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
3436096 6200 NULL Crocosphaera watsonii
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Crocosphaera_watsonii
-------------------------------------------------------------------
Crocosphaera watsonii, species, cyanobacteria
Crocosphaera, genus, cyanobacteria
Chroococcales, order, cyanobacteria
Cyanobacteria (blue-green algae), phylum, cyanobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 6216513
# phrap: 5431137
# db:
altered.
6200000
5949216 +/- 366399
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 44204
Number of reads with percent X's >= 20%: 403 = 0.4%
Number of reads with percent X's >= 50%: 154 = 0.2%
Number of reads with percent X's >= 80%: 15 = 0.0%
Total reads in project: 89802
Total bp X'd : 2721424
reads >= 20% >= 50% >= 80% screened
Nr with L09136 17662 176 79 9
Nr with pCC1Fos 2185 2 0 0
Nr with pMCL200_JGI_XZX+XZK 24357 225 75 6
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 3861
Number of reads with percent X's >= 20%: 2377 = 23.3%
Number of reads with percent X's >= 50%: 2071 = 20.3%
Number of reads with percent X's >= 80%: 1670 = 16.4%
Total reads in project: 10194
Total bp X'd : 2065108
reads >= 20% >= 50% >= 80% screened
Nr with L09136 555 394 379 302
Nr with LRS 79 79 77 69
Nr with pCC1Fos 36 2 2 0
Nr with pMCL200_JGI_XZX+XZK 3191 1902 1613 1299
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 30907130
C = 19787582
G = 19414973
T = 30071045
N = 658747
X = 4913181
GC fraction = 0.37
Total = 105752658
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436096_fasta.screen.contigs
-------------------------------------------------------------------
A 1982038
C 1164709
G 1167108
T 1963748
N 594
fraction GC = 0.37
total bases = 6278197
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 ACCN reads.list > grep.reads.list.ACCN
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACCN 4 500
-------------------------------------------------------------------
#Found 14929 total values totalling 49781668.0000. <3334.561458 +/- 793.259368>
#Range: [ 481 - 64698 ]
#Most likely bin: [ 3000 - 3500 ] 5124 counts
#Median bin: [ 3000 - 3500 ] 5124 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 2 0.00 0.00 ]
| 500 - 1000 : [ 4 0.00 0.00 ]
|X 1000 - 1500 : [ 108 0.01 0.01 ]
|X 1500 - 2000 : [ 143 0.01 0.02 ]
|XXX 2000 - 2500 : [ 336 0.02 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 3797 0.25 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 5124 0.34 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3368 0.23 0.86 ]
|XXXXXXXXXXXXXXX 4000 - 4500 : [ 1913 0.13 0.99 ]
|X 4500 - 5000 : [ 130 0.01 1.00 ]
#...
| 20000 - 20500 : [ 1 0.00 1.00 ]
| 20500 - 21000 : [ 1 0.00 1.00 ]
#...
| 21500 - 22000 : [ 1 0.00 1.00 ]
#...
| 64500 - 65000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACCO reads.list > grep.reads.list.ACCO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACCO 4 500
-------------------------------------------------------------------
#Found 9076 total values totalling 57830856.0000. <6371.843984 +/- 1489.846234>
#Range: [ 100 - 73891 ]
#Most likely bin: [ 6000 - 6500 ] 2139 counts
#Median bin: [ 6500 - 7000 ] 2074 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 5 0.00 0.00 ]
| 500 - 1000 : [ 19 0.00 0.00 ]
|X 1000 - 1500 : [ 44 0.00 0.01 ]
|XX 1500 - 2000 : [ 85 0.01 0.02 ]
|X 2000 - 2500 : [ 68 0.01 0.02 ]
|X 2500 - 3000 : [ 73 0.01 0.03 ]
|X 3000 - 3500 : [ 77 0.01 0.04 ]
|XX 3500 - 4000 : [ 91 0.01 0.05 ]
|XXX 4000 - 4500 : [ 135 0.01 0.07 ]
|XXXX 4500 - 5000 : [ 215 0.02 0.09 ]
|XXXXXXX 5000 - 5500 : [ 392 0.04 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1156 0.13 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2139 0.24 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2074 0.23 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1423 0.16 0.88 ]
|XXXXXXXXXXXXXXX 7500 - 8000 : [ 785 0.09 0.97 ]
|XXXXX 8000 - 8500 : [ 270 0.03 1.00 ]
| 8500 - 9000 : [ 17 0.00 1.00 ]
#...
| 9500 - 10000 : [ 1 0.00 1.00 ]
#...
