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
3634498 4500 NULL Shewanella putrefaciens
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Shewanella_putrefaciens
-------------------------------------------------------------------
Shewanellaceae, family, g-proteobacteria
Alteromonadales, order, g-proteobacteria
Shewanella putrefaciens, species, g-proteobacteria
Shewanella, genus, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4587675
# phrap: 4264346
# db:
altered.
4500000
4450673 +/- 136528
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 11867
Number of reads with percent X's >= 20%: 160 = 0.3%
Number of reads with percent X's >= 50%: 104 = 0.2%
Number of reads with percent X's >= 80%: 31 = 0.0%
Total reads in project: 63146
Total bp X'd : 515229
reads >= 20% >= 50% >= 80% screened
Nr with L09136 10644 30 19 7
Nr with pCC1Fos 975 0 0 0
Nr with pMCL200_JGI_XZX+XZK 248 130 85 24
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 3
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: 33
Total bp X'd : 113
reads >= 20% >= 50% >= 80% screened
Nr with L09136 2 0 0 0
Nr with pCC1Fos 1 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 16565164
C = 13419249
G = 13379286
T = 16376796
N = 234373
X = 515229
GC fraction = 0.44
Total = 60490097
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634498_fasta.screen.contigs
-------------------------------------------------------------------
A 1303837
C 1051153
G 993968
T 1253073
N 90
fraction GC = 0.44
total bases = 4602121
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 AIBX reads.list > grep.reads.list.AIBX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBX 4 500
-------------------------------------------------------------------
#Found 10893 total values totalling 35229583.0000. <3234.148811 +/- 1363.672590>
#Range: [ 942 - 94681 ]
#Most likely bin: [ 3000 - 3500 ] 6363 counts
#Median bin: [ 3000 - 3500 ] 6363 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 17 0.00 0.00 ]
| 1500 - 2000 : [ 33 0.00 0.00 ]
|X 2000 - 2500 : [ 174 0.02 0.02 ]
|XXXXXXXXXXXXXXX 2500 - 3000 : [ 2331 0.21 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 6363 0.58 0.82 ]
|XXXXXXXXXXXX 3500 - 4000 : [ 1963 0.18 1.00 ]
| 4000 - 4500 : [ 5 0.00 1.00 ]
#...
| 10000 - 10500 : [ 1 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
#...
| 26000 - 26500 : [ 1 0.00 1.00 ]
#...
| 68000 - 68500 : [ 1 0.00 1.00 ]
#...
| 79500 - 80000 : [ 1 0.00 1.00 ]
#...
| 94500 - 95000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBY reads.list > grep.reads.list.AIBY
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBY 4 500
-------------------------------------------------------------------
#Found 12793 total values totalling 92967178.0000. <7267.034941 +/- 4209.184283>
#Range: [ 461 - 219478 ]
#Most likely bin: [ 6500 - 7000 ] 2534 counts
#Median bin: [ 7000 - 7500 ] 2518 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
| 500 - 1000 : [ 3 0.00 0.00 ]
| 1000 - 1500 : [ 20 0.00 0.00 ]
| 1500 - 2000 : [ 24 0.00 0.00 ]
| 2000 - 2500 : [ 31 0.00 0.01 ]
|X 2500 - 3000 : [ 38 0.00 0.01 ]
|X 3000 - 3500 : [ 37 0.00 0.01 ]
|X 3500 - 4000 : [ 40 0.00 0.02 ]
|X 4000 - 4500 : [ 45 0.00 0.02 ]
|X 4500 - 5000 : [ 54 0.00 0.02 ]
|XXX 5000 - 5500 : [ 201 0.02 0.04 ]
|XXXXXXXXXXX 5500 - 6000 : [ 679 0.05 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1810 0.14 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2534 0.20 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 2518 0.20 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 2157 0.17 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1509 0.12 0.91 ]
|XXXXXXXXXXXXXX 8500 - 9000 : [ 886 0.07 0.98 ]
|XXX 9000 - 9500 : [ 180 0.01 1.00 ]
| 9500 - 10000 : [ 3 0.00 1.00 ]
| 10000 - 10500 : [ 1 0.00 1.00 ]
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 11500 - 12000 : [ 1 0.00 1.00 ]
#...
