.23 ]
|XXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1298 0.02 0.25 ]
|XXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1381 0.02 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1608 0.03 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1739 0.03 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1875 0.03 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1942 0.03 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 2107 0.03 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 2251 0.04 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 2231 0.04 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 2494 0.04 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 2554 0.04 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 2741 0.04 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 2772 0.04 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 2865 0.05 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 2768 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 2639 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 2405 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 2212 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 1835 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1764 0.03 0.92 ]
|XXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1330 0.02 0.94 ]
|XXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1083 0.02 0.96 ]
|XXXXXXXXXXX 0.615 - 0.62 : [ 775 0.01 0.97 ]
|XXXXXXXX 0.62 - 0.625 : [ 549 0.01 0.98 ]
|XXXXXX 0.625 - 0.63 : [ 430 0.01 0.98 ]
|XXXXX 0.63 - 0.635 : [ 332 0.01 0.99 ]
|XX 0.635 - 0.64 : [ 177 0.00 0.99 ]
|XX 0.64 - 0.645 : [ 160 0.00 0.99 ]
|X 0.645 - 0.65 : [ 94 0.00 1.00 ]
|X 0.65 - 0.655 : [ 76 0.00 1.00 ]
|X 0.655 - 0.66 : [ 39 0.00 1.00 ]
| 0.66 - 0.665 : [ 32 0.00 1.00 ]
| 0.665 - 0.67 : [ 34 0.00 1.00 ]
| 0.67 - 0.675 : [ 22 0.00 1.00 ]
| 0.675 - 0.68 : [ 14 0.00 1.00 ]
| 0.68 - 0.685 : [ 21 0.00 1.00 ]
| 0.685 - 0.69 : [ 13 0.00 1.00 ]
| 0.69 - 0.695 : [ 8 0.00 1.00 ]
| 0.695 - 0.7 : [ 4 0.00 1.00 ]
| 0.7 - 0.705 : [ 3 0.00 1.00 ]
| 0.705 - 0.71 : [ 6 0.00 1.00 ]
| 0.71 - 0.715 : [ 3 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 : [ 6 0.00 1.00 ]
| 0.73 - 0.735 : [ 3 0.00 1.00 ]
| 0.735 - 0.74 : [ 1 0.00 1.00 ]
| 0.74 - 0.745 : [ 2 0.00 1.00 ]
#...
| 0.75 - 0.755 : [ 2 0.00 1.00 ]
#...
| 0.76 - 0.765 : [ 3 0.00 1.00 ]
#...
| 0.775 - 0.78 : [ 2 0.00 1.00 ]
| 0.78 - 0.785 : [ 1 0.00 1.00 ]
#...
| 0.8 - 0.805 : [ 1 0.00 1.00 ]
#...
| 0.815 - 0.82 : [ 1 0.00 1.00 ]
#...
| 0.83 - 0.835 : [ 1 0.00 1.00 ]
#...
| 0.84 - 0.845 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 131. 707 reads; 74540 bp (untrimmed), 73966 (trimmed).
Contig 132. 734 reads; 40104 bp (untrimmed), 40077 (trimmed).
Contig 133. 810 reads; 56229 bp (untrimmed), 56110 (trimmed).
Contig 134. 839 reads; 51090 bp (untrimmed), 50741 (trimmed).
Contig 135. 865 reads; 64669 bp (untrimmed), 64403 (trimmed).
Contig 136. 884 reads; 59351 bp (untrimmed), 59045 (trimmed).
Contig 137. 907 reads; 62215 bp (untrimmed), 62056 (trimmed).
Contig 138. 964 reads; 69006 bp (untrimmed), 68983 (trimmed).
Contig 139. 1114 reads; 80618 bp (untrimmed), 80528 (trimmed).
Contig 140. 1141 reads; 77872 bp (untrimmed), 77487 (trimmed).
Contig 141. 1244 reads; 75249 bp (untrimmed), 75210 (trimmed).
Contig 142. 1311 reads; 79500 bp (untrimmed), 79270 (trimmed).
Contig 143. 1328 reads; 73350 bp (untrimmed), 73120 (trimmed).
Contig 144. 1338 reads; 93589 bp (untrimmed), 93401 (trimmed).
Contig 145. 1356 reads; 86779 bp (untrimmed), 86730 (trimmed).
Contig 146. 1418 reads; 96401 bp (untrimmed), 96318 (trimmed).
Contig 147. 1805 reads; 138045 bp (untrimmed), 138002 (trimmed).
Contig 148. 1941 reads; 118454 bp (untrimmed), 118352 (trimmed).
Contig 149. 2045 reads; 119103 bp (untrimmed), 119077 (trimmed).
Contig 150. 2414 reads; 135199 bp (untrimmed), 134995 (trimmed).
