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
3436373 4700 269483 Burkholderia sp.
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Burkholderia_sp.
-------------------------------------------------------------------
Burkholderiaceae, family, b-proteobacteria
Burkholderiales, order, b-proteobacteria
Burkholderia sp., 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: 8670967
# phrap: 8347874
# db:
altered.
4700000
7239613 +/- 1800615
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 83422
Number of reads with percent X's >= 20%: 882 = 0.7%
Number of reads with percent X's >= 50%: 406 = 0.3%
Number of reads with percent X's >= 80%: 43 = 0.0%
Total reads in project: 120083
Total bp X'd : 5606883
reads >= 20% >= 50% >= 80% screened
Nr with L09136 22538 239 103 3
Nr with pCC1Fos 3166 2 0 0
Nr with pMCL200_JGI_XZX+XZK 57718 641 303 40
-------------------------------------------------------------------
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 = 21397161
C = 38642078
G = 38651981
T = 21072937
N = 445712
X = 5606883
GC fraction = 0.61
Total = 125816752
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436373_fasta.screen.contigs
-------------------------------------------------------------------
A 1468672
C 2902799
G 2857723
T 1464094
N 1271
fraction GC = 0.66
total bases = 8694559
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 AADE reads.list > grep.reads.list.AADE
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AADE 4 500
-------------------------------------------------------------------
#Found 23522 total values totalling 105623696.0000. <4490.421563 +/- 17570.911694>
#Range: [ 869 - 1258450 ]
#Most likely bin: [ 3500 - 4000 ] 5514 counts
#Median bin: [ 4000 - 4500 ] 4743 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
|X 1000 - 1500 : [ 88 0.00 0.00 ]
|X 1500 - 2000 : [ 126 0.01 0.01 ]
|X 2000 - 2500 : [ 196 0.01 0.02 ]
|XXXXXXX 2500 - 3000 : [ 949 0.04 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4419 0.19 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 5514 0.23 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 4743 0.20 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 3816 0.16 0.84 ]
|XXXXXXXXXXXXXXXXXX 5000 - 5500 : [ 2526 0.11 0.95 ]
|XXXXXXX 5500 - 6000 : [ 974 0.04 0.99 ]
|X 6000 - 6500 : [ 138 0.01 1.00 ]
| 6500 - 7000 : [ 6 0.00 1.00 ]
#...
| 13500 - 14000 : [ 1 0.00 1.00 ]
#...
| 16000 - 16500 : [ 1 0.00 1.00 ]
#...
| 18000 - 18500 : [ 1 0.00 1.00 ]
#...
| 35000 - 35500 : [ 1 0.00 1.00 ]
#...
| 37500 - 38000 : [ 1 0.00 1.00 ]
#...
| 45500 - 46000 : [ 1 0.00 1.00 ]
#...
| 75500 - 76000 : [ 1 0.00 1.00 ]
#...
| 95500 - 96000 : [ 1 0.00 1.00 ]
#...
| 96500 - 97000 : [ 1 0.00 1.00 ]
#...
| 112000 - 112500 : [ 1 0.00 1.00 ]
#...
| 113000 - 113500 : [ 1 0.00 1.00 ]
#...
| 126000 - 126500 : [ 1 0.00 1.00 ]
#...
| 171000 - 171500 : [ 1 0.00 1.00 ]
#...
| 178000 - 178500 : [ 1 0.00 1.00 ]
#...
| 260000 - 260500 : [ 1 0.00 1.00 ]
#...
| 264500 - 265000 : [ 1 0.00 1.00 ]
#...
| 315500 - 316000 : [ 1 0.00 1.00 ]
#...
| 538000 - 538500 : [ 1 0.00 1.00 ]
#...
| 646500 - 647000 : [ 1 0.00 1.00 ]
#...
| 671000 - 671500 : [ 1 0.00 1.00 ]
#...
| 782000 - 782500 : [ 1 0.00 1.00 ]
#...
| 1032000 - 1032500 : [ 1 0.00 1.00 ]
#...
| 1102500 - 1103000 : [ 1 0.00 1.00 ]
#...
| 1148500 - 1149000 : [ 1 0.00 1.00 ]
#...
| 1258000 - 1258500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACTP reads.list > grep.reads.list.ACTP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACTP 4 500
-------------------------------------------------------------------
#Found 21224 total values totalling 208541996.0000. <9825.763098 +/- 14743.898555>
#Range: [ 200 - 1006508 ]
#Most likely bin: [ 9500 - 10000 ] 2257 counts
#Median bin: [ 9500 - 10000 ] 2257 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 6 0.00 0.00 ]
#...
