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
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Project Size(KB) TaxID GenusSpecies
3634477 3300 119484 Syntrophobacter fumaroxidans
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Syntrophobacter_fumaroxidans
-------------------------------------------------------------------
Syntrophobacteraceae, family, d-proteobacteria
Syntrophobacterales, order, d-proteobacteria
Syntrophobacter fumaroxidans, species, d-proteobacteria
delta/epsilon subdivisions, subphylum, proteobacteria
Syntrophobacter, genus, d-proteobacteria
Deltaproteobacteria, class, d-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4888872
# phrap: 4523471
# db:
altered.
3300000
4237447 +/- 679453
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 9559
Number of reads with percent X's >= 20%: 92 = 0.2%
Number of reads with percent X's >= 50%: 37 = 0.1%
Number of reads with percent X's >= 80%: 5 = 0.0%
Total reads in project: 40796
Total bp X'd : 400855
reads >= 20% >= 50% >= 80% screened
Nr with L09136 8770 72 32 1
Nr with pCC1Fos 764 0 0 0
Nr with pMCL200_JGI_XZX+XZK 25 20 5 4
-------------------------------------------------------------------
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 = 7488870
C = 10929376
G = 11073123
T = 7353881
N = 180429
X = 400855
GC fraction = 0.59
Total = 37426534
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634477_fasta.screen.contigs
-------------------------------------------------------------------
A 983167
C 1467793
G 1475104
T 981385
N 108
fraction GC = 0.60
total bases = 4907557
Libraries and Reads
-------------------------------------------------------------------
Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
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-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYI reads.list > grep.reads.list.AHYI
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYI 4 500
-------------------------------------------------------------------
#Found 8222 total values totalling 26877827.0000. <3269.013257 +/- 2276.526724>
#Range: [ 573 - 128961 ]
#Most likely bin: [ 3000 - 3500 ] 2992 counts
#Median bin: [ 3000 - 3500 ] 2992 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 12 0.00 0.00 ]
| 1000 - 1500 : [ 29 0.00 0.00 ]
| 1500 - 2000 : [ 25 0.00 0.01 ]
|X 2000 - 2500 : [ 105 0.01 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2722 0.33 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2992 0.36 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2057 0.25 0.97 ]
|XXXX 4000 - 4500 : [ 273 0.03 1.00 ]
#...
| 22500 - 23000 : [ 1 0.00 1.00 ]
#...
| 45000 - 45500 : [ 1 0.00 1.00 ]
#...
| 48000 - 48500 : [ 1 0.00 1.00 ]
#...
| 64500 - 65000 : [ 1 0.00 1.00 ]
#...
| 72000 - 72500 : [ 1 0.00 1.00 ]
#...
| 114500 - 115000 : [ 1 0.00 1.00 ]
#...
| 128500 - 129000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYK reads.list > grep.reads.list.AHYK
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYK 4 500
-------------------------------------------------------------------
#Found 7288 total values totalling 49012535.0000. <6725.100851 +/- 966.185649>
#Range: [ 1028 - 48959 ]
#Most likely bin: [ 6000 - 6500 ] 2090 counts
#Median bin: [ 6500 - 7000 ] 2003 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 6 0.00 0.00 ]
| 1500 - 2000 : [ 15 0.00 0.00 ]
| 2000 - 2500 : [ 11 0.00 0.00 ]
| 2500 - 3000 : [ 18 0.00 0.01 ]
| 3000 - 3500 : [ 14 0.00 0.01 ]
| 3500 - 4000 : [ 10 0.00 0.01 ]
| 4000 - 4500 : [ 6 0.00 0.01 ]
| 4500 - 5000 : [ 9 0.00 0.01 ]
| 5000 - 5500 : [ 7 0.00 0.01 ]
|XXXXXXXXXXXX 5500 - 6000 : [ 604 0.08 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2090 0.29 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2003 0.27 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1568 0.22 0.87 ]
|XXXXXXXXXXXXXXXXX 7500 - 8000 : [ 897 0.12 1.00 ]
|X 8000 - 8500 : [ 27 0.00 1.00 ]
#...
