Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-13-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
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: 3071025
# phrap: 2925968
# db:
altered.
2500000
2832331 +/- 242340
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 9231
Number of reads with percent X's >= 20%: 353 = 0.9%
Number of reads with percent X's >= 50%: 208 = 0.5%
Number of reads with percent X's >= 80%: 33 = 0.1%
Total reads in project: 38733
Total bp X'd : 527556
reads >= 20% >= 50% >= 80% screened
Nr with L09136 7807 179 98 12
Nr with pCC1Fos 1131 0 0 0
Nr with pMCL200_JGI_XZX+XZK 293 174 110 21
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 35
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: 107
Total bp X'd : 1268
reads >= 20% >= 50% >= 80% screened
Nr with L09136 5 0 0 0
Nr with pCC1Fos 30 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 10505663
C = 7687257
G = 7689347
T = 10326631
N = 191931
X = 527556
GC fraction = 0.42
Total = 36928385
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3635662_fasta.screen.contigs
-------------------------------------------------------------------
A 891457
C 649481
G 652282
T 887809
N 49
fraction GC = 0.42
total bases = 3081078
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 8413 total values totalling 30287164.0000. <3600.043266 +/- 3408.994307>
#Range: [ 722 - 221512 ]
#Most likely bin: [ 3500 - 4000 ] 2875 counts
#Median bin: [ 3500 - 4000 ] 2875 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 16 0.00 0.00 ]
|X 1000 - 1500 : [ 64 0.01 0.01 ]
|XX 1500 - 2000 : [ 132 0.02 0.03 ]
|XXX 2000 - 2500 : [ 240 0.03 0.05 ]
|XXXXXX 2500 - 3000 : [ 460 0.05 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2841 0.34 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2875 0.34 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1548 0.18 0.97 ]
|XXX 4500 - 5000 : [ 225 0.03 1.00 ]
| 5000 - 5500 : [ 9 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
#...
| 220500 - 221000 : [ 1 0.00 1.00 ]
#...
| 221500 - 222000 : [ 1 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 7412 total values totalling 46633346.0000. <6291.600917 +/- 4392.070246>
#Range: [ 956 - 224773 ]
#Most likely bin: [ 6000 - 6500 ] 1877 counts
#Median bin: [ 6000 - 6500 ] 1877 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
|X 1000 - 1500 : [ 45 0.01 0.01 ]
|X 1500 - 2000 : [ 47 0.01 0.01 ]
|X 2000 - 2500 : [ 63 0.01 0.02 ]
|X 2500 - 3000 : [ 59 0.01 0.03 ]
|XX 3000 - 3500 : [ 92 0.01 0.04 ]
|XX 3500 - 4000 : [ 111 0.01 0.06 ]
|XXX 4000 - 4500 : [ 151 0.02 0.08 ]
|XXXXX 4500 - 5000 : [ 234 0.03 0.11 ]
|XXXXXXXXXX 5000 - 5500 : [ 449 0.06 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1152 0.16 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1877 0.25 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1546 0.21 0.79 ]
|XXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 947 0.13 0.91 ]
|XXXXXXXXXX 7500 - 8000 : [ 487 0.07 0.98 ]
|XXX 8000 - 8500 : [ 140 0.02 1.00 ]
| 8500 - 9000 : [ 3 0.00 1.00 ]
#...
| 18500 - 19000 : [ 1 0.00 1.00 ]
#...
| 23500 - 24000 : [ 1 0.00 1.00 ]
#...
| 34000 - 34500 : [ 1 0.00 1.00 ]
#...
| 49000 - 49500 : [ 1 0.00 1.00 ]
#...
| 193500 - 194000 : [ 1 0.00 1.00 ]
#...
| 222500 - 223000 : [ 1 0.00 1.00 ]
#...
| 224500 - 225000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APOY reads.list > grep.reads.list.APOY
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APOY 4 500
-------------------------------------------------------------------
#Found 484 total values totalling 18084396.0000. <37364.454545 +/- 3263.956615>
#Range: [ 27995 - 46842 ]
#Most likely bin: [ 35000 - 35500 ] 31 counts
#Median bin: [ 37000 - 37500 ] 27 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 27500 - 28000 : [ 1 0.00 0.00 ]
|X 28000 - 28500 : [ 1 0.00 0.00 ]
#...
