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
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3635487 3000 1757 Thermoanaerobacter ethanolicus
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Thermoanaerobacter_ethanolicus
-------------------------------------------------------------------
Thermoanaerobacteriaceae, family, eubacteria
Clostridia, class, eubacteria
Thermoanaerobacteriales, order, eubacteria
Thermoanaerobacter ethanolicus, species, eubacteria
Thermoanaerobacter, genus, eubacteria
Firmicutes (Gram-positive bacteria), phylum, eubacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2108068
# phrap: 1803712
# db:
altered.
3000000
2303926 +/- 507639
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 3443
Number of reads with percent X's >= 20%: 825 = 5.4%
Number of reads with percent X's >= 50%: 784 = 5.1%
Number of reads with percent X's >= 80%: 713 = 4.7%
Total reads in project: 15326
Total bp X'd : 779091
reads >= 20% >= 50% >= 80% screened
Nr with L09136 2919 310 300 272
Nr with LRS 20 20 20 20
Nr with pMCL200_JGI_XZX+XZK 504 495 464 421
-------------------------------------------------------------------
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 = 4325755
C = 2506673
G = 2432433
T = 4194115
N = 69359
X = 779091
GC fraction = 0.35
Total = 14307426
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3635487_fasta.screen.contigs
-------------------------------------------------------------------
A 699655
C 375401
G 366720
T 705182
N 439
fraction GC = 0.35
total bases = 2147397
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 AOTU reads.list > grep.reads.list.AOTU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOTU 4 500
-------------------------------------------------------------------
#Found 2528 total values totalling 8201880.0000. <3244.414557 +/- 702.190941>
#Range: [ 652 - 20223 ]
#Most likely bin: [ 3000 - 3500 ] 1326 counts
#Median bin: [ 3000 - 3500 ] 1326 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 8 0.00 0.00 ]
| 1000 - 1500 : [ 8 0.00 0.01 ]
| 1500 - 2000 : [ 7 0.00 0.01 ]
| 2000 - 2500 : [ 14 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 630 0.25 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1326 0.52 0.79 ]
|XXXXXXXXXXXXXXX 3500 - 4000 : [ 512 0.20 0.99 ]
| 4000 - 4500 : [ 8 0.00 0.99 ]
#...
| 5500 - 6000 : [ 1 0.00 0.99 ]
| 6000 - 6500 : [ 6 0.00 1.00 ]
| 6500 - 7000 : [ 3 0.00 1.00 ]
#...
| 12000 - 12500 : [ 1 0.00 1.00 ]
#...
| 14000 - 14500 : [ 1 0.00 1.00 ]
| 14500 - 15000 : [ 1 0.00 1.00 ]
#...
| 17000 - 17500 : [ 1 0.00 1.00 ]
#...
| 20000 - 20500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTW reads.list > grep.reads.list.AOTW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOTW 4 500
-------------------------------------------------------------------
#Found 2092 total values totalling 13854208.0000. <6622.470363 +/- 1224.799719>
#Range: [ 999 - 21836 ]
#Most likely bin: [ 6000 - 6500 ] 583 counts
#Median bin: [ 6500 - 7000 ] 446 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
|X 1000 - 1500 : [ 13 0.01 0.01 ]
| 1500 - 2000 : [ 6 0.00 0.01 ]
|X 2000 - 2500 : [ 8 0.00 0.01 ]
|X 2500 - 3000 : [ 13 0.01 0.02 ]
|X 3000 - 3500 : [ 12 0.01 0.03 ]
|X 3500 - 4000 : [ 12 0.01 0.03 ]
|X 4000 - 4500 : [ 9 0.00 0.04 ]
| 4500 - 5000 : [ 5 0.00 0.04 ]
| 5000 - 5500 : [ 5 0.00 0.04 ]
|XXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 302 0.14 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 583 0.28 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 446 0.21 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 343 0.16 0.84 ]
|XXXXXXXXXXXXXXXX 7500 - 8000 : [ 230 0.11 0.95 ]
|XXXXX 8000 - 8500 : [ 80 0.04 0.99 ]
| 8500 - 9000 : [ 3 0.00 0.99 ]
| 9000 - 9500 : [ 3 0.00 0.99 ]
| 9500 - 10000 : [ 7 0.00 0.99 ]
| 10000 - 10500 : [ 2 0.00 1.00 ]
| 10500 - 11000 : [ 3 0.00 1.00 ]
| 11000 - 11500 : [ 1 0.00 1.00 ]
#...