|XX 1000 - 1500 : [ 140 0.01 0.01 ]
|XXXX 1500 - 2000 : [ 213 0.01 0.02 ]
|XXX 2000 - 2500 : [ 191 0.01 0.03 ]
|XXX 2500 - 3000 : [ 185 0.01 0.03 ]
|XXXX 3000 - 3500 : [ 205 0.01 0.04 ]
|XXX 3500 - 4000 : [ 182 0.01 0.05 ]
|XXXX 4000 - 4500 : [ 222 0.01 0.06 ]
|XXXXX 4500 - 5000 : [ 267 0.01 0.08 ]
|XXXXX 5000 - 5500 : [ 300 0.01 0.09 ]
|XXXXXXX 5500 - 6000 : [ 379 0.02 0.11 ]
|XXXXXXXX 6000 - 6500 : [ 441 0.02 0.13 ]
|XXXXXXXXX 6500 - 7000 : [ 509 0.02 0.15 ]
|XXXXXXXXXXX 7000 - 7500 : [ 617 0.03 0.18 ]
|XXXXXXXXXXXXXXX 7500 - 8000 : [ 837 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1196 0.06 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 1670 0.08 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 1994 0.09 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 2257 0.11 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 2136 0.10 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10500 - 11000 : [ 1922 0.09 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 11000 - 11500 : [ 1448 0.07 0.82 ]
|XXXXXXXXXXXXXXXXXXXXX 11500 - 12000 : [ 1166 0.05 0.87 ]
|XXXXXXXXXXXXXXXX 12000 - 12500 : [ 882 0.04 0.91 ]
|XXXXXXXXXXXX 12500 - 13000 : [ 650 0.03 0.94 ]
|XXXXXXXX 13000 - 13500 : [ 475 0.02 0.97 ]
|XXXXX 13500 - 14000 : [ 278 0.01 0.98 ]
|XXX 14000 - 14500 : [ 187 0.01 0.99 ]
|XX 14500 - 15000 : [ 104 0.00 0.99 ]
|X 15000 - 15500 : [ 70 0.00 1.00 ]
|X 15500 - 16000 : [ 38 0.00 1.00 ]
| 16000 - 16500 : [ 12 0.00 1.00 ]
| 16500 - 17000 : [ 5 0.00 1.00 ]
| 17000 - 17500 : [ 5 0.00 1.00 ]
#...
| 22000 - 22500 : [ 1 0.00 1.00 ]
#...
| 27000 - 27500 : [ 1 0.00 1.00 ]
#...
| 37000 - 37500 : [ 1 0.00 1.00 ]
#...
| 48500 - 49000 : [ 1 0.00 1.00 ]
#...
| 64000 - 64500 : [ 1 0.00 1.00 ]
#...
| 82000 - 82500 : [ 1 0.00 1.00 ]
#...
| 84000 - 84500 : [ 1 0.00 1.00 ]
#...
| 106000 - 106500 : [ 2 0.00 1.00 ]
| 106500 - 107000 : [ 1 0.00 1.00 ]
#...
| 108500 - 109000 : [ 1 0.00 1.00 ]
#...
| 117500 - 118000 : [ 1 0.00 1.00 ]
#...
| 127000 - 127500 : [ 1 0.00 1.00 ]
#...
| 132000 - 132500 : [ 1 0.00 1.00 ]
#...
| 178500 - 179000 : [ 1 0.00 1.00 ]
#...
| 191000 - 191500 : [ 1 0.00 1.00 ]
#...
| 226500 - 227000 : [ 1 0.00 1.00 ]
#...
| 239000 - 239500 : [ 1 0.00 1.00 ]
#...
| 250500 - 251000 : [ 1 0.00 1.00 ]
#...
| 261500 - 262000 : [ 1 0.00 1.00 ]
#...
| 262500 - 263000 : [ 1 0.00 1.00 ]
#...
| 266500 - 267000 : [ 1 0.00 1.00 ]
#...
| 269500 - 270000 : [ 1 0.00 1.00 ]
#...
| 278500 - 279000 : [ 1 0.00 1.00 ]
#...
| 282000 - 282500 : [ 1 0.00 1.00 ]
#...
| 287500 - 288000 : [ 1 0.00 1.00 ]
#...
| 353500 - 354000 : [ 1 0.00 1.00 ]
#...
| 371500 - 372000 : [ 1 0.00 1.00 ]
#...
| 437500 - 438000 : [ 1 0.00 1.00 ]
#...
| 580000 - 580500 : [ 1 0.00 1.00 ]
#...
| 603500 - 604000 : [ 1 0.00 1.00 ]
#...
| 623000 - 623500 : [ 1 0.00 1.00 ]
#...
| 646000 - 646500 : [ 1 0.00 1.00 ]
#...
| 892500 - 893000 : [ 1 0.00 1.00 ]
#...
| 1006500 - 1007000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAHR reads.list > grep.reads.list.AAHR
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAHR 4 500
-------------------------------------------------------------------
#Found 2610 total values totalling 23473256.0000. <8993.584674 +/- 23807.437874>
#Range: [ 536 - 929573 ]
#Most likely bin: [ 8500 - 9000 ] 305 counts
#Median bin: [ 8500 - 9000 ] 305 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 8 0.00 0.00 ]
|XXXXX 1000 - 1500 : [ 39 0.01 0.02 ]
|XXXXXX 1500 - 2000 : [ 49 0.02 0.04 ]
|XXXXXXX 2000 - 2500 : [ 54 0.02 0.06 ]
|XXXXX 2500 - 3000 : [ 38 0.01 0.07 ]
|XXXXXXX 3000 - 3500 : [ 55 0.02 0.09 ]
|XXXXX 3500 - 4000 : [ 35 0.01 0.11 ]
|XXXX 4000 - 4500 : [ 33 0.01 0.12 ]
|XXXXXX 4500 - 5000 : [ 47 0.02 0.14 ]
|XXXXXX 5000 - 5500 : [ 48 0.02 0.16 ]
|XXXXXXX 5500 - 6000 : [ 51 0.02 0.18 ]
|XXXXXXX 6000 - 6500 : [ 50 0.02 0.19 ]
|XXXXXXXXXX 6500 - 7000 : [ 80 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 140 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 184 0.07 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 299 0.11 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 305 0.12 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 286 0.11 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 210 0.08 0.77 ]
|XXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 161 0.06 0.83 ]
|XXXXXXXXXXXXXXXXXX 10500 - 11000 : [ 141 0.05 0.89 ]
|XXXXXXXXXXX 11000 - 11500 : [ 87 0.03 0.92 ]
|XXXXXXXXXX 11500 - 12000 : [ 75 0.03 0.95 ]
|XXXXXXXX 12000 - 12500 : [ 58 0.02 0.97 ]
|XXXX 12500 - 13000 : [ 32 0.01 0.98 ]
|XXX 13000 - 13500 : [ 21 0.01 0.99 ]
|XX 13500 - 14000 : [ 12 0.00 1.00 ]
|X 14000 - 14500 : [ 6 0.00 1.00 ]
| 14500 - 15000 : [ 1 0.00 1.00 ]
#...