|X 30500 - 31000 : [ 1 0.00 0.01 ]
|XXXXXXXX 31000 - 31500 : [ 6 0.01 0.02 ]
|XXXXXXXXX 31500 - 32000 : [ 7 0.01 0.03 ]
|XXXXXXXXXXXXXX 32000 - 32500 : [ 11 0.02 0.06 ]
|XXXXXXXXXXXXXXX 32500 - 33000 : [ 12 0.02 0.08 ]
|XXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 16 0.03 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 21 0.04 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 26 0.05 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 21 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 31 0.06 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 26 0.05 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 26 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 30 0.06 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 27 0.06 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 24 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 17 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 24 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 29 0.06 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 25 0.05 0.79 ]
|XXXXXXXXXXXXXXX 40000 - 40500 : [ 12 0.02 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 23 0.05 0.86 ]
|XXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 14 0.03 0.89 ]
|XXXXXXXXXXXXXX 41500 - 42000 : [ 11 0.02 0.91 ]
|XXXXXXXXX 42000 - 42500 : [ 7 0.01 0.93 ]
|XXXXXXXXXXXXXX 42500 - 43000 : [ 11 0.02 0.95 ]
|XXXXXXXX 43000 - 43500 : [ 6 0.01 0.96 ]
|XXXXXX 43500 - 44000 : [ 5 0.01 0.97 ]
|XXXXXXXX 44000 - 44500 : [ 6 0.01 0.99 ]
|X 44500 - 45000 : [ 1 0.00 0.99 ]
|XXX 45000 - 45500 : [ 2 0.00 0.99 ]
|XXX 45500 - 46000 : [ 2 0.00 1.00 ]
#...
|XXX 46500 - 47000 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# APOY 36378 +- 6096 (n=247)
# APOX 6070 +- 1413 (n=3816)
# APOW 3406 +- 687 (n=4268)
-------------------------------------------------------------------
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 21399 88 619 92 627
APOX 19968 86 726 95 686 19968 86 738 95 724
APOY 3072 80 604 89 570 2784 82 625 90 651
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
APOW 10710 91 625 95 639 10689 85 612 90 615
APOX 9984 86 729 95 716 9984 87 746 94 733
APOY 1248 82 655 89 653 1536 83 601 91 649
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3635662_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
112 19067 10151 90.63 94.41 APOW @
104 17266 8785 84.47 87.99 APOX @
16 2400 1398 87.38 91.02 APOY @
] 38733 20334 87.65 cumulative total@@
LIBRARY PLATE ID COUNT [ APOW 112 APOX 104 APOY 16 ] for 232 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 44151 total values totalling 25857806.0000. <585.667505 +/- 274.100748>
#Range: [ 0 - 932 ]
#Most likely bin: [ 750 - 800 ] 8659 counts
#Median bin: [ 700 - 750 ] 5995 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 5248 0.12 0.12 ]
|XXX 50 - 100 : [ 565 0.01 0.13 ]
|XX 100 - 150 : [ 513 0.01 0.14 ]
|XX 150 - 200 : [ 499 0.01 0.15 ]
|XXX 200 - 250 : [ 601 0.01 0.17 ]
|XXX 250 - 300 : [ 667 0.02 0.18 ]
|XXX 300 - 350 : [ 728 0.02 0.20 ]
|XXXX 350 - 400 : [ 787 0.02 0.22 ]
|XXXX 400 - 450 : [ 898 0.02 0.24 ]
|XXXXX 450 - 500 : [ 1030 0.02 0.26 ]
|XXXXXX 500 - 550 : [ 1276 0.03 0.29 ]
|XXXXXXXXX 550 - 600 : [ 1887 0.04 0.33 ]
|XXXXXXXXXXXX 600 - 650 : [ 2635 0.06 0.39 ]
|XXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4153 0.09 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5995 0.14 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8659 0.20 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6774 0.15 0.97 ]
|XXXXXX 850 - 900 : [ 1206 0.03 1.00 ]
| 900 - 950 : [ 30 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 21399 total values totalling 11694057.0000. <546.476798 +/- 261.546682>
