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 in progress (or initial analysis of completed)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3635662 2500 NULL Psychrobacter cryohalolentis
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Psychrobacter_cryohalolentis
-------------------------------------------------------------------
Psychrobacter cryohalolentis, species, g-proteobacteria
Psychrobacter, genus, g-proteobacteria
Moraxellaceae, family, g-proteobacteria
Pseudomonadales, order, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2712348
# phrap: 2263739
# db:
altered.
2500000
2492029 +/- 183230
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 3622
Number of reads with percent X's >= 20%: 782 = 5.1%
Number of reads with percent X's >= 50%: 714 = 4.7%
Number of reads with percent X's >= 80%: 596 = 3.9%
Total reads in project: 15315
Total bp X'd : 778394
reads >= 20% >= 50% >= 80% screened
Nr with L09136 2972 168 140 100
Nr with LRS 17 17 12 8
Nr with pMCL200_JGI_XZX+XZK 633 597 562 488
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 717
Number of reads with percent X's >= 20%: 650 = 32.3%
Number of reads with percent X's >= 50%: 623 = 31.0%
Number of reads with percent X's >= 80%: 568 = 28.2%
Total reads in project: 2012
Total bp X'd : 590117
reads >= 20% >= 50% >= 80% screened
Nr with L09136 186 123 116 97
Nr with LRS 17 17 12 8
Nr with pMCL200_JGI_XZX+XZK 514 510 495 463
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 4031007
C = 3053965
G = 3007408
T = 3930525
N = 90947
X = 778394
GC fraction = 0.41
Total = 14892246
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3635662_fasta.screen.contigs
-------------------------------------------------------------------
A 817342
C 599274
G 601452
T 815594
N 623
fraction GC = 0.42
total bases = 2834285
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 APOW reads.list > grep.reads.list.APOW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APOW 4 500
-------------------------------------------------------------------
#Found 1864 total values totalling 6496814.0000. <3485.415236 +/- 641.810442>
#Range: [ 660 - 5181 ]
#Most likely bin: [ 3000 - 3500 ] 631 counts
#Median bin: [ 3500 - 4000 ] 607 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 8 0.00 0.00 ]
|X 1000 - 1500 : [ 21 0.01 0.02 ]
|XX 1500 - 2000 : [ 38 0.02 0.04 ]
|XXXXX 2000 - 2500 : [ 76 0.04 0.08 ]
|XXXXXXXX 2500 - 3000 : [ 121 0.06 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 631 0.34 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 607 0.33 0.81 ]
|XXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 314 0.17 0.97 ]
|XXX 4500 - 5000 : [ 46 0.02 1.00 ]
| 5000 - 5500 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APOX reads.list > grep.reads.list.APOX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APOX 4 500
-------------------------------------------------------------------
#Found 1262 total values totalling 7657927.0000. <6068.087956 +/- 1648.348125>
#Range: [ 956 - 29330 ]
#Most likely bin: [ 6000 - 6500 ] 303 counts
#Median bin: [ 6000 - 6500 ] 303 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
|XX 1000 - 1500 : [ 18 0.01 0.02 ]
|XXX 1500 - 2000 : [ 20 0.02 0.03 ]
|XXX 2000 - 2500 : [ 21 0.02 0.05 ]
|XX 2500 - 3000 : [ 13 0.01 0.06 ]
|XX 3000 - 3500 : [ 17 0.01 0.07 ]
|XX 3500 - 4000 : [ 17 0.01 0.08 ]
|XXXXX 4000 - 4500 : [ 40 0.03 0.12 ]
|XXXXXX 4500 - 5000 : [ 43 0.03 0.15 ]
|XXXXXXXXXX 5000 - 5500 : [ 74 0.06 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 184 0.15 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 303 0.24 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 253 0.20 0.80 ]
|XXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 160 0.13 0.92 ]
|XXXXXXXXXX 7500 - 8000 : [ 77 0.06 0.98 ]
|XX 8000 - 8500 : [ 18 0.01 1.00 ]
#...
| 21000 - 21500 : [ 1 0.00 1.00 ]
| 21500 - 22000 : [ 1 0.00 1.00 ]
#...