| 23500 - 24000 : [ 1 0.00 1.00 ]
#...
| 38500 - 39000 : [ 1 0.00 1.00 ]
#...
| 48500 - 49000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYN reads.list > grep.reads.list.AHYN
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYN 4 500
-------------------------------------------------------------------
#Found 638 total values totalling 24561800.0000. <38498.119122 +/- 3599.925277>
#Range: [ 27347 - 46560 ]
#Most likely bin: [ 38000 - 38500 ] 38 counts
#Median bin: [ 38000 - 38500 ] 38 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 27000 - 27500 : [ 1 0.00 0.00 ]
|X 27500 - 28000 : [ 1 0.00 0.00 ]
|XX 28000 - 28500 : [ 2 0.00 0.01 ]
|XX 28500 - 29000 : [ 2 0.00 0.01 ]
#...
|X 29500 - 30000 : [ 1 0.00 0.01 ]
#...
|X 30500 - 31000 : [ 1 0.00 0.01 ]
|XXXXXX 31000 - 31500 : [ 6 0.01 0.02 ]
|XXXXXXXX 31500 - 32000 : [ 8 0.01 0.03 ]
|XXXXXXXXX 32000 - 32500 : [ 9 0.01 0.05 ]
|XXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 18 0.03 0.08 ]
|XXXXXXXXXXXXXXXXX 33000 - 33500 : [ 16 0.03 0.10 ]
|XXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 17 0.03 0.13 ]
|XXXXXXXXXXXXXXXX 34000 - 34500 : [ 15 0.02 0.15 ]
|XXXXXXXXXXXXXXXXX 34500 - 35000 : [ 16 0.03 0.18 ]
|XXXXXXXXXXX 35000 - 35500 : [ 10 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 34 0.05 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 24 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 36 0.06 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 29 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 36 0.06 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 38 0.06 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 27 0.04 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 29 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 28 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 30 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 28 0.04 0.72 ]
|XXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 20 0.03 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 31 0.05 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 29 0.05 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 33 0.05 0.90 ]
|XXXXXXXXXXXXXXXX 43000 - 43500 : [ 15 0.02 0.92 ]
|XXXXXXXXXXXXXXXXX 43500 - 44000 : [ 16 0.03 0.95 ]
|XXXXXXXXX 44000 - 44500 : [ 9 0.01 0.96 ]
|XXXXXXXXXXXXX 44500 - 45000 : [ 12 0.02 0.98 ]
|XXXXXX 45000 - 45500 : [ 6 0.01 0.99 ]
|XX 45500 - 46000 : [ 2 0.00 1.00 ]
|XX 46000 - 46500 : [ 2 0.00 1.00 ]
|X 46500 - 47000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHYK 6688 +- 1184 (n=3640)
# AHYN 38441 +- 3682 (n=320)
# AHYI 3100 +- 906 (n=4088)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634477_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
AHYI 21504 93 615 96 643 21415 93 616 95 621
AHYK 17664 97 794 98 773 17664 97 794 98 786
AHYN 3840 92 669 96 662 3840 92 677 96 687
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHYI 10704 93 616 95 624 10711 93 616 95 618
AHYK 8832 97 794 99 786 8832 97 794 98 786
AHYN 1920 91 678 96 677 1920 92 676 97 696
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634477_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
112 20101 10403 92.88 96.75 AHYI @
92 17104 8594 93.41 97.31 AHYK @
