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
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634642 10000 1854 Frankia sp.
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Frankia_sp.
-------------------------------------------------------------------
Actinobacteria, phylum, actinobacteria
Frankineae, suborder, high GC Gram+
Actinobacteridae, subclass, high GC Gram+
Frankiaceae, family, high GC Gram+
Actinomycetales, order, high GC Gram+
Frankia sp., species, high GC Gram+
Frankia, genus, high GC Gram+
Actinobacteria (class) (high G+C Gram-positive bacteria), class, high GC Gram+
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 8943736
# phrap: 8690932
# db:
altered.
10000000
9211556 +/- 566986
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 26773
Number of reads with percent X's >= 20%: 902 = 0.7%
Number of reads with percent X's >= 50%: 509 = 0.4%
Number of reads with percent X's >= 80%: 51 = 0.0%
Total reads in project: 125786
Total bp X'd : 1404442
reads >= 20% >= 50% >= 80% screened
Nr with L09136 22161 316 161 18
Nr with pCC1Fos 3817 1 0 0
Nr with pMCL200_JGI_XZX+XZK 795 585 348 33
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 22
Number of reads with percent X's >= 20%: 3 = 1.8%
Number of reads with percent X's >= 50%: 1 = 0.6%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 171
Total bp X'd : 1828
reads >= 20% >= 50% >= 80% screened
Nr with L09136 14 1 1 0
Nr with pCC1Fos 5 1 0 0
Nr with pMCL200_JGI_XZX+XZK 3 1 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 18430660
C = 40925655
G = 39577440
T = 19384456
N = 525838
X = 1404442
GC fraction = 0.67
Total = 120248491
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634642_fasta.screen.contigs
-------------------------------------------------------------------
A 1326295
C 3239306
G 3202503
T 1312926
N 385
fraction GC = 0.71
total bases = 9081415
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 AISX reads.list > grep.reads.list.AISX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AISX 4 500
-------------------------------------------------------------------
#Found 24751 total values totalling 82589655.0000. <3336.820937 +/- 1458.238693>
#Range: [ 200 - 222216 ]
#Most likely bin: [ 3000 - 3500 ] 13354 counts
#Median bin: [ 3000 - 3500 ] 13354 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 2 0.00 0.00 ]
| 500 - 1000 : [ 21 0.00 0.00 ]
|X 1000 - 1500 : [ 210 0.01 0.01 ]
|X 1500 - 2000 : [ 243 0.01 0.02 ]
|XX 2000 - 2500 : [ 588 0.02 0.04 ]
|XXXXXX 2500 - 3000 : [ 1854 0.07 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 13354 0.54 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 8207 0.33 0.99 ]
|X 4000 - 4500 : [ 267 0.01 1.00 ]
#...
| 5500 - 6000 : [ 1 0.00 1.00 ]
#...
| 7000 - 7500 : [ 1 0.00 1.00 ]
#...
| 12000 - 12500 : [ 1 0.00 1.00 ]
#...
| 19000 - 19500 : [ 1 0.00 1.00 ]
#...
| 222000 - 222500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AISY reads.list > grep.reads.list.AISY
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AISY 4 500
-------------------------------------------------------------------
#Found 21278 total values totalling 124034508.0000. <5829.237146 +/- 1249.970431>
#Range: [ 186 - 81254 ]
#Most likely bin: [ 5500 - 6000 ] 6070 counts
#Median bin: [ 5500 - 6000 ] 6070 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 2 0.00 0.00 ]
| 500 - 1000 : [ 26 0.00 0.00 ]
|X 1000 - 1500 : [ 199 0.01 0.01 ]
|X 1500 - 2000 : [ 203 0.01 0.02 ]
|X 2000 - 2500 : [ 189 0.01 0.03 ]
|X 2500 - 3000 : [ 197 0.01 0.04 ]
|X 3000 - 3500 : [ 192 0.01 0.05 ]
|XX 3500 - 4000 : [ 286 0.01 0.06 ]
|XXX 4000 - 4500 : [ 457 0.02 0.08 ]
|XXXXX 4500 - 5000 : [ 792 0.04 0.12 ]
|XXXXXXXXXXXXXX 5000 - 5500 : [ 2139 0.10 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 6070 0.29 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 5785 0.27 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 3628 0.17 0.95 ]
|XXXXXXX 7000 - 7500 : [ 1090 0.05 1.00 ]
| 7500 - 8000 : [ 13 0.00 1.00 ]
| 8000 - 8500 : [ 3 0.00 1.00 ]
| 8500 - 9000 : [ 2 0.00 1.00 ]
| 9000 - 9500 : [ 1 0.00 1.00 ]
#...