| 20000 - 20500 : [ 1 0.00 1.00 ]
#...
| 56500 - 57000 : [ 1 0.00 1.00 ]
#...
| 398500 - 399000 : [ 1 0.00 1.00 ]
#...
| 685000 - 685500 : [ 1 0.00 1.00 ]
#...
| 929500 - 930000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAHS reads.list > grep.reads.list.AAHS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAHS 4 500
-------------------------------------------------------------------
#Found 2746 total values totalling 105014292.0000. <38242.640932 +/- 3787.776052>
#Range: [ 25765 - 47722 ]
#Most likely bin: [ 38000 - 38500 ] 138 counts
#Median bin: [ 38000 - 38500 ] 138 counts
#Histogram Bins Count Fraction Cum_Fraction
| 25500 - 26000 : [ 1 0.00 0.00 ]
#...
| 26500 - 27000 : [ 1 0.00 0.00 ]
|X 27000 - 27500 : [ 2 0.00 0.00 ]
| 27500 - 28000 : [ 1 0.00 0.00 ]
| 28000 - 28500 : [ 1 0.00 0.00 ]
|X 28500 - 29000 : [ 4 0.00 0.00 ]
|X 29000 - 29500 : [ 4 0.00 0.01 ]
|XXX 29500 - 30000 : [ 10 0.00 0.01 ]
|XXX 30000 - 30500 : [ 11 0.00 0.01 ]
|XXXXX 30500 - 31000 : [ 18 0.01 0.02 ]
|XXXXXXXXX 31000 - 31500 : [ 31 0.01 0.03 ]
|XXXXXXXXXX 31500 - 32000 : [ 35 0.01 0.04 ]
|XXXXXXXXXXX 32000 - 32500 : [ 37 0.01 0.06 ]
|XXXXXXXXXXXXXX 32500 - 33000 : [ 48 0.02 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 85 0.03 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 89 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 108 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 100 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 120 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 117 0.04 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 121 0.04 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 125 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 130 0.05 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 129 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 138 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 133 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 136 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 123 0.04 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 112 0.04 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 92 0.03 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 96 0.03 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 102 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 75 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 73 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 70 0.03 0.90 ]
|XXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 69 0.03 0.93 ]
|XXXXXXXXXXXXXXX 44000 - 44500 : [ 52 0.02 0.95 ]
|XXXXXXXXXXXX 44500 - 45000 : [ 40 0.01 0.96 ]
|XXXXXXXXXX 45000 - 45500 : [ 36 0.01 0.97 ]
|XXXXXXXX 45500 - 46000 : [ 26 0.01 0.98 ]
|XXXXX 46000 - 46500 : [ 16 0.01 0.99 ]
|XXXX 46500 - 47000 : [ 15 0.01 0.99 ]
|XXX 47000 - 47500 : [ 12 0.00 1.00 ]
|X 47500 - 48000 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AAHR 7876 +- 2810 (n=1289)
# AADE 3997 +- 875 (n=11915)
# AAHS 38295 +- 3855 (n=1393)
# ACTP 9103 +- 2710 (n=10822)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436373_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
AADE 57984 -1 -1 98 681 54771 99 632 100 645
AAHR 7680 -1 -1 96 577 6732 99 575 100 625
AAHS 7680 -1 -1 94 617 6987 99 663 100 672
ACTP 58656 -1 -1 97 662 51593 99 637 100 690
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AADE 27010 99 626 100 641 27761 99 638 100 648
AAHR 3318 99 553 100 610 3414 100 595 100 640
AAHS 3538 98 676 100 669 3449 99 649 100 675
ACTP 25952 99 636 100 699 25641 99 637 100 682
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436373_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 120083 60948 90.70 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 3436373_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 120083 total values totalling 75440260.0000. <628.234305 +/- 148.743645>
#Range: [ 15 - 1012 ]
#Most likely bin: [ 700 - 750 ] 26778 counts
#Median bin: [ 650 - 700 ] 25198 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 208 0.00 0.00 ]
|X 50 - 100 : [ 697 0.01 0.01 ]
|XX 100 - 150 : [ 1081 0.01 0.02 ]
|XX 150 - 200 : [ 1184 0.01 0.03 ]