| 14500 - 15000 : [ 1 0.00 1.00 ]
#...
| 17500 - 18000 : [ 1 0.00 1.00 ]
#...
| 18500 - 19000 : [ 1 0.00 1.00 ]
#...
| 23000 - 23500 : [ 1 0.00 1.00 ]
#...
| 27000 - 27500 : [ 2 0.00 1.00 ]
#...
| 29500 - 30000 : [ 1 0.00 1.00 ]
#...
| 44000 - 44500 : [ 1 0.00 1.00 ]
#...
| 48000 - 48500 : [ 1 0.00 1.00 ]
#...
| 52500 - 53000 : [ 1 0.00 1.00 ]
#...
| 70000 - 70500 : [ 1 0.00 1.00 ]
#...
| 98000 - 98500 : [ 1 0.00 1.00 ]
#...
| 99500 - 100000 : [ 1 0.00 1.00 ]
#...
| 100500 - 101000 : [ 1 0.00 1.00 ]
#...
| 122000 - 122500 : [ 1 0.00 1.00 ]
#...
| 152000 - 152500 : [ 1 0.00 1.00 ]
#...
| 167000 - 167500 : [ 1 0.00 1.00 ]
#...
| 169000 - 169500 : [ 1 0.00 1.00 ]
#...
| 218500 - 219000 : [ 1 0.00 1.00 ]
| 219000 - 219500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBZ reads.list > grep.reads.list.AIBZ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBZ 4 500
-------------------------------------------------------------------
#Found 1015 total values totalling 38592300.0000. <38021.970443 +/- 3585.353328>
#Range: [ 12611 - 46549 ]
#Most likely bin: [ 35500 - 36000 ] 66 counts
#Median bin: [ 38000 - 38500 ] 48 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 12500 - 13000 : [ 1 0.00 0.00 ]
#...
|X 21000 - 21500 : [ 1 0.00 0.00 ]
#...
|X 25500 - 26000 : [ 1 0.00 0.00 ]
#...
|X 26500 - 27000 : [ 1 0.00 0.00 ]
#...
|X 27500 - 28000 : [ 1 0.00 0.00 ]
#...
|X 28500 - 29000 : [ 1 0.00 0.01 ]
|X 29000 - 29500 : [ 2 0.00 0.01 ]
|XX 29500 - 30000 : [ 4 0.00 0.01 ]
|XXX 30000 - 30500 : [ 5 0.00 0.02 ]
|XXX 30500 - 31000 : [ 5 0.00 0.02 ]
|X 31000 - 31500 : [ 2 0.00 0.02 ]
|XXXXXXXX 31500 - 32000 : [ 13 0.01 0.04 ]
|XXXXXXXX 32000 - 32500 : [ 14 0.01 0.05 ]
|XXXXXXXXXX 32500 - 33000 : [ 16 0.02 0.07 ]
|XXXXXXXXXXXXXXXXX 33000 - 33500 : [ 28 0.03 0.09 ]
|XXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 32 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 37 0.04 0.16 ]
|XXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 30 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 50 0.05 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 66 0.07 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 45 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 59 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 37 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 54 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 48 0.05 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 49 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 58 0.06 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 38 0.04 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 42 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 52 0.05 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 43 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 34 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 31 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 33 0.03 0.92 ]
|XXXXXXXXXXXXXXX 43000 - 43500 : [ 25 0.02 0.94 ]
|XXXXXXXXXXX 43500 - 44000 : [ 18 0.02 0.96 ]
|XXXXXXXXXXX 44000 - 44500 : [ 18 0.02 0.98 ]
|XXXXX 44500 - 45000 : [ 8 0.01 0.99 ]
|XXX 45000 - 45500 : [ 5 0.00 0.99 ]
|XXX 45500 - 46000 : [ 5 0.00 1.00 ]
|X 46000 - 46500 : [ 2 0.00 1.00 ]
|X 46500 - 47000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIBX 3133 +- 351 (n=5405)
# AIBY 7047 +- 1288 (n=6480)
# AIBZ 38153 +- 3639 (n=512)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634498_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
AIBX 25344 -1 -1 98 738 25906 96 733 97 738