Contig 151. 2613 reads; 165612 bp (untrimmed), 165474 (trimmed).
Contig 152. 2715 reads; 178999 bp (untrimmed), 178832 (trimmed).
Contig 153. 2821 reads; 180310 bp (untrimmed), 180212 (trimmed).
Contig 154. 2832 reads; 167455 bp (untrimmed), 167347 (trimmed).
Contig 155. 3008 reads; 203969 bp (untrimmed), 203829 (trimmed).
Contig 156. 3213 reads; 185250 bp (untrimmed), 185214 (trimmed).
Contig 157. 6108 reads; 375956 bp (untrimmed), 375956 (trimmed).
--------------------------------------------------------------
Totals 63701 reads; 4565308 bp (untrimmed), 4543111 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4558771 bases = 12.11 +- 5.77 = 0.31 +- 4.87
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 146 total values totalling 1076.8900. <7.375959 +/- 4.397277>
#Range: [ 1.19 - 16.50 ]
#Most likely bin: [ 1.5 - 2 ] 12 counts
#Median bin: [ 7 - 7.5 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 1 - 1.5 : [ 3 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 12 0.08 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 8 0.05 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 12 0.08 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 9 0.06 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 7 0.05 0.35 ]
|XXXXXXXXXXXXX 4 - 4.5 : [ 4 0.03 0.38 ]
|XXXXXXXXXXXXX 4.5 - 5 : [ 4 0.03 0.40 ]
|XXXXXXXXXX 5 - 5.5 : [ 3 0.02 0.42 ]
|XXX 5.5 - 6 : [ 1 0.01 0.43 ]
|XXXXXXXXXXXXX 6 - 6.5 : [ 4 0.03 0.46 ]
|XXXXXXXXXXXXX 6.5 - 7 : [ 4 0.03 0.49 ]
|XXXXXXXXXX 7 - 7.5 : [ 3 0.02 0.51 ]
|XXXXXXXXXXXXXXXXX 7.5 - 8 : [ 5 0.03 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 7 0.05 0.59 ]
|XXX 8.5 - 9 : [ 1 0.01 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 9 0.06 0.66 ]
|XXXXXXXXXX 9.5 - 10 : [ 3 0.02 0.68 ]
|XXXXXXXXXXXXXXXXX 10 - 10.5 : [ 5 0.03 0.71 ]
|XXXXXXXXXX 10.5 - 11 : [ 3 0.02 0.73 ]
|XXXXXXXXXXXXXXXXX 11 - 11.5 : [ 5 0.03 0.77 ]
|XXXXXXXXXX 11.5 - 12 : [ 3 0.02 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 7 0.05 0.84 ]
|XXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 6 0.04 0.88 ]
|XXX 13 - 13.5 : [ 1 0.01 0.88 ]
|XXXXXXXXXXXXX 13.5 - 14 : [ 4 0.03 0.91 ]
|XXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 6 0.04 0.95 ]
|XXXXXXX 14.5 - 15 : [ 2 0.01 0.97 ]
|XXX 15 - 15.5 : [ 1 0.01 0.97 ]
|XXXXXXXXXX 15.5 - 16 : [ 3 0.02 0.99 ]
#...
|XXX 16.5 - 17 : [ 1 0.01 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 102 total values totalling 966.3900. <9.474412 +/- 3.575712>
#Range: [ 2.59 - 16.50 ]
#Most likely bin: [ 9 - 9.5 ] 9 counts
#Median bin: [ 9 - 9.5 ] 9 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 2.5 - 3 : [ 2 0.02 0.02 ]
|XXXXXXXXXXXXX 3 - 3.5 : [ 3 0.03 0.05 ]
|XXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 4 0.04 0.09 ]
|XXXXXXXXXXXXX 4 - 4.5 : [ 3 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 4 0.04 0.16 ]
|XXXXXXXXX 5 - 5.5 : [ 2 0.02 0.18 ]
|XXXX 5.5 - 6 : [ 1 0.01 0.19 ]
|XXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 4 0.04 0.23 ]
|XXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 4 0.04 0.26 ]
|XXXXXXXXXXXXX 7 - 7.5 : [ 3 0.03 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 5 0.05 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 7 0.07 0.41 ]
|XXXX 8.5 - 9 : [ 1 0.01 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 9 0.09 0.51 ]
|XXXXXXXXXXXXX 9.5 - 10 : [ 3 0.03 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 5 0.05 0.59 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 3 0.03 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 5 0.05 0.67 ]
|XXXXXXXXXXXXX 11.5 - 12 : [ 3 0.03 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 7 0.07 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 6 0.06 0.82 ]
|XXXX 13 - 13.5 : [ 1 0.01 0.83 ]
|XXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 4 0.04 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 6 0.06 0.93 ]
|XXXXXXXXX 14.5 - 15 : [ 2 0.02 0.95 ]
|XXXX 15 - 15.5 : [ 1 0.01 0.96 ]
|XXXXXXXXXXXXX 15.5 - 16 : [ 3 0.03 0.99 ]
#...
