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 in progress (or initial analysis of completed)
-------------------------------------------------------------------
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Project information from 'PROJECTS' db
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Project Size(KB) TaxID GenusSpecies
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh
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Genome size estimates
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# contigs: 3419079
# phrap: 1603964
# db:
altered.
10000000
5007681 +/- 3607039
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Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
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Number of reads with X's: 0
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: 13241
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
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Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
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Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
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A = 2325004
C = 3777211
G = 3776733
T = 2295253
N = 60544
X = 453998
GC fraction = 0.60
Total = 12688743
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Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3635729_fasta.screen.contigs
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A 736766
C 1302041
G 1303416
T 734582
N 68773
fraction GC = 0.63
total bases = 4145578
Libraries and Reads
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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 APZO reads.list > grep.reads.list.APZO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APZO 4 500
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#Found 121 total values totalling 337203.0000. <2786.801653 +/- 665.481167>
#Range: [ 1236 - 4181 ]
#Most likely bin: [ 3000 - 3500 ] 36 counts
#Median bin: [ 2500 - 3000 ] 29 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1000 - 1500 : [ 1 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXXXXX 1500 - 2000 : [ 20 0.17 0.17 ]
|XXXXXXXXXXXXXXXXXXXXX 2000 - 2500 : [ 19 0.16 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 29 0.24 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 36 0.30 0.87 ]
|XXXXXXXXXXXXXXXXX 3500 - 4000 : [ 15 0.12 0.99 ]
|X 4000 - 4500 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APZP reads.list > grep.reads.list.APZP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APZP 4 500
-------------------------------------------------------------------
#Found 5 total values totalling 18633.0000. <3726.600000 +/- 1631.532114>
#Range: [ 1933 - 6741 ]
#Most likely bin: [ 0 - 500 ] 1 counts
#Median bin: [ 3000 - 3500 ] 1 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1500 - 2000 : [ 1 0.20 0.20 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 1 0.20 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1 0.20 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1 0.20 0.80 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1 0.20 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
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# APZP 3726 +- 1824 (n=5)
# APZO 2556 +- 1003 (n=133)
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Library / Read Quality summary
extracted from 3635729_fasta.screen.trimQ15.SaF and database (md_run table)
* note J15 is Jazz trimmed length, Q20 is count of Quality 20+ bases
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DB |----J15---| |----Q20---| Fasta |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
APZO 81792 94 694 97 692 5561 98 583 100 596
APZP 46848 92 752 97 718 7680 89 743 95 730
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
APZO 2791 98 585 100 603 2770 97 581 100 589
APZP 3840 91 742 97 728 3840 88 745 93 732
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reads2plates summary
extracted from file: 3635729_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
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plate(s) reads clones N/plate avg% LIBRARY @
40 5561 2993 74.83 77.94 APZO @
41 7680 3840 93.66 97.56 APZP @
] 13241 6833 84.36 cumulative total@@
LIBRARY PLATE ID COUNT [ APZO 40 APZP 41 ] for 81 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.
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trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3635729_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 13241 total values totalling 8286922.0000. <625.853183 +/- 230.918738>
#Range: [ 0 - 932 ]
#Most likely bin: [ 750 - 800 ] 2356 counts
#Median bin: [ 700 - 750 ] 1993 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXX 0 - 50 : [ 809 0.06 0.06 ]
|XX 50 - 100 : [ 139 0.01 0.07 ]
|XX 100 - 150 : [ 127 0.01 0.08 ]
|XXX 150 - 200 : [ 149 0.01 0.09 ]
|XXX 200 - 250 : [ 167 0.01 0.11 ]
|XXX 250 - 300 : [ 163 0.01 0.12 ]
|XXX 300 - 350 : [ 188 0.01 0.13 ]
|XXXX 350 - 400 : [ 213 0.02 0.15 ]
|XXXXXX 400 - 450 : [ 339 0.03 0.17 ]
|XXXXXX 450 - 500 : [ 345 0.03 0.20 ]