AIBY 40320 96 790 95 709 40122 85 679 89 674
AIBZ 3840 -1 -1 90 535 3839 86 590 90 594
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIBX 12859 96 722 98 737 13047 96 745 97 739
AIBY 19882 81 674 86 665 20240 90 683 93 682
AIBZ 1919 87 598 90 600 1920 86 581 90 589
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634498_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
132 24983 12353 93.58 97.48 AIBX @
208 34779 18749 90.14 93.90 AIBY @
20 3384 1754 87.70 91.35 AIBZ @
] 63146 32856 91.27 cumulative total@@
LIBRARY PLATE ID COUNT [ AIBX 132 AIBY 208 AIBZ 20 ] for 360 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 3634498_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 69867 total values totalling 43613339.0000. <624.233744 +/- 263.138490>
#Range: [ 0 - 935 ]
#Most likely bin: [ 800 - 850 ] 15032 counts
#Median bin: [ 700 - 750 ] 8544 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXX 0 - 50 : [ 6395 0.09 0.09 ]
|XXX 50 - 100 : [ 979 0.01 0.11 ]
|XX 100 - 150 : [ 817 0.01 0.12 ]
|XX 150 - 200 : [ 835 0.01 0.13 ]
|XX 200 - 250 : [ 780 0.01 0.14 ]
|XXX 250 - 300 : [ 942 0.01 0.15 ]
|XXX 300 - 350 : [ 975 0.01 0.17 ]
|XXX 350 - 400 : [ 984 0.01 0.18 ]
|XXX 400 - 450 : [ 1129 0.02 0.20 ]
|XXXX 450 - 500 : [ 1449 0.02 0.22 ]
|XXXXX 500 - 550 : [ 1890 0.03 0.25 ]
|XXXXXXX 550 - 600 : [ 2508 0.04 0.28 ]
|XXXXXXXXX 600 - 650 : [ 3427 0.05 0.33 ]
|XXXXXXXXXXXXX 650 - 700 : [ 4919 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8544 0.12 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 14827 0.21 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 15032 0.22 0.95 ]
|XXXXXXXXX 850 - 900 : [ 3374 0.05 1.00 ]
| 900 - 950 : [ 61 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBX 3634498_fasta.screen.trimQ15.SaF > reads.trim15.AIBX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBX.rl 2 50
-------------------------------------------------------------------
#Found 25906 total values totalling 18292958.0000. <706.128233 +/- 178.438449>
#Range: [ 0 - 917 ]
#Most likely bin: [ 750 - 800 ] 8039 counts
#Median bin: [ 750 - 800 ] 8039 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 0 - 50 : [ 892 0.03 0.03 ]
| 50 - 100 : [ 97 0.00 0.04 ]
| 100 - 150 : [ 88 0.00 0.04 ]
|X 150 - 200 : [ 123 0.00 0.05 ]
|X 200 - 250 : [ 109 0.00 0.05 ]
|X 250 - 300 : [ 132 0.01 0.06 ]
|X 300 - 350 : [ 174 0.01 0.06 ]
|X 350 - 400 : [ 168 0.01 0.07 ]
|X 400 - 450 : [ 201 0.01 0.08 ]
|X 450 - 500 : [ 255 0.01 0.09 ]
|XX 500 - 550 : [ 356 0.01 0.10 ]
|XXX 550 - 600 : [ 536 0.02 0.12 ]
|XXXXX 600 - 650 : [ 1014 0.04 0.16 ]
|XXXXXXXXXXX 650 - 700 : [ 2231 0.09 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5151 0.20 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8039 0.31 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5520 0.21 0.97 ]
|XXXX 850 - 900 : [ 812 0.03 1.00 ]
| 900 - 950 : [ 8 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBY 3634498_fasta.screen.trimQ15.SaF > reads.trim15.AIBY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBY.rl 2 50
-------------------------------------------------------------------
#Found 40122 total values totalling 23359639.0000. <582.215219 +/- 294.521608>
#Range: [ 0 - 935 ]
#Most likely bin: [ 800 - 850 ] 9465 counts
#Median bin: [ 700 - 750 ] 2792 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 5053 0.13 0.13 ]
|XXX 50 - 100 : [ 801 0.02 0.15 ]
