Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-12-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3436384 8900 269482 Burkholderia vietnamiensis
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Burkholderia_vietnamiensis
-------------------------------------------------------------------
Burkholderiaceae, family, b-proteobacteria
Burkholderia cepacia complex, species group, b-proteobacteria
Burkholderiales, order, b-proteobacteria
Burkholderia vietnamiensis, species, b-proteobacteria
Burkholderia, genus, b-proteobacteria
Betaproteobacteria, class, b-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 8406303
# phrap: 7724716
# db:
altered.
8900000
8343673 +/- 481847
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 0
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: 110083
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 20297045
C = 35300278
G = 34717966
T = 20302414
N = 584185
X = 7213443
GC fraction = 0.59
Total = 118415331
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436384_fasta.screen.contigs
-------------------------------------------------------------------
A 1463481
C 2796057
G 2774503
T 1460763
N 6036
fraction GC = 0.66
total bases = 8500840
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 ACTO reads.list > grep.reads.list.ACTO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACTO 4 500
-------------------------------------------------------------------
#Found 16696 total values totalling 164602645.0000. <9858.807199 +/- 4891.828169>
#Range: [ 120 - 316607 ]
#Most likely bin: [ 9500 - 10000 ] 1866 counts
#Median bin: [ 9500 - 10000 ] 1866 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 18 0.00 0.00 ]
| 500 - 1000 : [ 10 0.00 0.00 ]
|XX 1000 - 1500 : [ 72 0.00 0.01 ]
|XXX 1500 - 2000 : [ 117 0.01 0.01 ]
|XX 2000 - 2500 : [ 115 0.01 0.02 ]
|XX 2500 - 3000 : [ 112 0.01 0.03 ]
|XX 3000 - 3500 : [ 100 0.01 0.03 ]
|XX 3500 - 4000 : [ 114 0.01 0.04 ]
|XX 4000 - 4500 : [ 110 0.01 0.05 ]
|XXX 4500 - 5000 : [ 142 0.01 0.05 ]
|XXX 5000 - 5500 : [ 139 0.01 0.06 ]
|XXXXX 5500 - 6000 : [ 211 0.01 0.08 ]
|XXXXX 6000 - 6500 : [ 237 0.01 0.09 ]
|XXXXXXX 6500 - 7000 : [ 339 0.02 0.11 ]
|XXXXXXXXX 7000 - 7500 : [ 431 0.03 0.14 ]
|XXXXXXXXXXXXXX 7500 - 8000 : [ 634 0.04 0.17 ]
|XXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 829 0.05 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 1268 0.08 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 1567 0.09 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 1866 0.11 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 1732 0.10 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10500 - 11000 : [ 1635 0.10 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11000 - 11500 : [ 1346 0.08 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXX 11500 - 12000 : [ 1082 0.06 0.85 ]
|XXXXXXXXXXXXXXXXXX 12000 - 12500 : [ 844 0.05 0.90 ]
|XXXXXXXXXXXXX 12500 - 13000 : [ 610 0.04 0.94 ]
|XXXXXXXXX 13000 - 13500 : [ 415 0.02 0.96 ]
|XXXXX 13500 - 14000 : [ 244 0.01 0.98 ]
|XXX 14000 - 14500 : [ 161 0.01 0.99 ]
|XX 14500 - 15000 : [ 87 0.01 0.99 ]
|X 15000 - 15500 : [ 42 0.00 1.00 ]
| 15500 - 16000 : [ 22 0.00 1.00 ]
| 16000 - 16500 : [ 11 0.00 1.00 ]
| 16500 - 17000 : [ 4 0.00 1.00 ]
| 17000 - 17500 : [ 4 0.00 1.00 ]
| 17500 - 18000 : [ 3 0.00 1.00 ]
#...
| 29000 - 29500 : [ 1 0.00 1.00 ]
#...
| 54500 - 55000 : [ 1 0.00 1.00 ]
#...
| 69500 - 70000 : [ 1 0.00 1.00 ]
#...
| 75000 - 75500 : [ 1 0.00 1.00 ]
| 75500 - 76000 : [ 1 0.00 1.00 ]
| 76000 - 76500 : [ 1 0.00 1.00 ]
| 76500 - 77000 : [ 2 0.00 1.00 ]
| 77000 - 77500 : [ 3 0.00 1.00 ]
| 77500 - 78000 : [ 1 0.00 1.00 ]
| 78000 - 78500 : [ 1 0.00 1.00 ]
| 78500 - 79000 : [ 2 0.00 1.00 ]
| 79000 - 79500 : [ 1 0.00 1.00 ]
#...
| 80500 - 81000 : [ 1 0.00 1.00 ]
#...
| 94000 - 94500 : [ 1 0.00 1.00 ]
#...
| 132500 - 133000 : [ 1 0.00 1.00 ]
| 133000 - 133500 : [ 1 0.00 1.00 ]
#...
| 186000 - 186500 : [ 1 0.00 1.00 ]
#...
| 266500 - 267000 : [ 1 0.00 1.00 ]
#...
| 316500 - 317000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAHU reads.list > grep.reads.list.AAHU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAHU 4 500
-------------------------------------------------------------------
#Found 1252 total values totalling 48222126.0000. <38516.075080 +/- 8564.043885>
#Range: [ 981 - 111851 ]
#Most likely bin: [ 37500 - 38000 ] 73 counts
#Median bin: [ 37500 - 38000 ] 73 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 1 0.00 0.00 ]
#...
