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: 12-13-2005
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
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Lactococcus_lactis
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Lactobacillales, order, eubacteria
Bacilli, class, eubacteria
Lactococcus lactis, species, eubacteria
Lactococcus (lactic streptococci), genus, eubacteria
Streptococcaceae, family, eubacteria
Firmicutes (Gram-positive bacteria), phylum, eubacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
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Genome size estimates
-------------------------------------------------------------------
# contigs: 220081
# phrap: 176359
# db:
altered.
198220 +/- 21861
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 1918
Number of reads with percent X's >= 20%: 16 = 0.4%
Number of reads with percent X's >= 50%: 7 = 0.2%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 4305
Total bp X'd : 75226
reads >= 20% >= 50% >= 80% screened
Nr with L09136 1918 16 7 0
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 50
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: 124
Total bp X'd : 1828
reads >= 20% >= 50% >= 80% screened
Nr with L09136 50 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 1104932
C = 589575
G = 590945
T = 1117301
N = 25840
X = 75226
GC fraction = 0.34
Total = 3503819
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436157_fasta.screen.contigs
-------------------------------------------------------------------
A 73533
C 37807
G 37809
T 72993
N 29
fraction GC = 0.34
total bases = 222171
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 WPE reads.list > grep.reads.list.WPE
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.WPE 4 500
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#Found 1599 total values totalling 3400475.0000. <2126.626016 +/- 329.184183>
#Range: [ 804 - 2952 ]
#Most likely bin: [ 2000 - 2500 ] 676 counts
#Median bin: [ 2000 - 2500 ] 676 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
|X 1000 - 1500 : [ 13 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1500 - 2000 : [ 652 0.41 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 2500 : [ 676 0.42 0.84 ]
|XXXXXXXXXXXXXXX 2500 - 3000 : [ 256 0.16 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
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# WPE 2037 +- 353 (n=806)
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Library / Read Quality summary
extracted from 3436157_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
WPE 4608 -1 -1 98 682 4305 100 695 100 701
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
WPE 2161 100 691 100 705 2144 100 700 100 696
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436157_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
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plate(s) reads clones LIBRARY @
] 4305 2198 91.58 cumulative total @@
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 3436157_fasta.screen.trimQ15.SaF 4 50
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#Found 4305 total values totalling 2987733.0000. <694.014634 +/- 77.179412>
#Range: [ 38 - 824 ]
#Most likely bin: [ 700 - 750 ] 1933 counts
#Median bin: [ 700 - 750 ] 1933 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 2 0.00 0.00 ]
| 50 - 100 : [ 7 0.00 0.00 ]
| 100 - 150 : [ 13 0.00 0.01 ]
| 150 - 200 : [ 9 0.00 0.01 ]
| 200 - 250 : [ 11 0.00 0.01 ]
| 250 - 300 : [ 8 0.00 0.01 ]
| 300 - 350 : [ 11 0.00 0.01 ]
| 350 - 400 : [ 17 0.00 0.02 ]
| 400 - 450 : [ 18 0.00 0.02 ]
| 450 - 500 : [ 12 0.00 0.03 ]
| 500 - 550 : [ 20 0.00 0.03 ]
| 550 - 600 : [ 23 0.01 0.04 ]
|XXXXX 600 - 650 : [ 229 0.05 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1547 0.36 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1933 0.45 0.90 ]
|XXXXXXXXX 750 - 800 : [ 422 0.10 0.99 ]
| 800 - 850 : [ 23 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for WPE
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep WPE 3436157_fasta.screen.trimQ15.SaF > reads.trim15.WPE.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.WPE.rl 2 50
-------------------------------------------------------------------