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 24000 - 24500 : [ 2 0.00 1.00 ]
#...
| 27000 - 27500 : [ 1 0.00 1.00 ]
#...
| 28000 - 28500 : [ 1 0.00 1.00 ]
#...
| 35000 - 35500 : [ 1 0.00 1.00 ]
#...
| 73500 - 74000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACCP reads.list > grep.reads.list.ACCP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACCP 4 500
-------------------------------------------------------------------
#Found 88 total values totalling 3102835.0000. <35259.488636 +/- 6104.699544>
#Range: [ 1651 - 42568 ]
#Most likely bin: [ 35500 - 36000 ] 11 counts
#Median bin: [ 35500 - 36000 ] 11 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 1500 - 2000 : [ 1 0.01 0.01 ]
#...
|XXXX 3000 - 3500 : [ 1 0.01 0.02 ]
#...
|XXXX 15000 - 15500 : [ 1 0.01 0.03 ]
#...
|XXXX 28500 - 29000 : [ 1 0.01 0.05 ]
|XXXX 29000 - 29500 : [ 1 0.01 0.06 ]
#...
|XXXX 30000 - 30500 : [ 1 0.01 0.07 ]
#...
|XXXX 31000 - 31500 : [ 1 0.01 0.08 ]
#...
|XXXXXXXXXXX 32000 - 32500 : [ 3 0.03 0.11 ]
|XXXX 32500 - 33000 : [ 1 0.01 0.12 ]
|XXXXXXXXXXX 33000 - 33500 : [ 3 0.03 0.16 ]
|XXXXXXXXXXX 33500 - 34000 : [ 3 0.03 0.19 ]
|XXXXXXX 34000 - 34500 : [ 2 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 9 0.10 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 6 0.07 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 11 0.12 0.51 ]
|XXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 5 0.06 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 9 0.10 0.67 ]
|XXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 5 0.06 0.73 ]
|XXXX 37500 - 38000 : [ 1 0.01 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 6 0.07 0.81 ]
|XXXXXXXXXXX 38500 - 39000 : [ 3 0.03 0.84 ]
|XXXXXXX 39000 - 39500 : [ 2 0.02 0.86 ]
|XXXXXXXXXXXXXXX 39500 - 40000 : [ 4 0.05 0.91 ]
|XXXXXXX 40000 - 40500 : [ 2 0.02 0.93 ]
|XXXXXXXXXXX 40500 - 41000 : [ 3 0.03 0.97 ]
#...
|XXXX 41500 - 42000 : [ 1 0.01 0.98 ]
|XXXX 42000 - 42500 : [ 1 0.01 0.99 ]
|XXXX 42500 - 43000 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# ACCP 32253 +- 10448 (n=35)
# ACCN 3193 +- 666 (n=7730)
# ACCO 6088 +- 1334 (n=4521)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436096_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
ACCN 48000 -1 -1 98 725 47849 95 681 97 696
ACCO 47616 -1 -1 92 621 47393 81 557 88 593
ACCP 5376 -1 -1 99 738 5376 97 732 99 749
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
ACCN 24142 95 686 98 705 23707 94 676 96 687
ACCO 23679 80 558 87 598 23714 81 555 89 589
ACCP 2688 97 745 99 746 2688 96 719 99 751
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436096_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
236 47849 22650 95.97 99.97 ACCN @
248 47393 23790 95.93 99.92 ACCO @
28 5376 2688 96.00 100.00 ACCP @
] 100618 49128 95.95 cumulative total@@
LIBRARY PLATE ID COUNT [ ACCN 236 ACCO 248 ACCP 28 ] for 512 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 3436096_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 100618 total values totalling 56069315.0000. <557.249349 +/- 257.244151>
#Range: [ 0 - 1015 ]