| 14000 - 14500 : [ 1 0.00 1.00 ]
#...
| 38500 - 39000 : [ 1 0.00 1.00 ]
#...
| 56000 - 56500 : [ 1 0.00 1.00 ]
#...
| 81000 - 81500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AISZ reads.list > grep.reads.list.AISZ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AISZ 4 500
-------------------------------------------------------------------
#Found 1223 total values totalling 50117972.0000. <40979.535568 +/- 4707.621278>
#Range: [ 12395 - 101501 ]
#Most likely bin: [ 41000 - 41500 ] 81 counts
#Median bin: [ 41000 - 41500 ] 81 counts
#Histogram Bins Count Fraction Cum_Fraction
| 12000 - 12500 : [ 1 0.00 0.00 ]
#...
| 17000 - 17500 : [ 1 0.00 0.00 ]
#...
| 23500 - 24000 : [ 1 0.00 0.00 ]
#...
| 27000 - 27500 : [ 1 0.00 0.00 ]
#...
| 28000 - 28500 : [ 1 0.00 0.00 ]
#...
| 30500 - 31000 : [ 1 0.00 0.00 ]
|X 31000 - 31500 : [ 3 0.00 0.01 ]
|XX 31500 - 32000 : [ 4 0.00 0.01 ]
|X 32000 - 32500 : [ 2 0.00 0.01 ]
|X 32500 - 33000 : [ 3 0.00 0.01 ]
|XXX 33000 - 33500 : [ 6 0.00 0.02 ]
|XXX 33500 - 34000 : [ 7 0.01 0.03 ]
|XXXX 34000 - 34500 : [ 8 0.01 0.03 ]
|XXXXXXXX 34500 - 35000 : [ 16 0.01 0.04 ]
|XXXXXXXX 35000 - 35500 : [ 16 0.01 0.06 ]
|XXXXXXX 35500 - 36000 : [ 14 0.01 0.07 ]
|XXXXXXXXXX 36000 - 36500 : [ 20 0.02 0.09 ]
|XXXXXXXXXXXXXXXXX 36500 - 37000 : [ 34 0.03 0.11 ]
|XXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 36 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 45 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 58 0.05 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 54 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 62 0.05 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 76 0.06 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 63 0.05 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 66 0.05 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 81 0.07 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 76 0.06 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 59 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 74 0.06 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 74 0.06 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 58 0.05 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 44000 - 44500 : [ 49 0.04 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXX 44500 - 45000 : [ 45 0.04 0.91 ]
|XXXXXXXXXXXXXXXXXX 45000 - 45500 : [ 37 0.03 0.94 ]
|XXXXXXXXXXXXXX 45500 - 46000 : [ 28 0.02 0.96 ]
|XXXXXXXXXXXX 46000 - 46500 : [ 25 0.02 0.99 ]
|XXXX 46500 - 47000 : [ 8 0.01 0.99 ]
|XX 47000 - 47500 : [ 5 0.00 1.00 ]
| 47500 - 48000 : [ 1 0.00 1.00 ]
#...
| 95000 - 95500 : [ 1 0.00 1.00 ]
#...
|X 99500 - 100000 : [ 2 0.00 1.00 ]
#...