|X 2500 - 3000 : [ 1 0.00 0.00 ]
#...
|X 27000 - 27500 : [ 2 0.00 0.00 ]
|X 27500 - 28000 : [ 2 0.00 0.00 ]
|XX 28000 - 28500 : [ 3 0.00 0.01 ]
|X 28500 - 29000 : [ 2 0.00 0.01 ]
|XX 29000 - 29500 : [ 4 0.00 0.01 ]
|XXX 29500 - 30000 : [ 5 0.00 0.02 ]
|XXXXX 30000 - 30500 : [ 9 0.01 0.02 ]
|XXXXXXXX 30500 - 31000 : [ 14 0.01 0.03 ]
|XXXXX 31000 - 31500 : [ 9 0.01 0.04 ]
|XXXXXXXXXXXXX 31500 - 32000 : [ 23 0.02 0.06 ]
|XXXXXXXXXXXXXXX 32000 - 32500 : [ 27 0.02 0.08 ]
|XXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 38 0.03 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 40 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 43 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 57 0.05 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 49 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 53 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 52 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 53 0.04 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 54 0.04 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 55 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 73 0.06 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 65 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 51 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 57 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 40 0.03 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 45 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 48 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 36 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 35 0.03 0.84 ]
|XXXXXXXXXXXXXXXXX 42000 - 42500 : [ 31 0.02 0.86 ]
|XXXXXXXXXXXXXXXXX 42500 - 43000 : [ 31 0.02 0.88 ]
|XXXXXXXXXXXXX 43000 - 43500 : [ 24 0.02 0.90 ]
|XXXXXXXXXX 43500 - 44000 : [ 18 0.01 0.92 ]
|XXXXXXXXXXXXX 44000 - 44500 : [ 23 0.02 0.94 ]
|XXXXXXXX 44500 - 45000 : [ 15 0.01 0.95 ]
|XXXXXXXX 45000 - 45500 : [ 15 0.01 0.96 ]
|XXXXXX 45500 - 46000 : [ 11 0.01 0.97 ]
|XXXXX 46000 - 46500 : [ 9 0.01 0.98 ]
|XXXXX 46500 - 47000 : [ 9 0.01 0.98 ]
|XX 47000 - 47500 : [ 3 0.00 0.99 ]
|X 47500 - 48000 : [ 2 0.00 0.99 ]
#...
|X 97500 - 98000 : [ 1 0.00 0.99 ]
#...
|X 99000 - 99500 : [ 1 0.00 0.99 ]
#...
|X 102000 - 102500 : [ 1 0.00 0.99 ]
#...
|X 103500 - 104000 : [ 1 0.00 0.99 ]
#...
|X 105000 - 105500 : [ 1 0.00 0.99 ]
|X 105500 - 106000 : [ 2 0.00 0.99 ]
#...
|X 107000 - 107500 : [ 1 0.00 0.99 ]
|X 107500 - 108000 : [ 1 0.00 1.00 ]
|X 108000 - 108500 : [ 1 0.00 1.00 ]
#...
|X 110000 - 110500 : [ 1 0.00 1.00 ]
|XX 110500 - 111000 : [ 3 0.00 1.00 ]
#...
|X 111500 - 112000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAHW reads.list > grep.reads.list.AAHW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAHW 4 500
-------------------------------------------------------------------
#Found 2469 total values totalling 16892311.0000. <6841.762252 +/- 5228.567567>
#Range: [ 764 - 122999 ]
#Most likely bin: [ 8500 - 9000 ] 216 counts
#Median bin: [ 7500 - 8000 ] 139 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 500 - 1000 : [ 54 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 1500 : [ 135 0.05 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 1500 - 2000 : [ 135 0.05 0.13 ]
|XXXXXXXXXXXXXXXXXXXX 2000 - 2500 : [ 106 0.04 0.17 ]
|XXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 109 0.04 0.22 ]
|XXXXXXXXXXXXXXXX 3000 - 3500 : [ 89 0.04 0.25 ]
|XXXXXXXXXXXXXXXX 3500 - 4000 : [ 85 0.03 0.29 ]
|XXXXXXXXXXX 4000 - 4500 : [ 59 0.02 0.31 ]
|XXXXXXXXXXXXXX 4500 - 5000 : [ 73 0.03 0.34 ]
|XXXXXXXXXXXX 5000 - 5500 : [ 63 0.03 0.37 ]
|XXXXXXXXXX 5500 - 6000 : [ 54 0.02 0.39 ]
|XXXXXXXXXXX 6000 - 6500 : [ 62 0.03 0.41 ]
|XXXXXXXXXXXXXXXX 6500 - 7000 : [ 88 0.04 0.45 ]
|XXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 101 0.04 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 139 0.06 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 187 0.08 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 216 0.09 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 179 0.07 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 165 0.07 0.85 ]
|XXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 114 0.05 0.90 ]
|XXXXXXXXXXXXXXXX 10500 - 11000 : [ 86 0.03 0.93 ]
|XXXXXXXXXXXX 11000 - 11500 : [ 67 0.03 0.96 ]
|XXXXXXX 11500 - 12000 : [ 38 0.02 0.97 ]
|XXXX 12000 - 12500 : [ 23 0.01 0.98 ]
|XXXX 12500 - 13000 : [ 20 0.01 0.99 ]
|X 13000 - 13500 : [ 7 0.00 0.99 ]
| 13500 - 14000 : [ 2 0.00 0.99 ]
|X 14000 - 14500 : [ 4 0.00 1.00 ]
| 14500 - 15000 : [ 1 0.00 1.00 ]
| 15000 - 15500 : [ 2 0.00 1.00 ]
#...