#Range: [ 0 - 932 ]
#Most likely bin: [ 750 - 800 ] 2655 counts
#Median bin: [ 600 - 650 ] 1846 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2164 0.10 0.10 ]
|XXXXXX 50 - 100 : [ 410 0.02 0.12 ]
|XXXXXX 100 - 150 : [ 393 0.02 0.14 ]
|XXXXXX 150 - 200 : [ 371 0.02 0.16 ]
|XXXXXXX 200 - 250 : [ 437 0.02 0.18 ]
|XXXXXXX 250 - 300 : [ 477 0.02 0.20 ]
|XXXXXXXX 300 - 350 : [ 514 0.02 0.22 ]
|XXXXXXXXX 350 - 400 : [ 565 0.03 0.25 ]
|XXXXXXXXXX 400 - 450 : [ 663 0.03 0.28 ]
|XXXXXXXXXXXX 450 - 500 : [ 789 0.04 0.32 ]
|XXXXXXXXXXXXXXX 500 - 550 : [ 1012 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1430 0.07 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1846 0.09 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2509 0.12 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2630 0.12 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2655 0.12 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2018 0.09 0.98 ]
|XXXXXXXX 850 - 900 : [ 503 0.02 1.00 ]
| 900 - 950 : [ 13 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 19968 total values totalling 12723171.0000. <637.178035 +/- 274.836006>
#Range: [ 0 - 917 ]
#Most likely bin: [ 750 - 800 ] 5622 counts
#Median bin: [ 750 - 800 ] 5622 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2639 0.13 0.13 ]
|X 50 - 100 : [ 105 0.01 0.14 ]
|X 100 - 150 : [ 74 0.00 0.14 ]
|X 150 - 200 : [ 101 0.01 0.15 ]
|X 200 - 250 : [ 104 0.01 0.15 ]
|X 250 - 300 : [ 81 0.00 0.16 ]
|X 300 - 350 : [ 105 0.01 0.16 ]
|X 350 - 400 : [ 110 0.01 0.17 ]
|X 400 - 450 : [ 134 0.01 0.17 ]
|X 450 - 500 : [ 178 0.01 0.18 ]
|X 500 - 550 : [ 203 0.01 0.19 ]
|XXX 550 - 600 : [ 359 0.02 0.21 ]
|XXXXX 600 - 650 : [ 635 0.03 0.24 ]
|XXXXXXXXXX 650 - 700 : [ 1447 0.07 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3064 0.15 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5622 0.28 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4431 0.22 0.97 ]
|XXXX 850 - 900 : [ 568 0.03 1.00 ]
| 900 - 950 : [ 8 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APOY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APOY 3635662_fasta.screen.trimQ15.SaF > reads.trim15.APOY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APOY.rl 2 50
-------------------------------------------------------------------
#Found 2784 total values totalling 1440578.0000. <517.448994 +/- 297.378337>
#Range: [ 0 - 919 ]
#Most likely bin: [ 0 - 50 ] 445 counts
#Median bin: [ 600 - 650 ] 154 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 445 0.16 0.16 ]
|XXXX 50 - 100 : [ 50 0.02 0.18 ]
|XXXX 100 - 150 : [ 46 0.02 0.19 ]
|XX 150 - 200 : [ 27 0.01 0.20 ]
|XXXXX 200 - 250 : [ 60 0.02 0.23 ]
|XXXXXXXXXX 250 - 300 : [ 109 0.04 0.26 ]
|XXXXXXXXXX 300 - 350 : [ 109 0.04 0.30 ]
|XXXXXXXXXX 350 - 400 : [ 112 0.04 0.34 ]
|XXXXXXXXX 400 - 450 : [ 101 0.04 0.38 ]
|XXXXXX 450 - 500 : [ 63 0.02 0.40 ]
|XXXXX 500 - 550 : [ 61 0.02 0.42 ]
|XXXXXXXXX 550 - 600 : [ 98 0.04 0.46 ]
|XXXXXXXXXXXXXX 600 - 650 : [ 154 0.06 0.52 ]
|XXXXXXXXXXXXXXXXXX 650 - 700 : [ 197 0.07 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 301 0.11 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 382 0.14 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 325 0.12 0.95 ]
|XXXXXXXXXXXX 850 - 900 : [ 135 0.05 1.00 ]
|X 900 - 950 : [ 9 0.00 1.00 ]
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 38629 total values totalling 16143.8782. <0.417921 +/- 0.046389>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.425 - 0.43 ] 1809 counts
#Median bin: [ 0.42 - 0.425 ] 1734 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.135 - 0.14 : [ 2 0.00 0.00 ]
#...