| 101500 - 102000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AISZ 40797 +- 3134 (n=553)
# AISX 3212 +- 512 (n=12278)
# AISY 5647 +- 1313 (n=10204)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634642_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
AISX 64128 -1 -1 96 618 63922 90 617 93 621
AISY 71136 -1 -1 90 531 70583 80 545 86 545
AISZ 11520 -1 -1 89 522 11520 84 565 90 582
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AISX 31777 88 599 93 608 32145 92 635 94 634
AISY 35516 82 558 88 562 35067 78 531 85 527
AISZ 5760 80 567 88 563 5760 88 563 92 601
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634642_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
60 9947 5533 92.22 96.06 AISZ @
332 58078 30526 91.95 95.78 AISX @
368 57761 32058 87.11 90.74 AISY @
] 125786 68117 89.63 cumulative total@@
LIBRARY PLATE ID COUNT [ AISZ 60 AISX 332 AISY 368 ] for 760 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 3634642_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 146025 total values totalling 71980343.0000. <492.931642 +/- 268.311499>
#Range: [ 0 - 925 ]
#Most likely bin: [ 0 - 50 ] 19219 counts
#Median bin: [ 550 - 600 ] 10190 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 19219 0.13 0.13 ]
|XXXXXXX 50 - 100 : [ 3428 0.02 0.16 ]
|XXXXXXX 100 - 150 : [ 3132 0.02 0.18 ]
|XXXXXXX 150 - 200 : [ 3301 0.02 0.20 ]
|XXXXXXXX 200 - 250 : [ 3628 0.02 0.22 ]
|XXXXXXXXX 250 - 300 : [ 4407 0.03 0.25 ]
|XXXXXXXXX 300 - 350 : [ 4521 0.03 0.29 ]
|XXXXXXXXXX 350 - 400 : [ 4985 0.03 0.32 ]
|XXXXXXXXXXXX 400 - 450 : [ 5574 0.04 0.36 ]
|XXXXXXXXXXXXX 450 - 500 : [ 6322 0.04 0.40 ]
|XXXXXXXXXXXXXXXXX 500 - 550 : [ 8096 0.06 0.46 ]
|XXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 10190 0.07 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 12841 0.09 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 15858 0.11 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 16774 0.11 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 14462 0.10 0.94 ]
|XXXXXXXXXXXXXXXXX 800 - 850 : [ 7944 0.05 0.99 ]
|XXX 850 - 900 : [ 1317 0.01 1.00 ]
| 900 - 950 : [ 26 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AISX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AISX 3634642_fasta.screen.trimQ15.SaF > reads.trim15.AISX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AISX.rl 2 50
-------------------------------------------------------------------
#Found 63922 total values totalling 35570323.0000. <556.464488 +/- 249.900435>
#Range: [ 0 - 925 ]
#Most likely bin: [ 700 - 750 ] 8714 counts
#Median bin: [ 600 - 650 ] 5631 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 5435 0.09 0.09 ]
|XXXXX 50 - 100 : [ 1056 0.02 0.10 ]
|XXXXX 100 - 150 : [ 1037 0.02 0.12 ]
|XXXXX 150 - 200 : [ 1132 0.02 0.14 ]
|XXXXXX 200 - 250 : [ 1292 0.02 0.16 ]
|XXXXXXX 250 - 300 : [ 1456 0.02 0.18 ]
|XXXXXXX 300 - 350 : [ 1564 0.02 0.20 ]
|XXXXXXXXX 350 - 400 : [ 1959 0.03 0.23 ]
|XXXXXXXXXX 400 - 450 : [ 2119 0.03 0.27 ]
|XXXXXXXXXXX 450 - 500 : [ 2441 0.04 0.30 ]
|XXXXXXXXXXXXXX 500 - 550 : [ 3084 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 4234 0.07 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 5631 0.09 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 7606 0.12 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8714 0.14 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8579 0.13 0.90 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5471 0.09 0.98 ]
|XXXXX 850 - 900 : [ 1089 0.02 1.00 ]
| 900 - 950 : [ 23 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AISY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AISY 3634642_fasta.screen.trimQ15.SaF > reads.trim15.AISY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AISY.rl 2 50
-------------------------------------------------------------------
#Found 70583 total values totalling 30905221.0000. <437.856439 +/- 271.515205>
#Range: [ 0 - 906 ]
#Most likely bin: [ 0 - 50 ] 12238 counts