#Most likely bin: [ 700 - 750 ] 16898 counts
#Median bin: [ 650 - 700 ] 12793 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 10267 0.10 0.10 ]
|XXXX 50 - 100 : [ 1737 0.02 0.12 ]
|XXXX 100 - 150 : [ 1485 0.01 0.13 ]
|XXXX 150 - 200 : [ 1517 0.02 0.15 ]
|XXXX 200 - 250 : [ 1658 0.02 0.17 ]
|XXXX 250 - 300 : [ 1838 0.02 0.18 ]
|XXXXX 300 - 350 : [ 2100 0.02 0.20 ]
|XXXXXX 350 - 400 : [ 2398 0.02 0.23 ]
|XXXXXXX 400 - 450 : [ 2849 0.03 0.26 ]
|XXXXXXXX 450 - 500 : [ 3469 0.03 0.29 ]
|XXXXXXXXXX 500 - 550 : [ 4241 0.04 0.33 ]
|XXXXXXXXXXXXXX 550 - 600 : [ 5916 0.06 0.39 ]
|XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 8630 0.09 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 12793 0.13 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 16898 0.17 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 14319 0.14 0.92 ]
|XXXXXXXXXXXXXXXX 800 - 850 : [ 6606 0.07 0.98 ]
|XXX 850 - 900 : [ 1321 0.01 0.99 ]
|X 900 - 950 : [ 489 0.00 1.00 ]
| 950 - 1000 : [ 84 0.00 1.00 ]
| 1000 - 1050 : [ 3 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACCN
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACCN 3436096_fasta.screen.trimQ15.SaF > reads.trim15.ACCN.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACCN.rl 2 50
-------------------------------------------------------------------
#Found 47849 total values totalling 30873431.0000. <645.226253 +/- 211.355067>
#Range: [ 0 - 1015 ]
#Most likely bin: [ 750 - 800 ] 10328 counts
#Median bin: [ 700 - 750 ] 9430 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXX 0 - 50 : [ 2137 0.04 0.04 ]
|XX 50 - 100 : [ 459 0.01 0.05 ]
|X 100 - 150 : [ 387 0.01 0.06 ]
|XX 150 - 200 : [ 416 0.01 0.07 ]
|XX 200 - 250 : [ 514 0.01 0.08 ]
|XX 250 - 300 : [ 561 0.01 0.09 ]
|XXX 300 - 350 : [ 668 0.01 0.11 ]
|XXX 350 - 400 : [ 786 0.02 0.12 ]
|XXXX 400 - 450 : [ 1015 0.02 0.15 ]
|XXXXX 450 - 500 : [ 1207 0.03 0.17 ]
|XXXXX 500 - 550 : [ 1332 0.03 0.20 ]
|XXXXXXXX 550 - 600 : [ 1995 0.04 0.24 ]
|XXXXXXXXXXXXX 600 - 650 : [ 3347 0.07 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 6045 0.13 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 9430 0.20 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 10328 0.22 0.85 ]
|XXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5511 0.12 0.96 ]
|XXXX 850 - 900 : [ 1140 0.02 0.99 ]
|XX 900 - 950 : [ 484 0.01 1.00 ]
| 950 - 1000 : [ 84 0.00 1.00 ]
| 1000 - 1050 : [ 3 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACCO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACCO 3436096_fasta.screen.trimQ15.SaF > reads.trim15.ACCO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACCO.rl 2 50
-------------------------------------------------------------------
#Found 47393 total values totalling 21392700.0000. <451.389446 +/- 265.382595>
#Range: [ 0 - 842 ]
#Most likely bin: [ 0 - 50 ] 7972 counts
#Median bin: [ 550 - 600 ] 3849 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 7972 0.17 0.17 ]
|XXXXXX 50 - 100 : [ 1251 0.03 0.19 ]
|XXXXX 100 - 150 : [ 1078 0.02 0.22 ]
|XXXXX 150 - 200 : [ 1087 0.02 0.24 ]
|XXXXXX 200 - 250 : [ 1130 0.02 0.26 ]