| 29000 - 29500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# APOX 5821 +- 1793 (n=658)
# APOW 3325 +- 689 (n=974)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3635662_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
APOW 21504 93 714 95 677 7635 81 547 87 557
APOX 19968 86 726 95 686 7680 87 751 94 743
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
APOW 3824 88 572 92 585 3811 75 517 82 525
APOX 3840 86 746 95 738 3840 87 757 94 747
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3635662_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
40 7635 3832 95.80 99.79 APOW @
40 7680 3840 96.00 100.00 APOX @
] 15315 7672 95.90 cumulative total@@
LIBRARY PLATE ID COUNT [ APOW 40 APOX 40 ] for 80 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 3635662_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 15315 total values totalling 8427171.0000. <550.256024 +/- 285.759140>
#Range: [ 0 - 917 ]
#Most likely bin: [ 750 - 800 ] 2619 counts
#Median bin: [ 650 - 700 ] 1520 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2169 0.14 0.14 ]
|XXXX 50 - 100 : [ 287 0.02 0.16 ]
|XXXX 100 - 150 : [ 251 0.02 0.18 ]
|XXX 150 - 200 : [ 217 0.01 0.19 ]
|XXXX 200 - 250 : [ 230 0.02 0.21 ]
|XXXX 250 - 300 : [ 235 0.02 0.22 ]
|XXXX 300 - 350 : [ 240 0.02 0.24 ]
|XXXXX 350 - 400 : [ 304 0.02 0.26 ]
|XXXXX 400 - 450 : [ 339 0.02 0.28 ]
|XXXXXX 450 - 500 : [ 413 0.03 0.31 ]
|XXXXXXXX 500 - 550 : [ 513 0.03 0.34 ]
|XXXXXXXXXXX 550 - 600 : [ 752 0.05 0.39 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 981 0.06 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1520 0.10 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2049 0.13 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2619 0.17 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1900 0.12 0.98 ]
|XXXX 850 - 900 : [ 288 0.02 1.00 ]
| 900 - 950 : [ 8 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APOW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APOW 3635662_fasta.screen.trimQ15.SaF > reads.trim15.APOW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APOW.rl 2 50
-------------------------------------------------------------------
#Found 7635 total values totalling 3420218.0000. <447.965684 +/- 260.970864>
#Range: [ 0 - 836 ]
#Most likely bin: [ 0 - 50 ] 1179 counts
#Median bin: [ 500 - 550 ] 467 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1179 0.15 0.15 ]
|XXXXXXXXX 50 - 100 : [ 251 0.03 0.19 ]
|XXXXXXXX 100 - 150 : [ 230 0.03 0.22 ]
|XXXXXX 150 - 200 : [ 182 0.02 0.24 ]
|XXXXXXX 200 - 250 : [ 195 0.03 0.27 ]
|XXXXXXX 250 - 300 : [ 210 0.03 0.29 ]
|XXXXXXX 300 - 350 : [ 213 0.03 0.32 ]
|XXXXXXXXX 350 - 400 : [ 272 0.04 0.36 ]
|XXXXXXXXXX 400 - 450 : [ 301 0.04 0.40 ]
|XXXXXXXXXXXX 450 - 500 : [ 358 0.05 0.44 ]
|XXXXXXXXXXXXXXXX 500 - 550 : [ 467 0.06 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 667 0.09 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 835 0.11 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1076 0.14 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 831 0.11 0.95 ]
|XXXXXXXXXXXX 750 - 800 : [ 340 0.04 1.00 ]