#Median bin: [ 500 - 550 ] 4576 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 12238 0.17 0.17 ]
|XXXXXXX 50 - 100 : [ 2064 0.03 0.20 ]
|XXXXXX 100 - 150 : [ 1860 0.03 0.23 ]
|XXXXXX 150 - 200 : [ 1955 0.03 0.26 ]
|XXXXXXX 200 - 250 : [ 2039 0.03 0.29 ]
|XXXXXXX 250 - 300 : [ 2084 0.03 0.32 ]
|XXXXXXXX 300 - 350 : [ 2353 0.03 0.35 ]
|XXXXXXXXX 350 - 400 : [ 2676 0.04 0.39 ]
|XXXXXXXXXX 400 - 450 : [ 3161 0.04 0.43 ]
|XXXXXXXXXXXX 450 - 500 : [ 3561 0.05 0.48 ]
|XXXXXXXXXXXXXXX 500 - 550 : [ 4576 0.06 0.55 ]
|XXXXXXXXXXXXXXXXX 550 - 600 : [ 5342 0.08 0.62 ]
|XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 6367 0.09 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 7020 0.10 0.81 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6390 0.09 0.90 ]
|XXXXXXXXXXXXXXX 750 - 800 : [ 4634 0.07 0.97 ]
|XXXXXXX 800 - 850 : [ 2062 0.03 1.00 ]
|X 850 - 900 : [ 198 0.00 1.00 ]
| 900 - 950 : [ 3 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AISZ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AISZ 3634642_fasta.screen.trimQ15.SaF > reads.trim15.AISZ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AISZ.rl 2 50
-------------------------------------------------------------------
#Found 11520 total values totalling 5504799.0000. <477.847135 +/- 270.416558>
#Range: [ 0 - 891 ]
#Most likely bin: [ 700 - 750 ] 1670 counts
#Median bin: [ 550 - 600 ] 614 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1546 0.13 0.13 ]
|XXXXXXX 50 - 100 : [ 308 0.03 0.16 ]
|XXXXXX 100 - 150 : [ 235 0.02 0.18 ]
|XXXXX 150 - 200 : [ 214 0.02 0.20 ]
|XXXXXXX 200 - 250 : [ 297 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 867 0.08 0.30 ]
|XXXXXXXXXXXXXX 300 - 350 : [ 604 0.05 0.35 ]
|XXXXXXXX 350 - 400 : [ 350 0.03 0.38 ]
|XXXXXXX 400 - 450 : [ 294 0.03 0.41 ]
|XXXXXXXX 450 - 500 : [ 320 0.03 0.44 ]
|XXXXXXXXXX 500 - 550 : [ 436 0.04 0.47 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 614 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 843 0.07 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1232 0.11 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1670 0.14 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1249 0.11 0.96 ]
|XXXXXXXXXX 800 - 850 : [ 411 0.04 1.00 ]
|X 850 - 900 : [ 30 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634642
-------------------------------------------------------------------
AISX.000001.000100 pUC18.fa LRS.fasta
AISX.000101.000200 pUC18.fa LRS.fasta
AISX.000201.000300 pUC18.fa LRS.fasta
AISX.000301.000400 pUC18.fa LRS.fasta
AISY.000001.000100 pMCL200.fa LRS.fasta
AISY.000101.000200 pMCL200.fa LRS.fasta
AISY.000201.000300 pMCL200.fa LRS.fasta
AISY.000301.000400 pMCL200.fa LRS.fasta
AISZ.000001.000100 pCC1Fos.fa LRS.fasta
AISX.000001.000100 pUC18.fa LRS.fasta
AISX.000101.000200 pUC18.fa LRS.fasta
AISX.000201.000300 pUC18.fa LRS.fasta
AISX.000301.000400 pUC18.fa LRS.fasta
AISY.000001.000100 pMCL200.fa LRS.fasta
AISY.000101.000200 pMCL200.fa LRS.fasta
AISY.000201.000300 pMCL200.fa LRS.fasta
AISY.000301.000400 pMCL200.fa LRS.fasta
AISZ.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634642_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634642_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 125270 total values totalling 88206.7974. <0.704133 +/- 0.046595>
#Range: [ 0.2895 - 1 ]
#Most likely bin: [ 0.71 - 0.715 ] 5836 counts
#Median bin: [ 0.705 - 0.71 ] 5793 counts
| 0.285 - 0.29 : [ 1 0.00 0.00 ]
#...
| 0.305 - 0.31 : [ 1 0.00 0.00 ]
| 0.31 - 0.315 : [ 1 0.00 0.00 ]
#...
| 0.325 - 0.33 : [ 2 0.00 0.00 ]
| 0.33 - 0.335 : [ 3 0.00 0.00 ]
#...
| 0.35 - 0.355 : [ 1 0.00 0.00 ]
#...
| 0.36 - 0.365 : [ 2 0.00 0.00 ]
#...
| 0.375 - 0.38 : [ 2 0.00 0.00 ]
#...
| 0.385 - 0.39 : [ 1 0.00 0.00 ]
| 0.39 - 0.395 : [ 5 0.00 0.00 ]
#...
| 0.405 - 0.41 : [ 1 0.00 0.00 ]
| 0.41 - 0.415 : [ 3 0.00 0.00 ]
| 0.415 - 0.42 : [ 2 0.00 0.00 ]
| 0.42 - 0.425 : [ 2 0.00 0.00 ]
| 0.425 - 0.43 : [ 2 0.00 0.00 ]
#...