20 3591 1857 92.85 96.72 AHYN @
] 40796 20854 93.10 cumulative total@@
LIBRARY PLATE ID COUNT [ AHYI 112 AHYK 92 AHYN 20 ] for 224 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 3634477_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 42919 total values totalling 28295201.0000. <659.269811 +/- 213.674818>
#Range: [ 0 - 938 ]
#Most likely bin: [ 800 - 850 ] 8446 counts
#Median bin: [ 700 - 750 ] 6409 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 0 - 50 : [ 1979 0.05 0.05 ]
|XX 50 - 100 : [ 360 0.01 0.05 ]
|X 100 - 150 : [ 302 0.01 0.06 ]
|X 150 - 200 : [ 309 0.01 0.07 ]
|XX 200 - 250 : [ 383 0.01 0.08 ]
|XX 250 - 300 : [ 445 0.01 0.09 ]
|XX 300 - 350 : [ 520 0.01 0.10 ]
|XXX 350 - 400 : [ 624 0.01 0.11 ]
|XXXX 400 - 450 : [ 801 0.02 0.13 ]
|XXXXX 450 - 500 : [ 1048 0.02 0.16 ]
|XXXXXX 500 - 550 : [ 1366 0.03 0.19 ]
|XXXXXXXXX 550 - 600 : [ 1940 0.05 0.23 ]
|XXXXXXXXXXXXXX 600 - 650 : [ 2917 0.07 0.30 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4410 0.10 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6409 0.15 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8436 0.20 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 8446 0.20 0.95 ]
|XXXXXXXXXX 850 - 900 : [ 2160 0.05 1.00 ]
| 900 - 950 : [ 64 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYI 3634477_fasta.screen.trimQ15.SaF > reads.trim15.AHYI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYI.rl 2 50
-------------------------------------------------------------------
#Found 21415 total values totalling 12323058.0000. <575.440486 +/- 208.665347>
#Range: [ 0 - 850 ]
#Most likely bin: [ 700 - 750 ] 4338 counts
#Median bin: [ 650 - 700 ] 3705 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 0 - 50 : [ 1175 0.05 0.05 ]
|XXX 50 - 100 : [ 276 0.01 0.07 ]
|XX 100 - 150 : [ 247 0.01 0.08 ]
|XX 150 - 200 : [ 261 0.01 0.09 ]
|XXX 200 - 250 : [ 299 0.01 0.11 ]
|XXX 250 - 300 : [ 351 0.02 0.12 ]
|XXXX 300 - 350 : [ 400 0.02 0.14 ]
|XXXXX 350 - 400 : [ 506 0.02 0.16 ]
|XXXXXX 400 - 450 : [ 673 0.03 0.20 ]
|XXXXXXXXX 450 - 500 : [ 946 0.04 0.24 ]
|XXXXXXXXXXX 500 - 550 : [ 1193 0.06 0.30 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 1747 0.08 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2562 0.12 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3705 0.17 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4338 0.20 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2457 0.11 0.99 ]
|XXX 800 - 850 : [ 278 0.01 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYK
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYK 3634477_fasta.screen.trimQ15.SaF > reads.trim15.AHYK.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYK.rl 2 50
-------------------------------------------------------------------
#Found 17664 total values totalling 13581723.0000. <768.892833 +/- 157.649671>
#Range: [ 0 - 931 ]
#Most likely bin: [ 800 - 850 ] 7586 counts
#Median bin: [ 800 - 850 ] 7586 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 0 - 50 : [ 533 0.03 0.03 ]
| 50 - 100 : [ 34 0.00 0.03 ]
| 100 - 150 : [ 29 0.00 0.03 ]
| 150 - 200 : [ 13 0.00 0.03 ]
| 200 - 250 : [ 36 0.00 0.04 ]
| 250 - 300 : [ 23 0.00 0.04 ]
| 300 - 350 : [ 30 0.00 0.04 ]
| 350 - 400 : [ 40 0.00 0.04 ]