| 74000 - 74500 : [ 2 0.00 1.00 ]
| 74500 - 75000 : [ 1 0.00 1.00 ]
#...
| 76500 - 77000 : [ 1 0.00 1.00 ]
#...
| 96000 - 96500 : [ 1 0.00 1.00 ]
#...
| 122500 - 123000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAHT reads.list > grep.reads.list.AAHT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAHT 4 500
-------------------------------------------------------------------
#Found 20382 total values totalling 80562773.0000. <3952.643166 +/- 3661.588535>
#Range: [ 750 - 282624 ]
#Most likely bin: [ 3500 - 4000 ] 4523 counts
#Median bin: [ 3500 - 4000 ] 4523 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 25 0.00 0.00 ]
|X 1000 - 1500 : [ 108 0.01 0.01 ]
|X 1500 - 2000 : [ 137 0.01 0.01 ]
|XXX 2000 - 2500 : [ 293 0.01 0.03 ]
|XXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2313 0.11 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4209 0.21 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 4523 0.22 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 4274 0.21 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 2992 0.15 0.93 ]
|XXXXXXXXXXX 5000 - 5500 : [ 1289 0.06 0.99 ]
|XX 5500 - 6000 : [ 188 0.01 1.00 ]
| 6000 - 6500 : [ 3 0.00 1.00 ]
| 6500 - 7000 : [ 2 0.00 1.00 ]
#...
| 8500 - 9000 : [ 1 0.00 1.00 ]
#...
| 16000 - 16500 : [ 1 0.00 1.00 ]
#...
| 19500 - 20000 : [ 1 0.00 1.00 ]
#...
| 20500 - 21000 : [ 1 0.00 1.00 ]
#...
| 45000 - 45500 : [ 1 0.00 1.00 ]
#...
| 51500 - 52000 : [ 1 0.00 1.00 ]
#...
| 68000 - 68500 : [ 1 0.00 1.00 ]
#...
| 69000 - 69500 : [ 1 0.00 1.00 ]
#...
| 70000 - 70500 : [ 2 0.00 1.00 ]
| 70500 - 71000 : [ 2 0.00 1.00 ]
| 71000 - 71500 : [ 2 0.00 1.00 ]
| 71500 - 72000 : [ 3 0.00 1.00 ]
#...
| 75500 - 76000 : [ 1 0.00 1.00 ]
#...
| 90500 - 91000 : [ 1 0.00 1.00 ]
#...
| 96000 - 96500 : [ 1 0.00 1.00 ]
#...
| 100000 - 100500 : [ 1 0.00 1.00 ]
#...
| 122500 - 123000 : [ 1 0.00 1.00 ]
#...
| 138000 - 138500 : [ 1 0.00 1.00 ]
#...
| 174500 - 175000 : [ 1 0.00 1.00 ]
#...
| 197500 - 198000 : [ 1 0.00 1.00 ]
#...
| 282500 - 283000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AAHT 3737 +- 862 (n=10398)
# ACTO 9328 +- 2768 (n=8459)
# AAHW 6122 +- 3548 (n=1343)
# AAHU 37643 +- 4224 (n=625)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436384_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
AAHT 52992 -1 -1 98 671 50928 99 647 100 655
AAHU 6144 -1 -1 95 585 5659 99 624 100 630
AAHW 7680 -1 -1 99 600 6979 99 568 100 633
ACTO 52992 -1 -1 98 663 46517 99 610 100 666
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AAHT 24820 99 632 100 646 26108 100 661 100 663
AAHU 2834 99 634 100 624 2825 99 613 100 636
AAHW 3447 98 572 100 646 3532 99 564 100 621
ACTO 23252 99 603 100 668 23265 99 617 100 663
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436384_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 117263 58339 95.95 cumulative total @@
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 3436384_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 110083 total values totalling 68257857.0000. <620.058111 +/- 154.718416>
#Range: [ 14 - 950 ]
#Most likely bin: [ 700 - 750 ] 26039 counts
#Median bin: [ 650 - 700 ] 24608 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 205 0.00 0.00 ]
|X 50 - 100 : [ 825 0.01 0.01 ]
|XX 100 - 150 : [ 1237 0.01 0.02 ]
|XX 150 - 200 : [ 1456 0.01 0.03 ]
|XXX 200 - 250 : [ 1813 0.02 0.05 ]
|XXX 250 - 300 : [ 1727 0.02 0.07 ]
|XXX 300 - 350 : [ 1982 0.02 0.08 ]
|XXX 350 - 400 : [ 2248 0.02 0.10 ]
|XXXX 400 - 450 : [ 2778 0.03 0.13 ]
|XXXXX 450 - 500 : [ 3518 0.03 0.16 ]
|XXXXXXXX 500 - 550 : [ 5253 0.05 0.21 ]
|XXXXXXXXXXXXX 550 - 600 : [ 8366 0.08 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 14862 0.14 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 24608 0.22 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 26039 0.24 0.88 ]
|XXXXXXXXXXXXXXXXXX 750 - 800 : [ 11856 0.11 0.99 ]
|XX 800 - 850 : [ 1181 0.01 1.00 ]
| 850 - 900 : [ 98 0.00 1.00 ]
| 900 - 950 : [ 30 0.00 1.00 ]
| 950 - 1000 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOUW
trimt JAZZ trim 15 readlength histogram for ACTO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACTO 3436384_fasta.screen.trimQ15.SaF > reads.trim15.ACTO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACTO.rl 2 50
-------------------------------------------------------------------
#Found 46517 total values totalling 28079458.0000. <603.638627 +/- 157.274333>
#Range: [ 14 - 854 ]
#Most likely bin: [ 650 - 700 ] 10466 counts
#Median bin: [ 650 - 700 ] 10466 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 103 0.00 0.00 ]
|XX 50 - 100 : [ 427 0.01 0.01 ]
|XX 100 - 150 : [ 614 0.01 0.02 ]
|XXX 150 - 200 : [ 678 0.01 0.04 ]
|XXX 200 - 250 : [ 797 0.02 0.06 ]
|XXX 250 - 300 : [ 786 0.02 0.07 ]
|XXXX 300 - 350 : [ 951 0.02 0.09 ]
|XXXX 350 - 400 : [ 1044 0.02 0.12 ]
|XXXXX 400 - 450 : [ 1386 0.03 0.15 ]
|XXXXXX 450 - 500 : [ 1691 0.04 0.18 ]
|XXXXXXXXXX 500 - 550 : [ 2632 0.06 0.24 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 4220 0.09 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 7118 0.15 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 10466 0.22 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 9776 0.21 0.92 ]
|XXXXXXXXXXXXXX 750 - 800 : [ 3552 0.08 0.99 ]
|X 800 - 850 : [ 274 0.01 1.00 ]