| 0.435 - 0.44 : [ 2 0.00 0.00 ]
| 0.44 - 0.445 : [ 4 0.00 0.00 ]
| 0.445 - 0.45 : [ 4 0.00 0.00 ]
| 0.45 - 0.455 : [ 9 0.00 0.00 ]
| 0.455 - 0.46 : [ 5 0.00 0.00 ]
| 0.46 - 0.465 : [ 7 0.00 0.00 ]
| 0.465 - 0.47 : [ 5 0.00 0.00 ]
| 0.47 - 0.475 : [ 6 0.00 0.00 ]
| 0.475 - 0.48 : [ 10 0.00 0.00 ]
| 0.48 - 0.485 : [ 13 0.00 0.00 ]
| 0.485 - 0.49 : [ 9 0.00 0.00 ]
| 0.49 - 0.495 : [ 12 0.00 0.00 ]
| 0.495 - 0.5 : [ 7 0.00 0.00 ]
| 0.5 - 0.505 : [ 36 0.00 0.00 ]
| 0.505 - 0.51 : [ 14 0.00 0.00 ]
| 0.51 - 0.515 : [ 16 0.00 0.00 ]
| 0.515 - 0.52 : [ 24 0.00 0.00 ]
| 0.52 - 0.525 : [ 25 0.00 0.00 ]
| 0.525 - 0.53 : [ 41 0.00 0.00 ]
| 0.53 - 0.535 : [ 70 0.00 0.00 ]
| 0.535 - 0.54 : [ 63 0.00 0.00 ]
|X 0.54 - 0.545 : [ 76 0.00 0.00 ]
|X 0.545 - 0.55 : [ 82 0.00 0.00 ]
|X 0.55 - 0.555 : [ 110 0.00 0.01 ]
|X 0.555 - 0.56 : [ 105 0.00 0.01 ]
|X 0.56 - 0.565 : [ 156 0.00 0.01 ]
|X 0.565 - 0.57 : [ 154 0.00 0.01 ]
|X 0.57 - 0.575 : [ 150 0.00 0.01 ]
|XX 0.575 - 0.58 : [ 222 0.00 0.01 ]
|XX 0.58 - 0.585 : [ 246 0.00 0.01 ]
|XX 0.585 - 0.59 : [ 312 0.00 0.02 ]
|XX 0.59 - 0.595 : [ 319 0.00 0.02 ]
|XXX 0.595 - 0.6 : [ 398 0.00 0.02 ]
|XXX 0.6 - 0.605 : [ 475 0.00 0.03 ]
|XXX 0.605 - 0.61 : [ 485 0.00 0.03 ]
|XXXX 0.61 - 0.615 : [ 647 0.01 0.03 ]
|XXXXX 0.615 - 0.62 : [ 714 0.01 0.04 ]
|XXXXXX 0.62 - 0.625 : [ 835 0.01 0.05 ]
|XXXXXXX 0.625 - 0.63 : [ 1029 0.01 0.06 ]
|XXXXXXXXX 0.63 - 0.635 : [ 1259 0.01 0.07 ]
|XXXXXXXXXX 0.635 - 0.64 : [ 1476 0.01 0.08 ]
|XXXXXXXXXXXX 0.64 - 0.645 : [ 1754 0.01 0.09 ]
|XXXXXXXXXXXXXX 0.645 - 0.65 : [ 2094 0.02 0.11 ]
|XXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 2453 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 2950 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 3204 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 3766 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 4130 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 4515 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 4906 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 5126 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 5290 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 5496 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 5711 0.05 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 5793 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 5836 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 5706 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 5545 0.04 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.725 - 0.73 : [ 5455 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.73 - 0.735 : [ 4984 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.735 - 0.74 : [ 4738 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.74 - 0.745 : [ 4189 0.03 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.745 - 0.75 : [ 3394 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.75 - 0.755 : [ 3545 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXX 0.755 - 0.76 : [ 2791 0.02 0.90 ]
