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
3634604 4500 60478 Shewanella amazonensis
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Shewanella_amazonensis
-------------------------------------------------------------------
Shewanellaceae, family, g-proteobacteria
Alteromonadales, order, g-proteobacteria
Shewanella amazonensis, species, g-proteobacteria
Shewanella, genus, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4252489
# phrap: 4716269
# db:
altered.
4500000
4489586 +/- 189480
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 14636
Number of reads with percent X's >= 20%: 1428 = 2.5%
Number of reads with percent X's >= 50%: 729 = 1.3%
Number of reads with percent X's >= 80%: 99 = 0.2%
Total reads in project: 57918
Total bp X'd : 1247081
reads >= 20% >= 50% >= 80% screened
Nr with L09136 11991 413 161 5
Nr with pCC1Fos 1407 43 6 0
Nr with pMCL200_JGI_XZX+XZK 1238 972 562 94
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 6
Number of reads with percent X's >= 20%: 3 = 10.0%
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: 30
Total bp X'd : 901
reads >= 20% >= 50% >= 80% screened
Nr with L09136 2 1 0 0
Nr with pCC1Fos 3 1 0 0
Nr with pMCL200_JGI_XZX+XZK 1 1 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 12583816
C = 14291827
G = 14424408
T = 12087105
N = 286307
X = 1247081
GC fraction = 0.52
Total = 54920544
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634604_fasta.screen.contigs
-------------------------------------------------------------------
A 994046
C 1146333
G 1140216
T 983801
N 137
fraction GC = 0.54
total bases = 4264533
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 AINZ reads.list > grep.reads.list.AINZ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AINZ 4 500
-------------------------------------------------------------------
#Found 11495 total values totalling 38690435.0000. <3365.849065 +/- 2721.459452>
#Range: [ 570 - 201879 ]
#Most likely bin: [ 3000 - 3500 ] 3681 counts
#Median bin: [ 3000 - 3500 ] 3681 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 79 0.01 0.01 ]
|XXX 1000 - 1500 : [ 253 0.02 0.03 ]
|XXX 1500 - 2000 : [ 287 0.02 0.05 ]
|XXXXX 2000 - 2500 : [ 470 0.04 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2221 0.19 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3681 0.32 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2449 0.21 0.82 ]
|XXXXXXXXXXXXXXXX 4000 - 4500 : [ 1498 0.13 0.95 ]
|XXXXXX 4500 - 5000 : [ 537 0.05 1.00 ]
| 5000 - 5500 : [ 17 0.00 1.00 ]
#...
| 88000 - 88500 : [ 1 0.00 1.00 ]
#...
| 183000 - 183500 : [ 1 0.00 1.00 ]
#...
| 201500 - 202000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOA reads.list > grep.reads.list.AIOA
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOA 4 500
-------------------------------------------------------------------
#Found 10897 total values totalling 60709683.0000. <5571.229054 +/- 1750.266991>
#Range: [ 182 - 29254 ]
#Most likely bin: [ 5500 - 6000 ] 1860 counts
#Median bin: [ 5500 - 6000 ] 1860 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
| 500 - 1000 : [ 11 0.00 0.00 ]
|XXXXXXX 1000 - 1500 : [ 309 0.03 0.03 ]
|XXXXXXX 1500 - 2000 : [ 334 0.03 0.06 ]
|XXXXXXXX 2000 - 2500 : [ 350 0.03 0.09 ]
|XXXXXXX 2500 - 3000 : [ 303 0.03 0.12 ]
|XXXXXXX 3000 - 3500 : [ 308 0.03 0.15 ]
|XXXXXX 3500 - 4000 : [ 300 0.03 0.18 ]
|XXXXXXXXX 4000 - 4500 : [ 419 0.04 0.21 ]
|XXXXXXXXXXXXX 4500 - 5000 : [ 611 0.06 0.27 ]
|XXXXXXXXXXXXXXXXXXXXX 5000 - 5500 : [ 985 0.09 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1860 0.17 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1794 0.16 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1288 0.12 0.81 ]
|XXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 900 0.08 0.90 ]
|XXXXXXXXXXXXXX 7500 - 8000 : [ 658 0.06 0.96 ]
|XXXXXXXX 8000 - 8500 : [ 365 0.03 0.99 ]
|XX 8500 - 9000 : [ 98 0.01 1.00 ]
| 9000 - 9500 : [ 1 0.00 1.00 ]
#...
| 12000 - 12500 : [ 1 0.00 1.00 ]
#...
| 29000 - 29500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOB reads.list > grep.reads.list.AIOB
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOB 4 500
-------------------------------------------------------------------
#Found 1127 total values totalling 41687809.0000. <36990.070098 +/- 3803.309715>
#Range: [ 545 - 47306 ]
#Most likely bin: [ 34500 - 35000 ] 69 counts
#Median bin: [ 36500 - 37000 ] 64 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 1 0.00 0.00 ]
#...