|X 800 - 850 : [ 28 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APOX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APOX 3635662_fasta.screen.trimQ15.SaF > reads.trim15.APOX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APOX.rl 2 50
-------------------------------------------------------------------
#Found 7680 total values totalling 5006953.0000. <651.947005 +/- 272.742206>
#Range: [ 0 - 917 ]
#Most likely bin: [ 750 - 800 ] 2279 counts
#Median bin: [ 750 - 800 ] 2279 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXX 0 - 50 : [ 990 0.13 0.13 ]
|X 50 - 100 : [ 36 0.00 0.13 ]
| 100 - 150 : [ 21 0.00 0.14 ]
|X 150 - 200 : [ 35 0.00 0.14 ]
|X 200 - 250 : [ 35 0.00 0.15 ]
| 250 - 300 : [ 25 0.00 0.15 ]
| 300 - 350 : [ 27 0.00 0.15 ]
|X 350 - 400 : [ 32 0.00 0.16 ]
|X 400 - 450 : [ 38 0.00 0.16 ]
|X 450 - 500 : [ 55 0.01 0.17 ]
|X 500 - 550 : [ 46 0.01 0.17 ]
|X 550 - 600 : [ 85 0.01 0.19 ]
|XXX 600 - 650 : [ 146 0.02 0.20 ]
|XXXXXXXX 650 - 700 : [ 444 0.06 0.26 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1218 0.16 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2279 0.30 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1872 0.24 0.96 ]
|XXXXX 850 - 900 : [ 288 0.04 1.00 ]
| 900 - 950 : [ 8 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APOY
trimt JAZZ trim 15 readlength histogram for ATSS
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3635662
-------------------------------------------------------------------
APOW.000001.000100 pUC18.fa LRS.fasta
APOW.000101.000200 pUC18.fa LRS.fasta
APOX.000001.000100 pMCL200.fa LRS.fasta
APOX.000101.000200 pMCL200.fa LRS.fasta
APOY.000001.000100 pCC1Fos.fa LRS.fasta
APOW.000001.000100 pUC18.fa LRS.fasta
APOW.000101.000200 pUC18.fa LRS.fasta
APOX.000001.000100 pMCL200.fa LRS.fasta
APOX.000101.000200 pMCL200.fa LRS.fasta
APOY.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3635662_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3635662_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 13181 total values totalling 5506.0369. <0.417725 +/- 0.048488>
#Range: [ 0.1875 - 1 ]
#Most likely bin: [ 0.425 - 0.43 ] 614 counts
#Median bin: [ 0.42 - 0.425 ] 578 counts
| 0.185 - 0.19 : [ 2 0.00 0.00 ]
#...
| 0.2 - 0.205 : [ 3 0.00 0.00 ]
| 0.205 - 0.21 : [ 1 0.00 0.00 ]
| 0.21 - 0.215 : [ 2 0.00 0.00 ]
| 0.215 - 0.22 : [ 2 0.00 0.00 ]
| 0.22 - 0.225 : [ 2 0.00 0.00 ]
| 0.225 - 0.23 : [ 4 0.00 0.00 ]
|X 0.23 - 0.235 : [ 9 0.00 0.00 ]
| 0.235 - 0.24 : [ 1 0.00 0.00 ]
| 0.24 - 0.245 : [ 5 0.00 0.00 ]
| 0.245 - 0.25 : [ 7 0.00 0.00 ]
|X 0.25 - 0.255 : [ 9 0.00 0.00 ]
|X 0.255 - 0.26 : [ 12 0.00 0.00 ]
|X 0.26 - 0.265 : [ 8 0.00 0.01 ]
|X 0.265 - 0.27 : [ 9 0.00 0.01 ]
| 0.27 - 0.275 : [ 7 0.00 0.01 ]
|X 0.275 - 0.28 : [ 11 0.00 0.01 ]
|X 0.28 - 0.285 : [ 20 0.00 0.01 ]
|XX 0.285 - 0.29 : [ 24 0.00 0.01 ]
|XX 0.29 - 0.295 : [ 25 0.00 0.01 ]
|XX 0.295 - 0.3 : [ 38 0.00 0.02 ]
|XX 0.3 - 0.305 : [ 29 0.00 0.02 ]
|XXX 0.305 - 0.31 : [ 46 0.00 0.02 ]
|XXXX 0.31 - 0.315 : [ 57 0.00 0.03 ]
|XXXX 0.315 - 0.32 : [ 60 0.00 0.03 ]
|XXXXX 0.32 - 0.325 : [ 75 0.01 0.04 ]
|XXXXX 0.325 - 0.33 : [ 83 0.01 0.04 ]
|XXXXXXX 0.33 - 0.335 : [ 100 0.01 0.05 ]
|XXXXXXX 0.335 - 0.34 : [ 105 0.01 0.06 ]
|XXXXXXXXXX 0.34 - 0.345 : [ 158 0.01 0.07 ]
|XXXXXXXXXX 0.345 - 0.35 : [ 151 0.01 0.08 ]
|XXXXXXXXXXXXXX 0.35 - 0.355 : [ 219 0.02 0.10 ]