| 14000 - 14500 : [ 1 0.00 1.00 ]
#...
| 17500 - 18000 : [ 1 0.00 1.00 ]
#...
| 18500 - 19000 : [ 1 0.00 1.00 ]
#...
| 21500 - 22000 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AOTU 3133 +- 808 (n=1273)
# AOTW 6481 +- 1385 (n=1083)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3635487_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
AOTU 15360 87 626 93 640 7646 88 604 93 619
AOTW 13056 90 779 96 736 7680 89 768 96 759
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AOTU 3829 88 609 94 623 3817 88 599 91 615
AOTW 3840 89 765 96 756 3840 90 771 95 762
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3635487_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
40 7680 3840 96.00 100.00 AOTW @
40 7646 3839 95.97 99.97 AOTU @
] 15326 7679 95.99 cumulative total@@
LIBRARY PLATE ID COUNT [ AOTW 40 AOTU 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.
-------------------------------------------------------------------
trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3635487_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 15326 total values totalling 9346774.0000. <609.863891 +/- 256.708372>
#Range: [ 0 - 892 ]
#Most likely bin: [ 750 - 800 ] 3365 counts
#Median bin: [ 700 - 750 ] 2350 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1655 0.11 0.11 ]
|X 50 - 100 : [ 84 0.01 0.11 ]
|X 100 - 150 : [ 94 0.01 0.12 ]
|X 150 - 200 : [ 99 0.01 0.13 ]
|XX 200 - 250 : [ 130 0.01 0.13 ]
|XX 250 - 300 : [ 163 0.01 0.15 ]
|XX 300 - 350 : [ 168 0.01 0.16 ]
|XXX 350 - 400 : [ 234 0.02 0.17 ]
|XXX 400 - 450 : [ 266 0.02 0.19 ]
|XXXX 450 - 500 : [ 339 0.02 0.21 ]
|XXXXX 500 - 550 : [ 451 0.03 0.24 ]
|XXXXXXXX 550 - 600 : [ 676 0.04 0.28 ]
|XXXXXXXXXXXXX 600 - 650 : [ 1104 0.07 0.36 ]
|XXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1580 0.10 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2350 0.15 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3365 0.22 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2321 0.15 0.98 ]
|XXX 850 - 900 : [ 247 0.02 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOTU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTU 3635487_fasta.screen.trimQ15.SaF > reads.trim15.AOTU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOTU.rl 2 50
-------------------------------------------------------------------
#Found 7646 total values totalling 4064324.0000. <531.562124 +/- 239.142355>
#Range: [ 0 - 850 ]
#Most likely bin: [ 650 - 700 ] 1391 counts
#Median bin: [ 600 - 650 ] 1029 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 862 0.11 0.11 ]
|XX 50 - 100 : [ 67 0.01 0.12 ]
|XX 100 - 150 : [ 76 0.01 0.13 ]
|XX 150 - 200 : [ 82 0.01 0.14 ]
|XXX 200 - 250 : [ 114 0.01 0.16 ]
|XXXX 250 - 300 : [ 139 0.02 0.18 ]
|XXXX 300 - 350 : [ 151 0.02 0.20 ]
|XXXXXX 350 - 400 : [ 209 0.03 0.22 ]
|XXXXXXX 400 - 450 : [ 236 0.03 0.25 ]
|XXXXXXXXX 450 - 500 : [ 302 0.04 0.29 ]
|XXXXXXXXXXXX 500 - 550 : [ 416 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXX 550 - 600 : [ 637 0.08 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1029 0.13 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1391 0.18 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1327 0.17 0.92 ]
