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)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
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Project Size(KB) TaxID GenusSpecies
3634608 4500 NULL Shewanella putrefaciens
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Shewanella_putrefaciens
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Shewanellaceae, family, g-proteobacteria
Alteromonadales, order, g-proteobacteria
Shewanella putrefaciens, 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
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# contigs: 5183512
# phrap: 3329177
# db:
altered.
4500000
4337563 +/- 765693
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
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Number of reads with X's: 3984
Number of reads with percent X's >= 20%: 648 = 4.2%
Number of reads with percent X's >= 50%: 598 = 3.9%
Number of reads with percent X's >= 80%: 492 = 3.2%
Total reads in project: 15264
Total bp X'd : 668249
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3416 95 66 44
Nr with LRS 36 36 36 29
Nr with pMCL200_JGI_XZX+XZK 532 517 496 419
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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 = 3641507
C = 3632955
G = 3540901
T = 3657878
N = 50798
X = 668249
GC fraction = 0.47
Total = 15192288
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634608_fasta.screen.contigs
-------------------------------------------------------------------
A 1404964
C 1363679
G 1357765
T 1398537
N 1689
fraction GC = 0.49
total bases = 5526634
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 AIOS reads.list > grep.reads.list.AIOS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOS 4 500
-------------------------------------------------------------------
#Found 853 total values totalling 2713303.0000. <3180.894490 +/- 729.607878>
#Range: [ 862 - 5227 ]
#Most likely bin: [ 3000 - 3500 ] 272 counts
#Median bin: [ 3000 - 3500 ] 272 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
|XXXX 1000 - 1500 : [ 27 0.03 0.03 ]
|XXXXX 1500 - 2000 : [ 37 0.04 0.08 ]
|XXXXX 2000 - 2500 : [ 34 0.04 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 227 0.27 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 272 0.32 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 147 0.17 0.87 ]
|XXXXXXXXXXXX 4000 - 4500 : [ 81 0.09 0.97 ]
|XXXX 4500 - 5000 : [ 24 0.03 1.00 ]
| 5000 - 5500 : [ 3 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOT reads.list > grep.reads.list.AIOT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOT 4 500
-------------------------------------------------------------------
#Found 182 total values totalling 993106.0000. <5456.626374 +/- 2164.032599>
#Range: [ 1131 - 8892 ]
#Most likely bin: [ 6000 - 6500 ] 39 counts
#Median bin: [ 6000 - 6500 ] 39 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXX 1000 - 1500 : [ 16 0.09 0.09 ]
|XXXXXXXXXX 1500 - 2000 : [ 10 0.05 0.14 ]
|XXXXXXXX 2000 - 2500 : [ 8 0.04 0.19 ]
|XXXX 2500 - 3000 : [ 4 0.02 0.21 ]
|XXXX 3000 - 3500 : [ 4 0.02 0.23 ]
|XXX 3500 - 4000 : [ 3 0.02 0.25 ]
|XXXXX 4000 - 4500 : [ 5 0.03 0.27 ]
|XX 4500 - 5000 : [ 2 0.01 0.29 ]
|XXX 5000 - 5500 : [ 3 0.02 0.30 ]
|XXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 19 0.10 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 39 0.21 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 33 0.18 0.80 ]
|XXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 18 0.10 0.90 ]
|XXXXXXX 7500 - 8000 : [ 7 0.04 0.94 ]
|XXXX 8000 - 8500 : [ 4 0.02 0.96 ]
|XXXXXXX 8500 - 9000 : [ 7 0.04 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIOS 3048 +- 839 (n=447)
# AIOT 4334 +- 2803 (n=120)
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Library / Read Quality summary
extracted from 3634608_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
AIOS 7680 -1 -1 96 748 7680 95 772 97 775
AIOT 7680 -1 -1 96 696 7584 89 734 96 725
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIOS 3840 97 755 98 770 3840 93 789 95 781
AIOT 3744 89 732 97 722 3840 90 736 96 727
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reads2plates summary
extracted from file: 3634608_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
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plate(s) reads clones N/plate avg% LIBRARY @