| 850 - 900 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAHU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAHU 3436384_fasta.screen.trimQ15.SaF > reads.trim15.AAHU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAHU.rl 2 50
-------------------------------------------------------------------
#Found 5659 total values totalling 3489611.0000. <616.647994 +/- 178.488096>
#Range: [ 25 - 832 ]
#Most likely bin: [ 700 - 750 ] 1765 counts
#Median bin: [ 650 - 700 ] 1173 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 13 0.00 0.00 ]
|X 50 - 100 : [ 58 0.01 0.01 ]
|XX 100 - 150 : [ 97 0.02 0.03 ]
|XXX 150 - 200 : [ 136 0.02 0.05 ]
|XXX 200 - 250 : [ 152 0.03 0.08 ]
|XXX 250 - 300 : [ 118 0.02 0.10 ]
|XXX 300 - 350 : [ 144 0.03 0.13 ]
|XXX 350 - 400 : [ 141 0.02 0.15 ]
|XX 400 - 450 : [ 107 0.02 0.17 ]
|XXX 450 - 500 : [ 112 0.02 0.19 ]
|XXXX 500 - 550 : [ 162 0.03 0.22 ]
|XXXXX 550 - 600 : [ 233 0.04 0.26 ]
|XXXXXXXXXXX 600 - 650 : [ 487 0.09 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1173 0.21 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1765 0.31 0.87 ]
|XXXXXXXXXXXXXXXX 750 - 800 : [ 713 0.13 0.99 ]
|X 800 - 850 : [ 48 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAHW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAHW 3436384_fasta.screen.trimQ15.SaF > reads.trim15.AAHW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAHW.rl 2 50
-------------------------------------------------------------------
#Found 6979 total values totalling 3911889.0000. <560.522854 +/- 152.242465>
#Range: [ 22 - 757 ]
#Most likely bin: [ 650 - 700 ] 1861 counts
#Median bin: [ 600 - 650 ] 1505 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 25 0.00 0.00 ]
|XX 50 - 100 : [ 76 0.01 0.01 ]
|XX 100 - 150 : [ 111 0.02 0.03 ]
|XXX 150 - 200 : [ 130 0.02 0.05 ]
|XXX 200 - 250 : [ 155 0.02 0.07 ]
|XXX 250 - 300 : [ 151 0.02 0.09 ]
|XXXX 300 - 350 : [ 166 0.02 0.12 ]
|XXXX 350 - 400 : [ 198 0.03 0.15 ]
|XXXXX 400 - 450 : [ 234 0.03 0.18 ]
|XXXXXXX 450 - 500 : [ 344 0.05 0.23 ]
|XXXXXXXXXXXX 500 - 550 : [ 560 0.08 0.31 ]
|XXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 967 0.14 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1505 0.22 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1861 0.27 0.93 ]
|XXXXXXXXXXX 700 - 750 : [ 494 0.07 1.00 ]
| 750 - 800 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOYK
trimt JAZZ trim 15 readlength histogram for APZC
trimt JAZZ trim 15 readlength histogram for AAHT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAHT 3436384_fasta.screen.trimQ15.SaF > reads.trim15.AAHT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAHT.rl 2 50
-------------------------------------------------------------------
#Found 50928 total values totalling 32776899.0000. <643.592896 +/- 145.417872>
#Range: [ 21 - 950 ]
#Most likely bin: [ 700 - 750 ] 14004 counts
#Median bin: [ 650 - 700 ] 11108 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 64 0.00 0.00 ]
|X 50 - 100 : [ 264 0.01 0.01 ]
|X 100 - 150 : [ 415 0.01 0.01 ]
|X 150 - 200 : [ 512 0.01 0.02 ]
|XX 200 - 250 : [ 709 0.01 0.04 ]
|XX 250 - 300 : [ 672 0.01 0.05 ]
|XX 300 - 350 : [ 721 0.01 0.07 ]
|XX 350 - 400 : [ 865 0.02 0.08 ]
|XXX 400 - 450 : [ 1051 0.02 0.10 ]
|XXXX 450 - 500 : [ 1371 0.03 0.13 ]
|XXXXX 500 - 550 : [ 1899 0.04 0.17 ]
|XXXXXXXX 550 - 600 : [ 2946 0.06 0.23 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 5752 0.11 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 11108 0.22 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 14004 0.27 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 7589 0.15 0.98 ]
|XX 800 - 850 : [ 859 0.02 1.00 ]
| 850 - 900 : [ 96 0.00 1.00 ]
| 900 - 950 : [ 30 0.00 1.00 ]
| 950 - 1000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436384
-------------------------------------------------------------------
AAHT.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AAHT.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AAHT.000201.000300 pUC18.fa pUC18.fa LRS.fasta
AAHU.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AAHW.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
ACTO.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
ACTO.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
ACTO.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
ACTO.000301.000400 pMCL200.fa pMCL200.fa LRS.fasta
AOUW.000001.000100
AAHT.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AAHT.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AAHT.000201.000300 pUC18.fa pUC18.fa LRS.fasta
AAHU.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AAHW.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
ACTO.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
ACTO.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
ACTO.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
ACTO.000301.000400 pMCL200.fa pMCL200.fa LRS.fasta
AOUW.000001.000100
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436384_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436384_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 111043 total values totalling 72724.8456. <0.654925 +/- 0.057917>
#Range: [ 0 - 0.9678 ]
#Most likely bin: [ 0.68 - 0.685 ] 4714 counts
#Median bin: [ 0.66 - 0.665 ] 4122 counts
| 0 - 0.005 : [ 2 0.00 0.00 ]
#...