|XXX 100 - 150 : [ 671 0.02 0.16 ]
|XXX 150 - 200 : [ 656 0.02 0.18 ]
|XXX 200 - 250 : [ 619 0.02 0.19 ]
|XXX 250 - 300 : [ 674 0.02 0.21 ]
|XXX 300 - 350 : [ 679 0.02 0.23 ]
|XXX 350 - 400 : [ 745 0.02 0.25 ]
|XXX 400 - 450 : [ 822 0.02 0.27 ]
|XXXX 450 - 500 : [ 1035 0.03 0.29 ]
|XXXXXX 500 - 550 : [ 1323 0.03 0.33 ]
|XXXXXXX 550 - 600 : [ 1648 0.04 0.37 ]
|XXXXXXXX 600 - 650 : [ 1955 0.05 0.42 ]
|XXXXXXXXX 650 - 700 : [ 2070 0.05 0.47 ]
|XXXXXXXXXXXX 700 - 750 : [ 2792 0.07 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6500 0.16 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 9465 0.24 0.93 ]
|XXXXXXXXXXX 850 - 900 : [ 2561 0.06 1.00 ]
| 900 - 950 : [ 53 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBZ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBZ 3634498_fasta.screen.trimQ15.SaF > reads.trim15.AIBZ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBZ.rl 2 50
-------------------------------------------------------------------
#Found 3839 total values totalling 1960742.0000. <510.742902 +/- 249.269173>
#Range: [ 0 - 855 ]
#Most likely bin: [ 650 - 700 ] 618 counts
#Median bin: [ 600 - 650 ] 458 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 450 0.12 0.12 ]
|XXXXX 50 - 100 : [ 81 0.02 0.14 ]
|XXXX 100 - 150 : [ 58 0.02 0.15 ]
|XXXX 150 - 200 : [ 56 0.01 0.17 ]
|XXX 200 - 250 : [ 52 0.01 0.18 ]
|XXXXXXXXX 250 - 300 : [ 136 0.04 0.22 ]
|XXXXXXXX 300 - 350 : [ 122 0.03 0.25 ]
|XXXXX 350 - 400 : [ 71 0.02 0.27 ]
|XXXXXXX 400 - 450 : [ 106 0.03 0.29 ]
|XXXXXXXXXX 450 - 500 : [ 159 0.04 0.34 ]
|XXXXXXXXXXXXXX 500 - 550 : [ 211 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 324 0.08 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 458 0.12 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 618 0.16 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 601 0.16 0.91 ]
|XXXXXXXXXXXXXXXXXXX 750 - 800 : [ 288 0.08 0.99 ]
|XXX 800 - 850 : [ 47 0.01 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATTI
trimt JAZZ trim 15 readlength histogram for ATTN
trimt JAZZ trim 15 readlength histogram for ATTO
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634498
-------------------------------------------------------------------
AIBX.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIBX.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIBY.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIBY.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AIBY.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
AIBZ.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AIBX.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIBX.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIBY.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIBY.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AIBY.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
AIBZ.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634498_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634498_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 62995 total values totalling 27977.8037. <0.444127 +/- 0.044337>
#Range: [ 0.0645 - 0.8 ]
#Most likely bin: [ 0.445 - 0.45 ] 3240 counts
#Median bin: [ 0.445 - 0.45 ] 3240 counts
#Entropy = 5.1587 bits
| 0.06 - 0.065 : [ 1 0.00 0.00 ]
#...
| 0.12 - 0.125 : [ 1 0.00 0.00 ]
| 0.125 - 0.13 : [ 1 0.00 0.00 ]
#...
| 0.15 - 0.155 : [ 1 0.00 0.00 ]
#...
| 0.16 - 0.165 : [ 3 0.00 0.00 ]
| 0.165 - 0.17 : [ 1 0.00 0.00 ]
| 0.17 - 0.175 : [ 1 0.00 0.00 ]
#...