| 400 - 450 : [ 42 0.00 0.04 ]
| 450 - 500 : [ 44 0.00 0.05 ]
| 500 - 550 : [ 46 0.00 0.05 ]
| 550 - 600 : [ 65 0.00 0.05 ]
|X 600 - 650 : [ 118 0.01 0.06 ]
|XX 650 - 700 : [ 319 0.02 0.08 ]
|XXXXXXX 700 - 750 : [ 1376 0.08 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5224 0.30 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7586 0.43 0.88 ]
|XXXXXXXXXXX 850 - 900 : [ 2046 0.12 1.00 ]
| 900 - 950 : [ 60 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYN
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYN 3634477_fasta.screen.trimQ15.SaF > reads.trim15.AHYN.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYN.rl 2 50
-------------------------------------------------------------------
#Found 3840 total values totalling 2390420.0000. <622.505208 +/- 239.438622>
#Range: [ 0 - 938 ]
#Most likely bin: [ 750 - 800 ] 755 counts
#Median bin: [ 700 - 750 ] 695 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXX 0 - 50 : [ 271 0.07 0.07 ]
|XXX 50 - 100 : [ 50 0.01 0.08 ]
|X 100 - 150 : [ 26 0.01 0.09 ]
|XX 150 - 200 : [ 35 0.01 0.10 ]
|XXX 200 - 250 : [ 48 0.01 0.11 ]
|XXXX 250 - 300 : [ 71 0.02 0.13 ]
|XXXXX 300 - 350 : [ 90 0.02 0.15 ]
|XXXX 350 - 400 : [ 78 0.02 0.17 ]
|XXXXX 400 - 450 : [ 86 0.02 0.20 ]
|XXX 450 - 500 : [ 58 0.02 0.21 ]
|XXXXXXX 500 - 550 : [ 127 0.03 0.24 ]
|XXXXXXX 550 - 600 : [ 128 0.03 0.28 ]
|XXXXXXXXXXXXX 600 - 650 : [ 237 0.06 0.34 ]
|XXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 386 0.10 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 695 0.18 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 755 0.20 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 582 0.15 0.97 ]
|XXXXXX 850 - 900 : [ 113 0.03 1.00 ]
| 900 - 950 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AXNU
trimt JAZZ trim 15 readlength histogram for AXNW
trimt JAZZ trim 15 readlength histogram for AXNX
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634477
-------------------------------------------------------------------
AHYI.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHYI.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AHYK.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AHYN.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AXNW.000001.000100
AHYI.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHYI.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AHYK.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AHYN.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AXNW.000001.000100
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634477_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634477_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 40759 total values totalling 24419.7625. <0.599126 +/- 0.041789>
#Range: [ 0.2551 - 0.9167 ]
#Most likely bin: [ 0.605 - 0.61 ] 2509 counts
#Median bin: [ 0.6 - 0.605 ] 2438 counts
#Entropy = 4.9689 bits
| 0.255 - 0.26 : [ 1 0.00 0.00 ]
| 0.26 - 0.265 : [ 2 0.00 0.00 ]
| 0.265 - 0.27 : [ 1 0.00 0.00 ]
| 0.27 - 0.275 : [ 2 0.00 0.00 ]
#...
| 0.28 - 0.285 : [ 3 0.00 0.00 ]
| 0.285 - 0.29 : [ 3 0.00 0.00 ]
| 0.29 - 0.295 : [ 2 0.00 0.00 ]
| 0.295 - 0.3 : [ 1 0.00 0.00 ]
| 0.3 - 0.305 : [ 1 0.00 0.00 ]
| 0.305 - 0.31 : [ 5 0.00 0.00 ]
| 0.31 - 0.315 : [ 2 0.00 0.00 ]
#...