|XXXXXXXX 500 - 550 : [ 489 0.04 0.24 ]
|XXXXXXXXXXX 550 - 600 : [ 672 0.05 0.29 ]
|XXXXXXXXXXXXXXXXXX 600 - 650 : [ 1039 0.08 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1545 0.12 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1993 0.15 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2356 0.18 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1920 0.15 0.96 ]
|XXXXXXXXXX 850 - 900 : [ 561 0.04 1.00 ]
| 900 - 950 : [ 27 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APZO
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Command: /usr/xpg4/bin/grep APZO 3635729_fasta.screen.trimQ15.SaF > reads.trim15.APZO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APZO.rl 2 50
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#Found 5561 total values totalling 3171265.0000. <570.268837 +/- 172.545435>
#Range: [ 22 - 834 ]
#Most likely bin: [ 650 - 700 ] 1134 counts
#Median bin: [ 600 - 650 ] 843 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 50 : [ 50 0.01 0.01 ]
|XXX 50 - 100 : [ 89 0.02 0.02 ]
|XXX 100 - 150 : [ 89 0.02 0.04 ]
|XXXX 150 - 200 : [ 101 0.02 0.06 ]
|XXXX 200 - 250 : [ 110 0.02 0.08 ]
|XXXX 250 - 300 : [ 117 0.02 0.10 ]
|XXXXX 300 - 350 : [ 134 0.02 0.12 ]
|XXXXXX 350 - 400 : [ 156 0.03 0.15 ]
|XXXXXXXXXX 400 - 450 : [ 278 0.05 0.20 ]
|XXXXXXXXXX 450 - 500 : [ 278 0.05 0.25 ]
|XXXXXXXXXXXXXXX 500 - 550 : [ 412 0.07 0.33 ]
|XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 537 0.10 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 843 0.15 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1134 0.20 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 912 0.16 0.94 ]
|XXXXXXXXXXX 750 - 800 : [ 302 0.05 1.00 ]
|X 800 - 850 : [ 19 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APZP
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Command: /usr/xpg4/bin/grep APZP 3635729_fasta.screen.trimQ15.SaF > reads.trim15.APZP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APZP.rl 2 50
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#Found 7680 total values totalling 5115657.0000. <666.101172 +/- 257.914331>
#Range: [ 0 - 932 ]
#Most likely bin: [ 750 - 800 ] 2054 counts
#Median bin: [ 750 - 800 ] 2054 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 0 - 50 : [ 759 0.10 0.10 ]
|X 50 - 100 : [ 50 0.01 0.11 ]
|X 100 - 150 : [ 38 0.00 0.11 ]
|X 150 - 200 : [ 48 0.01 0.12 ]
|X 200 - 250 : [ 57 0.01 0.12 ]
|X 250 - 300 : [ 46 0.01 0.13 ]
|X 300 - 350 : [ 54 0.01 0.14 ]
|X 350 - 400 : [ 57 0.01 0.14 ]
|X 400 - 450 : [ 61 0.01 0.15 ]
|X 450 - 500 : [ 67 0.01 0.16 ]
|X 500 - 550 : [ 77 0.01 0.17 ]
|XXX 550 - 600 : [ 135 0.02 0.19 ]
|XXXX 600 - 650 : [ 196 0.03 0.21 ]
|XXXXXXXX 650 - 700 : [ 411 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1081 0.14 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2054 0.27 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1901 0.25 0.92 ]
|XXXXXXXXXXX 850 - 900 : [ 561 0.07 1.00 ]
|X 900 - 950 : [ 27 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APZS
trimt JAZZ trim 15 readlength histogram for AZYA
trimt JAZZ trim 15 readlength histogram for AZYB
trimt JAZZ trim 15 readlength histogram for AZYC
trimt JAZZ trim 15 readlength histogram for SBXG
trimt JAZZ trim 15 readlength histogram for BIXY
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Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3635729
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APZO.000001.000100 pUC18.fa pUC18.fa LRS.fasta
APZO.000101.000200 pUC18.fa pUC18.fa LRS.fasta
APZO.000201.000300 pUC18.fa pUC18.fa LRS.fasta
APZO.000301.000400 pUC18.fa pUC18.fa LRS.fasta
APZO.000401.000500 pUC18.fa pUC18.fa LRS.fasta
APZP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
APZP.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
APZP.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
APZS.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
BIXY.000001.000100 pSMART-HCKan.fa pSMART-HCKan.fa LRS.fasta
APZO.000001.000100 pUC18.fa pUC18.fa LRS.fasta
APZO.000101.000200 pUC18.fa pUC18.fa LRS.fasta
APZO.000201.000300 pUC18.fa pUC18.fa LRS.fasta
APZO.000301.000400 pUC18.fa pUC18.fa LRS.fasta
APZO.000401.000500 pUC18.fa pUC18.fa LRS.fasta
APZP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
APZP.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
APZP.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
APZS.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
BIXY.000001.000100 pSMART-HCKan.fa pSMART-HCKan.fa LRS.fasta
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GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3635729_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
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Contigs and Assemblies
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Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
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Contig 2774. 12 reads; 4867 bp (untrimmed), 4672 (trimmed).
Contig 2775. 12 reads; 5462 bp (untrimmed), 5381 (trimmed).
Contig 2776. 12 reads; 3389 bp (untrimmed), 3168 (trimmed).
Contig 2777. 13 reads; 3975 bp (untrimmed), 3761 (trimmed).