| 0.18 - 0.185 : [ 1 0.00 0.00 ]
#...
| 0.19 - 0.195 : [ 2 0.00 0.00 ]
| 0.195 - 0.2 : [ 1 0.00 0.00 ]
| 0.2 - 0.205 : [ 1 0.00 0.00 ]
#...
| 0.22 - 0.225 : [ 2 0.00 0.00 ]
| 0.225 - 0.23 : [ 4 0.00 0.00 ]
| 0.23 - 0.235 : [ 2 0.00 0.00 ]
| 0.235 - 0.24 : [ 4 0.00 0.00 ]
| 0.24 - 0.245 : [ 5 0.00 0.00 ]
| 0.245 - 0.25 : [ 4 0.00 0.00 ]
| 0.25 - 0.255 : [ 8 0.00 0.00 ]
| 0.255 - 0.26 : [ 10 0.00 0.00 ]
| 0.26 - 0.265 : [ 11 0.00 0.00 ]
| 0.265 - 0.27 : [ 18 0.00 0.00 ]
| 0.27 - 0.275 : [ 35 0.00 0.00 ]
| 0.275 - 0.28 : [ 31 0.00 0.00 ]
|X 0.28 - 0.285 : [ 41 0.00 0.00 ]
|X 0.285 - 0.29 : [ 43 0.00 0.00 ]
|X 0.29 - 0.295 : [ 47 0.00 0.00 ]
|X 0.295 - 0.3 : [ 61 0.00 0.01 ]
|X 0.3 - 0.305 : [ 78 0.00 0.01 ]
|X 0.305 - 0.31 : [ 83 0.00 0.01 ]
|X 0.31 - 0.315 : [ 96 0.00 0.01 ]
|X 0.315 - 0.32 : [ 90 0.00 0.01 ]
|X 0.32 - 0.325 : [ 103 0.00 0.01 ]
|XX 0.325 - 0.33 : [ 122 0.00 0.01 ]
|X 0.33 - 0.335 : [ 117 0.00 0.02 ]
|XX 0.335 - 0.34 : [ 142 0.00 0.02 ]
|XX 0.34 - 0.345 : [ 185 0.00 0.02 ]
|XXX 0.345 - 0.35 : [ 203 0.00 0.02 ]
|XXX 0.35 - 0.355 : [ 257 0.00 0.03 ]
|XXXX 0.355 - 0.36 : [ 313 0.00 0.03 ]
|XXXXX 0.36 - 0.365 : [ 393 0.01 0.04 ]
|XXXXX 0.365 - 0.37 : [ 444 0.01 0.05 ]
|XXXXXXX 0.37 - 0.375 : [ 546 0.01 0.06 ]
|XXXXXXXX 0.375 - 0.38 : [ 682 0.01 0.07 ]
|XXXXXXXXXX 0.38 - 0.385 : [ 841 0.01 0.08 ]
|XXXXXXXXXXXX 0.385 - 0.39 : [ 959 0.02 0.10 ]
|XXXXXXXXXXXXXXX 0.39 - 0.395 : [ 1185 0.02 0.11 ]
|XXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 1357 0.02 0.14 ]
|XXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 1694 0.03 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 1844 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 2107 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 2271 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 2612 0.04 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 2844 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 3037 0.05 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 3097 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 3177 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 3240 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 3164 0.05 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 3005 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 2990 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 2738 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 2514 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 2227 0.04 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 1976 0.03 0.84 ]
|XXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1733 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1445 0.02 0.89 ]