| 0.165 - 0.17 : [ 1 0.00 0.00 ]
| 0.17 - 0.175 : [ 1 0.00 0.00 ]
#...
| 0.18 - 0.185 : [ 1 0.00 0.00 ]
| 0.185 - 0.19 : [ 1 0.00 0.00 ]
| 0.19 - 0.195 : [ 1 0.00 0.00 ]
| 0.195 - 0.2 : [ 1 0.00 0.00 ]
| 0.2 - 0.205 : [ 3 0.00 0.00 ]
#...
| 0.21 - 0.215 : [ 4 0.00 0.00 ]
| 0.215 - 0.22 : [ 5 0.00 0.00 ]
| 0.22 - 0.225 : [ 3 0.00 0.00 ]
| 0.225 - 0.23 : [ 6 0.00 0.00 ]
| 0.23 - 0.235 : [ 8 0.00 0.00 ]
| 0.235 - 0.24 : [ 4 0.00 0.00 ]
| 0.24 - 0.245 : [ 11 0.00 0.00 ]
| 0.245 - 0.25 : [ 11 0.00 0.00 ]
|X 0.25 - 0.255 : [ 23 0.00 0.00 ]
|X 0.255 - 0.26 : [ 27 0.00 0.00 ]
| 0.26 - 0.265 : [ 21 0.00 0.00 ]
|X 0.265 - 0.27 : [ 29 0.00 0.00 ]
|X 0.27 - 0.275 : [ 28 0.00 0.00 ]
|X 0.275 - 0.28 : [ 37 0.00 0.01 ]
|X 0.28 - 0.285 : [ 42 0.00 0.01 ]
|X 0.285 - 0.29 : [ 58 0.00 0.01 ]
|X 0.29 - 0.295 : [ 64 0.00 0.01 ]
|XX 0.295 - 0.3 : [ 88 0.00 0.01 ]
|XX 0.3 - 0.305 : [ 99 0.00 0.02 ]
|XXX 0.305 - 0.31 : [ 118 0.00 0.02 ]
|XXX 0.31 - 0.315 : [ 137 0.00 0.02 ]
|XXX 0.315 - 0.32 : [ 156 0.00 0.03 ]
|XXXXX 0.32 - 0.325 : [ 211 0.01 0.03 ]
|XXXXX 0.325 - 0.33 : [ 219 0.01 0.04 ]
|XXXXXX 0.33 - 0.335 : [ 251 0.01 0.04 ]
|XXXXXXX 0.335 - 0.34 : [ 301 0.01 0.05 ]
|XXXXXXXXX 0.34 - 0.345 : [ 406 0.01 0.06 ]
|XXXXXXXXXXX 0.345 - 0.35 : [ 493 0.01 0.07 ]
|XXXXXXXXXXXXXX 0.35 - 0.355 : [ 616 0.02 0.09 ]
|XXXXXXXXXXXXXX 0.355 - 0.36 : [ 642 0.02 0.11 ]
|XXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 710 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 826 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 867 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 984 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 1161 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 1207 0.03 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 1279 0.03 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 1224 0.03 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 1479 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 1466 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 1667 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 1631 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 1734 0.04 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 1809 0.05 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 1761 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 1749 0.05 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 1756 0.05 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 1662 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 1622 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 1494 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 1216 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 1100 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 896 0.02 0.92 ]
|XXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 715 0.02 0.94 ]
|XXXXXXXXXXXXX 0.48 - 0.485 : [ 589 0.02 0.95 ]
|XXXXXXXXXX 0.485 - 0.49 : [ 443 0.01 0.96 ]
|XXXXXXXX 0.49 - 0.495 : [ 349 0.01 0.97 ]
|XXXX 0.495 - 0.5 : [ 190 0.00 0.98 ]
|XXXXX 0.5 - 0.505 : [ 226 0.01 0.98 ]
|XXX 0.505 - 0.51 : [ 136 0.00 0.99 ]
|XXX 0.51 - 0.515 : [ 125 0.00 0.99 ]
|XX 0.515 - 0.52 : [ 88 0.00 0.99 ]
|XX 0.52 - 0.525 : [ 73 0.00 0.99 ]
|X 0.525 - 0.53 : [ 51 0.00 0.99 ]
|X 0.53 - 0.535 : [ 31 0.00 1.00 ]
|X 0.535 - 0.54 : [ 29 0.00 1.00 ]
|X 0.54 - 0.545 : [ 24 0.00 1.00 ]
| 0.545 - 0.55 : [ 15 0.00 1.00 ]
|X 0.55 - 0.555 : [ 25 0.00 1.00 ]
| 0.555 - 0.56 : [ 10 0.00 1.00 ]
| 0.56 - 0.565 : [ 8 0.00 1.00 ]
| 0.565 - 0.57 : [ 13 0.00 1.00 ]
| 0.57 - 0.575 : [ 7 0.00 1.00 ]
| 0.575 - 0.58 : [ 7 0.00 1.00 ]
| 0.58 - 0.585 : [ 5 0.00 1.00 ]
| 0.585 - 0.59 : [ 5 0.00 1.00 ]
| 0.59 - 0.595 : [ 1 0.00 1.00 ]
| 0.595 - 0.6 : [ 2 0.00 1.00 ]
| 0.6 - 0.605 : [ 1 0.00 1.00 ]
| 0.605 - 0.61 : [ 4 0.00 1.00 ]
| 0.61 - 0.615 : [ 1 0.00 1.00 ]
| 0.615 - 0.62 : [ 1 0.00 1.00 ]
| 0.62 - 0.625 : [ 2 0.00 1.00 ]
| 0.625 - 0.63 : [ 4 0.00 1.00 ]
#...
| 0.645 - 0.65 : [ 1 0.00 1.00 ]
| 0.65 - 0.655 : [ 2 0.00 1.00 ]
| 0.655 - 0.66 : [ 3 0.00 1.00 ]
| 0.66 - 0.665 : [ 1 0.00 1.00 ]
| 0.665 - 0.67 : [ 1 0.00 1.00 ]
| 0.67 - 0.675 : [ 1 0.00 1.00 ]
| 0.675 - 0.68 : [ 2 0.00 1.00 ]
| 0.68 - 0.685 : [ 2 0.00 1.00 ]
| 0.685 - 0.69 : [ 1 0.00 1.00 ]
#...
| 0.695 - 0.7 : [ 1 0.00 1.00 ]
| 0.7 - 0.705 : [ 2 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 36. 315 reads; 28200 bp (untrimmed), 28172 (trimmed).
Contig 37. 332 reads; 36536 bp (untrimmed), 35692 (trimmed).
Contig 38. 375 reads; 41451 bp (untrimmed), 41408 (trimmed).
Contig 39. 425 reads; 39905 bp (untrimmed), 39886 (trimmed).
Contig 40. 432 reads; 38755 bp (untrimmed), 38707 (trimmed).
Contig 41. 467 reads; 49913 bp (untrimmed), 49698 (trimmed).
Contig 42. 467 reads; 45515 bp (untrimmed), 44914 (trimmed).
Contig 43. 505 reads; 50184 bp (untrimmed), 49713 (trimmed).
Contig 44. 540 reads; 52115 bp (untrimmed), 52037 (trimmed).
Contig 45. 583 reads; 58364 bp (untrimmed), 58244 (trimmed).
Contig 46. 592 reads; 62094 bp (untrimmed), 62053 (trimmed).
Contig 47. 599 reads; 47618 bp (untrimmed), 47518 (trimmed).
Contig 48. 636 reads; 63856 bp (untrimmed), 63752 (trimmed).
Contig 49. 730 reads; 72327 bp (untrimmed), 71867 (trimmed).
Contig 50. 730 reads; 65133 bp (untrimmed), 64913 (trimmed).
Contig 51. 846 reads; 69136 bp (untrimmed), 68807 (trimmed).
Contig 52. 955 reads; 75080 bp (untrimmed), 74892 (trimmed).
Contig 53. 981 reads; 81653 bp (untrimmed), 81501 (trimmed).