|XXXXXXXXXXXXXXXX 750 - 800 : [ 569 0.07 0.99 ]
|X 800 - 850 : [ 38 0.00 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOTW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTW 3635487_fasta.screen.trimQ15.SaF > reads.trim15.AOTW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOTW.rl 2 50
-------------------------------------------------------------------
#Found 7680 total values totalling 5282450.0000. <687.819010 +/- 249.779355>
#Range: [ 0 - 892 ]
#Most likely bin: [ 750 - 800 ] 2796 counts
#Median bin: [ 750 - 800 ] 2796 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 0 - 50 : [ 793 0.10 0.10 ]
| 50 - 100 : [ 17 0.00 0.11 ]
| 100 - 150 : [ 18 0.00 0.11 ]
| 150 - 200 : [ 17 0.00 0.11 ]
| 200 - 250 : [ 16 0.00 0.11 ]
| 250 - 300 : [ 24 0.00 0.12 ]
| 300 - 350 : [ 17 0.00 0.12 ]
| 350 - 400 : [ 25 0.00 0.12 ]
| 400 - 450 : [ 30 0.00 0.12 ]
|X 450 - 500 : [ 37 0.00 0.13 ]
|X 500 - 550 : [ 35 0.00 0.13 ]
|X 550 - 600 : [ 39 0.01 0.14 ]
|X 600 - 650 : [ 75 0.01 0.15 ]
|XXX 650 - 700 : [ 189 0.02 0.17 ]
|XXXXXXXXXXXXXXX 700 - 750 : [ 1023 0.13 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2796 0.36 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2283 0.30 0.97 ]
|XXXX 850 - 900 : [ 246 0.03 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOTX
trimt JAZZ trim 15 readlength histogram for AUFP
trimt JAZZ trim 15 readlength histogram for AUFS
trimt JAZZ trim 15 readlength histogram for AUFT
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3635487
-------------------------------------------------------------------
AOTU.000001.000100 pUC18.fa LRS.fasta
AOTW.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AOTX.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AUFP.000001.000100
AOTU.000001.000100 pUC18.fa LRS.fasta
AOTW.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AOTX.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AUFP.000001.000100
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3635487_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
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Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 313. 138 reads; 16376 bp (untrimmed), 16347 (trimmed).
Contig 314. 144 reads; 18558 bp (untrimmed), 18514 (trimmed).
Contig 315. 150 reads; 17512 bp (untrimmed), 17450 (trimmed).
Contig 316. 154 reads; 9409 bp (untrimmed), 9388 (trimmed).
Contig 317. 160 reads; 25404 bp (untrimmed), 25377 (trimmed).
Contig 318. 163 reads; 25770 bp (untrimmed), 25752 (trimmed).
Contig 319. 172 reads; 19974 bp (untrimmed), 19944 (trimmed).
Contig 320. 179 reads; 20231 bp (untrimmed), 20156 (trimmed).
Contig 321. 179 reads; 21969 bp (untrimmed), 21800 (trimmed).
Contig 322. 181 reads; 25457 bp (untrimmed), 25233 (trimmed).
Contig 323. 184 reads; 22435 bp (untrimmed), 22420 (trimmed).
Contig 324. 189 reads; 22235 bp (untrimmed), 22198 (trimmed).
Contig 325. 191 reads; 21039 bp (untrimmed), 20646 (trimmed).
Contig 326. 199 reads; 25127 bp (untrimmed), 24924 (trimmed).
Contig 327. 201 reads; 27463 bp (untrimmed), 27399 (trimmed).
Contig 328. 202 reads; 23353 bp (untrimmed), 23330 (trimmed).
Contig 329. 210 reads; 27955 bp (untrimmed), 27879 (trimmed).