|XXXXXXXXXXXXXX 0.495 - 0.5 : [ 1100 0.02 0.91 ]
|XXXXXXXXXXXXXX 0.5 - 0.505 : [ 1158 0.02 0.93 ]
|XXXXXXXXXXX 0.505 - 0.51 : [ 864 0.01 0.94 ]
|XXXXXXXXX 0.51 - 0.515 : [ 731 0.01 0.95 ]
|XXXXXXX 0.515 - 0.52 : [ 589 0.01 0.96 ]
|XXXXXX 0.52 - 0.525 : [ 507 0.01 0.97 ]
|XXXXX 0.525 - 0.53 : [ 408 0.01 0.98 ]
|XXXX 0.53 - 0.535 : [ 331 0.01 0.98 ]
|XXX 0.535 - 0.54 : [ 219 0.00 0.99 ]
|XX 0.54 - 0.545 : [ 161 0.00 0.99 ]
|XX 0.545 - 0.55 : [ 122 0.00 0.99 ]
|X 0.55 - 0.555 : [ 102 0.00 0.99 ]
|X 0.555 - 0.56 : [ 55 0.00 0.99 ]
|X 0.56 - 0.565 : [ 61 0.00 0.99 ]
|X 0.565 - 0.57 : [ 53 0.00 1.00 ]
| 0.57 - 0.575 : [ 38 0.00 1.00 ]
| 0.575 - 0.58 : [ 28 0.00 1.00 ]
| 0.58 - 0.585 : [ 26 0.00 1.00 ]
| 0.585 - 0.59 : [ 29 0.00 1.00 ]
|X 0.59 - 0.595 : [ 50 0.00 1.00 ]
| 0.595 - 0.6 : [ 24 0.00 1.00 ]
| 0.6 - 0.605 : [ 28 0.00 1.00 ]
| 0.605 - 0.61 : [ 9 0.00 1.00 ]
| 0.61 - 0.615 : [ 13 0.00 1.00 ]
| 0.615 - 0.62 : [ 7 0.00 1.00 ]
| 0.62 - 0.625 : [ 5 0.00 1.00 ]
| 0.625 - 0.63 : [ 5 0.00 1.00 ]
| 0.63 - 0.635 : [ 3 0.00 1.00 ]
| 0.635 - 0.64 : [ 3 0.00 1.00 ]
| 0.64 - 0.645 : [ 4 0.00 1.00 ]
| 0.645 - 0.65 : [ 3 0.00 1.00 ]
| 0.65 - 0.655 : [ 4 0.00 1.00 ]
| 0.655 - 0.66 : [ 2 0.00 1.00 ]
| 0.66 - 0.665 : [ 1 0.00 1.00 ]
#...
| 0.8 - 0.805 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 76. 772 reads; 64741 bp (untrimmed), 64739 (trimmed).
Contig 77. 783 reads; 52187 bp (untrimmed), 51984 (trimmed).
Contig 78. 803 reads; 59644 bp (untrimmed), 59502 (trimmed).
Contig 79. 856 reads; 63320 bp (untrimmed), 63230 (trimmed).
Contig 80. 913 reads; 77814 bp (untrimmed), 77791 (trimmed).
Contig 81. 1049 reads; 67420 bp (untrimmed), 67144 (trimmed).
Contig 82. 1076 reads; 93534 bp (untrimmed), 93450 (trimmed).
Contig 83. 1087 reads; 78498 bp (untrimmed), 78473 (trimmed).
Contig 84. 1126 reads; 75202 bp (untrimmed), 74998 (trimmed).
Contig 85. 1190 reads; 87309 bp (untrimmed), 87235 (trimmed).
Contig 86. 1195 reads; 98668 bp (untrimmed), 98644 (trimmed).
Contig 87. 1235 reads; 84850 bp (untrimmed), 84797 (trimmed).
Contig 88. 1334 reads; 116148 bp (untrimmed), 115917 (trimmed).
Contig 89. 1380 reads; 106457 bp (untrimmed), 106347 (trimmed).
Contig 90. 1419 reads; 91159 bp (untrimmed), 91062 (trimmed).
Contig 91. 1928 reads; 127330 bp (untrimmed), 127231 (trimmed).
Contig 92. 2083 reads; 138592 bp (untrimmed), 138404 (trimmed).
Contig 93. 2230 reads; 150516 bp (untrimmed), 149942 (trimmed).
Contig 94. 2413 reads; 148775 bp (untrimmed), 148750 (trimmed).
Contig 95. 2485 reads; 160687 bp (untrimmed), 160633 (trimmed).
Contig 96. 2730 reads; 182695 bp (untrimmed), 182685 (trimmed).