|XXXXXXXXXXXXXXXXX 0.76 - 0.765 : [ 2455 0.02 0.92 ]
|XXXXXXXXXXXXXX 0.765 - 0.77 : [ 2004 0.02 0.94 ]
|XXXXXXXXXXX 0.77 - 0.775 : [ 1615 0.01 0.95 ]
|XXXXXXXXX 0.775 - 0.78 : [ 1349 0.01 0.96 ]
|XXXXXXX 0.78 - 0.785 : [ 1079 0.01 0.97 ]
|XXXXXX 0.785 - 0.79 : [ 816 0.01 0.98 ]
|XXXX 0.79 - 0.795 : [ 648 0.01 0.98 ]
|XXX 0.795 - 0.8 : [ 427 0.00 0.99 ]
|XXX 0.8 - 0.805 : [ 421 0.00 0.99 ]
|XX 0.805 - 0.81 : [ 298 0.00 0.99 ]
|XX 0.81 - 0.815 : [ 246 0.00 0.99 ]
|X 0.815 - 0.82 : [ 176 0.00 0.99 ]
|X 0.82 - 0.825 : [ 137 0.00 1.00 ]
|X 0.825 - 0.83 : [ 109 0.00 1.00 ]
|X 0.83 - 0.835 : [ 76 0.00 1.00 ]
| 0.835 - 0.84 : [ 58 0.00 1.00 ]
| 0.84 - 0.845 : [ 69 0.00 1.00 ]
| 0.845 - 0.85 : [ 52 0.00 1.00 ]
| 0.85 - 0.855 : [ 43 0.00 1.00 ]
| 0.855 - 0.86 : [ 23 0.00 1.00 ]
| 0.86 - 0.865 : [ 20 0.00 1.00 ]
| 0.865 - 0.87 : [ 22 0.00 1.00 ]
| 0.87 - 0.875 : [ 8 0.00 1.00 ]
| 0.875 - 0.88 : [ 24 0.00 1.00 ]
| 0.88 - 0.885 : [ 16 0.00 1.00 ]
| 0.885 - 0.89 : [ 5 0.00 1.00 ]
| 0.89 - 0.895 : [ 4 0.00 1.00 ]
| 0.895 - 0.9 : [ 2 0.00 1.00 ]
| 0.9 - 0.905 : [ 7 0.00 1.00 ]
| 0.905 - 0.91 : [ 5 0.00 1.00 ]
| 0.91 - 0.915 : [ 5 0.00 1.00 ]
| 0.915 - 0.92 : [ 1 0.00 1.00 ]
#...
| 0.925 - 0.93 : [ 5 0.00 1.00 ]
| 0.93 - 0.935 : [ 2 0.00 1.00 ]
| 0.935 - 0.94 : [ 2 0.00 1.00 ]
| 0.94 - 0.945 : [ 1 0.00 1.00 ]
| 0.945 - 0.95 : [ 2 0.00 1.00 ]
#...
| 0.955 - 0.96 : [ 2 0.00 1.00 ]
#...
| 0.965 - 0.97 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 3 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 268. 1181 reads; 74450 bp (untrimmed), 74403 (trimmed).
Contig 269. 1186 reads; 81071 bp (untrimmed), 80927 (trimmed).
Contig 270. 1199 reads; 85825 bp (untrimmed), 85522 (trimmed).
Contig 271. 1224 reads; 93236 bp (untrimmed), 92637 (trimmed).
Contig 272. 1251 reads; 88799 bp (untrimmed), 87293 (trimmed).
Contig 273. 1274 reads; 81615 bp (untrimmed), 81565 (trimmed).
Contig 274. 1277 reads; 93706 bp (untrimmed), 93564 (trimmed).
Contig 275. 1304 reads; 90597 bp (untrimmed), 90597 (trimmed).
Contig 276. 1366 reads; 88335 bp (untrimmed), 87753 (trimmed).
Contig 277. 1389 reads; 108604 bp (untrimmed), 107779 (trimmed).
Contig 278. 1417 reads; 85106 bp (untrimmed), 83712 (trimmed).
Contig 279. 1441 reads; 95457 bp (untrimmed), 94596 (trimmed).
Contig 280. 1512 reads; 105479 bp (untrimmed), 105432 (trimmed).
Contig 281. 1615 reads; 108368 bp (untrimmed), 108232 (trimmed).
Contig 282. 1677 reads; 111781 bp (untrimmed), 110843 (trimmed).
Contig 283. 1688 reads; 112147 bp (untrimmed), 110860 (trimmed).
Contig 284. 1689 reads; 110561 bp (untrimmed), 109765 (trimmed).
Contig 285. 1717 reads; 116678 bp (untrimmed), 116678 (trimmed).
Contig 286. 1806 reads; 125906 bp (untrimmed), 124575 (trimmed).
Contig 287. 1894 reads; 133273 bp (untrimmed), 133243 (trimmed).
Contig 288. 1960 reads; 144852 bp (untrimmed), 144086 (trimmed).
Contig 289. 2473 reads; 171417 bp (untrimmed), 171272 (trimmed).