#Found 4305 total values totalling 2987733.0000. <694.014634 +/- 77.179412>
#Range: [ 38 - 824 ]
#Most likely bin: [ 700 - 750 ] 1933 counts
#Median bin: [ 700 - 750 ] 1933 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 2 0.00 0.00 ]
| 50 - 100 : [ 7 0.00 0.00 ]
| 100 - 150 : [ 13 0.00 0.01 ]
| 150 - 200 : [ 9 0.00 0.01 ]
| 200 - 250 : [ 11 0.00 0.01 ]
| 250 - 300 : [ 8 0.00 0.01 ]
| 300 - 350 : [ 11 0.00 0.01 ]
| 350 - 400 : [ 17 0.00 0.02 ]
| 400 - 450 : [ 18 0.00 0.02 ]
| 450 - 500 : [ 12 0.00 0.03 ]
| 500 - 550 : [ 20 0.00 0.03 ]
| 550 - 600 : [ 23 0.01 0.04 ]
|XXXXX 600 - 650 : [ 229 0.05 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1547 0.36 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1933 0.45 0.90 ]
|XXXXXXXXX 750 - 800 : [ 422 0.10 0.99 ]
| 800 - 850 : [ 23 0.01 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436157
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GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436157_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436157_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 4302 total values totalling 1462.2583. <0.339902 +/- 0.038209>
#Range: [ 0.2186 - 0.6977 ]
#Most likely bin: [ 0.325 - 0.33 ] 259 counts
#Median bin: [ 0.335 - 0.34 ] 208 counts
| 0.215 - 0.22 : [ 1 0.00 0.00 ]
| 0.22 - 0.225 : [ 1 0.00 0.00 ]
| 0.225 - 0.23 : [ 2 0.00 0.00 ]
| 0.23 - 0.235 : [ 3 0.00 0.00 ]
|X 0.235 - 0.24 : [ 4 0.00 0.00 ]
|X 0.24 - 0.245 : [ 7 0.00 0.00 ]
|X 0.245 - 0.25 : [ 6 0.00 0.01 ]
|XX 0.25 - 0.255 : [ 15 0.00 0.01 ]
|XXX 0.255 - 0.26 : [ 18 0.00 0.01 ]
|XXXXXX 0.26 - 0.265 : [ 42 0.01 0.02 ]
|XXXXXXX 0.265 - 0.27 : [ 44 0.01 0.03 ]
|XXXXXXX 0.27 - 0.275 : [ 48 0.01 0.04 ]
|XXXXXXXXX 0.275 - 0.28 : [ 58 0.01 0.06 ]
|XXXXXXXXX 0.28 - 0.285 : [ 57 0.01 0.07 ]
|XXXXXXXXXX 0.285 - 0.29 : [ 66 0.02 0.09 ]
|XXXXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 115 0.03 0.11 ]
|XXXXXXXXXXXXXXXX 0.295 - 0.3 : [ 102 0.02 0.14 ]
|XXXXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 135 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 163 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 200 0.05 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 208 0.05 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 220 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 259 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 227 0.05 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 208 0.05 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 218 0.05 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 225 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 198 0.05 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 195 0.05 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 193 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 169 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 147 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 141 0.03 0.86 ]
|XXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 107 0.02 0.88 ]
|XXXXXXXXXXXXX 0.385 - 0.39 : [ 86 0.02 0.90 ]
|XXXXXXXXXXXX 0.39 - 0.395 : [ 78 0.02 0.92 ]
|XXXXXXXXXXXX 0.395 - 0.4 : [ 77 0.02 0.94 ]
|XXXXXXXXX 0.4 - 0.405 : [ 58 0.01 0.95 ]
|XXXXXXX 0.405 - 0.41 : [ 47 0.01 0.96 ]
|XXXXXXX 0.41 - 0.415 : [ 44 0.01 0.97 ]
|XXXXX 0.415 - 0.42 : [ 34 0.01 0.98 ]
|XX 0.42 - 0.425 : [ 14 0.00 0.99 ]
|XXX 0.425 - 0.43 : [ 22 0.01 0.99 ]
|X 0.43 - 0.435 : [ 4 0.00 0.99 ]
|XX 0.435 - 0.44 : [ 11 0.00 0.99 ]
|X 0.44 - 0.445 : [ 6 0.00 1.00 ]
|X 0.445 - 0.45 : [ 7 0.00 1.00 ]
|X 0.45 - 0.455 : [ 6 0.00 1.00 ]
| 0.455 - 0.46 : [ 1 0.00 1.00 ]
#...
| 0.465 - 0.47 : [ 2 0.00 1.00 ]
| 0.47 - 0.475 : [ 1 0.00 1.00 ]
#...
| 0.64 - 0.645 : [ 1 0.00 1.00 ]
#...
| 0.695 - 0.7 : [ 1 0.00 1.00 ]
Contigs and Assemblies
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Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
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Contig 16. 5 reads; 2083 bp (untrimmed), 2035 (trimmed).
Contig 17. 6 reads; 1466 bp (untrimmed), 1463 (trimmed).
Contig 18. 6 reads; 1984 bp (untrimmed), 1952 (trimmed).
Contig 19. 6 reads; 2713 bp (untrimmed), 2696 (trimmed).
Contig 20. 6 reads; 1729 bp (untrimmed), 1700 (trimmed).
Contig 21. 7 reads; 2409 bp (untrimmed), 2386 (trimmed).