| 0.19 - 0.195 : [ 1 0.00 0.00 ]
#...
| 0.255 - 0.26 : [ 1 0.00 0.00 ]
#...
| 0.265 - 0.27 : [ 1 0.00 0.00 ]
| 0.27 - 0.275 : [ 1 0.00 0.00 ]
| 0.275 - 0.28 : [ 2 0.00 0.00 ]
#...
| 0.285 - 0.29 : [ 1 0.00 0.00 ]
| 0.29 - 0.295 : [ 4 0.00 0.00 ]
| 0.295 - 0.3 : [ 6 0.00 0.00 ]
| 0.3 - 0.305 : [ 6 0.00 0.00 ]
| 0.305 - 0.31 : [ 6 0.00 0.00 ]
| 0.31 - 0.315 : [ 10 0.00 0.00 ]
| 0.315 - 0.32 : [ 10 0.00 0.00 ]
| 0.32 - 0.325 : [ 10 0.00 0.00 ]
| 0.325 - 0.33 : [ 12 0.00 0.00 ]
| 0.33 - 0.335 : [ 14 0.00 0.00 ]
| 0.335 - 0.34 : [ 17 0.00 0.00 ]
| 0.34 - 0.345 : [ 14 0.00 0.00 ]
| 0.345 - 0.35 : [ 15 0.00 0.00 ]
| 0.35 - 0.355 : [ 13 0.00 0.00 ]
| 0.355 - 0.36 : [ 13 0.00 0.00 ]
| 0.36 - 0.365 : [ 12 0.00 0.00 ]
| 0.365 - 0.37 : [ 20 0.00 0.00 ]
| 0.37 - 0.375 : [ 12 0.00 0.00 ]
| 0.375 - 0.38 : [ 24 0.00 0.00 ]
| 0.38 - 0.385 : [ 25 0.00 0.00 ]
| 0.385 - 0.39 : [ 22 0.00 0.00 ]
| 0.39 - 0.395 : [ 18 0.00 0.00 ]
| 0.395 - 0.4 : [ 14 0.00 0.00 ]
| 0.4 - 0.405 : [ 17 0.00 0.00 ]
| 0.405 - 0.41 : [ 16 0.00 0.00 ]
| 0.41 - 0.415 : [ 17 0.00 0.00 ]
| 0.415 - 0.42 : [ 22 0.00 0.00 ]
| 0.42 - 0.425 : [ 23 0.00 0.00 ]
| 0.425 - 0.43 : [ 28 0.00 0.00 ]
| 0.43 - 0.435 : [ 35 0.00 0.00 ]
| 0.435 - 0.44 : [ 39 0.00 0.00 ]
| 0.44 - 0.445 : [ 40 0.00 0.00 ]
| 0.445 - 0.45 : [ 36 0.00 0.01 ]
| 0.45 - 0.455 : [ 49 0.00 0.01 ]
| 0.455 - 0.46 : [ 51 0.00 0.01 ]
| 0.46 - 0.465 : [ 58 0.00 0.01 ]
|X 0.465 - 0.47 : [ 66 0.00 0.01 ]
|X 0.47 - 0.475 : [ 61 0.00 0.01 ]
|X 0.475 - 0.48 : [ 60 0.00 0.01 ]
|X 0.48 - 0.485 : [ 86 0.00 0.01 ]
|X 0.485 - 0.49 : [ 85 0.00 0.01 ]
|X 0.49 - 0.495 : [ 76 0.00 0.01 ]
|X 0.495 - 0.5 : [ 73 0.00 0.01 ]
|X 0.5 - 0.505 : [ 166 0.00 0.01 ]
|X 0.505 - 0.51 : [ 160 0.00 0.01 ]
|XX 0.51 - 0.515 : [ 183 0.00 0.02 ]
|XX 0.515 - 0.52 : [ 226 0.00 0.02 ]
|XX 0.52 - 0.525 : [ 276 0.00 0.02 ]
|XXX 0.525 - 0.53 : [ 388 0.00 0.02 ]
|XXXX 0.53 - 0.535 : [ 417 0.00 0.03 ]
|XXXX 0.535 - 0.54 : [ 453 0.00 0.03 ]
|XXXXX 0.54 - 0.545 : [ 552 0.00 0.04 ]
|XXXXXX 0.545 - 0.55 : [ 698 0.01 0.04 ]
|XXXXXXX 0.55 - 0.555 : [ 828 0.01 0.05 ]
|XXXXXXXX 0.555 - 0.56 : [ 890 0.01 0.06 ]
|XXXXXXXXX 0.56 - 0.565 : [ 1079 0.01 0.07 ]
|XXXXXXXXXXX 0.565 - 0.57 : [ 1254 0.01 0.08 ]
|XXXXXXXXXXX 0.57 - 0.575 : [ 1346 0.01 0.09 ]
|XXXXXXXXXXXXX 0.575 - 0.58 : [ 1483 0.01 0.10 ]
|XXXXXXXXXXXXX 0.58 - 0.585 : [ 1541 0.01 0.12 ]
|XXXXXXXXXXXXXX 0.585 - 0.59 : [ 1625 0.01 0.13 ]
|XXXXXXXXXXXXXXX 0.59 - 0.595 : [ 1794 0.02 0.15 ]
|XXXXXXXXXXXXXXX 0.595 - 0.6 : [ 1770 0.02 0.17 ]
|XXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 2021 0.02 0.18 ]
|XXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 2031 0.02 0.20 ]
|XXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 2220 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 2431 0.02 0.24 ]
|XXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 2524 0.02 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 2663 0.02 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 2822 0.03 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 3074 0.03 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 3323 0.03 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 3536 0.03 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 3691 0.03 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 3863 0.03 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 4122 0.04 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 4292 0.04 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 4418 0.04 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 4439 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 4714 0.04 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 4545 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 4449 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 4050 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 3915 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 3451 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 3091 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 2532 0.02 0.91 ]
|XXXXXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 2261 0.02 0.93 ]
|XXXXXXXXXXXXXXX 0.725 - 0.73 : [ 1778 0.02 0.94 ]
|XXXXXXXXXXXXX 0.73 - 0.735 : [ 1488 0.01 0.96 ]
|XXXXXXXXXX 0.735 - 0.74 : [ 1122 0.01 0.97 ]
|XXXXXXXX 0.74 - 0.745 : [ 886 0.01 0.97 ]
|XXXXX 0.745 - 0.75 : [ 589 0.01 0.98 ]
|XXXXX 0.75 - 0.755 : [ 567 0.01 0.98 ]
|XXX 0.755 - 0.76 : [ 344 0.00 0.99 ]
|XXX 0.76 - 0.765 : [ 329 0.00 0.99 ]
|XX 0.765 - 0.77 : [ 219 0.00 0.99 ]
|XX 0.77 - 0.775 : [ 184 0.00 0.99 ]
|X 0.775 - 0.78 : [ 127 0.00 0.99 ]
|X 0.78 - 0.785 : [ 109 0.00 1.00 ]
|X 0.785 - 0.79 : [ 66 0.00 1.00 ]
| 0.79 - 0.795 : [ 57 0.00 1.00 ]
| 0.795 - 0.8 : [ 35 0.00 1.00 ]
|X 0.8 - 0.805 : [ 62 0.00 1.00 ]
| 0.805 - 0.81 : [ 41 0.00 1.00 ]
| 0.81 - 0.815 : [ 28 0.00 1.00 ]
| 0.815 - 0.82 : [ 24 0.00 1.00 ]
| 0.82 - 0.825 : [ 19 0.00 1.00 ]
| 0.825 - 0.83 : [ 19 0.00 1.00 ]
| 0.83 - 0.835 : [ 17 0.00 1.00 ]
| 0.835 - 0.84 : [ 10 0.00 1.00 ]
| 0.84 - 0.845 : [ 6 0.00 1.00 ]
| 0.845 - 0.85 : [ 6 0.00 1.00 ]
| 0.85 - 0.855 : [ 11 0.00 1.00 ]
| 0.855 - 0.86 : [ 4 0.00 1.00 ]
| 0.86 - 0.865 : [ 6 0.00 1.00 ]
| 0.865 - 0.87 : [ 4 0.00 1.00 ]
| 0.87 - 0.875 : [ 2 0.00 1.00 ]
| 0.875 - 0.88 : [ 5 0.00 1.00 ]
| 0.88 - 0.885 : [ 9 0.00 1.00 ]
| 0.885 - 0.89 : [ 2 0.00 1.00 ]
| 0.89 - 0.895 : [ 1 0.00 1.00 ]
#...
| 0.9 - 0.905 : [ 3 0.00 1.00 ]
| 0.905 - 0.91 : [ 2 0.00 1.00 ]
| 0.91 - 0.915 : [ 2 0.00 1.00 ]
| 0.915 - 0.92 : [ 1 0.00 1.00 ]
| 0.92 - 0.925 : [ 4 0.00 1.00 ]
| 0.925 - 0.93 : [ 1 0.00 1.00 ]
#...
| 0.935 - 0.94 : [ 1 0.00 1.00 ]
#...
| 0.95 - 0.955 : [ 1 0.00 1.00 ]
#...
| 0.965 - 0.97 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 411. 1376 reads; 104658 bp (untrimmed), 103440 (trimmed).
Contig 412. 1395 reads; 105311 bp (untrimmed), 104877 (trimmed).