Contig 330. 211 reads; 29558 bp (untrimmed), 29510 (trimmed).
Contig 331. 224 reads; 13411 bp (untrimmed), 13386 (trimmed).
Contig 332. 233 reads; 28638 bp (untrimmed), 28612 (trimmed).
Contig 333. 261 reads; 32334 bp (untrimmed), 32215 (trimmed).
Contig 334. 267 reads; 25457 bp (untrimmed), 25389 (trimmed).
Contig 335. 360 reads; 50740 bp (untrimmed), 50694 (trimmed).
Contig 336. 367 reads; 42111 bp (untrimmed), 41994 (trimmed).
Contig 337. 394 reads; 40443 bp (untrimmed), 40384 (trimmed).
Contig 338. 538 reads; 66174 bp (untrimmed), 66171 (trimmed).
Contig 339. 768 reads; 76377 bp (untrimmed), 76317 (trimmed).
--------------------------------------------------------------
Totals 13665 reads; 2147397 bp (untrimmed), 2108068 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2139176 bases = 5.39 +- 3.44 = 0.74 +- 3.01
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 327 total values totalling 1224.5900. <3.744924 +/- 1.911650>
#Range: [ 1.07 - 14.71 ]
#Most likely bin: [ 2 - 2.5 ] 44 counts
#Median bin: [ 3 - 3.5 ] 32 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXX 1 - 1.5 : [ 13 0.04 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 41 0.13 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 44 0.13 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 40 0.12 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 32 0.10 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 34 0.10 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 26 0.08 0.70 ]
|XXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 22 0.07 0.77 ]
|XXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 23 0.07 0.84 ]
|XXXXXXXXXXXXXX 5.5 - 6 : [ 15 0.05 0.89 ]
|XXXXXX 6 - 6.5 : [ 7 0.02 0.91 ]
|XXXXXXXXX 6.5 - 7 : [ 10 0.03 0.94 ]
|XXXXXXXXXX 7 - 7.5 : [ 11 0.03 0.97 ]
|XXX 7.5 - 8 : [ 3 0.01 0.98 ]
|X 8 - 8.5 : [ 1 0.00 0.98 ]
|XX 8.5 - 9 : [ 2 0.01 0.99 ]
|X 9 - 9.5 : [ 1 0.00 0.99 ]
#...
|XX 14.5 - 15 : [ 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 178 total values totalling 852.4900. <4.789270 +/- 1.812296>
#Range: [ 1.98 - 14.71 ]
#Most likely bin: [ 3.5 - 4 ] 28 counts
#Median bin: [ 4 - 4.5 ] 22 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1.5 - 2 : [ 1 0.01 0.01 ]
|XXXXXXXXX 2 - 2.5 : [ 6 0.03 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 16 0.09 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 16 0.09 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 28 0.16 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 22 0.12 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 19 0.11 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 21 0.12 0.72 ]
|XXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 14 0.08 0.80 ]
|XXXXXXXXXX 6 - 6.5 : [ 7 0.04 0.84 ]
|XXXXXXXXXXXXX 6.5 - 7 : [ 9 0.05 0.89 ]
|XXXXXXXXXXXXXXXX 7 - 7.5 : [ 11 0.06 0.96 ]
|XXXX 7.5 - 8 : [ 3 0.02 0.97 ]
|X 8 - 8.5 : [ 1 0.01 0.98 ]
|XXX 8.5 - 9 : [ 2 0.01 0.99 ]
#...