Contig 54. 1404 reads; 127894 bp (untrimmed), 127647 (trimmed).
Contig 55. 1506 reads; 142077 bp (untrimmed), 141972 (trimmed).
Contig 56. 1602 reads; 126356 bp (untrimmed), 126163 (trimmed).
Contig 57. 1700 reads; 142310 bp (untrimmed), 142102 (trimmed).
Contig 58. 2306 reads; 201764 bp (untrimmed), 201669 (trimmed).
Contig 59. 2673 reads; 238458 bp (untrimmed), 237942 (trimmed).
Contig 60. 3137 reads; 289794 bp (untrimmed), 289612 (trimmed).
Contig 61. 4722 reads; 407247 bp (untrimmed), 407125 (trimmed).
Contig 62. 5908 reads; 42277 bp (untrimmed), 42083 (trimmed).
--------------------------------------------------------------
Totals 38626 reads; 3081078 bp (untrimmed), 3071025 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3080552 bases = 11.01 +- 13.97 = 0.16 +- 3.95
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 61 total values totalling 572.3500. <9.382787 +/- 14.813447>
#Range: [ 1.63 - 122.51 ]
#Most likely bin: [ 9.5 - 10 ] 7 counts
#Median bin: [ 8 - 8.5 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 1.5 - 2 : [ 1 0.02 0.02 ]
|XXXXXX 2 - 2.5 : [ 1 0.02 0.03 ]
|XXXXXX 2.5 - 3 : [ 1 0.02 0.05 ]
|XXXXXX 3 - 3.5 : [ 1 0.02 0.07 ]
|XXXXXXXXXXXXXXXXX 3.5 - 4 : [ 3 0.05 0.11 ]
|XXXXXXXXXXXXXXXXX 4 - 4.5 : [ 3 0.05 0.16 ]
|XXXXXXXXXXX 4.5 - 5 : [ 2 0.03 0.20 ]
|XXXXXXXXXXXXXXXXX 5 - 5.5 : [ 3 0.05 0.25 ]
|XXXXXXXXXXX 5.5 - 6 : [ 2 0.03 0.28 ]
|XXXXXXXXXXXXXXXXX 6 - 6.5 : [ 3 0.05 0.33 ]
|XXXXXX 6.5 - 7 : [ 1 0.02 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 5 0.08 0.43 ]
|XXXXXXXXXXXXXXXXX 7.5 - 8 : [ 3 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 6 0.10 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 5 0.08 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 5 0.08 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 7 0.11 0.85 ]
|XXXXXX 10 - 10.5 : [ 1 0.02 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 5 0.08 0.95 ]
|XXXXXXXXXXX 11 - 11.5 : [ 2 0.03 0.98 ]
#...
|XXXXXX 122.5 - 123 : [ 1 0.02 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 54 total values totalling 548.4400. <10.156296 +/- 15.570949>
#Range: [ 3.53 - 122.51 ]
#Most likely bin: [ 9.5 - 10 ] 7 counts
#Median bin: [ 8 - 8.5 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 3.5 - 4 : [ 2 0.04 0.04 ]
|XXXXXXXXXXXXXXXXX 4 - 4.5 : [ 3 0.06 0.09 ]
|XXXXXX 4.5 - 5 : [ 1 0.02 0.11 ]
|XXXXXXXXXXX 5 - 5.5 : [ 2 0.04 0.15 ]
|XXXXXXXXXXX 5.5 - 6 : [ 2 0.04 0.19 ]
|XXXXXXXXXXXXXXXXX 6 - 6.5 : [ 3 0.06 0.24 ]
|XXXXXX 6.5 - 7 : [ 1 0.02 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 5 0.09 0.35 ]
|XXXXXXXXXXXXXXXXX 7.5 - 8 : [ 3 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 6 0.11 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 5 0.09 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 5 0.09 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 7 0.13 0.83 ]
|XXXXXX 10 - 10.5 : [ 1 0.02 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 5 0.09 0.94 ]
|XXXXXXXXXXX 11 - 11.5 : [ 2 0.04 0.98 ]
#...