Contig 290. 2772 reads; 193384 bp (untrimmed), 192988 (trimmed).
Contig 291. 3154 reads; 205232 bp (untrimmed), 204909 (trimmed).
Contig 292. 3518 reads; 225823 bp (untrimmed), 225735 (trimmed).
Contig 293. 5216 reads; 358124 bp (untrimmed), 357659 (trimmed).
Contig 294. 5238 reads; 361826 bp (untrimmed), 361824 (trimmed).
--------------------------------------------------------------
Totals 125615 reads; 9081415 bp (untrimmed), 8943736 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 9077640 bases = 11.27 +- 4.63 = 0.26 +- 3.65
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 289 total values totalling 2650.6500. <9.171799 +/- 3.142717>
#Range: [ 1.19 - 14.81 ]
#Most likely bin: [ 10.5 - 11 ] 32 counts
#Median bin: [ 10 - 10.5 ] 24 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1 - 1.5 : [ 1 0.00 0.00 ]
|XXXXXXXX 1.5 - 2 : [ 6 0.02 0.02 ]
|XXXXXXXXX 2 - 2.5 : [ 7 0.02 0.05 ]
|XXXXXXXXX 2.5 - 3 : [ 7 0.02 0.07 ]
|XXXXX 3 - 3.5 : [ 4 0.01 0.09 ]
|XXXXXX 3.5 - 4 : [ 5 0.02 0.10 ]
|XXXXX 4 - 4.5 : [ 4 0.01 0.12 ]
|XXXXXX 4.5 - 5 : [ 5 0.02 0.13 ]
|XXXXX 5 - 5.5 : [ 4 0.01 0.15 ]
|XXXXXXXXXXXXXX 5.5 - 6 : [ 11 0.04 0.19 ]
|XXXXXXXX 6 - 6.5 : [ 6 0.02 0.21 ]
|XXXXXXXXX 6.5 - 7 : [ 7 0.02 0.23 ]
|XXXXXXXXXXXX 7 - 7.5 : [ 10 0.03 0.27 ]
|XXXXXXXXX 7.5 - 8 : [ 7 0.02 0.29 ]
|XXXXXXXXXX 8 - 8.5 : [ 8 0.03 0.32 ]
|XXXXXXXXXXXX 8.5 - 9 : [ 10 0.03 0.35 ]
|XXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 17 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 16 0.06 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 24 0.08 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 32 0.11 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 29 0.10 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 21 0.07 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 21 0.07 0.91 ]
|XXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 14 0.05 0.96 ]
|XXXXXXXXXXXX 13 - 13.5 : [ 10 0.03 0.99 ]
|XX 13.5 - 14 : [ 2 0.01 1.00 ]
#...
|X 14.5 - 15 : [ 1 0.00 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 255 total values totalling 2542.5000. <9.970588 +/- 2.342494>
#Range: [ 2.55 - 14.81 ]
#Most likely bin: [ 10.5 - 11 ] 32 counts
#Median bin: [ 10.5 - 11 ] 32 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 2.5 - 3 : [ 1 0.00 0.00 ]
|X 3 - 3.5 : [ 1 0.00 0.01 ]
|XXXX 3.5 - 4 : [ 3 0.01 0.02 ]
|XXXX 4 - 4.5 : [ 3 0.01 0.03 ]
|XXXX 4.5 - 5 : [ 3 0.01 0.04 ]
|XXXXX 5 - 5.5 : [ 4 0.02 0.06 ]
|XXXXXX 5.5 - 6 : [ 5 0.02 0.08 ]
|XXXXXXXX 6 - 6.5 : [ 6 0.02 0.10 ]
|XXXXXXXXX 6.5 - 7 : [ 7 0.03 0.13 ]
|XXXXXXXXXXXX 7 - 7.5 : [ 10 0.04 0.17 ]
|XXXXXXXXX 7.5 - 8 : [ 7 0.03 0.20 ]
|XXXXXXXXXX 8 - 8.5 : [ 8 0.03 0.23 ]
|XXXXXXXXXXXX 8.5 - 9 : [ 10 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 17 0.07 0.33 ]
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 16 0.06 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 24 0.09 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 32 0.13 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 29 0.11 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 21 0.08 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 21 0.08 0.89 ]
|XXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 14 0.05 0.95 ]
|XXXXXXXXXXXX 13 - 13.5 : [ 10 0.04 0.99 ]
|XX 13.5 - 14 : [ 2 0.01 1.00 ]
#...