|XXXXXX 250 - 300 : [ 1241 0.03 0.29 ]
|XXXXXXX 300 - 350 : [ 1389 0.03 0.32 ]
|XXXXXXXX 350 - 400 : [ 1559 0.03 0.35 ]
|XXXXXXXXX 400 - 450 : [ 1748 0.04 0.39 ]
|XXXXXXXXXXX 450 - 500 : [ 2194 0.05 0.44 ]
|XXXXXXXXXXXXXX 500 - 550 : [ 2860 0.06 0.50 ]
|XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 3849 0.08 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 5107 0.11 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 6363 0.13 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6311 0.13 0.95 ]
|XXXXXXXXXXX 750 - 800 : [ 2129 0.04 1.00 ]
|X 800 - 850 : [ 125 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACCP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACCP 3436096_fasta.screen.trimQ15.SaF > reads.trim15.ACCP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACCP.rl 2 50
-------------------------------------------------------------------
#Found 5376 total values totalling 3803184.0000. <707.437500 +/- 172.724825>
#Range: [ 0 - 908 ]
#Most likely bin: [ 750 - 800 ] 1862 counts
#Median bin: [ 750 - 800 ] 1862 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 0 - 50 : [ 158 0.03 0.03 ]
|X 50 - 100 : [ 27 0.01 0.03 ]
| 100 - 150 : [ 20 0.00 0.04 ]
| 150 - 200 : [ 14 0.00 0.04 ]
| 200 - 250 : [ 14 0.00 0.04 ]
|X 250 - 300 : [ 36 0.01 0.05 ]
|X 300 - 350 : [ 43 0.01 0.06 ]
|X 350 - 400 : [ 53 0.01 0.07 ]
|XX 400 - 450 : [ 86 0.02 0.08 ]
|X 450 - 500 : [ 68 0.01 0.10 ]
|X 500 - 550 : [ 49 0.01 0.11 ]
|XX 550 - 600 : [ 72 0.01 0.12 ]
|XXXX 600 - 650 : [ 176 0.03 0.15 ]
|XXXXXXXX 650 - 700 : [ 385 0.07 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1157 0.22 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1862 0.35 0.78 ]
|XXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 970 0.18 0.97 ]
|XXXX 850 - 900 : [ 181 0.03 1.00 ]
| 900 - 950 : [ 5 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436096
-------------------------------------------------------------------
ACCN.000001.000100 pUC18.fa.4 LRS.fasta
ACCN.000101.000200 pUC18.fa LRS.fasta
ACCN.000201.000300 pUC18.fa LRS.fasta
ACCO.000001.000100 pMCL200.fa.4 LRS.fasta
ACCO.000101.000200 pMCL200.fa LRS.fasta
ACCO.000201.000300 pMCL200.fa LRS.fasta
ACCP.000001.000100 pCC1Fos.fa.4 LRS.fasta
ACCN.000001.000100 pUC18.fa.4 LRS.fasta
ACCN.000101.000200 pUC18.fa LRS.fasta
ACCN.000201.000300 pUC18.fa LRS.fasta
ACCO.000001.000100 pMCL200.fa.4 LRS.fasta
ACCO.000101.000200 pMCL200.fa LRS.fasta
ACCO.000201.000300 pMCL200.fa LRS.fasta
ACCP.000001.000100 pCC1Fos.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436096_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436096_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 90491 total values totalling 33514.1373. <0.370359 +/- 0.053110>
#Range: [ 0 - 0.822 ]
#Most likely bin: [ 0.35 - 0.355 ] 3686 counts
#Median bin: [ 0.365 - 0.37 ] 3395 counts
| 0 - 0.005 : [ 2 0.00 0.00 ]
#...
| 0.08 - 0.085 : [ 1 0.00 0.00 ]
#...
| 0.095 - 0.1 : [ 1 0.00 0.00 ]
#...
| 0.105 - 0.11 : [ 1 0.00 0.00 ]
#...
| 0.12 - 0.125 : [ 1 0.00 0.00 ]
| 0.125 - 0.13 : [ 2 0.00 0.00 ]
#...
| 0.135 - 0.14 : [ 2 0.00 0.00 ]
#...