|XXXXXXXXXXXXXX 0.355 - 0.36 : [ 210 0.02 0.11 ]
|XXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 249 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 279 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 314 0.02 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 341 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 404 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 393 0.03 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 422 0.03 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 391 0.03 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 492 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 498 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 526 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 544 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 578 0.04 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 614 0.05 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 592 0.04 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 577 0.04 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 596 0.05 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 543 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 538 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 525 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 420 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 389 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 305 0.02 0.91 ]
|XXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 248 0.02 0.93 ]
|XXXXXXXXXXXXX 0.48 - 0.485 : [ 198 0.02 0.95 ]
|XXXXXXXXXXX 0.485 - 0.49 : [ 163 0.01 0.96 ]
|XXXXXXX 0.49 - 0.495 : [ 110 0.01 0.97 ]
|XXXXXX 0.495 - 0.5 : [ 85 0.01 0.97 ]
|XXXXX 0.5 - 0.505 : [ 82 0.01 0.98 ]
|XXX 0.505 - 0.51 : [ 44 0.00 0.98 ]
|XXX 0.51 - 0.515 : [ 49 0.00 0.99 ]
|XXX 0.515 - 0.52 : [ 40 0.00 0.99 ]
|XX 0.52 - 0.525 : [ 30 0.00 0.99 ]
|X 0.525 - 0.53 : [ 22 0.00 0.99 ]
|X 0.53 - 0.535 : [ 13 0.00 0.99 ]
|X 0.535 - 0.54 : [ 14 0.00 1.00 ]
|X 0.54 - 0.545 : [ 9 0.00 1.00 ]
| 0.545 - 0.55 : [ 7 0.00 1.00 ]
| 0.55 - 0.555 : [ 4 0.00 1.00 ]
| 0.555 - 0.56 : [ 4 0.00 1.00 ]
| 0.56 - 0.565 : [ 1 0.00 1.00 ]
| 0.565 - 0.57 : [ 5 0.00 1.00 ]
| 0.57 - 0.575 : [ 3 0.00 1.00 ]
| 0.575 - 0.58 : [ 2 0.00 1.00 ]
| 0.58 - 0.585 : [ 2 0.00 1.00 ]
| 0.585 - 0.59 : [ 3 0.00 1.00 ]
#...
| 0.615 - 0.62 : [ 1 0.00 1.00 ]
| 0.62 - 0.625 : [ 1 0.00 1.00 ]
| 0.625 - 0.63 : [ 2 0.00 1.00 ]
#...
| 0.64 - 0.645 : [ 1 0.00 1.00 ]
| 0.645 - 0.65 : [ 1 0.00 1.00 ]
| 0.65 - 0.655 : [ 1 0.00 1.00 ]
| 0.655 - 0.66 : [ 1 0.00 1.00 ]
| 0.66 - 0.665 : [ 1 0.00 1.00 ]
| 0.665 - 0.67 : [ 2 0.00 1.00 ]
#...
| 0.69 - 0.695 : [ 1 0.00 1.00 ]
| 0.695 - 0.7 : [ 1 0.00 1.00 ]
| 0.7 - 0.705 : [ 2 0.00 1.00 ]
#...
| 0.725 - 0.73 : [ 1 0.00 1.00 ]
#...
| 0.735 - 0.74 : [ 1 0.00 1.00 ]
#...
| 0.77 - 0.775 : [ 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 670. 67 reads; 13580 bp (untrimmed), 13275 (trimmed).
Contig 671. 67 reads; 10922 bp (untrimmed), 10581 (trimmed).
Contig 672. 67 reads; 11757 bp (untrimmed), 11736 (trimmed).
Contig 673. 71 reads; 12949 bp (untrimmed), 12798 (trimmed).
Contig 674. 72 reads; 6364 bp (untrimmed), 6129 (trimmed).
Contig 675. 72 reads; 18677 bp (untrimmed), 18453 (trimmed).