|XX 200 - 250 : [ 1593 0.01 0.04 ]
|XX 250 - 300 : [ 1558 0.01 0.05 ]
|XXX 300 - 350 : [ 2107 0.02 0.07 ]
|XXXX 350 - 400 : [ 2407 0.02 0.09 ]
|XXXXX 400 - 450 : [ 3055 0.03 0.12 ]
|XXXXXX 450 - 500 : [ 4021 0.03 0.15 ]
|XXXXXXXXX 500 - 550 : [ 6077 0.05 0.20 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 9994 0.08 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 16618 0.14 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 25198 0.21 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 26778 0.22 0.85 ]
|XXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 14206 0.12 0.97 ]
|XXXX 800 - 850 : [ 2702 0.02 1.00 ]
|X 850 - 900 : [ 406 0.00 1.00 ]
| 900 - 950 : [ 162 0.00 1.00 ]
| 950 - 1000 : [ 27 0.00 1.00 ]
| 1000 - 1050 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AADE
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AADE 3436373_fasta.screen.trimQ15.SaF > reads.trim15.AADE.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AADE.rl 2 50
-------------------------------------------------------------------
#Found 54771 total values totalling 34445001.0000. <628.891220 +/- 152.911871>
#Range: [ 22 - 1012 ]
#Most likely bin: [ 700 - 750 ] 11406 counts
#Median bin: [ 650 - 700 ] 10016 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 45 0.00 0.00 ]
|X 50 - 100 : [ 237 0.00 0.01 ]
|X 100 - 150 : [ 417 0.01 0.01 ]
|XX 150 - 200 : [ 565 0.01 0.02 ]
|XXX 200 - 250 : [ 852 0.02 0.04 ]
|XXX 250 - 300 : [ 777 0.01 0.05 ]
|XXX 300 - 350 : [ 981 0.02 0.07 ]
|XXXXX 350 - 400 : [ 1330 0.02 0.10 ]
|XXXXXX 400 - 450 : [ 1750 0.03 0.13 ]
|XXXXXXXX 450 - 500 : [ 2219 0.04 0.17 ]
|XXXXXXXXXXX 500 - 550 : [ 3000 0.05 0.22 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 4324 0.08 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 6760 0.12 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 10016 0.18 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 11406 0.21 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 7882 0.14 0.96 ]
|XXXXXX 800 - 850 : [ 1739 0.03 0.99 ]
|X 850 - 900 : [ 288 0.01 1.00 ]
|X 900 - 950 : [ 152 0.00 1.00 ]
| 950 - 1000 : [ 27 0.00 1.00 ]
| 1000 - 1050 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOUY
trimt JAZZ trim 15 readlength histogram for ACTP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACTP 3436373_fasta.screen.trimQ15.SaF > reads.trim15.ACTP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACTP.rl 2 50
-------------------------------------------------------------------
#Found 51593 total values totalling 32572976.0000. <631.344872 +/- 142.108187>
#Range: [ 15 - 938 ]
#Most likely bin: [ 650 - 700 ] 13074 counts
#Median bin: [ 650 - 700 ] 13074 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 110 0.00 0.00 ]
|X 50 - 100 : [ 380 0.01 0.01 ]
|XX 100 - 150 : [ 517 0.01 0.02 ]
|X 150 - 200 : [ 472 0.01 0.03 ]
|XX 200 - 250 : [ 563 0.01 0.04 ]
|XX 250 - 300 : [ 575 0.01 0.05 ]
|XX 300 - 350 : [ 736 0.01 0.06 ]
|XX 350 - 400 : [ 810 0.02 0.08 ]
|XXX 400 - 450 : [ 1046 0.02 0.10 ]
|XXXX 450 - 500 : [ 1390 0.03 0.13 ]
|XXXXXXX 500 - 550 : [ 2186 0.04 0.17 ]
|XXXXXXXXXXXX 550 - 600 : [ 3787 0.07 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 7681 0.15 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 13074 0.25 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 12969 0.25 0.90 ]
|XXXXXXXXXXXXXXX 750 - 800 : [ 4760 0.09 0.99 ]
|X 800 - 850 : [ 480 0.01 1.00 ]
| 850 - 900 : [ 49 0.00 1.00 ]
| 900 - 950 : [ 8 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOYN
trimt JAZZ trim 15 readlength histogram for APZB
trimt JAZZ trim 15 readlength histogram for AAHR
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAHR 3436373_fasta.screen.trimQ15.SaF > reads.trim15.AAHR.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAHR.rl 2 50
-------------------------------------------------------------------
#Found 6732 total values totalling 3843740.0000. <570.965538 +/- 125.585482>
#Range: [ 23 - 775 ]
#Most likely bin: [ 600 - 650 ] 1603 counts
#Median bin: [ 550 - 600 ] 1543 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 24 0.00 0.00 ]
|X 50 - 100 : [ 22 0.00 0.01 ]
|X 100 - 150 : [ 52 0.01 0.01 ]