|XXXXXX 122.5 - 123 : [ 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 3 4 reads 2321 bases = 1.63 +- 0.60 = 0.89 +- 0.70
Contig 5 4 reads 1401 bases = 2.22 +- 1.15 = 2.22 +- 1.15
Contig 2 3 reads 1014 bases = 2.67 +- 0.55 = 2.67 +- 0.55
Contig 4 4 reads 1244 bases = 3.16 +- 1.21 = 3.16 +- 1.21
Contig 10 18 reads 4638 bases = 3.53 +- 1.96 = 1.34 +- 2.16
Contig 11 25 reads 5768 bases = 3.81 +- 2.02 = 2.43 +- 2.15
Contig 6 6 reads 1221 bases = 3.98 +- 1.57 = 1.52 +- 0.51
Contig 9 13 reads 2712 bases = 4.00 +- 1.59 = 4.00 +- 1.59
Contig 15 37 reads 7941 bases = 4.06 +- 1.79 = 0.57 +- 3.07
Contig 13 29 reads 5627 bases = 4.35 +- 2.04 = 1.70 +- 1.29
Contig 14 37 reads 6407 bases = 4.76 +- 1.70 = 0.57 +- 3.38
Contig 7 7 reads 1384 bases = 4.78 +- 2.51 = 4.78 +- 2.51
Contig 19 65 reads 11168 bases = 5.07 +- 2.45 = 0.90 +- 3.09
Contig 17 48 reads 7452 bases = 5.14 +- 2.63 = 0.56 +- 1.94
Contig 8 12 reads 1886 bases = 5.47 +- 2.93 = 0.25 +- 1.67
Contig 18 60 reads 8843 bases = 5.68 +- 2.64 = 0.27 +- 3.28
Contig 21 71 reads 10221 bases = 5.83 +- 2.78 = 1.33 +- 3.71
Contig 20 67 reads 9231 bases = 6.16 +- 2.47 = 0.32 +- 3.44
Contig 23 102 reads 14072 bases = 6.17 +- 2.82 = 0.24 +- 3.72
Contig 25 117 reads 15619 bases = 6.40 +- 2.40 = 0.28 +- 4.37
Contig 55 1506 reads 142077 bases = 9.30 +- 3.80 = -0.03 +- 3.76
Contig 39 425 reads 39905 bases = 9.33 +- 3.25 = 0.50 +- 3.20
Contig 22 93 reads 9016 bases = 9.39 +- 5.26 = 0.53 +- 2.16
Contig 60 3137 reads 289794 bases = 9.47 +- 3.60 = -0.01 +- 3.52
Contig 36 315 reads 28200 bases = 9.66 +- 3.55 = 0.36 +- 3.86
Contig 54 1404 reads 127894 bases = 9.70 +- 3.68 = 0.05 +- 3.41
Contig 50 730 reads 65133 bases = 9.78 +- 4.29 = 0.07 +- 3.65
Contig 59 2673 reads 238458 bases = 9.83 +- 3.48 = 0.05 +- 3.42
Contig 40 432 reads 38755 bases = 9.94 +- 3.25 = 0.09 +- 3.33
Contig 58 2306 reads 201764 bases = 9.95 +- 3.45 = 0.03 +- 3.86
Contig 29 206 reads 18078 bases = 9.98 +- 4.45 = 0.67 +- 3.43
Contig 61 4722 reads 407247 bases = 10.26 +- 3.78 = -0.01 +- 3.60
Contig 57 1700 reads 142310 bases = 10.51 +- 6.98 = 0.22 +- 4.60
Contig 53 981 reads 81653 bases = 10.60 +- 3.91 = 0.11 +- 3.43
Contig 33 249 reads 19909 bases = 10.63 +- 5.08 = 0.27 +- 5.63
Contig 47 599 reads 47618 bases = 10.76 +- 4.26 = 0.90 +- 3.99
Contig 51 846 reads 69136 bases = 10.81 +- 3.82 = 0.15 +- 3.78
Contig 56 1602 reads 126356 bases = 11.10 +- 3.70 = 0.08 +- 3.88
Contig 52 955 reads 75080 bases = 11.22 +- 4.15 = -0.04 +- 3.84
Contig 62 5908 reads 42277 bases = 122.51 +- 20.65 = 0.50 +- 13.14
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 25
Chimeric reads = 119
Suspect alignments = 327
-------------------------------------------------------------------
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.23Sep04.QD