| 0.145 - 0.15 : [ 2 0.00 0.00 ]
| 0.15 - 0.155 : [ 5 0.00 0.00 ]
| 0.155 - 0.16 : [ 3 0.00 0.00 ]
| 0.16 - 0.165 : [ 5 0.00 0.00 ]
| 0.165 - 0.17 : [ 4 0.00 0.00 ]
| 0.17 - 0.175 : [ 6 0.00 0.00 ]
| 0.175 - 0.18 : [ 6 0.00 0.00 ]
| 0.18 - 0.185 : [ 10 0.00 0.00 ]
| 0.185 - 0.19 : [ 8 0.00 0.00 ]
| 0.19 - 0.195 : [ 14 0.00 0.00 ]
| 0.195 - 0.2 : [ 4 0.00 0.00 ]
| 0.2 - 0.205 : [ 15 0.00 0.00 ]
| 0.205 - 0.21 : [ 14 0.00 0.00 ]
| 0.21 - 0.215 : [ 18 0.00 0.00 ]
| 0.215 - 0.22 : [ 21 0.00 0.00 ]
| 0.22 - 0.225 : [ 22 0.00 0.00 ]
| 0.225 - 0.23 : [ 32 0.00 0.00 ]
| 0.23 - 0.235 : [ 32 0.00 0.00 ]
| 0.235 - 0.24 : [ 42 0.00 0.00 ]
|X 0.24 - 0.245 : [ 73 0.00 0.00 ]
|X 0.245 - 0.25 : [ 62 0.00 0.00 ]
|X 0.25 - 0.255 : [ 132 0.00 0.01 ]
|XX 0.255 - 0.26 : [ 162 0.00 0.01 ]
|XXX 0.26 - 0.265 : [ 271 0.00 0.01 ]
|XXXX 0.265 - 0.27 : [ 351 0.00 0.01 ]
|XXXXXX 0.27 - 0.275 : [ 536 0.01 0.02 ]
|XXXXXXXXXX 0.275 - 0.28 : [ 917 0.01 0.03 ]
|XXXXXXXXXXXX 0.28 - 0.285 : [ 1146 0.01 0.04 ]
|XXXXXXXXXXXXXX 0.285 - 0.29 : [ 1266 0.01 0.06 ]
|XXXXXXXXXXXXXX 0.29 - 0.295 : [ 1308 0.01 0.07 ]
|XXXXXXXXXXXXXXX 0.295 - 0.3 : [ 1427 0.02 0.09 ]
|XXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 1595 0.02 0.11 ]
|XXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 1748 0.02 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 2009 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 2155 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 2437 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 2671 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 2765 0.03 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 3006 0.03 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 3422 0.04 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 3640 0.04 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 3686 0.04 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 3569 0.04 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 3598 0.04 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 3395 0.04 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 3138 0.03 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 3154 0.03 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 2959 0.03 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 2753 0.03 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 2705 0.03 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 2377 0.03 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 2425 0.03 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 2213 0.02 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 2230 0.02 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 2084 0.02 0.81 ]
|XXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 1941 0.02 0.84 ]
|XXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 1944 0.02 0.86 ]
|XXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 1781 0.02 0.88 ]
|XXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 1682 0.02 0.90 ]
|XXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 1565 0.02 0.91 ]
|XXXXXXXXXXXXXXX 0.445 - 0.45 : [ 1425 0.02 0.93 ]
|XXXXXXXXXXXXX 0.45 - 0.455 : [ 1174 0.01 0.94 ]
|XXXXXXXXXXX 0.455 - 0.46 : [ 994 0.01 0.95 ]
|XXXXXXXXXX 0.46 - 0.465 : [ 887 0.01 0.96 ]
|XXXXXXXX 0.465 - 0.47 : [ 706 0.01 0.97 ]
|XXXXXX 0.47 - 0.475 : [ 579 0.01 0.98 ]
|XXXX 0.475 - 0.48 : [ 400 0.00 0.98 ]
|XXXX 0.48 - 0.485 : [ 361 0.00 0.98 ]
|XXX 0.485 - 0.49 : [ 263 0.00 0.99 ]
|XX 0.49 - 0.495 : [ 176 0.00 0.99 ]
|X 0.495 - 0.5 : [ 115 0.00 0.99 ]
|XX 0.5 - 0.505 : [ 208 0.00 0.99 ]
|X 0.505 - 0.51 : [ 70 0.00 0.99 ]
|X 0.51 - 0.515 : [ 79 0.00 0.99 ]
|X 0.515 - 0.52 : [ 65 0.00 1.00 ]
| 0.52 - 0.525 : [ 41 0.00 1.00 ]
|X 0.525 - 0.53 : [ 47 0.00 1.00 ]
| 0.53 - 0.535 : [ 37 0.00 1.00 ]
| 0.535 - 0.54 : [ 37 0.00 1.00 ]
| 0.54 - 0.545 : [ 45 0.00 1.00 ]
| 0.545 - 0.55 : [ 28 0.00 1.00 ]
| 0.55 - 0.555 : [ 23 0.00 1.00 ]
| 0.555 - 0.56 : [ 19 0.00 1.00 ]
| 0.56 - 0.565 : [ 19 0.00 1.00 ]
| 0.565 - 0.57 : [ 25 0.00 1.00 ]
| 0.57 - 0.575 : [ 11 0.00 1.00 ]
| 0.575 - 0.58 : [ 11 0.00 1.00 ]
| 0.58 - 0.585 : [ 7 0.00 1.00 ]
| 0.585 - 0.59 : [ 11 0.00 1.00 ]
| 0.59 - 0.595 : [ 8 0.00 1.00 ]
| 0.595 - 0.6 : [ 2 0.00 1.00 ]
| 0.6 - 0.605 : [ 7 0.00 1.00 ]
| 0.605 - 0.61 : [ 5 0.00 1.00 ]
| 0.61 - 0.615 : [ 2 0.00 1.00 ]
| 0.615 - 0.62 : [ 6 0.00 1.00 ]
| 0.62 - 0.625 : [ 2 0.00 1.00 ]
| 0.625 - 0.63 : [ 3 0.00 1.00 ]
| 0.63 - 0.635 : [ 1 0.00 1.00 ]
#...