|X 150 - 200 : [ 58 0.01 0.02 ]
|X 200 - 250 : [ 60 0.01 0.03 ]
|XX 250 - 300 : [ 92 0.01 0.05 ]
|XXXXXXX 300 - 350 : [ 282 0.04 0.09 ]
|XXX 350 - 400 : [ 134 0.02 0.11 ]
|XXXX 400 - 450 : [ 167 0.02 0.13 ]
|XXXXXXX 450 - 500 : [ 284 0.04 0.17 ]
|XXXXXXXXXXXXXXXXX 500 - 550 : [ 693 0.10 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1543 0.23 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1603 0.24 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1152 0.17 0.92 ]
|XXXXXXXXXXXXX 700 - 750 : [ 539 0.08 1.00 ]
|X 750 - 800 : [ 27 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAHS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAHS 3436373_fasta.screen.trimQ15.SaF > reads.trim15.AAHS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAHS.rl 2 50
-------------------------------------------------------------------
#Found 6987 total values totalling 4578543.0000. <655.294547 +/- 169.331306>
#Range: [ 26 - 914 ]
#Most likely bin: [ 700 - 750 ] 1864 counts
#Median bin: [ 700 - 750 ] 1864 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 29 0.00 0.00 ]
|X 50 - 100 : [ 58 0.01 0.01 ]
|XX 100 - 150 : [ 95 0.01 0.03 ]
|XX 150 - 200 : [ 89 0.01 0.04 ]
|XXX 200 - 250 : [ 118 0.02 0.06 ]
|XX 250 - 300 : [ 114 0.02 0.07 ]
|XX 300 - 350 : [ 108 0.02 0.09 ]
|XXX 350 - 400 : [ 133 0.02 0.11 ]
|XX 400 - 450 : [ 92 0.01 0.12 ]
|XXX 450 - 500 : [ 128 0.02 0.14 ]
|XXXX 500 - 550 : [ 198 0.03 0.17 ]
|XXXXXXX 550 - 600 : [ 340 0.05 0.21 ]
|XXXXXXXXXXXX 600 - 650 : [ 574 0.08 0.30 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 956 0.14 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1864 0.27 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1537 0.22 0.92 ]
|XXXXXXXXXX 800 - 850 : [ 483 0.07 0.99 ]
|X 850 - 900 : [ 69 0.01 1.00 ]
| 900 - 950 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436373
-------------------------------------------------------------------
AADE.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AADE.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AADE.000201.000300 pUC18.fa pUC18.fa LRS.fasta
AADE.000301.000400 pUC18.fa pUC18.fa LRS.fasta
AAHR.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AAHS.000001.000100 pCC1Fos.fa.4 LRS.fasta
ACTP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
ACTP.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
ACTP.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
ACTP.000301.000400 pMCL200.fa pMCL200.fa LRS.fasta
APZB.000001.000100
AADE.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AADE.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AADE.000201.000300 pUC18.fa pUC18.fa LRS.fasta
AADE.000301.000400 pUC18.fa pUC18.fa LRS.fasta
AAHR.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AAHS.000001.000100 pCC1Fos.fa.4 LRS.fasta
ACTP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
ACTP.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
ACTP.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
ACTP.000301.000400 pMCL200.fa pMCL200.fa LRS.fasta
APZB.000001.000100
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436373_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436373_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 119836 total values totalling 79058.1550. <0.659720 +/- 0.047490>
#Range: [ 0.0789 - 1 ]
#Most likely bin: [ 0.675 - 0.68 ] 6583 counts
#Median bin: [ 0.665 - 0.67 ] 6347 counts
| 0.075 - 0.08 : [ 1 0.00 0.00 ]
#...
| 0.22 - 0.225 : [ 1 0.00 0.00 ]
#...
| 0.255 - 0.26 : [ 1 0.00 0.00 ]
#...
| 0.27 - 0.275 : [ 1 0.00 0.00 ]
#...
| 0.295 - 0.3 : [ 1 0.00 0.00 ]
| 0.3 - 0.305 : [ 2 0.00 0.00 ]
| 0.305 - 0.31 : [ 3 0.00 0.00 ]
#...
| 0.315 - 0.32 : [ 1 0.00 0.00 ]
| 0.32 - 0.325 : [ 2 0.00 0.00 ]
| 0.325 - 0.33 : [ 3 0.00 0.00 ]
| 0.33 - 0.335 : [ 2 0.00 0.00 ]
#...
| 0.345 - 0.35 : [ 1 0.00 0.00 ]
#...
| 0.355 - 0.36 : [ 1 0.00 0.00 ]
| 0.36 - 0.365 : [ 2 0.00 0.00 ]
| 0.365 - 0.37 : [ 2 0.00 0.00 ]
| 0.37 - 0.375 : [ 2 0.00 0.00 ]
| 0.375 - 0.38 : [ 4 0.00 0.00 ]
| 0.38 - 0.385 : [ 7 0.00 0.00 ]
| 0.385 - 0.39 : [ 2 0.00 0.00 ]
| 0.39 - 0.395 : [ 21 0.00 0.00 ]
| 0.395 - 0.4 : [ 1 0.00 0.00 ]