Contig 97. 3220 reads; 237605 bp (untrimmed), 237126 (trimmed).
Contig 98. 3277 reads; 226719 bp (untrimmed), 226657 (trimmed).
Contig 99. 3349 reads; 218948 bp (untrimmed), 218869 (trimmed).
Contig 100. 3718 reads; 253585 bp (untrimmed), 253488 (trimmed).
Contig 101. 4025 reads; 257632 bp (untrimmed), 257610 (trimmed).
Contig 102. 4625 reads; 300434 bp (untrimmed), 300258 (trimmed).
--------------------------------------------------------------
Totals 62548 reads; 4602121 bp (untrimmed), 4587675 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4602121 bases = 12.22 +- 5.30 = 0.25 +- 4.53
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 102 total values totalling 790.0100. <7.745196 +/- 4.411390>
#Range: [ 1.38 - 14.56 ]
#Most likely bin: [ 2.5 - 3 ] 10 counts
#Median bin: [ 7.5 - 8 ] 4 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXX 1 - 1.5 : [ 2 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 7 0.07 0.09 ]
|XXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 5 0.05 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 10 0.10 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 7 0.07 0.30 ]
|XXXXXXXX 3.5 - 4 : [ 2 0.02 0.32 ]
|XXXX 4 - 4.5 : [ 1 0.01 0.33 ]
|XXXXXXXXXXXXXXXX 4.5 - 5 : [ 4 0.04 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 7 0.07 0.44 ]
|XXXXXXXX 5.5 - 6 : [ 2 0.02 0.46 ]
#...
|XXXX 6.5 - 7 : [ 1 0.01 0.47 ]
#...
|XXXXXXXXXXXXXXXX 7.5 - 8 : [ 4 0.04 0.51 ]
#...
|XXXXXXXXXXXX 8.5 - 9 : [ 3 0.03 0.54 ]
#...
|XXXXXXXXXXXX 9.5 - 10 : [ 3 0.03 0.57 ]
|XXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 5 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 5 0.05 0.67 ]
|XXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 5 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 6 0.06 0.81 ]
|XXXXXXXX 12.5 - 13 : [ 2 0.02 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 7 0.07 0.90 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 7 0.07 0.97 ]
|XXXXXXXX 14 - 14.5 : [ 2 0.02 0.99 ]
|XXXX 14.5 - 15 : [ 1 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 74 total values totalling 719.1300. <9.717973 +/- 3.528063>
#Range: [ 2.35 - 14.56 ]
#Most likely bin: [ 13 - 13.5 ] 7 counts
#Median bin: [ 10.5 - 11 ] 5 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 2 - 2.5 : [ 1 0.01 0.01 ]
|XXXXXX 2.5 - 3 : [ 1 0.01 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 4 0.05 0.08 ]
#...
|XXXXXX 4 - 4.5 : [ 1 0.01 0.09 ]
|XXXXXXXXXXXXXXXXX 4.5 - 5 : [ 3 0.04 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 7 0.09 0.23 ]
|XXXXXXXXXXX 5.5 - 6 : [ 2 0.03 0.26 ]
#...
|XXXXXX 6.5 - 7 : [ 1 0.01 0.27 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 4 0.05 0.32 ]
#...
|XXXXXXXXXXXXXXXXX 8.5 - 9 : [ 3 0.04 0.36 ]
#...