Contig 676. 73 reads; 13760 bp (untrimmed), 13706 (trimmed).
Contig 677. 76 reads; 16474 bp (untrimmed), 16435 (trimmed).
Contig 678. 78 reads; 18152 bp (untrimmed), 18095 (trimmed).
Contig 679. 84 reads; 18168 bp (untrimmed), 18137 (trimmed).
Contig 680. 85 reads; 15995 bp (untrimmed), 15693 (trimmed).
Contig 681. 89 reads; 12846 bp (untrimmed), 12331 (trimmed).
Contig 682. 95 reads; 17724 bp (untrimmed), 17610 (trimmed).
Contig 683. 97 reads; 19673 bp (untrimmed), 19226 (trimmed).
Contig 684. 100 reads; 19782 bp (untrimmed), 19743 (trimmed).
Contig 685. 100 reads; 20317 bp (untrimmed), 20176 (trimmed).
Contig 686. 103 reads; 18721 bp (untrimmed), 18700 (trimmed).
Contig 687. 106 reads; 24285 bp (untrimmed), 23970 (trimmed).
Contig 688. 107 reads; 20901 bp (untrimmed), 20662 (trimmed).
Contig 689. 114 reads; 27983 bp (untrimmed), 27935 (trimmed).
Contig 690. 115 reads; 25280 bp (untrimmed), 24951 (trimmed).
Contig 691. 119 reads; 20942 bp (untrimmed), 20827 (trimmed).
Contig 692. 131 reads; 27149 bp (untrimmed), 26943 (trimmed).
Contig 693. 134 reads; 23546 bp (untrimmed), 23380 (trimmed).
Contig 694. 140 reads; 22233 bp (untrimmed), 22135 (trimmed).
Contig 695. 145 reads; 29913 bp (untrimmed), 29789 (trimmed).
Contig 696. 2070 reads; 42008 bp (untrimmed), 41971 (trimmed).
--------------------------------------------------------------
Totals 13303 reads; 2834285 bp (untrimmed), 2712348 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2830562 bases = 4.03 +- 5.14 = 0.63 +- 2.06
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 686 total values totalling 2058.9300. <3.001356 +/- 1.803678>
#Range: [ 1.07 - 42.08 ]
#Most likely bin: [ 3 - 3.5 ] 120 counts
#Median bin: [ 2.5 - 3 ] 113 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXX 1 - 1.5 : [ 41 0.06 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 100 0.15 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 103 0.15 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 113 0.16 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 120 0.17 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 109 0.16 0.85 ]
|XXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 59 0.09 0.94 ]
|XXXXXXXX 4.5 - 5 : [ 24 0.03 0.98 ]
|XXXX 5 - 5.5 : [ 13 0.02 0.99 ]
| 5.5 - 6 : [ 1 0.00 1.00 ]
| 6 - 6.5 : [ 1 0.00 1.00 ]
#...
| 9.5 - 10 : [ 1 0.00 1.00 ]
#...
| 42 - 42.5 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Histogram of Major Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000
-------------------------------------------------------------------
#Found 335 total values totalling 1256.6900. <3.751313 +/- 2.242213>
#Range: [ 1.83 - 42.08 ]
#Most likely bin: [ 3.5 - 4 ] 96 counts
#Median bin: [ 3.5 - 4 ] 96 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1.5 - 2 : [ 2 0.01 0.01 ]
|XXXXXXXX 2 - 2.5 : [ 18 0.05 0.06 ]
|XXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 43 0.13 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 83 0.25 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 96 0.29 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 53 0.16 0.88 ]
|XXXXXXXXXX 4.5 - 5 : [ 24 0.07 0.95 ]
|XXXXX 5 - 5.5 : [ 12 0.04 0.99 ]
| 5.5 - 6 : [ 1 0.00 0.99 ]
| 6 - 6.5 : [ 1 0.00 0.99 ]
#...
| 9.5 - 10 : [ 1 0.00 1.00 ]
#...