| 0.4 - 0.405 : [ 7 0.00 0.00 ]
| 0.405 - 0.41 : [ 8 0.00 0.00 ]
| 0.41 - 0.415 : [ 9 0.00 0.00 ]
| 0.415 - 0.42 : [ 11 0.00 0.00 ]
| 0.42 - 0.425 : [ 13 0.00 0.00 ]
| 0.425 - 0.43 : [ 10 0.00 0.00 ]
| 0.43 - 0.435 : [ 14 0.00 0.00 ]
| 0.435 - 0.44 : [ 25 0.00 0.00 ]
| 0.44 - 0.445 : [ 28 0.00 0.00 ]
| 0.445 - 0.45 : [ 26 0.00 0.00 ]
| 0.45 - 0.455 : [ 37 0.00 0.00 ]
| 0.455 - 0.46 : [ 48 0.00 0.00 ]
| 0.46 - 0.465 : [ 42 0.00 0.00 ]
| 0.465 - 0.47 : [ 51 0.00 0.00 ]
| 0.47 - 0.475 : [ 80 0.00 0.00 ]
| 0.475 - 0.48 : [ 81 0.00 0.00 ]
|X 0.48 - 0.485 : [ 96 0.00 0.01 ]
|X 0.485 - 0.49 : [ 130 0.00 0.01 ]
|X 0.49 - 0.495 : [ 140 0.00 0.01 ]
|X 0.495 - 0.5 : [ 114 0.00 0.01 ]
|X 0.5 - 0.505 : [ 181 0.00 0.01 ]
|X 0.505 - 0.51 : [ 139 0.00 0.01 ]
|X 0.51 - 0.515 : [ 184 0.00 0.01 ]
|X 0.515 - 0.52 : [ 243 0.00 0.01 ]
|X 0.52 - 0.525 : [ 229 0.00 0.02 ]
|XX 0.525 - 0.53 : [ 345 0.00 0.02 ]
|XX 0.53 - 0.535 : [ 338 0.00 0.02 ]
|XX 0.535 - 0.54 : [ 368 0.00 0.03 ]
|XXX 0.54 - 0.545 : [ 474 0.00 0.03 ]
|XXX 0.545 - 0.55 : [ 490 0.00 0.03 ]
|XXX 0.55 - 0.555 : [ 497 0.00 0.04 ]
|XXX 0.555 - 0.56 : [ 532 0.00 0.04 ]
|XXXX 0.56 - 0.565 : [ 581 0.00 0.05 ]
|XXXX 0.565 - 0.57 : [ 611 0.01 0.05 ]
|XXXX 0.57 - 0.575 : [ 694 0.01 0.06 ]
|XXXXX 0.575 - 0.58 : [ 789 0.01 0.06 ]
|XXXXX 0.58 - 0.585 : [ 877 0.01 0.07 ]
|XXXXXX 0.585 - 0.59 : [ 1053 0.01 0.08 ]
|XXXXXXX 0.59 - 0.595 : [ 1130 0.01 0.09 ]
|XXXXXXX 0.595 - 0.6 : [ 1137 0.01 0.10 ]
|XXXXXXXX 0.6 - 0.605 : [ 1369 0.01 0.11 ]
|XXXXXXXXX 0.605 - 0.61 : [ 1548 0.01 0.12 ]
|XXXXXXXXXXX 0.61 - 0.615 : [ 1806 0.02 0.14 ]
|XXXXXXXXXXXXX 0.615 - 0.62 : [ 2116 0.02 0.16 ]
|XXXXXXXXXXXXXXX 0.62 - 0.625 : [ 2399 0.02 0.18 ]
|XXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 2909 0.02 0.20 ]
|XXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 3368 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 3805 0.03 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 4253 0.04 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 4655 0.04 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 5389 0.04 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 5798 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 6092 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 6347 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 6479 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 6583 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 6472 0.05 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 6209 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 5538 0.05 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 5078 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 4481 0.04 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 3577 0.03 0.90 ]
|XXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 2908 0.02 0.93 ]
|XXXXXXXXXXXXXX 0.715 - 0.72 : [ 2223 0.02 0.95 ]
|XXXXXXXXXX 0.72 - 0.725 : [ 1703 0.01 0.96 ]
|XXXXXXXX 0.725 - 0.73 : [ 1317 0.01 0.97 ]
|XXXXXX 0.73 - 0.735 : [ 944 0.01 0.98 ]
|XXXX 0.735 - 0.74 : [ 718 0.01 0.98 ]
|XXX 0.74 - 0.745 : [ 492 0.00 0.99 ]
|XX 0.745 - 0.75 : [ 308 0.00 0.99 ]
|XX 0.75 - 0.755 : [ 317 0.00 0.99 ]
|X 0.755 - 0.76 : [ 183 0.00 1.00 ]
|X 0.76 - 0.765 : [ 124 0.00 1.00 ]
|X 0.765 - 0.77 : [ 86 0.00 1.00 ]
| 0.77 - 0.775 : [ 63 0.00 1.00 ]
| 0.775 - 0.78 : [ 39 0.00 1.00 ]
| 0.78 - 0.785 : [ 38 0.00 1.00 ]
| 0.785 - 0.79 : [ 35 0.00 1.00 ]
| 0.79 - 0.795 : [ 29 0.00 1.00 ]
| 0.795 - 0.8 : [ 15 0.00 1.00 ]
| 0.8 - 0.805 : [ 20 0.00 1.00 ]
| 0.805 - 0.81 : [ 13 0.00 1.00 ]
| 0.81 - 0.815 : [ 17 0.00 1.00 ]
| 0.815 - 0.82 : [ 9 0.00 1.00 ]
| 0.82 - 0.825 : [ 7 0.00 1.00 ]
| 0.825 - 0.83 : [ 7 0.00 1.00 ]
| 0.83 - 0.835 : [ 9 0.00 1.00 ]
| 0.835 - 0.84 : [ 1 0.00 1.00 ]
| 0.84 - 0.845 : [ 6 0.00 1.00 ]
#...
| 0.85 - 0.855 : [ 2 0.00 1.00 ]
#...
| 0.86 - 0.865 : [ 1 0.00 1.00 ]
#...
| 0.875 - 0.88 : [ 1 0.00 1.00 ]
| 0.88 - 0.885 : [ 1 0.00 1.00 ]
#...
| 0.9 - 0.905 : [ 1 0.00 1.00 ]
| 0.905 - 0.91 : [ 1 0.00 1.00 ]
| 0.91 - 0.915 : [ 2 0.00 1.00 ]
#...
| 0.93 - 0.935 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 62. 1262 reads; 107517 bp (untrimmed), 107517 (trimmed).