Contig 22. 7 reads; 2810 bp (untrimmed), 2622 (trimmed).
Contig 23. 7 reads; 2482 bp (untrimmed), 2458 (trimmed).
Contig 24. 8 reads; 2070 bp (untrimmed), 2050 (trimmed).
Contig 25. 8 reads; 3006 bp (untrimmed), 2937 (trimmed).
Contig 26. 10 reads; 3116 bp (untrimmed), 3093 (trimmed).
Contig 27. 10 reads; 1240 bp (untrimmed), 1221 (trimmed).
Contig 28. 12 reads; 3710 bp (untrimmed), 3644 (trimmed).
Contig 29. 12 reads; 4352 bp (untrimmed), 4220 (trimmed).
Contig 30. 13 reads; 4998 bp (untrimmed), 4896 (trimmed).
Contig 31. 19 reads; 4754 bp (untrimmed), 4748 (trimmed).
Contig 32. 24 reads; 5944 bp (untrimmed), 5903 (trimmed).
Contig 33. 95 reads; 3290 bp (untrimmed), 3271 (trimmed).
Contig 34. 116 reads; 1507 bp (untrimmed), 1497 (trimmed).
Contig 35. 129 reads; 11430 bp (untrimmed), 11392 (trimmed).
Contig 36. 168 reads; 15006 bp (untrimmed), 14951 (trimmed).
Contig 37. 310 reads; 19393 bp (untrimmed), 19393 (trimmed).
Contig 38. 353 reads; 5285 bp (untrimmed), 5249 (trimmed).
Contig 39. 449 reads; 31751 bp (untrimmed), 31751 (trimmed).
Contig 40. 649 reads; 6484 bp (untrimmed), 6301 (trimmed).
Contig 41. 652 reads; 45337 bp (untrimmed), 45337 (trimmed).
Contig 42. 1041 reads; 7815 bp (untrimmed), 7783 (trimmed).
--------------------------------------------------------------
Totals 4181 reads; 222171 bp (untrimmed), 220081 (trimmed).
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Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
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depth.out contains 222171 bases = 14.53 +- 24.41 = 0.45 +- 4.36
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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 42 total values totalling 434.5200. <10.345714 +/- 21.582079>
#Range: [ 1.25 - 103.59 ]
#Most likely bin: [ 1.5 - 2 ] 11 counts
#Median bin: [ 2 - 2.5 ] 10 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 1 - 1.5 : [ 4 0.10 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 11 0.26 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 10 0.24 0.60 ]
|XXXXXXX 2.5 - 3 : [ 2 0.05 0.64 ]
|XXXXXXXXXXXXXXX 3 - 3.5 : [ 4 0.10 0.74 ]
#...
|XXXX 6 - 6.5 : [ 1 0.02 0.76 ]
#...
|XXXXXXX 8.5 - 9 : [ 2 0.05 0.81 ]
#...
|XXXX 10.5 - 11 : [ 1 0.02 0.83 ]
|XXXX 11 - 11.5 : [ 1 0.02 0.86 ]
#...
|XXXX 12 - 12.5 : [ 1 0.02 0.88 ]
#...
|XXXX 20 - 20.5 : [ 1 0.02 0.90 ]
#...
|XXXX 51.5 - 52 : [ 1 0.02 0.93 ]
#...
|XXXX 59 - 59.5 : [ 1 0.02 0.95 ]
#...
|XXXX 77 - 77.5 : [ 1 0.02 0.98 ]
#...
|XXXX 103.5 - 104 : [ 1 0.02 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 15 total values totalling 320.0900. <21.339333 +/- 30.089486>
#Range: [ 2.02 - 103.59 ]
#Most likely bin: [ 2 - 2.5 ] 3 counts
#Median bin: [ 8.5 - 9 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 3 0.20 0.20 ]
|XXXXXXXXXXXXX 2.5 - 3 : [ 1 0.07 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 2 0.13 0.40 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 2 0.13 0.53 ]
#...
|XXXXXXXXXXXXX 10.5 - 11 : [ 1 0.07 0.60 ]
|XXXXXXXXXXXXX 11 - 11.5 : [ 1 0.07 0.67 ]
#...
|XXXXXXXXXXXXX 12 - 12.5 : [ 1 0.07 0.73 ]
#...
|XXXXXXXXXXXXX 20 - 20.5 : [ 1 0.07 0.80 ]
#...
|XXXXXXXXXXXXX 51.5 - 52 : [ 1 0.07 0.87 ]
#...
|XXXXXXXXXXXXX 77 - 77.5 : [ 1 0.07 0.93 ]
#...