| 42 - 42.5 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 44 2 reads 1465 bases = 1.07 +- 0.25 = -0.23 +- 0.94
Contig 18 2 reads 976 bases = 1.10 +- 0.30 = -0.90 +- 0.30
Contig 30 2 reads 888 bases = 1.10 +- 0.30 = 0.90 +- 0.30
Contig 85 2 reads 981 bases = 1.11 +- 0.31 = -0.89 +- 0.31
Contig 61 2 reads 1059 bases = 1.18 +- 0.39 = 0.82 +- 0.39
Contig 80 2 reads 1163 bases = 1.18 +- 0.38 = -0.04 +- 0.91
Contig 57 2 reads 1630 bases = 1.19 +- 0.39 = 1.19 +- 0.39
Contig 36 2 reads 1639 bases = 1.20 +- 0.40 = 1.20 +- 0.40
Contig 69 2 reads 1539 bases = 1.20 +- 0.40 = 1.20 +- 0.40
Contig 33 2 reads 1583 bases = 1.23 +- 0.42 = 1.23 +- 0.42
Contig 35 2 reads 976 bases = 1.23 +- 0.42 = 1.23 +- 0.42
Contig 40 2 reads 1039 bases = 1.24 +- 0.43 = 1.24 +- 0.43
Contig 12 2 reads 1435 bases = 1.25 +- 0.43 = -0.20 +- 0.85
Contig 74 2 reads 1315 bases = 1.27 +- 0.45 = -0.10 +- 0.85
Contig 104 3 reads 2404 bases = 1.28 +- 0.45 = 0.49 +- 0.69
Contig 138 3 reads 2174 bases = 1.28 +- 0.45 = 1.28 +- 0.45
Contig 27 2 reads 1293 bases = 1.29 +- 0.45 = 1.29 +- 0.45
Contig 25 2 reads 1046 bases = 1.30 +- 0.46 = -0.02 +- 0.84
Contig 16 2 reads 1509 bases = 1.31 +- 0.46 = -0.05 +- 0.83
Contig 68 2 reads 1475 bases = 1.31 +- 0.46 = 1.31 +- 0.46
Contig 575 26 reads 4383 bases = 4.87 +- 2.70 = 0.76 +- 1.98
Contig 566 24 reads 4220 bases = 4.91 +- 1.89 = 1.24 +- 1.19
Contig 672 67 reads 11757 bases = 4.94 +- 3.88 = 0.02 +- 2.76
Contig 693 134 reads 23546 bases = 5.01 +- 1.98 = 0.11 +- 2.10
Contig 450 13 reads 2388 bases = 5.03 +- 2.36 = 0.51 +- 1.20
Contig 691 119 reads 20942 bases = 5.05 +- 2.01 = 0.15 +- 2.02
Contig 565 24 reads 4229 bases = 5.07 +- 2.10 = 0.48 +- 2.90
Contig 585 27 reads 4784 bases = 5.20 +- 3.10 = 0.95 +- 1.95
Contig 370 10 reads 1317 bases = 5.21 +- 2.11 = 1.50 +- 1.39
Contig 457 14 reads 2485 bases = 5.21 +- 2.74 = 1.39 +- 2.22
Contig 438 13 reads 2172 bases = 5.24 +- 2.13 = 0.05 +- 2.87
Contig 465 14 reads 2356 bases = 5.28 +- 1.96 = 2.00 +- 1.78
Contig 462 14 reads 2316 bases = 5.34 +- 2.06 = 0.43 +- 1.87
Contig 637 41 reads 6489 bases = 5.38 +- 2.04 = 0.49 +- 1.96
Contig 694 140 reads 22233 bases = 5.46 +- 2.21 = 0.10 +- 2.52
Contig 671 67 reads 10922 bases = 5.48 +- 2.53 = 0.44 +- 2.36
Contig 681 89 reads 12846 bases = 5.77 +- 2.61 = 0.27 +- 3.39
Contig 601 31 reads 4143 bases = 6.03 +- 2.68 = 0.99 +- 1.63
Contig 674 72 reads 6364 bases = 9.66 +- 5.05 = 2.27 +- 2.37
Contig 696 2070 reads 42008 bases = 42.08 +- 8.41 = 0.49 +- 6.76
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 322
HQ Discrepant reads = 222
Chimeric reads = 52
Suspect alignments = 74
-------------------------------------------------------------------
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/microbe2/3635662/edit_dir.12Aug04.QC