Contig 63. 1368 reads; 102274 bp (untrimmed), 102114 (trimmed).
Contig 64. 1384 reads; 124442 bp (untrimmed), 124406 (trimmed).
Contig 65. 1454 reads; 102862 bp (untrimmed), 102862 (trimmed).
Contig 66. 1459 reads; 125758 bp (untrimmed), 125755 (trimmed).
Contig 67. 1477 reads; 106909 bp (untrimmed), 106901 (trimmed).
Contig 68. 1829 reads; 130219 bp (untrimmed), 129508 (trimmed).
Contig 69. 1894 reads; 140334 bp (untrimmed), 140334 (trimmed).
Contig 70. 2035 reads; 167225 bp (untrimmed), 167225 (trimmed).
Contig 71. 2089 reads; 154655 bp (untrimmed), 154201 (trimmed).
Contig 72. 2130 reads; 137229 bp (untrimmed), 137209 (trimmed).
Contig 73. 2934 reads; 220190 bp (untrimmed), 219531 (trimmed).
Contig 74. 3059 reads; 204648 bp (untrimmed), 204648 (trimmed).
Contig 75. 3081 reads; 215496 bp (untrimmed), 215496 (trimmed).
Contig 76. 3267 reads; 216876 bp (untrimmed), 215691 (trimmed).
Contig 77. 3388 reads; 254607 bp (untrimmed), 254217 (trimmed).
Contig 78. 3996 reads; 289567 bp (untrimmed), 288811 (trimmed).
Contig 79. 4437 reads; 339048 bp (untrimmed), 338953 (trimmed).
Contig 80. 4482 reads; 337248 bp (untrimmed), 337097 (trimmed).
Contig 81. 4494 reads; 297684 bp (untrimmed), 297518 (trimmed).
Contig 82. 4663 reads; 334352 bp (untrimmed), 334352 (trimmed).
Contig 83. 4948 reads; 351066 bp (untrimmed), 350002 (trimmed).
Contig 84. 5135 reads; 400502 bp (untrimmed), 400420 (trimmed).
Contig 85. 5733 reads; 416639 bp (untrimmed), 416639 (trimmed).
Contig 86. 5974 reads; 413329 bp (untrimmed), 413256 (trimmed).
Contig 87. 6875 reads; 563773 bp (untrimmed), 563372 (trimmed).
Contig 88. 21718 reads; 1344188 bp (untrimmed), 1344092 (trimmed).
--------------------------------------------------------------
Totals 119902 reads; 8694559 bp (untrimmed), 8670967 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 8686147 bases = 11.64 +- 4.19 = 0.13 +- 3.85
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 76 total values totalling 670.0800. <8.816842 +/- 4.018458>
#Range: [ 1.11 - 18.93 ]
#Most likely bin: [ 11 - 11.5 ] 12 counts
#Median bin: [ 9.5 - 10 ] 4 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 1 - 1.5 : [ 2 0.03 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 7 0.09 0.12 ]
#...
|XXXXXXX 2.5 - 3 : [ 2 0.03 0.14 ]
#...
|XXXXXXXXXXXXXXXXX 3.5 - 4 : [ 5 0.07 0.21 ]
|XXX 4 - 4.5 : [ 1 0.01 0.22 ]
#...
|XXX 5.5 - 6 : [ 1 0.01 0.24 ]
|XXX 6 - 6.5 : [ 1 0.01 0.25 ]
|XXXXXXXXXX 6.5 - 7 : [ 3 0.04 0.29 ]
|XXX 7 - 7.5 : [ 1 0.01 0.30 ]
|XXXXXXXXXX 7.5 - 8 : [ 3 0.04 0.34 ]
|XXXXXXX 8 - 8.5 : [ 2 0.03 0.37 ]
|XXXXXXX 8.5 - 9 : [ 2 0.03 0.39 ]
|XXXXXXXXXXXXX 9 - 9.5 : [ 4 0.05 0.45 ]
|XXXXXXXXXXXXX 9.5 - 10 : [ 4 0.05 0.50 ]
|XXXXXXXXXX 10 - 10.5 : [ 3 0.04 0.54 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 4 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 12 0.16 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.09 0.84 ]
|XXXXXXXXXX 12 - 12.5 : [ 3 0.04 0.88 ]
|XXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 6 0.08 0.96 ]
#...
|XXX 13.5 - 14 : [ 1 0.01 0.97 ]
#...
|XXX 18 - 18.5 : [ 1 0.01 0.99 ]
|XXX 18.5 - 19 : [ 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 60 total values totalling 627.9900. <10.466500 +/- 2.649154>
#Range: [ 3.65 - 18.93 ]
#Most likely bin: [ 11 - 11.5 ] 12 counts
#Median bin: [ 11 - 11.5 ] 12 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 3.5 - 4 : [ 2 0.03 0.03 ]
#...