|X 14.5 - 15 : [ 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 7 2 reads 1534 bases = 1.19 +- 0.39 = 0.07 +- 0.90
Contig 12 3 reads 1459 bases = 1.58 +- 0.85 = 0.36 +- 1.01
Contig 13 3 reads 1662 bases = 1.59 +- 0.64 = 0.58 +- 0.49
Contig 6 2 reads 595 bases = 1.60 +- 0.49 = -0.32 +- 0.55
Contig 10 3 reads 1718 bases = 1.67 +- 0.71 = 1.67 +- 0.71
Contig 17 4 reads 1916 bases = 1.76 +- 0.76 = 0.02 +- 1.58
Contig 22 5 reads 1667 bases = 1.76 +- 1.13 = 1.27 +- 1.37
Contig 18 4 reads 1010 bases = 2.15 +- 1.31 = -0.40 +- 0.68
Contig 23 6 reads 2020 bases = 2.15 +- 1.40 = 0.26 +- 1.70
Contig 19 4 reads 1588 bases = 2.19 +- 0.77 = 0.95 +- 0.61
Contig 8 3 reads 973 bases = 2.21 +- 0.89 = 1.16 +- 0.36
Contig 9 3 reads 943 bases = 2.25 +- 0.47 = 2.25 +- 0.47
Contig 11 3 reads 810 bases = 2.32 +- 0.81 = 1.24 +- 0.43
Contig 21 5 reads 1144 bases = 2.37 +- 1.56 = 1.60 +- 0.79
Contig 14 3 reads 1046 bases = 2.52 +- 0.76 = 2.52 +- 0.76
Contig 37 13 reads 4036 bases = 2.55 +- 1.14 = 1.44 +- 1.53
Contig 15 4 reads 1392 bases = 2.57 +- 1.30 = 1.09 +- 1.45
Contig 26 8 reads 2089 bases = 2.57 +- 1.12 = 1.52 +- 1.35
Contig 28 8 reads 2399 bases = 2.64 +- 1.54 = 0.98 +- 1.33
Contig 16 4 reads 969 bases = 2.70 +- 1.25 = 1.41 +- 0.53
Contig 254 830 reads 52791 bases = 12.60 +- 4.89 = 0.50 +- 4.33
Contig 228 583 reads 37441 bases = 12.65 +- 4.54 = 0.33 +- 3.63
Contig 128 160 reads 11068 bases = 12.66 +- 5.83 = 1.72 +- 4.03
Contig 234 627 reads 42072 bases = 12.66 +- 4.30 = 0.20 +- 3.90
Contig 81 54 reads 3631 bases = 12.75 +- 5.13 = 1.95 +- 2.89
Contig 184 338 reads 22485 bases = 12.76 +- 5.23 = 0.60 +- 3.70
Contig 218 523 reads 33365 bases = 12.84 +- 4.54 = 0.66 +- 3.94
Contig 233 614 reads 38692 bases = 13.03 +- 4.53 = 0.48 +- 3.38
Contig 276 1366 reads 88335 bases = 13.04 +- 4.60 = 0.32 +- 4.06
Contig 226 573 reads 35692 bases = 13.11 +- 4.22 = 0.09 +- 4.23
Contig 291 3154 reads 205232 bases = 13.16 +- 6.73 = 0.05 +- 3.72
Contig 292 3518 reads 225823 bases = 13.23 +- 4.66 = 0.17 +- 4.06
Contig 158 258 reads 15647 bases = 13.27 +- 5.09 = 0.65 +- 4.53
Contig 250 791 reads 50699 bases = 13.32 +- 3.64 = 0.11 +- 4.06
Contig 131 166 reads 10667 bases = 13.37 +- 5.26 = 0.19 +- 3.66
Contig 278 1417 reads 85106 bases = 13.37 +- 9.19 = 0.22 +- 3.82
Contig 273 1274 reads 81615 bases = 13.38 +- 3.94 = 0.25 +- 3.80
Contig 75 44 reads 2808 bases = 13.57 +- 8.99 = 0.71 +- 3.08
Contig 196 428 reads 25931 bases = 13.80 +- 5.33 = 0.42 +- 3.08
Contig 142 199 reads 11288 bases = 14.81 +- 5.74 = 1.13 +- 3.60
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1407
HQ Discrepant reads = 456
Chimeric reads = 276
Suspect alignments = 570
-------------------------------------------------------------------
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/genome4/3634642/edit_dir.06Jul04.QD