|XXX 14.5 - 15 : [ 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 25 2 reads 1804 bases = 1.07 +- 0.25 = 1.07 +- 0.25
Contig 38 2 reads 1518 bases = 1.15 +- 0.36 = 1.15 +- 0.36
Contig 20 2 reads 1220 bases = 1.16 +- 0.37 = 1.16 +- 0.37
Contig 16 2 reads 1257 bases = 1.19 +- 0.39 = 1.19 +- 0.39
Contig 11 2 reads 1185 bases = 1.28 +- 0.45 = 1.28 +- 0.45
Contig 35 2 reads 1474 bases = 1.31 +- 0.46 = 1.31 +- 0.46
Contig 32 2 reads 843 bases = 1.33 +- 0.47 = 1.33 +- 0.47
Contig 14 2 reads 780 bases = 1.38 +- 0.49 = 1.38 +- 0.49
Contig 24 2 reads 1041 bases = 1.38 +- 0.48 = 1.38 +- 0.48
Contig 60 3 reads 1892 bases = 1.40 +- 0.49 = 0.35 +- 1.25
Contig 12 2 reads 1026 bases = 1.44 +- 0.50 = 1.44 +- 0.50
Contig 13 2 reads 872 bases = 1.47 +- 0.50 = 1.47 +- 0.50
Contig 79 4 reads 2331 bases = 1.49 +- 0.55 = 0.61 +- 1.19
Contig 29 2 reads 1211 bases = 1.52 +- 0.50 = 1.52 +- 0.50
Contig 118 7 reads 3097 bases = 1.55 +- 0.58 = 1.00 +- 1.14
Contig 17 2 reads 763 bases = 1.57 +- 0.49 = 0.26 +- 0.60
Contig 55 3 reads 1414 bases = 1.58 +- 0.49 = 1.58 +- 0.49
Contig 53 3 reads 1494 bases = 1.61 +- 0.64 = 1.61 +- 0.64
Contig 27 2 reads 956 bases = 1.62 +- 0.49 = 1.62 +- 0.49
Contig 86 4 reads 1827 bases = 1.62 +- 0.61 = 1.62 +- 0.61
Contig 236 28 reads 3416 bases = 7.05 +- 3.46 = 1.37 +- 3.84
Contig 321 179 reads 21969 bases = 7.09 +- 3.21 = 0.08 +- 3.66
Contig 276 62 reads 7576 bases = 7.10 +- 4.21 = 3.27 +- 2.01
Contig 323 184 reads 22435 bases = 7.10 +- 3.18 = 0.00 +- 3.65
Contig 315 150 reads 17512 bases = 7.13 +- 3.97 = 0.78 +- 2.80
Contig 291 83 reads 10074 bases = 7.15 +- 3.06 = 0.75 +- 4.35
Contig 324 189 reads 22235 bases = 7.16 +- 4.04 = 0.13 +- 3.81
Contig 264 45 reads 5358 bases = 7.19 +- 6.13 = 2.58 +- 2.92
Contig 328 202 reads 23353 bases = 7.30 +- 2.82 = 0.05 +- 2.65
Contig 336 367 reads 42111 bases = 7.42 +- 3.47 = 0.47 +- 2.90
Contig 319 172 reads 19974 bases = 7.48 +- 3.84 = 0.40 +- 4.42
Contig 320 179 reads 20231 bases = 7.63 +- 3.62 = 1.17 +- 2.58
Contig 308 122 reads 13753 bases = 7.69 +- 3.36 = 1.08 +- 3.01
Contig 325 191 reads 21039 bases = 7.71 +- 3.24 = 0.35 +- 2.75
Contig 337 394 reads 40443 bases = 8.29 +- 3.58 = 0.51 +- 4.30
Contig 339 768 reads 76377 bases = 8.53 +- 4.99 = 0.03 +- 3.43
Contig 334 267 reads 25457 bases = 8.87 +- 3.33 = 0.03 +- 2.94
Contig 206 18 reads 1685 bases = 9.45 +- 5.28 = 4.40 +- 4.06
Contig 316 154 reads 9409 bases = 14.62 +- 7.59 = 0.81 +- 3.97
Contig 331 224 reads 13411 bases = 14.71 +- 6.77 = 0.80 +- 3.59
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 469
HQ Discrepant reads = 57
Chimeric reads = 15
Suspect alignments = 64
-------------------------------------------------------------------
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/microbe2/3635487/edit_dir.03Nov04.QC