|XXX 5.5 - 6 : [ 1 0.02 0.05 ]
|XXX 6 - 6.5 : [ 1 0.02 0.07 ]
|XXXXXXX 6.5 - 7 : [ 2 0.03 0.10 ]
|XXX 7 - 7.5 : [ 1 0.02 0.12 ]
|XXXXXXXXXX 7.5 - 8 : [ 3 0.05 0.17 ]
|XXXXXXX 8 - 8.5 : [ 2 0.03 0.20 ]
|XXXXXXX 8.5 - 9 : [ 2 0.03 0.23 ]
|XXXXXXXXXXXXX 9 - 9.5 : [ 4 0.07 0.30 ]
|XXXXXXXXXXXXX 9.5 - 10 : [ 4 0.07 0.37 ]
|XXXXXXXXXX 10 - 10.5 : [ 3 0.05 0.42 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 4 0.07 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 12 0.20 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.12 0.80 ]
|XXXXXXXXXX 12 - 12.5 : [ 3 0.05 0.85 ]
|XXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 6 0.10 0.95 ]
#...
|XXX 13.5 - 14 : [ 1 0.02 0.97 ]
#...
|XXX 18 - 18.5 : [ 1 0.02 0.98 ]
|XXX 18.5 - 19 : [ 1 0.02 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 7 2 reads 997 bases = 1.11 +- 0.32 = -0.38 +- 0.86
Contig 21 6 reads 1202 bases = 1.42 +- 1.39 = 1.08 +- 0.28
Contig 12 3 reads 1571 bases = 1.54 +- 0.83 = 0.20 +- 0.96
Contig 10 2 reads 1032 bases = 1.70 +- 0.46 = 0.11 +- 0.53
Contig 13 3 reads 1429 bases = 1.74 +- 0.87 = 0.83 +- 0.38
Contig 9 2 reads 1051 bases = 1.82 +- 0.38 = 1.82 +- 0.38
Contig 14 3 reads 952 bases = 1.84 +- 0.99 = 1.00 +- 0.00
Contig 8 2 reads 754 bases = 1.87 +- 0.34 = -0.05 +- 0.36
Contig 17 4 reads 1324 bases = 1.99 +- 1.03 = 0.80 +- 0.85
Contig 20 5 reads 1589 bases = 2.55 +- 1.13 = 2.55 +- 1.13
Contig 25 8 reads 2355 bases = 2.75 +- 1.59 = 1.34 +- 1.62
Contig 22 6 reads 1394 bases = 3.51 +- 1.74 = 2.23 +- 0.95
Contig 23 8 reads 1866 bases = 3.61 +- 1.73 = 1.75 +- 0.78
Contig 30 28 reads 6097 bases = 3.65 +- 1.31 = 1.94 +- 2.12
Contig 19 5 reads 1295 bases = 3.69 +- 1.52 = 3.69 +- 1.52
Contig 26 13 reads 2646 bases = 3.72 +- 1.30 = 1.00 +- 1.05
Contig 28 20 reads 1142 bases = 4.33 +- 7.22 = 1.18 +- 0.38
Contig 33 41 reads 6481 bases = 5.59 +- 2.49 = 2.36 +- 3.71
Contig 34 61 reads 8392 bases = 6.14 +- 2.42 = 1.00 +- 4.93
Contig 27 14 reads 694 bases = 6.62 +- 6.44 = -0.57 +- 0.50
Contig 52 524 reads 37719 bases = 11.47 +- 5.22 = 0.45 +- 3.96
Contig 78 3996 reads 289567 bases = 11.66 +- 3.84 = -0.05 +- 3.78
Contig 85 5733 reads 416639 bases = 11.67 +- 3.83 = -0.03 +- 3.78
Contig 67 1477 reads 106909 bases = 11.68 +- 4.01 = 0.32 +- 3.85
Contig 68 1829 reads 130219 bases = 11.68 +- 3.89 = 0.15 +- 3.66
Contig 83 4948 reads 351066 bases = 11.75 +- 3.89 = 0.22 +- 3.79
Contig 82 4663 reads 334352 bases = 11.89 +- 3.90 = -0.01 +- 3.76
Contig 65 1454 reads 102862 bases = 11.94 +- 3.73 = 0.26 +- 5.23
Contig 75 3081 reads 215496 bases = 12.07 +- 3.81 = 0.18 +- 3.74
Contig 86 5974 reads 413329 bases = 12.36 +- 4.03 = 0.16 +- 4.22
Contig 48 408 reads 28121 bases = 12.39 +- 4.71 = 0.02 +- 4.29
Contig 74 3059 reads 204648 bases = 12.65 +- 4.22 = 0.12 +- 3.90
Contig 58 995 reads 63998 bases = 12.71 +- 3.98 = 0.01 +- 3.91
Contig 81 4494 reads 297684 bases = 12.79 +- 4.03 = 0.18 +- 3.86
Contig 76 3267 reads 216876 bases = 12.81 +- 4.42 = 0.00 +- 3.82
Contig 51 515 reads 33480 bases = 12.82 +- 4.71 = 0.54 +- 3.78
Contig 72 2130 reads 137229 bases = 12.82 +- 4.16 = 0.12 +- 3.95
Contig 88 21718 reads 1344188 bases = 13.68 +- 4.24 = 0.01 +- 4.11
Contig 36 78 reads 3580 bases = 18.01 +- 11.31 = 11.46 +- 7.84
Contig 38 104 reads 4708 bases = 18.93 +- 19.42 = 6.47 +- 6.11
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 2114
HQ Discrepant reads = 39
Chimeric reads = 118
Suspect alignments = 250
-------------------------------------------------------------------
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/finished2/microbe/3436373/edit_dir.14Nov03.QD