|XXXXXXXXXXXXX 103.5 - 104 : [ 1 0.07 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 4 3 reads 1974 bases = 1.25 +- 0.43 = 0.39 +- 1.12
Contig 9 3 reads 1752 bases = 1.34 +- 0.47 = 0.47 +- 1.24
Contig 3 3 reads 1687 bases = 1.41 +- 0.49 = 1.41 +- 0.49
Contig 7 3 reads 1541 bases = 1.48 +- 0.50 = 0.58 +- 1.15
Contig 12 4 reads 1853 bases = 1.60 +- 0.49 = -0.01 +- 0.74
Contig 11 4 reads 1849 bases = 1.63 +- 0.63 = 0.01 +- 1.44
Contig 1 2 reads 941 bases = 1.70 +- 0.46 = 0.00 +- 0.55
Contig 16 5 reads 2083 bases = 1.76 +- 0.70 = 0.26 +- 0.77
Contig 8 3 reads 1346 bases = 1.76 +- 0.73 = 1.76 +- 0.73
Contig 14 5 reads 2222 bases = 1.78 +- 0.76 = 0.38 +- 1.04
Contig 19 6 reads 2713 bases = 1.80 +- 0.64 = -0.01 +- 1.66
Contig 2 3 reads 1291 bases = 1.85 +- 0.78 = 1.85 +- 0.78
Contig 6 3 reads 1284 bases = 1.87 +- 0.79 = 1.87 +- 0.79
Contig 5 3 reads 1196 bases = 1.92 +- 0.81 = 1.92 +- 0.81
Contig 22 7 reads 2810 bases = 1.94 +- 0.56 = 0.28 +- 1.40
Contig 13 5 reads 1927 bases = 2.01 +- 0.90 = 0.42 +- 1.16
Contig 25 8 reads 3006 bases = 2.02 +- 0.81 = 0.54 +- 0.97
Contig 30 13 reads 4998 bases = 2.02 +- 0.83 = 0.16 +- 1.16
Contig 15 5 reads 1919 bases = 2.06 +- 1.11 = 1.20 +- 0.47
Contig 29 12 reads 4352 bases = 2.14 +- 1.49 = 0.70 +- 0.72
Contig 18 6 reads 1984 bases = 2.32 +- 0.84 = 0.01 +- 0.78
Contig 20 6 reads 1729 bases = 2.46 +- 0.57 = 0.56 +- 0.74
Contig 26 10 reads 3116 bases = 2.48 +- 0.95 = 0.46 +- 1.71
Contig 28 12 reads 3710 bases = 2.51 +- 0.91 = 0.08 +- 1.55
Contig 10 4 reads 1225 bases = 2.56 +- 1.09 = 1.24 +- 1.44
Contig 24 8 reads 2070 bases = 3.03 +- 0.91 = 0.79 +- 0.91
Contig 32 24 reads 5944 bases = 3.03 +- 1.11 = 0.35 +- 2.15
Contig 17 6 reads 1466 bases = 3.05 +- 1.20 = 0.95 +- 2.35
Contig 31 19 reads 4754 bases = 3.08 +- 1.01 = 0.16 +- 1.79
Contig 27 10 reads 1240 bases = 6.28 +- 2.60 = 6.28 +- 2.60
Contig 36 168 reads 15006 bases = 8.60 +- 3.44 = 0.09 +- 2.55
Contig 35 129 reads 11430 bases = 8.62 +- 3.81 = 0.33 +- 2.44
Contig 39 449 reads 31751 bases = 10.91 +- 5.08 = 0.18 +- 3.79
Contig 41 652 reads 45337 bases = 11.07 +- 5.45 = 0.13 +- 4.14
Contig 37 310 reads 19393 bases = 12.43 +- 4.71 = 0.08 +- 3.92
Contig 33 95 reads 3290 bases = 20.37 +- 10.43 = 1.14 +- 4.57
Contig 38 353 reads 5285 bases = 51.78 +- 18.10 = 0.35 +- 7.86
Contig 34 116 reads 1507 bases = 59.22 +- 32.44 = 1.93 +- 4.59
Contig 40 649 reads 6484 bases = 77.46 +- 32.92 = 2.05 +- 14.02
Contig 42 1041 reads 7815 bases = 103.59 +- 30.51 = 1.76 +- 8.58
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 80
HQ Discrepant reads = 5
Chimeric reads = 9
Suspect alignments = 82
-------------------------------------------------------------------
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/bermuda/draft004/prefin/projects/3436157/edit_dir.20Jan04.QD