Contig 413. 1403 reads; 101633 bp (untrimmed), 101633 (trimmed).
Contig 414. 1431 reads; 117224 bp (untrimmed), 117224 (trimmed).
Contig 415. 1455 reads; 109276 bp (untrimmed), 108965 (trimmed).
Contig 416. 1528 reads; 110998 bp (untrimmed), 110778 (trimmed).
Contig 417. 1693 reads; 122012 bp (untrimmed), 121990 (trimmed).
Contig 418. 1711 reads; 134088 bp (untrimmed), 134041 (trimmed).
Contig 419. 1861 reads; 136641 bp (untrimmed), 136335 (trimmed).
Contig 420. 1971 reads; 113936 bp (untrimmed), 113734 (trimmed).
Contig 421. 2146 reads; 151454 bp (untrimmed), 151443 (trimmed).
Contig 422. 2175 reads; 175326 bp (untrimmed), 174053 (trimmed).
Contig 423. 2200 reads; 157251 bp (untrimmed), 156698 (trimmed).
Contig 424. 2215 reads; 156400 bp (untrimmed), 156148 (trimmed).
Contig 425. 2290 reads; 155407 bp (untrimmed), 154639 (trimmed).
Contig 426. 2420 reads; 170713 bp (untrimmed), 169899 (trimmed).
Contig 427. 2596 reads; 203504 bp (untrimmed), 203260 (trimmed).
Contig 428. 2599 reads; 188937 bp (untrimmed), 188937 (trimmed).
Contig 429. 3003 reads; 215158 bp (untrimmed), 215086 (trimmed).
Contig 430. 3055 reads; 208182 bp (untrimmed), 207896 (trimmed).
Contig 431. 3397 reads; 248528 bp (untrimmed), 248416 (trimmed).
Contig 432. 3637 reads; 276692 bp (untrimmed), 276493 (trimmed).
Contig 433. 4011 reads; 272815 bp (untrimmed), 272814 (trimmed).
Contig 434. 4379 reads; 306857 bp (untrimmed), 306857 (trimmed).
Contig 435. 5666 reads; 375696 bp (untrimmed), 375696 (trimmed).
Contig 436. 6026 reads; 403452 bp (untrimmed), 403413 (trimmed).
Contig 437. 7026 reads; 411416 bp (untrimmed), 411398 (trimmed).
--------------------------------------------------------------
Totals 111638 reads; 8500840 bp (untrimmed), 8406303 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 8386930 bases = 10.79 +- 5.16 = 0.26 +- 3.65
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 259 total values totalling 1794.5500. <6.928764 +/- 5.007920>
#Range: [ 1.00 - 46.82 ]
#Most likely bin: [ 1.5 - 2 ] 28 counts
#Median bin: [ 7 - 7.5 ] 5 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 18 0.07 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 28 0.11 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 23 0.09 0.27 ]
|XXXXXXXXXXX 2.5 - 3 : [ 8 0.03 0.30 ]
|XXXXXXXXXXXXX 3 - 3.5 : [ 9 0.03 0.33 ]
|XXXXXXXXXXXXXXXXX 3.5 - 4 : [ 12 0.05 0.38 ]
|XXXXXXXXX 4 - 4.5 : [ 6 0.02 0.40 ]
|XXXXXX 4.5 - 5 : [ 4 0.02 0.42 ]
|XXXX 5 - 5.5 : [ 3 0.01 0.43 ]
|XXX 5.5 - 6 : [ 2 0.01 0.44 ]
|XXXXXXXXXX 6 - 6.5 : [ 7 0.03 0.46 ]
|XXXXXXX 6.5 - 7 : [ 5 0.02 0.48 ]
|XXXXXXX 7 - 7.5 : [ 5 0.02 0.50 ]
|XXXXXXXXXX 7.5 - 8 : [ 7 0.03 0.53 ]
|XXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 15 0.06 0.59 ]
|XXXXXXXXXXXXXXXXX 8.5 - 9 : [ 12 0.05 0.63 ]
|XXXXXXXXXXXXXXXXX 9 - 9.5 : [ 12 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 16 0.06 0.74 ]
|XXXXXXXXXXXXXXXX 10 - 10.5 : [ 11 0.04 0.78 ]
|XXXXXXXXXXXXXXXX 10.5 - 11 : [ 11 0.04 0.83 ]
|XXXXXXXXXXXXXXXXX 11 - 11.5 : [ 12 0.05 0.87 ]
|XXXXXXXXXXXXXXXXX 11.5 - 12 : [ 12 0.05 0.92 ]
|XXXXXXXXXXXXX 12 - 12.5 : [ 9 0.03 0.95 ]
|X 12.5 - 13 : [ 1 0.00 0.96 ]
|XXXX 13 - 13.5 : [ 3 0.01 0.97 ]
#...
|XXXX 14 - 14.5 : [ 3 0.01 0.98 ]
#...
|XXX 16.5 - 17 : [ 2 0.01 0.99 ]
#...
|X 19 - 19.5 : [ 1 0.00 0.99 ]
#...
|X 32 - 32.5 : [ 1 0.00 1.00 ]
#...