Contig 2778. 13 reads; 4722 bp (untrimmed), 4669 (trimmed).
Contig 2779. 13 reads; 5128 bp (untrimmed), 4921 (trimmed).
Contig 2780. 14 reads; 4658 bp (untrimmed), 4329 (trimmed).
Contig 2781. 14 reads; 3495 bp (untrimmed), 3442 (trimmed).
Contig 2782. 14 reads; 4797 bp (untrimmed), 4596 (trimmed).
Contig 2783. 15 reads; 4198 bp (untrimmed), 4162 (trimmed).
Contig 2784. 15 reads; 4187 bp (untrimmed), 3868 (trimmed).
Contig 2785. 16 reads; 6220 bp (untrimmed), 6066 (trimmed).
Contig 2786. 16 reads; 4777 bp (untrimmed), 4479 (trimmed).
Contig 2787. 16 reads; 6792 bp (untrimmed), 6273 (trimmed).
Contig 2788. 16 reads; 6019 bp (untrimmed), 5460 (trimmed).
Contig 2789. 17 reads; 3659 bp (untrimmed), 3495 (trimmed).
Contig 2790. 17 reads; 5452 bp (untrimmed), 5402 (trimmed).
Contig 2791. 19 reads; 5210 bp (untrimmed), 4995 (trimmed).
Contig 2792. 19 reads; 5250 bp (untrimmed), 5165 (trimmed).
Contig 2793. 19 reads; 7128 bp (untrimmed), 6909 (trimmed).
Contig 2794. 22 reads; 3329 bp (untrimmed), 3225 (trimmed).
Contig 2795. 23 reads; 5695 bp (untrimmed), 5336 (trimmed).
Contig 2796. 25 reads; 7354 bp (untrimmed), 7081 (trimmed).
Contig 2797. 27 reads; 4937 bp (untrimmed), 4888 (trimmed).
Contig 2798. 29 reads; 4810 bp (untrimmed), 4570 (trimmed).
Contig 2799. 33 reads; 6362 bp (untrimmed), 6174 (trimmed).
Contig 2800. 65 reads; 6382 bp (untrimmed), 6275 (trimmed).
--------------------------------------------------------------
Totals 8014 reads; 4145578 bp (untrimmed), 3419079 (trimmed).
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Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
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depth.out contains 3413151 bases = 1.72 +- 1.00 = 0.62 +- 1.15
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Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
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#Found 2011 total values totalling 3317.7400. <1.649796 +/- 0.479106>
#Range: [ 1.00 - 7.49 ]
#Most likely bin: [ 1 - 1.5 ] 850 counts
#Median bin: [ 1.5 - 2 ] 800 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 850 0.42 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 800 0.40 0.82 ]
|XXXXXXXXXXXX 2 - 2.5 : [ 247 0.12 0.94 ]
|XXXX 2.5 - 3 : [ 91 0.05 0.99 ]
|X 3 - 3.5 : [ 14 0.01 1.00 ]
| 3.5 - 4 : [ 4 0.00 1.00 ]
| 4 - 4.5 : [ 1 0.00 1.00 ]
| 4.5 - 5 : [ 2 0.00 1.00 ]
| 5 - 5.5 : [ 1 0.00 1.00 ]
#...
| 7 - 7.5 : [ 1 0.00 1.00 ]
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Histogram of Major Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000
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#Found 63 total values totalling 169.7000. <2.693651 +/- 0.927426>
#Range: [ 1.57 - 7.49 ]
#Most likely bin: [ 2 - 2.5 ] 21 counts
#Median bin: [ 2.5 - 3 ] 20 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 10 0.16 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 21 0.33 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 20 0.32 0.81 ]
|XXXXXXXX 3 - 3.5 : [ 4 0.06 0.87 ]
|XXXXXX 3.5 - 4 : [ 3 0.05 0.92 ]
|XX 4 - 4.5 : [ 1 0.02 0.94 ]
|XXXX 4.5 - 5 : [ 2 0.03 0.97 ]
|XX 5 - 5.5 : [ 1 0.02 0.98 ]
#...