| 0.64 - 0.645 : [ 3 0.00 1.00 ]
| 0.645 - 0.65 : [ 2 0.00 1.00 ]
| 0.65 - 0.655 : [ 1 0.00 1.00 ]
| 0.655 - 0.66 : [ 2 0.00 1.00 ]
#...
| 0.665 - 0.67 : [ 2 0.00 1.00 ]
| 0.67 - 0.675 : [ 2 0.00 1.00 ]
#...
| 0.68 - 0.685 : [ 3 0.00 1.00 ]
#...
| 0.695 - 0.7 : [ 1 0.00 1.00 ]
| 0.7 - 0.705 : [ 2 0.00 1.00 ]
#...
| 0.805 - 0.81 : [ 1 0.00 1.00 ]
| 0.81 - 0.815 : [ 1 0.00 1.00 ]
#...
| 0.82 - 0.825 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 270. 783 reads; 53172 bp (untrimmed), 52948 (trimmed).
Contig 271. 806 reads; 47024 bp (untrimmed), 46944 (trimmed).
Contig 272. 840 reads; 63469 bp (untrimmed), 63004 (trimmed).
Contig 273. 847 reads; 56743 bp (untrimmed), 56719 (trimmed).
Contig 274. 853 reads; 61938 bp (untrimmed), 61361 (trimmed).
Contig 275. 855 reads; 54528 bp (untrimmed), 54466 (trimmed).
Contig 276. 862 reads; 59719 bp (untrimmed), 59566 (trimmed).
Contig 277. 898 reads; 56823 bp (untrimmed), 56552 (trimmed).
Contig 278. 902 reads; 50565 bp (untrimmed), 50535 (trimmed).
Contig 279. 942 reads; 65869 bp (untrimmed), 65290 (trimmed).
Contig 280. 991 reads; 76125 bp (untrimmed), 75733 (trimmed).
Contig 281. 998 reads; 67869 bp (untrimmed), 67866 (trimmed).
Contig 282. 1005 reads; 67837 bp (untrimmed), 67691 (trimmed).
Contig 283. 1012 reads; 59024 bp (untrimmed), 59024 (trimmed).
Contig 284. 1027 reads; 71227 bp (untrimmed), 71173 (trimmed).
Contig 285. 1056 reads; 63961 bp (untrimmed), 63961 (trimmed).
Contig 286. 1067 reads; 65115 bp (untrimmed), 64808 (trimmed).
Contig 287. 1153 reads; 79311 bp (untrimmed), 79237 (trimmed).
Contig 288. 1175 reads; 73589 bp (untrimmed), 73589 (trimmed).
Contig 289. 1178 reads; 77101 bp (untrimmed), 77101 (trimmed).
Contig 290. 1250 reads; 87183 bp (untrimmed), 86752 (trimmed).
Contig 291. 1281 reads; 82272 bp (untrimmed), 81609 (trimmed).
Contig 292. 1403 reads; 103799 bp (untrimmed), 103755 (trimmed).
Contig 293. 1615 reads; 104631 bp (untrimmed), 104537 (trimmed).
Contig 294. 1745 reads; 121450 bp (untrimmed), 121243 (trimmed).
Contig 295. 1894 reads; 127897 bp (untrimmed), 127768 (trimmed).
Contig 296. 2069 reads; 130245 bp (untrimmed), 130217 (trimmed).