|XXXXXXXXXXXXXXXXX 9.5 - 10 : [ 3 0.04 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 5 0.07 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 5 0.07 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 5 0.07 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 6 0.08 0.74 ]
|XXXXXXXXXXX 12.5 - 13 : [ 2 0.03 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 7 0.09 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 7 0.09 0.96 ]
|XXXXXXXXXXX 14 - 14.5 : [ 2 0.03 0.99 ]
|XXXXXX 14.5 - 15 : [ 1 0.01 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 1852 bases = 1.38 +- 0.49 = 0.66 +- 1.09
Contig 3 3 reads 1927 bases = 1.49 +- 0.51 = 1.49 +- 0.51
Contig 8 4 reads 2219 bases = 1.62 +- 0.74 = 0.75 +- 1.23
Contig 1 3 reads 1774 bases = 1.65 +- 0.68 = 1.65 +- 0.68
Contig 22 6 reads 3344 bases = 1.67 +- 0.47 = 0.45 +- 1.58
Contig 2 3 reads 1587 bases = 1.76 +- 0.75 = 1.76 +- 0.75
Contig 13 5 reads 2473 bases = 1.84 +- 0.64 = 0.45 +- 1.03
Contig 9 4 reads 2207 bases = 1.84 +- 0.92 = 1.84 +- 0.92
Contig 14 5 reads 2269 bases = 1.90 +- 0.67 = 0.36 +- 1.17
Contig 20 6 reads 2360 bases = 2.31 +- 0.87 = 2.31 +- 0.87
Contig 31 11 reads 4064 bases = 2.35 +- 1.16 = 0.52 +- 1.73
Contig 5 4 reads 1400 bases = 2.41 +- 1.10 = -0.38 +- 0.92
Contig 7 4 reads 1580 bases = 2.44 +- 1.18 = 1.22 +- 1.37
Contig 6 4 reads 1463 bases = 2.49 +- 1.02 = 1.36 +- 1.22
Contig 15 5 reads 1753 bases = 2.52 +- 0.77 = 0.55 +- 0.52
Contig 25 8 reads 2473 bases = 2.59 +- 1.10 = 1.87 +- 1.37
Contig 18 5 reads 1580 bases = 2.81 +- 1.36 = 2.81 +- 1.36
Contig 21 6 reads 1773 bases = 2.81 +- 1.63 = 2.50 +- 1.33
Contig 23 7 reads 2250 bases = 2.84 +- 1.65 = 1.24 +- 1.50
Contig 19 5 reads 1457 bases = 2.88 +- 1.29 = 1.51 +- 0.59
Contig 83 1087 reads 78498 bases = 12.41 +- 4.97 = 0.22 +- 4.26
Contig 71 645 reads 45828 bases = 12.67 +- 5.26 = 0.58 +- 4.54
Contig 60 251 reads 17458 bases = 12.92 +- 5.09 = 2.29 +- 4.61
Contig 98 3277 reads 226719 bases = 13.11 +- 4.66 = 0.34 +- 4.52
Contig 87 1235 reads 84850 bases = 13.13 +- 7.95 = 0.49 +- 4.29
Contig 100 3718 reads 253585 bases = 13.14 +- 5.37 = 0.18 +- 4.77
Contig 93 2230 reads 150516 bases = 13.26 +- 5.31 = 0.11 +- 4.34
Contig 77 783 reads 52187 bases = 13.41 +- 4.55 = 0.60 +- 5.05
Contig 84 1126 reads 75202 bases = 13.41 +- 4.82 = 0.78 +- 4.84
Contig 96 2730 reads 182695 bases = 13.45 +- 4.62 = 0.09 +- 4.71
Contig 91 1928 reads 127330 bases = 13.62 +- 5.57 = -0.08 +- 4.44
Contig 92 2083 reads 138592 bases = 13.63 +- 4.64 = 0.26 +- 4.10
Contig 99 3349 reads 218948 bases = 13.71 +- 4.95 = 0.06 +- 4.96
Contig 41 39 reads 2530 bases = 13.86 +- 8.27 = 2.80 +- 3.06
Contig 102 4625 reads 300434 bases = 13.87 +- 4.93 = 0.14 +- 4.65
Contig 95 2485 reads 160687 bases = 13.91 +- 5.43 = 0.06 +- 5.24
Contig 81 1049 reads 67420 bases = 13.94 +- 4.62 = 0.12 +- 4.46
Contig 90 1419 reads 91159 bases = 14.03 +- 5.20 = 0.08 +- 4.92
Contig 101 4025 reads 257632 bases = 14.06 +- 4.75 = 0.17 +- 4.64
Contig 94 2413 reads 148775 bases = 14.56 +- 5.36 = 0.31 +- 4.80
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 158
HQ Discrepant reads = 37
Chimeric reads = 135
Suspect alignments = 425
-------------------------------------------------------------------
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/microbe5/3634498/edit_dir.04Jan05.QD