|X 46.5 - 47 : [ 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 156 total values totalling 1409.4200. <9.034744 +/- 2.586462>
#Range: [ 3.19 - 16.76 ]
#Most likely bin: [ 9.5 - 10 ] 16 counts
#Median bin: [ 9 - 9.5 ] 11 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXX 3 - 3.5 : [ 3 0.02 0.02 ]
|XXXXXXXXXXXX 3.5 - 4 : [ 5 0.03 0.05 ]
|XXXXXXXXXXXXXXX 4 - 4.5 : [ 6 0.04 0.09 ]
|XXXXXXXX 4.5 - 5 : [ 3 0.02 0.11 ]
|XXXXX 5 - 5.5 : [ 2 0.01 0.12 ]
|XXXXX 5.5 - 6 : [ 2 0.01 0.13 ]
|XXXXXXXXXXXXXXX 6 - 6.5 : [ 6 0.04 0.17 ]
|XXXXXXXXXXXX 6.5 - 7 : [ 5 0.03 0.21 ]
|XXXXXXXXXX 7 - 7.5 : [ 4 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 7 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 15 0.10 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 12 0.08 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 11 0.07 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 16 0.10 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 11 0.07 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 11 0.07 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 12 0.08 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 11 0.07 0.91 ]
|XXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 8 0.05 0.96 ]
#...
|XXXXX 13 - 13.5 : [ 2 0.01 0.97 ]
#...
|XXXXXXXX 14 - 14.5 : [ 3 0.02 0.99 ]
#...
|XX 16.5 - 17 : [ 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 142 2 reads 545 bases = 1.00 +- 0.04 = -1.00 +- 0.04
Contig 276 13 reads 1000 bases = 1.04 +- 0.29 = 1.03 +- 0.25
Contig 143 2 reads 1024 bases = 1.10 +- 0.30 = 1.10 +- 0.30
Contig 204 2 reads 936 bases = 1.16 +- 0.37 = -0.58 +- 0.71
Contig 217 2 reads 1528 bases = 1.20 +- 0.40 = -0.04 +- 0.90
Contig 108 2 reads 1723 bases = 1.21 +- 0.41 = 1.21 +- 0.41
Contig 166 2 reads 945 bases = 1.21 +- 0.41 = -0.01 +- 0.89
Contig 129 2 reads 1671 bases = 1.26 +- 0.44 = -0.02 +- 0.86
Contig 179 2 reads 1129 bases = 1.28 +- 0.45 = 0.03 +- 0.85
Contig 196 2 reads 1192 bases = 1.35 +- 0.48 = 1.35 +- 0.48
Contig 237 3 reads 1643 bases = 1.36 +- 0.72 = 1.36 +- 0.72
Contig 95 2 reads 781 bases = 1.37 +- 0.48 = 1.37 +- 0.48
Contig 131 2 reads 621 bases = 1.39 +- 0.49 = 0.61 +- 0.49
Contig 200 2 reads 1245 bases = 1.39 +- 0.49 = -0.10 +- 0.78
Contig 209 2 reads 1161 bases = 1.41 +- 0.49 = -0.10 +- 0.76
Contig 230 3 reads 1318 bases = 1.41 +- 0.79 = 1.41 +- 0.79
Contig 225 3 reads 1708 bases = 1.45 +- 0.50 = 0.42 +- 0.61
Contig 244 4 reads 855 bases = 1.46 +- 0.99 = -0.75 +- 0.52
Contig 123 2 reads 1028 bases = 1.50 +- 0.50 = 1.50 +- 0.50
Contig 138 2 reads 1482 bases = 1.51 +- 0.50 = -0.01 +- 0.70
Contig 301 38 reads 1314 bases = 12.13 +- 8.93 = -0.25 +- 0.84
Contig 391 558 reads 39121 bases = 12.14 +- 4.23 = 0.06 +- 3.67
Contig 425 2290 reads 155407 bases = 12.15 +- 3.89 = 0.35 +- 3.56
Contig 409 1141 reads 75564 bases = 12.18 +- 4.16 = 0.16 +- 3.40
Contig 435 5666 reads 375696 bases = 12.19 +- 4.06 = 0.07 +- 3.75
Contig 368 282 reads 19257 bases = 12.20 +- 5.11 = 0.38 +- 3.40
Contig 436 6026 reads 403452 bases = 12.23 +- 4.68 = 0.19 +- 3.70
Contig 349 188 reads 12511 bases = 12.41 +- 3.88 = 0.27 +- 2.47
Contig 302 39 reads 1641 bases = 12.57 +- 17.47 = 0.33 +- 0.94
Contig 407 1108 reads 68554 bases = 13.03 +- 4.84 = 0.09 +- 3.89
Contig 378 363 reads 23215 bases = 13.07 +- 4.50 = 0.41 +- 3.03
Contig 291 25 reads 1353 bases = 13.39 +- 8.97 = 3.53 +- 2.31
Contig 359 245 reads 14347 bases = 14.04 +- 4.86 = 0.30 +- 4.86
Contig 437 7026 reads 411416 bases = 14.08 +- 11.15 = -0.05 +- 4.06
Contig 420 1971 reads 113936 bases = 14.25 +- 8.63 = 0.06 +- 3.69
Contig 282 17 reads 750 bases = 16.61 +- 0.86 = 0.75 +- 0.74
Contig 381 383 reads 18981 bases = 16.76 +- 5.93 = 0.35 +- 4.24
Contig 309 57 reads 985 bases = 19.09 +- 23.11 = 0.55 +- 0.99
Contig 311 62 reads 1547 bases = 32.27 +- 21.57 = 0.77 +- 2.98
Contig 326 101 reads 1793 bases = 46.82 +- 40.33 = 2.79 +- 3.59
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 95
Chimeric reads = 261
Suspect alignments = 467
-------------------------------------------------------------------
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/microbe5/3436384/edit_dir.13Nov03.QD