--------------------------------------------------------------
Totals 90424 reads; 6278197 bp (untrimmed), 6216513 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 6270265 bases = 11.43 +- 5.56 = 0.46 +- 3.98
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 282 total values totalling 2881.2300. <10.217128 +/- 3.904328>
#Range: [ 1.10 - 45.31 ]
#Most likely bin: [ 11 - 11.5 ] 29 counts
#Median bin: [ 10.5 - 11 ] 26 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 1 - 1.5 : [ 3 0.01 0.01 ]
|XXX 1.5 - 2 : [ 2 0.01 0.02 ]
|XXXX 2 - 2.5 : [ 3 0.01 0.03 ]
|XXXXXXX 2.5 - 3 : [ 5 0.02 0.05 ]
|XXXX 3 - 3.5 : [ 3 0.01 0.06 ]
|XXX 3.5 - 4 : [ 2 0.01 0.06 ]
|XXXXXX 4 - 4.5 : [ 4 0.01 0.08 ]
|XXX 4.5 - 5 : [ 2 0.01 0.09 ]
|XXXXXX 5 - 5.5 : [ 4 0.01 0.10 ]
|XXXXXXX 5.5 - 6 : [ 5 0.02 0.12 ]
|XXXX 6 - 6.5 : [ 3 0.01 0.13 ]
|XXXXXXXXXXXX 6.5 - 7 : [ 9 0.03 0.16 ]
|XXXXXXXXXXXXXX 7 - 7.5 : [ 10 0.04 0.20 ]
|XXXXXXXXXXXX 7.5 - 8 : [ 9 0.03 0.23 ]
|XXXXXXXXXXXXXXX 8 - 8.5 : [ 11 0.04 0.27 ]
|XXXXXXXXXXXX 8.5 - 9 : [ 9 0.03 0.30 ]
|XXXXXXXXXXXX 9 - 9.5 : [ 9 0.03 0.33 ]
|XXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 14 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 15 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 26 0.09 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 29 0.10 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 27 0.10 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 21 0.07 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 18 0.06 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 19 0.07 0.93 ]
|XXXXXXXXXXXXXX 13.5 - 14 : [ 10 0.04 0.96 ]
|XXXX 14 - 14.5 : [ 3 0.01 0.98 ]
|XXX 14.5 - 15 : [ 2 0.01 0.98 ]
|X 15 - 15.5 : [ 1 0.00 0.99 ]
#...
|XXX 17 - 17.5 : [ 2 0.01 0.99 ]
#...
|X 30 - 30.5 : [ 1 0.00 1.00 ]
#...
|X 45 - 45.5 : [ 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 251 total values totalling 2671.3600. <10.642869 +/- 2.413118>
#Range: [ 3.34 - 17.20 ]
#Most likely bin: [ 11 - 11.5 ] 28 counts
#Median bin: [ 11 - 11.5 ] 28 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 3 - 3.5 : [ 1 0.00 0.00 ]
|X 3.5 - 4 : [ 1 0.00 0.01 ]
|XXXX 4 - 4.5 : [ 3 0.01 0.02 ]
|X 4.5 - 5 : [ 1 0.00 0.02 ]
|XXXX 5 - 5.5 : [ 3 0.01 0.04 ]
|XXXXXX 5.5 - 6 : [ 4 0.02 0.05 ]
|XXXX 6 - 6.5 : [ 3 0.01 0.06 ]
|XXXXXXXXXXX 6.5 - 7 : [ 8 0.03 0.10 ]
|XXXXXXX 7 - 7.5 : [ 5 0.02 0.12 ]
|XXXXXXXXXXXXX 7.5 - 8 : [ 9 0.04 0.15 ]
|XXXXXXXXXXXXXXXX 8 - 8.5 : [ 11 0.04 0.20 ]
|XXXXXXXXXXXXX 8.5 - 9 : [ 9 0.04 0.23 ]
|XXXXXXXXXXX 9 - 9.5 : [ 8 0.03 0.26 ]
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 14 0.06 0.32 ]
|XXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 15 0.06 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 26 0.10 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 28 0.11 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 27 0.11 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 20 0.08 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 18 0.07 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 19 0.08 0.93 ]
|XXXXXXXXXXXXXX 13.5 - 14 : [ 10 0.04 0.97 ]
|XXXX 14 - 14.5 : [ 3 0.01 0.98 ]
|XXX 14.5 - 15 : [ 2 0.01 0.99 ]
|X 15 - 15.5 : [ 1 0.00 0.99 ]
#...