|X 26000 - 26500 : [ 1 0.00 0.00 ]
#...
|X 27500 - 28000 : [ 1 0.00 0.00 ]
|X 28000 - 28500 : [ 1 0.00 0.00 ]
|XX 28500 - 29000 : [ 3 0.00 0.01 ]
|XX 29000 - 29500 : [ 4 0.00 0.01 ]
|X 29500 - 30000 : [ 2 0.00 0.01 ]
|XXX 30000 - 30500 : [ 6 0.01 0.02 ]
|XXXXXXX 30500 - 31000 : [ 12 0.01 0.03 ]
|XXXXXXXXX 31000 - 31500 : [ 16 0.01 0.04 ]
|XXXXXXXXXXXXX 31500 - 32000 : [ 23 0.02 0.06 ]
|XXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 35 0.03 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 49 0.04 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 47 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 39 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 59 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 69 0.06 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 67 0.06 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 52 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 59 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 64 0.06 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 57 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 46 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 44 0.04 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 41 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 35 0.03 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 42 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 35 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 35 0.03 0.84 ]
|XXXXXXXXXXXXXX 41000 - 41500 : [ 25 0.02 0.86 ]
|XXXXXXXXXXXXXXX 41500 - 42000 : [ 26 0.02 0.88 ]
|XXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 31 0.03 0.91 ]
|XXXXXXXXXXXXXX 42500 - 43000 : [ 25 0.02 0.93 ]
|XXXXXXXXXX 43000 - 43500 : [ 18 0.02 0.95 ]
|XXXXXXXXXXXX 43500 - 44000 : [ 20 0.02 0.97 ]
|XXXXX 44000 - 44500 : [ 8 0.01 0.97 ]
|XXXXXX 44500 - 45000 : [ 11 0.01 0.98 ]
|XXX 45000 - 45500 : [ 6 0.01 0.99 ]
|XXX 45500 - 46000 : [ 6 0.01 0.99 ]
|XX 46000 - 46500 : [ 4 0.00 1.00 ]
#...
|X 47000 - 47500 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIOA 5249 +- 2015 (n=5768)
# AIOB 36835 +- 4026 (n=558)
# AINZ 3124 +- 818 (n=6418)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634604_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
AINZ 33024 89 604 94 635 4606 87 570 92 587
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AINZ 2113 85 539 92 559 2493 89 596 93 610
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634604_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
176 24550 12559 71.36 74.33 AIOA @
148 29610 13324 90.03 93.78 AINZ @
24 3758 2017 84.04 87.54 AIOB @
] 57918 27900 80.17 cumulative total@@
LIBRARY PLATE ID COUNT [ AINZ 148 AIOA 176 AIOB 24 ] for 348 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 3634604_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 4606 total values totalling 2300624.0000. <499.484151 +/- 250.078749>
#Range: [ 0 - 958 ]
#Most likely bin: [ 650 - 700 ] 598 counts
#Median bin: [ 550 - 600 ] 447 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 488 0.11 0.11 ]
|XXXXXXX 50 - 100 : [ 103 0.02 0.13 ]
|XXXXXX 100 - 150 : [ 94 0.02 0.15 ]
|XXXXXX 150 - 200 : [ 97 0.02 0.17 ]
|XXXXXXXX 200 - 250 : [ 120 0.03 0.20 ]
|XXXXXXXX 250 - 300 : [ 125 0.03 0.22 ]
|XXXXXXXXX 300 - 350 : [ 137 0.03 0.25 ]
|XXXXXXXXXXX 350 - 400 : [ 160 0.03 0.29 ]
|XXXXXXXXXXXXXX 400 - 450 : [ 203 0.04 0.33 ]
|XXXXXXXXXXXXXXX 450 - 500 : [ 221 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXX 500 - 550 : [ 271 0.06 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 447 0.10 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 568 0.12 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 598 0.13 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 500 0.11 0.90 ]