|XXXX 16.5 - 17 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 18 2 reads 1545 bases = 1.19 +- 0.39 = -0.16 +- 0.88
Contig 15 2 reads 1070 bases = 1.35 +- 0.48 = 1.35 +- 0.48
Contig 27 3 reads 1873 bases = 1.43 +- 0.50 = 0.44 +- 0.61
Contig 9 2 reads 1157 bases = 1.62 +- 0.49 = 1.62 +- 0.49
Contig 13 2 reads 921 bases = 1.68 +- 0.47 = -0.32 +- 0.47
Contig 20 2 reads 1091 bases = 1.69 +- 0.46 = 0.01 +- 0.56
Contig 19 2 reads 858 bases = 1.71 +- 0.45 = -0.21 +- 0.49
Contig 22 2 reads 1055 bases = 1.72 +- 0.45 = 0.06 +- 0.52
Contig 11 2 reads 750 bases = 1.73 +- 0.44 = 1.73 +- 0.44
Contig 12 2 reads 1071 bases = 1.74 +- 0.44 = 0.14 +- 0.49
Contig 26 3 reads 1522 bases = 1.79 +- 0.74 = 0.58 +- 0.99
Contig 7 2 reads 652 bases = 1.87 +- 0.34 = -0.02 +- 0.36
Contig 17 2 reads 735 bases = 1.94 +- 0.24 = -0.00 +- 0.24
Contig 16 2 reads 730 bases = 1.97 +- 0.16 = -0.03 +- 0.16
Contig 32 4 reads 1621 bases = 1.98 +- 1.03 = 1.98 +- 1.03
Contig 28 3 reads 1367 bases = 2.01 +- 0.73 = 0.83 +- 1.17
Contig 30 4 reads 1585 bases = 2.20 +- 1.06 = 2.20 +- 1.06
Contig 25 3 reads 1203 bases = 2.23 +- 0.84 = 2.23 +- 0.84
Contig 37 5 reads 2046 bases = 2.24 +- 1.10 = 1.41 +- 0.49
Contig 40 6 reads 2280 bases = 2.34 +- 0.79 = 0.76 +- 0.51
Contig 155 3008 reads 203969 bases = 12.84 +- 5.10 = 0.13 +- 5.16
Contig 121 455 reads 30313 bases = 12.98 +- 3.86 = 0.74 +- 4.57
Contig 152 2715 reads 178999 bases = 13.20 +- 6.64 = -0.03 +- 5.20
Contig 153 2821 reads 180310 bases = 13.57 +- 5.07 = 0.05 +- 5.12
Contig 151 2613 reads 165612 bases = 13.70 +- 5.19 = 0.16 +- 4.73
Contig 145 1356 reads 86779 bases = 13.71 +- 4.99 = 0.44 +- 4.60
Contig 122 503 reads 31283 bases = 13.92 +- 5.65 = 0.38 +- 4.75
Contig 157 6108 reads 375956 bases = 14.00 +- 5.04 = 0.05 +- 4.88
Contig 102 224 reads 13985 bases = 14.01 +- 8.25 = 2.09 +- 4.03
Contig 134 839 reads 51090 bases = 14.20 +- 5.43 = 0.20 +- 5.31
Contig 148 1941 reads 118454 bases = 14.22 +- 4.95 = 0.05 +- 5.21
Contig 142 1311 reads 79500 bases = 14.29 +- 5.32 = 0.32 +- 4.62
Contig 141 1244 reads 75249 bases = 14.46 +- 5.02 = 0.20 +- 4.97
Contig 154 2832 reads 167455 bases = 14.64 +- 4.87 = 0.14 +- 4.79
Contig 149 2045 reads 119103 bases = 14.74 +- 5.62 = 0.22 +- 4.89
Contig 156 3213 reads 185250 bases = 15.10 +- 4.95 = 0.18 +- 5.05
Contig 150 2414 reads 135199 bases = 15.54 +- 5.37 = 0.34 +- 5.05
Contig 143 1328 reads 73350 bases = 15.61 +- 5.45 = 0.23 +- 5.10
Contig 132 734 reads 40104 bases = 15.81 +- 5.02 = 1.05 +- 4.31
Contig 77 55 reads 2882 bases = 16.50 +- 11.93 = 15.55 +- 10.68
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 771
HQ Discrepant reads = 66
Chimeric reads = 142
Suspect alignments = 322
-------------------------------------------------------------------
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/microbe5/3634499/edit_dir.16Jul04.QD