| 0.32 - 0.325 : [ 4 0.00 0.00 ]
| 0.325 - 0.33 : [ 3 0.00 0.00 ]
| 0.33 - 0.335 : [ 4 0.00 0.00 ]
| 0.335 - 0.34 : [ 10 0.00 0.00 ]
| 0.34 - 0.345 : [ 4 0.00 0.00 ]
| 0.345 - 0.35 : [ 6 0.00 0.00 ]
| 0.35 - 0.355 : [ 8 0.00 0.00 ]
| 0.355 - 0.36 : [ 9 0.00 0.00 ]
| 0.36 - 0.365 : [ 10 0.00 0.00 ]
| 0.365 - 0.37 : [ 9 0.00 0.00 ]
| 0.37 - 0.375 : [ 13 0.00 0.00 ]
| 0.375 - 0.38 : [ 7 0.00 0.00 ]
| 0.38 - 0.385 : [ 8 0.00 0.00 ]
| 0.385 - 0.39 : [ 13 0.00 0.00 ]
| 0.39 - 0.395 : [ 13 0.00 0.00 ]
| 0.395 - 0.4 : [ 11 0.00 0.00 ]
| 0.4 - 0.405 : [ 19 0.00 0.00 ]
| 0.405 - 0.41 : [ 7 0.00 0.00 ]
| 0.41 - 0.415 : [ 14 0.00 0.00 ]
| 0.415 - 0.42 : [ 15 0.00 0.01 ]
| 0.42 - 0.425 : [ 13 0.00 0.01 ]
| 0.425 - 0.43 : [ 18 0.00 0.01 ]
| 0.43 - 0.435 : [ 20 0.00 0.01 ]
| 0.435 - 0.44 : [ 17 0.00 0.01 ]
| 0.44 - 0.445 : [ 18 0.00 0.01 ]
|X 0.445 - 0.45 : [ 33 0.00 0.01 ]
| 0.45 - 0.455 : [ 31 0.00 0.01 ]
|X 0.455 - 0.46 : [ 33 0.00 0.01 ]
|X 0.46 - 0.465 : [ 47 0.00 0.01 ]
|X 0.465 - 0.47 : [ 33 0.00 0.01 ]
|X 0.47 - 0.475 : [ 44 0.00 0.01 ]
|X 0.475 - 0.48 : [ 49 0.00 0.01 ]
|X 0.48 - 0.485 : [ 65 0.00 0.02 ]
|X 0.485 - 0.49 : [ 81 0.00 0.02 ]
|XX 0.49 - 0.495 : [ 102 0.00 0.02 ]
|XX 0.495 - 0.5 : [ 108 0.00 0.02 ]
|XX 0.5 - 0.505 : [ 151 0.00 0.03 ]
|XX 0.505 - 0.51 : [ 150 0.00 0.03 ]
|XXX 0.51 - 0.515 : [ 159 0.00 0.03 ]
|XXX 0.515 - 0.52 : [ 192 0.00 0.04 ]
|XXX 0.52 - 0.525 : [ 217 0.01 0.04 ]
|XXXXX 0.525 - 0.53 : [ 296 0.01 0.05 ]
|XXXXX 0.53 - 0.535 : [ 324 0.01 0.06 ]
|XXXXXXX 0.535 - 0.54 : [ 411 0.01 0.07 ]
|XXXXXXX 0.54 - 0.545 : [ 421 0.01 0.08 ]
|XXXXXXXXX 0.545 - 0.55 : [ 544 0.01 0.09 ]
|XXXXXXXXXX 0.55 - 0.555 : [ 656 0.02 0.11 ]
|XXXXXXXXXXXXX 0.555 - 0.56 : [ 821 0.02 0.13 ]
|XXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 981 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1173 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1377 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1586 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1832 0.04 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 2035 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 2223 0.05 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 2298 0.06 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 2438 0.06 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 2509 0.06 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 2385 0.06 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 2417 0.06 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 2101 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 1925 0.05 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 1631 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 1489 0.04 0.87 ]
|XXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 1181 0.03 0.90 ]
|XXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 1008 0.02 0.93 ]
|XXXXXXXXXXXX 0.65 - 0.655 : [ 737 0.02 0.95 ]
|XXXXXXXXX 0.655 - 0.66 : [ 584 0.01 0.96 ]
|XXXXXXX 0.66 - 0.665 : [ 463 0.01 0.97 ]
|XXXXX 0.665 - 0.67 : [ 341 0.01 0.98 ]
|XXXX 0.67 - 0.675 : [ 240 0.01 0.99 ]
|XX 0.675 - 0.68 : [ 135 0.00 0.99 ]
|XX 0.68 - 0.685 : [ 119 0.00 0.99 ]
|X 0.685 - 0.69 : [ 75 0.00 0.99 ]
|X 0.69 - 0.695 : [ 62 0.00 1.00 ]
|X 0.695 - 0.7 : [ 34 0.00 1.00 ]
| 0.7 - 0.705 : [ 23 0.00 1.00 ]
| 0.705 - 0.71 : [ 28 0.00 1.00 ]
| 0.71 - 0.715 : [ 13 0.00 1.00 ]
| 0.715 - 0.72 : [ 7 0.00 1.00 ]
| 0.72 - 0.725 : [ 7 0.00 1.00 ]
| 0.725 - 0.73 : [ 6 0.00 1.00 ]
| 0.73 - 0.735 : [ 8 0.00 1.00 ]
| 0.735 - 0.74 : [ 5 0.00 1.00 ]
| 0.74 - 0.745 : [ 1 0.00 1.00 ]
#...
| 0.75 - 0.755 : [ 2 0.00 1.00 ]
| 0.755 - 0.76 : [ 2 0.00 1.00 ]
| 0.76 - 0.765 : [ 3 0.00 1.00 ]
| 0.765 - 0.77 : [ 2 0.00 1.00 ]
#...
| 0.78 - 0.785 : [ 2 0.00 1.00 ]
| 0.785 - 0.79 : [ 2 0.00 1.00 ]
#...
| 0.8 - 0.805 : [ 1 0.00 1.00 ]
#...
| 0.82 - 0.825 : [ 1 0.00 1.00 ]
#...
| 0.86 - 0.865 : [ 1 0.00 1.00 ]
#...
| 0.89 - 0.895 : [ 1 0.00 1.00 ]
#...
| 0.915 - 0.92 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 140. 415 reads; 50481 bp (untrimmed), 50445 (trimmed).
Contig 141. 425 reads; 57481 bp (untrimmed), 57370 (trimmed).
Contig 142. 504 reads; 65311 bp (untrimmed), 65285 (trimmed).
Contig 143. 553 reads; 61821 bp (untrimmed), 61758 (trimmed).
Contig 144. 572 reads; 66506 bp (untrimmed), 66283 (trimmed).
Contig 145. 573 reads; 76081 bp (untrimmed), 76027 (trimmed).
Contig 146. 609 reads; 69032 bp (untrimmed), 69008 (trimmed).
Contig 147. 727 reads; 86274 bp (untrimmed), 86059 (trimmed).
Contig 148. 770 reads; 85210 bp (untrimmed), 85187 (trimmed).
Contig 149. 772 reads; 96078 bp (untrimmed), 96054 (trimmed).
Contig 150. 785 reads; 83198 bp (untrimmed), 83097 (trimmed).
Contig 151. 787 reads; 81255 bp (untrimmed), 81177 (trimmed).
Contig 152. 789 reads; 85618 bp (untrimmed), 85287 (trimmed).
Contig 153. 844 reads; 97431 bp (untrimmed), 97310 (trimmed).
Contig 154. 850 reads; 95302 bp (untrimmed), 95231 (trimmed).
Contig 155. 859 reads; 93558 bp (untrimmed), 93265 (trimmed).
Contig 156. 932 reads; 101115 bp (untrimmed), 101063 (trimmed).
Contig 157. 980 reads; 106789 bp (untrimmed), 106734 (trimmed).
Contig 158. 1001 reads; 103326 bp (untrimmed), 103300 (trimmed).