40 7680 3840 96.00 100.00 AIOS @
40 7584 3840 96.00 100.00 AIOT @
] 15264 7680 96.00 cumulative total@@
LIBRARY PLATE ID COUNT [ AIOS 40 AIOT 40 ] for 80 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 3634608_fasta.screen.trimQ15.SaF 4 50
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#Found 15264 total values totalling 10616011.0000. <695.493383 +/- 226.144882>
#Range: [ 0 - 946 ]
#Most likely bin: [ 750 - 800 ] 4815 counts
#Median bin: [ 750 - 800 ] 4815 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 0 - 50 : [ 1128 0.07 0.07 ]
|X 50 - 100 : [ 64 0.00 0.08 ]
| 100 - 150 : [ 31 0.00 0.08 ]
| 150 - 200 : [ 31 0.00 0.08 ]
| 200 - 250 : [ 47 0.00 0.09 ]
| 250 - 300 : [ 52 0.00 0.09 ]
|X 300 - 350 : [ 94 0.01 0.09 ]
|X 350 - 400 : [ 122 0.01 0.10 ]
|X 400 - 450 : [ 162 0.01 0.11 ]
|X 450 - 500 : [ 143 0.01 0.12 ]
|XX 500 - 550 : [ 184 0.01 0.13 ]
|XX 550 - 600 : [ 191 0.01 0.15 ]
|XX 600 - 650 : [ 271 0.02 0.17 ]
|XXXXX 650 - 700 : [ 646 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2303 0.15 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4815 0.32 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4080 0.27 0.94 ]
|XXXXXXX 850 - 900 : [ 879 0.06 1.00 ]
| 900 - 950 : [ 21 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOS 3634608_fasta.screen.trimQ15.SaF > reads.trim15.AIOS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOS.rl 2 50
-------------------------------------------------------------------
#Found 7680 total values totalling 5639016.0000. <734.246875 +/- 183.558355>
#Range: [ 0 - 946 ]
#Most likely bin: [ 750 - 800 ] 2767 counts
#Median bin: [ 750 - 800 ] 2767 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 0 - 50 : [ 360 0.05 0.05 ]
| 50 - 100 : [ 16 0.00 0.05 ]
| 100 - 150 : [ 9 0.00 0.05 ]
| 150 - 200 : [ 7 0.00 0.05 ]
| 200 - 250 : [ 18 0.00 0.05 ]
| 250 - 300 : [ 19 0.00 0.06 ]
| 300 - 350 : [ 17 0.00 0.06 ]
| 350 - 400 : [ 19 0.00 0.06 ]
| 400 - 450 : [ 21 0.00 0.06 ]
| 450 - 500 : [ 33 0.00 0.07 ]
|X 500 - 550 : [ 46 0.01 0.07 ]
|X 550 - 600 : [ 43 0.01 0.08 ]
|X 600 - 650 : [ 83 0.01 0.09 ]
|XXXX 650 - 700 : [ 267 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXX 700 - 750 : [ 1228 0.16 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2767 0.36 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2218 0.29 0.93 ]
|XXXXXXX 850 - 900 : [ 495 0.06 1.00 ]
| 900 - 950 : [ 14 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOT
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Command: /usr/xpg4/bin/grep AIOT 3634608_fasta.screen.trimQ15.SaF > reads.trim15.AIOT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOT.rl 2 50
-------------------------------------------------------------------
#Found 7584 total values totalling 4976995.0000. <656.249341 +/- 256.416196>
#Range: [ 0 - 918 ]
#Most likely bin: [ 750 - 800 ] 2048 counts
#Median bin: [ 750 - 800 ] 2048 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 0 - 50 : [ 768 0.10 0.10 ]
|X 50 - 100 : [ 48 0.01 0.11 ]
| 100 - 150 : [ 22 0.00 0.11 ]
| 150 - 200 : [ 24 0.00 0.11 ]
|X 200 - 250 : [ 29 0.00 0.12 ]
|X 250 - 300 : [ 33 0.00 0.12 ]
|XX 300 - 350 : [ 77 0.01 0.13 ]
|XX 350 - 400 : [ 103 0.01 0.15 ]
|XXX 400 - 450 : [ 141 0.02 0.16 ]
|XX 450 - 500 : [ 110 0.01 0.18 ]
|XXX 500 - 550 : [ 138 0.02 0.20 ]
|XXX 550 - 600 : [ 148 0.02 0.22 ]
|XXXX 600 - 650 : [ 188 0.02 0.24 ]
|XXXXXXX 650 - 700 : [ 379 0.05 0.29 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1075 0.14 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2048 0.27 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1862 0.25 0.95 ]
|XXXXXXXX 850 - 900 : [ 384 0.05 1.00 ]
| 900 - 950 : [ 7 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOU
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Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634608
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AIOS.000001.000100 pUC18.fa LRS.fasta
AIOT.000001.000100 pMCL200.fa LRS.fasta
AIOS.000001.000100 pUC18.fa LRS.fasta
AIOT.000001.000100 pMCL200.fa LRS.fasta
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GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634608_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 2468. 26 reads; 7526 bp (untrimmed), 7483 (trimmed).