|XXX 17 - 17.5 : [ 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 13 2 reads 1384 bases = 1.10 +- 0.30 = -0.03 +- 0.95
Contig 11 2 reads 982 bases = 1.47 +- 0.50 = -0.53 +- 0.50
Contig 12 2 reads 1365 bases = 1.48 +- 0.50 = 1.48 +- 0.50
Contig 9 2 reads 808 bases = 1.65 +- 0.48 = 1.65 +- 0.48
Contig 10 2 reads 1115 bases = 1.77 +- 0.42 = 1.77 +- 0.42
Contig 21 6 reads 2193 bases = 2.31 +- 1.21 = 1.62 +- 1.65
Contig 14 3 reads 1303 bases = 2.34 +- 0.83 = 2.34 +- 0.83
Contig 29 8 reads 2690 bases = 2.42 +- 1.19 = 0.37 +- 2.01
Contig 18 4 reads 1612 bases = 2.50 +- 1.40 = 1.07 +- 1.32
Contig 19 5 reads 1753 bases = 2.69 +- 1.41 = 2.69 +- 1.41
Contig 16 4 reads 1080 bases = 2.71 +- 1.25 = 0.86 +- 1.27
Contig 25 6 reads 2078 bases = 2.76 +- 1.89 = 2.76 +- 1.89
Contig 23 6 reads 2038 bases = 2.81 +- 1.97 = 2.81 +- 1.97
Contig 20 5 reads 1282 bases = 3.04 +- 1.42 = 3.04 +- 1.42
Contig 28 8 reads 1967 bases = 3.16 +- 2.05 = 2.35 +- 1.53
Contig 31 10 reads 2363 bases = 3.34 +- 2.50 = 1.37 +- 1.91
Contig 24 6 reads 1216 bases = 3.89 +- 1.81 = 1.10 +- 1.10
Contig 36 12 reads 2401 bases = 3.98 +- 2.32 = 1.07 +- 1.79
Contig 33 10 reads 2213 bases = 4.06 +- 2.02 = 3.15 +- 1.49
Contig 45 17 reads 3290 bases = 4.22 +- 2.35 = 2.54 +- 3.34
Contig 271 806 reads 47024 bases = 13.62 +- 4.29 = 1.04 +- 3.69
Contig 267 755 reads 42906 bases = 13.80 +- 4.12 = 0.23 +- 4.50
Contig 165 217 reads 12604 bases = 13.82 +- 7.78 = 1.01 +- 2.59
Contig 283 1012 reads 59024 bases = 13.83 +- 5.67 = 0.12 +- 4.38
Contig 143 179 reads 10074 bases = 13.84 +- 5.05 = 0.70 +- 3.36
Contig 119 125 reads 7294 bases = 13.85 +- 4.54 = 2.91 +- 3.72
Contig 190 305 reads 17752 bases = 13.90 +- 5.29 = 0.17 +- 3.48
Contig 137 163 reads 9524 bases = 13.91 +- 4.48 = 0.84 +- 4.47
Contig 142 179 reads 10540 bases = 13.91 +- 3.75 = -0.10 +- 2.80
Contig 83 57 reads 3148 bases = 13.92 +- 12.27 = 1.31 +- 1.49
Contig 183 275 reads 15853 bases = 14.17 +- 4.72 = -0.03 +- 3.42
Contig 278 902 reads 50565 bases = 14.25 +- 6.99 = 0.04 +- 4.40
Contig 138 168 reads 9249 bases = 14.30 +- 7.57 = -0.05 +- 4.48
Contig 155 199 reads 10743 bases = 14.55 +- 12.93 = 0.40 +- 4.39
Contig 218 432 reads 21389 bases = 14.96 +- 9.60 = -0.11 +- 7.75
Contig 153 198 reads 10364 bases = 15.30 +- 11.53 = 1.31 +- 3.85
Contig 117 122 reads 5454 bases = 17.15 +- 17.68 = 3.16 +- 5.45
Contig 257 666 reads 30745 bases = 17.20 +- 21.01 = -0.18 +- 4.66
Contig 67 32 reads 750 bases = 30.30 +- 3.10 = 0.39 +- 1.42
Contig 113 112 reads 1993 bases = 45.31 +- 40.19 = 1.28 +- 3.66
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1165
HQ Discrepant reads = 165
Chimeric reads = 170
Suspect alignments = 658
-------------------------------------------------------------------
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: -8)
A C G T N X
A 1 -8 -8 -8 0 -9
C -8 1 -8 -8 0 -9
G -8 -8 1 -8 0 -9
T -8 -8 -8 1 0 -9
N 0 0 0 0 0 0
X -9 -9 -9 -9 0 -9
gap_init: -10
gap_ext: -9
ins_gap_ext: -9
del_gap_ext: -9
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 55
maxmatch: 80
max_group_size: 20
minscore: 75
bandwidth: 14
indexwordsize: 10
vector_bound: 50
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 20
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -8
confirm_score: 30
node_seg: 48
node_space: 24
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/finished2/microbe/3436096/edit_dir.27Sep05.QD