Contig 159. 1015 reads; 119701 bp (untrimmed), 119607 (trimmed).
Contig 160. 1020 reads; 115058 bp (untrimmed), 115042 (trimmed).
Contig 161. 1162 reads; 129465 bp (untrimmed), 129409 (trimmed).
Contig 162. 1166 reads; 142566 bp (untrimmed), 142264 (trimmed).
Contig 163. 1198 reads; 125412 bp (untrimmed), 125256 (trimmed).
Contig 164. 1350 reads; 160654 bp (untrimmed), 160609 (trimmed).
Contig 165. 1517 reads; 175229 bp (untrimmed), 175206 (trimmed).
Contig 166. 2339 reads; 233121 bp (untrimmed), 233100 (trimmed).
--------------------------------------------------------------
Totals 40747 reads; 4907557 bp (untrimmed), 4888872 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4907557 bases = 7.11 +- 3.08 = 0.25 +- 2.92
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 166 total values totalling 933.1200. <5.621205 +/- 1.979081>
#Range: [ 1.30 - 11.30 ]
#Most likely bin: [ 6.5 - 7 ] 21 counts
#Median bin: [ 6 - 6.5 ] 15 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 1 - 1.5 : [ 1 0.01 0.01 ]
|XXXX 1.5 - 2 : [ 2 0.01 0.02 ]
|XXXXXXXXXXXXX 2 - 2.5 : [ 7 0.04 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 13 0.08 0.14 ]
|XXXXXXXXXXXXX 3 - 3.5 : [ 7 0.04 0.18 ]
|XXXXXXXXXXXXXXXXX 3.5 - 4 : [ 9 0.05 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 17 0.10 0.34 ]
|XXXXXXXXXXXXX 4.5 - 5 : [ 7 0.04 0.38 ]
|XXXXXXXXXXXXXXX 5 - 5.5 : [ 8 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 11 0.07 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 15 0.09 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 21 0.13 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 17 0.10 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 19 0.11 0.93 ]
|XXXXXXXXXXX 8 - 8.5 : [ 6 0.04 0.96 ]
|XXXXXXXX 8.5 - 9 : [ 4 0.02 0.99 ]
#...
|XXXX 11 - 11.5 : [ 2 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 142 total values totalling 864.9500. <6.091197 +/- 1.703115>
#Range: [ 2.50 - 11.30 ]
#Most likely bin: [ 6.5 - 7 ] 21 counts
#Median bin: [ 6 - 6.5 ] 15 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 2.5 - 3 : [ 6 0.04 0.04 ]
|XXXXXXXXXX 3 - 3.5 : [ 5 0.04 0.08 ]
|XXXXXXXXXXXXXXXXX 3.5 - 4 : [ 9 0.06 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 15 0.11 0.25 ]
|XXXXXXXX 4.5 - 5 : [ 4 0.03 0.27 ]
|XXXXXXXXXXXXXXX 5 - 5.5 : [ 8 0.06 0.33 ]
|XXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 11 0.08 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 15 0.11 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 21 0.15 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 17 0.12 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 19 0.13 0.92 ]
|XXXXXXXXXXX 8 - 8.5 : [ 6 0.04 0.96 ]
|XXXXXXXX 8.5 - 9 : [ 4 0.03 0.99 ]
#...