Contig 2469. 26 reads; 10697 bp (untrimmed), 10579 (trimmed).
Contig 2470. 26 reads; 7556 bp (untrimmed), 7396 (trimmed).
Contig 2471. 26 reads; 10862 bp (untrimmed), 10764 (trimmed).
Contig 2472. 27 reads; 5165 bp (untrimmed), 5124 (trimmed).
Contig 2473. 27 reads; 6276 bp (untrimmed), 6276 (trimmed).
Contig 2474. 27 reads; 8275 bp (untrimmed), 8216 (trimmed).
Contig 2475. 28 reads; 10565 bp (untrimmed), 10541 (trimmed).
Contig 2476. 29 reads; 11056 bp (untrimmed), 10591 (trimmed).
Contig 2477. 29 reads; 9760 bp (untrimmed), 9694 (trimmed).
Contig 2478. 30 reads; 10508 bp (untrimmed), 10317 (trimmed).
Contig 2479. 31 reads; 10849 bp (untrimmed), 10299 (trimmed).
Contig 2480. 31 reads; 9096 bp (untrimmed), 9074 (trimmed).
Contig 2481. 32 reads; 11311 bp (untrimmed), 11005 (trimmed).
Contig 2482. 35 reads; 5451 bp (untrimmed), 5232 (trimmed).
Contig 2483. 37 reads; 10332 bp (untrimmed), 10163 (trimmed).
Contig 2484. 38 reads; 9425 bp (untrimmed), 9395 (trimmed).
Contig 2485. 39 reads; 12113 bp (untrimmed), 12072 (trimmed).
Contig 2486. 42 reads; 12191 bp (untrimmed), 12147 (trimmed).
Contig 2487. 43 reads; 8673 bp (untrimmed), 8458 (trimmed).
Contig 2488. 47 reads; 9041 bp (untrimmed), 8996 (trimmed).
Contig 2489. 49 reads; 13919 bp (untrimmed), 13899 (trimmed).
Contig 2490. 60 reads; 11725 bp (untrimmed), 11594 (trimmed).
Contig 2491. 71 reads; 14174 bp (untrimmed), 13957 (trimmed).
Contig 2492. 112 reads; 22762 bp (untrimmed), 22737 (trimmed).
Contig 2493. 128 reads; 23083 bp (untrimmed), 23063 (trimmed).
Contig 2494. 129 reads; 19954 bp (untrimmed), 19922 (trimmed).
--------------------------------------------------------------
Totals 13095 reads; 5526634 bp (untrimmed), 5183512 (trimmed).
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Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
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depth.out contains 5470729 bases = 2.20 +- 1.31 = 0.76 +- 1.36
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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 2418 total values totalling 4883.2000. <2.019520 +/- 0.621022>
#Range: [ 1.04 - 6.02 ]
#Most likely bin: [ 1.5 - 2 ] 897 counts
#Median bin: [ 1.5 - 2 ] 897 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 476 0.20 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 897 0.37 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 571 0.24 0.80 ]
|XXXXXXXXXXXXXX 2.5 - 3 : [ 306 0.13 0.93 ]
|XXXXX 3 - 3.5 : [ 106 0.04 0.97 ]
|XX 3.5 - 4 : [ 44 0.02 0.99 ]
| 4 - 4.5 : [ 8 0.00 1.00 ]
| 4.5 - 5 : [ 5 0.00 1.00 ]
| 5 - 5.5 : [ 3 0.00 1.00 ]
| 5.5 - 6 : [ 1 0.00 1.00 ]
| 6 - 6.5 : [ 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
-------------------------------------------------------------------
#Found 274 total values totalling 772.5200. <2.819416 +/- 0.655618>
#Range: [ 1.65 - 6.02 ]
#Most likely bin: [ 2.5 - 3 ] 103 counts
#Median bin: [ 2.5 - 3 ] 103 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 1.5 - 2 : [ 12 0.04 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 80 0.29 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 103 0.38 0.71 ]
|XXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 47 0.17 0.88 ]
|XXXXXXX 3.5 - 4 : [ 18 0.07 0.95 ]
|XX 4 - 4.5 : [ 6 0.02 0.97 ]
|XX 4.5 - 5 : [ 4 0.01 0.99 ]
|X 5 - 5.5 : [ 2 0.01 0.99 ]
| 5.5 - 6 : [ 1 0.00 1.00 ]
| 6 - 6.5 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 392 2 reads 1888 bases = 1.04 +- 0.19 = -0.04 +- 0.98
Contig 447 2 reads 1627 bases = 1.04 +- 0.21 = 0.06 +- 0.98
Contig 72 2 reads 1806 bases = 1.04 +- 0.19 = -0.01 +- 0.98
Contig 159 2 reads 1855 bases = 1.05 +- 0.21 = -0.05 +- 0.97
Contig 316 2 reads 1806 bases = 1.05 +- 0.22 = 0.04 +- 0.97
Contig 345 2 reads 1848 bases = 1.05 +- 0.23 = -0.01 +- 0.97
Contig 513 2 reads 1826 bases = 1.05 +- 0.21 = 1.05 +- 0.21
Contig 709 2 reads 1547 bases = 1.05 +- 0.21 = 0.20 +- 0.95
Contig 177 2 reads 1776 bases = 1.06 +- 0.23 = 1.06 +- 0.23
Contig 187 2 reads 1823 bases = 1.06 +- 0.24 = -0.02 +- 0.97
Contig 203 2 reads 1848 bases = 1.06 +- 0.23 = -0.03 +- 0.97
Contig 256 2 reads 1866 bases = 1.06 +- 0.24 = 1.06 +- 0.24
Contig 289 2 reads 1759 bases = 1.06 +- 0.24 = 0.01 +- 0.97
Contig 307 2 reads 1708 bases = 1.06 +- 0.25 = -0.03 +- 0.97
Contig 457 2 reads 1867 bases = 1.06 +- 0.25 = -0.02 +- 0.97
Contig 134 2 reads 1857 bases = 1.07 +- 0.25 = 1.07 +- 0.25
Contig 175 2 reads 1725 bases = 1.07 +- 0.25 = 1.07 +- 0.25
Contig 185 2 reads 1748 bases = 1.07 +- 0.25 = 1.07 +- 0.25
Contig 436 2 reads 1125 bases = 1.07 +- 0.26 = 1.07 +- 0.26
Contig 642 2 reads 1857 bases = 1.07 +- 0.26 = 1.07 +- 0.26
Contig 1914 6 reads 1446 bases = 3.91 +- 1.70 = 1.28 +- 0.87
Contig 2436 19 reads 4491 bases = 3.97 +- 1.77 = 0.28 +- 1.12
Contig 2465 25 reads 5709 bases = 4.09 +- 4.02 = 0.97 +- 2.12
Contig 2473 27 reads 6276 bases = 4.09 +- 3.35 = 0.98 +- 2.24
Contig 2185 9 reads 2113 bases = 4.10 +- 1.31 = 2.38 +- 0.84
Contig 2047 7 reads 1550 bases = 4.14 +- 1.91 = 1.73 +- 1.01
Contig 2237 10 reads 2141 bases = 4.40 +- 2.13 = 2.61 +- 2.49
Contig 2487 43 reads 8673 bases = 4.43 +- 2.17 = 0.10 +- 2.42
Contig 2355 13 reads 2712 bases = 4.44 +- 1.31 = 3.06 +- 1.29
Contig 2492 112 reads 22762 bases = 4.45 +- 2.24 = 0.13 +- 2.17
Contig 2491 71 reads 14174 bases = 4.64 +- 1.92 = 0.48 +- 2.66
Contig 1921 6 reads 1195 bases = 4.72 +- 1.80 = -0.17 +- 0.99
Contig 2490 60 reads 11725 bases = 4.76 +- 1.72 = 0.12 +- 2.57
Contig 2488 47 reads 9041 bases = 4.79 +- 2.54 = 0.13 +- 2.27
Contig 2472 27 reads 5165 bases = 4.82 +- 3.17 = 1.96 +- 1.78
Contig 2493 128 reads 23083 bases = 5.09 +- 4.08 = 0.08 +- 2.42
Contig 2435 19 reads 3347 bases = 5.28 +- 4.75 = 2.02 +- 2.48
Contig 2215 9 reads 1579 bases = 5.33 +- 2.93 = 2.88 +- 1.99
Contig 2482 35 reads 5451 bases = 5.60 +- 6.59 = 0.23 +- 1.37
Contig 2494 129 reads 19954 bases = 6.02 +- 2.37 = 0.19 +- 2.50
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 284
HQ Discrepant reads = 314
Chimeric reads = 56
Suspect alignments = 39
-------------------------------------------------------------------
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/microbe3/3634608/edit_dir.07Jul04.QC