|XX 7 - 7.5 : [ 1 0.02 1.00 ]
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Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
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Contig 1710 2 reads 546 bases = 1.00 +- 0.04 = 1.00 +- 0.04
Contig 1120 2 reads 1608 bases = 1.02 +- 0.15 = -0.01 +- 0.99
Contig 1125 2 reads 1663 bases = 1.02 +- 0.15 = -0.27 +- 0.95
Contig 895 2 reads 1632 bases = 1.02 +- 0.15 = -0.11 +- 0.98
Contig 1024 2 reads 1932 bases = 1.03 +- 0.18 = 1.03 +- 0.18
Contig 1313 2 reads 1654 bases = 1.03 +- 0.18 = 1.03 +- 0.18
Contig 1405 2 reads 1238 bases = 1.03 +- 0.18 = -0.12 +- 0.97
Contig 1423 2 reads 1373 bases = 1.03 +- 0.17 = 0.24 +- 0.96
Contig 1556 2 reads 1503 bases = 1.03 +- 0.18 = 1.03 +- 0.18
Contig 1622 2 reads 1619 bases = 1.03 +- 0.18 = 1.03 +- 0.18
Contig 1641 2 reads 1717 bases = 1.03 +- 0.17 = 1.03 +- 0.17
Contig 912 2 reads 1337 bases = 1.03 +- 0.17 = -0.08 +- 0.98
Contig 977 2 reads 1732 bases = 1.03 +- 0.16 = -0.11 +- 0.98
Contig 1079 2 reads 1420 bases = 1.04 +- 0.20 = -0.10 +- 0.97
Contig 1118 2 reads 1260 bases = 1.04 +- 0.19 = 0.19 +- 0.96
Contig 1279 2 reads 1784 bases = 1.04 +- 0.20 = 1.04 +- 0.20
Contig 1340 2 reads 1742 bases = 1.04 +- 0.19 = 1.04 +- 0.19
Contig 1479 2 reads 1915 bases = 1.04 +- 0.21 = 1.04 +- 0.21
Contig 1503 2 reads 1614 bases = 1.04 +- 0.19 = -0.22 +- 0.96
Contig 1529 2 reads 2182 bases = 1.04 +- 0.20 = 0.00 +- 0.98
Contig 2594 6 reads 1692 bases = 3.11 +- 1.77 = 1.16 +- 0.67
Contig 2603 6 reads 1582 bases = 3.13 +- 1.83 = -0.54 +- 1.04
Contig 2781 14 reads 3495 bases = 3.15 +- 1.54 = 0.64 +- 1.99
Contig 2311 4 reads 1173 bases = 3.16 +- 1.08 = 1.39 +- 0.95
Contig 2746 10 reads 2653 bases = 3.16 +- 2.00 = 0.66 +- 1.50
Contig 2590 6 reads 1417 bases = 3.21 +- 1.37 = 1.22 +- 0.73
Contig 2531 6 reads 1576 bases = 3.26 +- 1.68 = 2.20 +- 0.97
Contig 2473 5 reads 1242 bases = 3.29 +- 1.61 = 0.49 +- 0.78
Contig 2652 7 reads 1869 bases = 3.29 +- 1.67 = 0.16 +- 1.54
Contig 2653 7 reads 1430 bases = 3.30 +- 1.51 = 0.31 +- 0.91
Contig 2795 23 reads 5695 bases = 3.34 +- 1.52 = 0.37 +- 1.54
Contig 2757 11 reads 2262 bases = 3.52 +- 1.38 = 1.52 +- 0.81
Contig 2789 17 reads 3659 bases = 3.56 +- 1.58 = 0.34 +- 1.65
Contig 2497 5 reads 925 bases = 3.61 +- 1.46 = 1.85 +- 1.26
Contig 2756 11 reads 2477 bases = 3.68 +- 1.65 = 0.07 +- 1.51
Contig 2799 33 reads 6362 bases = 4.44 +- 3.50 = 1.98 +- 2.11
Contig 2797 27 reads 4937 bases = 4.55 +- 3.27 = 0.80 +- 2.74
Contig 2798 29 reads 4810 bases = 4.68 +- 2.00 = -0.64 +- 1.55
Contig 2794 22 reads 3329 bases = 5.00 +- 1.98 = -0.09 +- 2.70
Contig 2800 65 reads 6382 bases = 7.49 +- 6.67 = 1.04 +- 3.38
Assembler Specific Info
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Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 124
Chimeric reads = 268
Suspect alignments = 52
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Assembly parameters
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phrap version SPS - 4.18 SUN Solaris 7,8
Score matrix /psf/QC/Applications/pphrap/matrix/score_matrix.8
A C G T N X
A 1 -8 -8 -8 0 0
C -8 1 -8 -8 0 0
G -8 -8 1 -8 0 0
T -8 -8 -8 1 0 0
N 0 0 0 0 0 0
X 0 0 0 0 0 0
gap_init: -10
gap_ext: -9
ins_gap_ext: -9
del_gap_ext: -9
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: 20
maxmatch: 45
max_group_size: 20
minscore: 35
bandwidth: 14
indexwordsize: 10
vector_bound: 10
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 19
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -8
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
File generated in /psf/project/assorted1/microbe/community/3635729/edit_dir.10plateQC