|XXXX 11 - 11.5 : [ 2 0.01 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 1 2 reads 1378 bases = 1.30 +- 0.46 = 0.01 +- 0.84
Contig 2 3 reads 739 bases = 1.53 +- 0.88 = 1.00 +- 0.00
Contig 5 4 reads 2282 bases = 1.64 +- 0.60 = 1.64 +- 0.60
Contig 8 5 reads 2129 bases = 2.03 +- 0.97 = 1.11 +- 0.48
Contig 14 6 reads 2514 bases = 2.04 +- 0.64 = 0.70 +- 0.95
Contig 6 5 reads 2099 bases = 2.06 +- 0.70 = 1.12 +- 1.27
Contig 19 8 reads 2258 bases = 2.26 +- 0.81 = -0.26 +- 1.23
Contig 16 6 reads 1686 bases = 2.32 +- 1.07 = 1.39 +- 1.74
Contig 3 4 reads 1535 bases = 2.42 +- 1.23 = 1.13 +- 1.03
Contig 22 9 reads 3197 bases = 2.46 +- 0.96 = 1.46 +- 1.12
Contig 33 14 reads 4396 bases = 2.50 +- 1.30 = 0.63 +- 1.36
Contig 32 13 reads 4261 bases = 2.52 +- 0.96 = 1.38 +- 1.83
Contig 4 4 reads 1424 bases = 2.69 +- 1.06 = 2.69 +- 1.06
Contig 27 12 reads 3051 bases = 2.74 +- 1.06 = 1.92 +- 1.08
Contig 9 5 reads 1096 bases = 2.74 +- 1.15 = 2.74 +- 1.15
Contig 26 11 reads 3223 bases = 2.80 +- 0.91 = 1.04 +- 2.47
Contig 38 16 reads 4696 bases = 2.82 +- 0.93 = 0.31 +- 2.41
Contig 18 7 reads 2212 bases = 2.83 +- 1.39 = 2.83 +- 1.39
Contig 15 6 reads 1907 bases = 2.87 +- 1.12 = 0.02 +- 0.83
Contig 37 16 reads 4922 bases = 2.88 +- 1.07 = 0.42 +- 0.91
Contig 154 850 reads 95302 bases = 7.73 +- 3.04 = 0.11 +- 2.91
Contig 84 126 reads 14170 bases = 7.73 +- 3.18 = 0.85 +- 2.87
Contig 161 1162 reads 129465 bases = 7.74 +- 2.78 = 0.11 +- 2.80
Contig 117 262 reads 28723 bases = 7.91 +- 2.65 = 0.12 +- 3.04
Contig 157 980 reads 106789 bases = 7.91 +- 3.18 = -0.02 +- 2.83
Contig 155 859 reads 93558 bases = 7.95 +- 3.08 = 0.03 +- 3.42
Contig 156 932 reads 101115 bases = 7.95 +- 2.62 = 0.07 +- 2.58
Contig 152 789 reads 85618 bases = 7.96 +- 3.11 = 0.18 +- 2.82
Contig 120 289 reads 29933 bases = 8.02 +- 3.24 = 0.50 +- 2.93
Contig 150 785 reads 83198 bases = 8.08 +- 2.78 = 0.10 +- 3.54
Contig 86 131 reads 14264 bases = 8.09 +- 3.38 = 0.38 +- 3.75
Contig 163 1198 reads 125412 bases = 8.30 +- 2.67 = -0.02 +- 3.39
Contig 158 1001 reads 103326 bases = 8.31 +- 2.90 = 0.09 +- 2.98
Contig 151 787 reads 81255 bases = 8.37 +- 2.93 = 0.31 +- 3.19
Contig 93 153 reads 15276 bases = 8.55 +- 3.18 = -0.06 +- 2.91
Contig 166 2339 reads 233121 bases = 8.59 +- 3.06 = 0.06 +- 3.10
Contig 123 295 reads 29715 bases = 8.66 +- 4.25 = 0.06 +- 3.21
Contig 103 185 reads 18278 bases = 8.69 +- 3.57 = 0.19 +- 3.47
Contig 106 194 reads 15127 bases = 11.01 +- 4.76 = 0.23 +- 5.19
Contig 115 259 reads 19226 bases = 11.30 +- 5.27 = 1.07 +- 3.35
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 198
HQ Discrepant reads = 61
Chimeric reads = 143
Suspect alignments = 167
-------------------------------------------------------------------
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/microbe4/3634477/edit_dir.03Dec04.QD