|XXXXXXXXXXXXXXXX 750 - 800 : [ 244 0.05 0.95 ]
|XXXXXXX 800 - 850 : [ 111 0.02 0.97 ]
|XXXXX 850 - 900 : [ 80 0.02 0.99 ]
|XX 900 - 950 : [ 36 0.01 1.00 ]
| 950 - 1000 : [ 3 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AINZ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AINZ 3634604_fasta.screen.trimQ15.SaF > reads.trim15.AINZ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AINZ.rl 2 50
-------------------------------------------------------------------
#Found 4606 total values totalling 2300624.0000. <499.484151 +/- 250.078749>
#Range: [ 0 - 958 ]
#Most likely bin: [ 650 - 700 ] 598 counts
#Median bin: [ 550 - 600 ] 447 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 488 0.11 0.11 ]
|XXXXXXX 50 - 100 : [ 103 0.02 0.13 ]
|XXXXXX 100 - 150 : [ 94 0.02 0.15 ]
|XXXXXX 150 - 200 : [ 97 0.02 0.17 ]
|XXXXXXXX 200 - 250 : [ 120 0.03 0.20 ]
|XXXXXXXX 250 - 300 : [ 125 0.03 0.22 ]
|XXXXXXXXX 300 - 350 : [ 137 0.03 0.25 ]
|XXXXXXXXXXX 350 - 400 : [ 160 0.03 0.29 ]
|XXXXXXXXXXXXXX 400 - 450 : [ 203 0.04 0.33 ]
|XXXXXXXXXXXXXXX 450 - 500 : [ 221 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXX 500 - 550 : [ 271 0.06 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 447 0.10 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 568 0.12 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 598 0.13 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 500 0.11 0.90 ]
|XXXXXXXXXXXXXXXX 750 - 800 : [ 244 0.05 0.95 ]
|XXXXXXX 800 - 850 : [ 111 0.02 0.97 ]
|XXXXX 850 - 900 : [ 80 0.02 0.99 ]
|XX 900 - 950 : [ 36 0.01 1.00 ]
| 950 - 1000 : [ 3 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOA
trimt JAZZ trim 15 readlength histogram for AIOB
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634604
-------------------------------------------------------------------
AINZ.000001.000100 pUC18.fa LRS.fasta
AINZ.000101.000200 pUC18.fa LRS.fasta
AIOA.000001.000100 pMCL200.fa LRS.fasta
AIOA.000101.000200 pMCL200.fa LRS.fasta
AIOB.000001.000100 pCC1Fos.fa LRS.fasta
AINZ.000001.000100 pUC18.fa LRS.fasta
AINZ.000101.000200 pUC18.fa LRS.fasta
AIOA.000001.000100 pMCL200.fa LRS.fasta
AIOA.000101.000200 pMCL200.fa LRS.fasta
AIOB.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634604_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634604_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 57668 total values totalling 31055.0652. <0.538515 +/- 0.044414>
#Range: [ 0.169 - 0.7917 ]
#Most likely bin: [ 0.55 - 0.555 ] 3278 counts
#Median bin: [ 0.54 - 0.545 ] 3041 counts
| 0.165 - 0.17 : [ 1 0.00 0.00 ]
#...
| 0.185 - 0.19 : [ 1 0.00 0.00 ]
#...
| 0.205 - 0.21 : [ 1 0.00 0.00 ]
#...
| 0.24 - 0.245 : [ 2 0.00 0.00 ]
#...
| 0.25 - 0.255 : [ 1 0.00 0.00 ]
| 0.255 - 0.26 : [ 1 0.00 0.00 ]
| 0.26 - 0.265 : [ 3 0.00 0.00 ]
| 0.265 - 0.27 : [ 3 0.00 0.00 ]
| 0.27 - 0.275 : [ 5 0.00 0.00 ]
| 0.275 - 0.28 : [ 3 0.00 0.00 ]
| 0.28 - 0.285 : [ 1 0.00 0.00 ]
| 0.285 - 0.29 : [ 5 0.00 0.00 ]
| 0.29 - 0.295 : [ 10 0.00 0.00 ]
| 0.295 - 0.3 : [ 7 0.00 0.00 ]
| 0.3 - 0.305 : [ 9 0.00 0.00 ]
| 0.305 - 0.31 : [ 11 0.00 0.00 ]
| 0.31 - 0.315 : [ 12 0.00 0.00 ]
| 0.315 - 0.32 : [ 24 0.00 0.00 ]
| 0.32 - 0.325 : [ 13 0.00 0.00 ]
| 0.325 - 0.33 : [ 18 0.00 0.00 ]
| 0.33 - 0.335 : [ 20 0.00 0.00 ]
| 0.335 - 0.34 : [ 15 0.00 0.00 ]
| 0.34 - 0.345 : [ 22 0.00 0.00 ]
| 0.345 - 0.35 : [ 31 0.00 0.00 ]
| 0.35 - 0.355 : [ 37 0.00 0.00 ]
| 0.355 - 0.36 : [ 26 0.00 0.00 ]
|X 0.36 - 0.365 : [ 43 0.00 0.01 ]
|X 0.365 - 0.37 : [ 51 0.00 0.01 ]
|X 0.37 - 0.375 : [ 66 0.00 0.01 ]
|X 0.375 - 0.38 : [ 57 0.00 0.01 ]
|X 0.38 - 0.385 : [ 89 0.00 0.01 ]
|X 0.385 - 0.39 : [ 82 0.00 0.01 ]
|X 0.39 - 0.395 : [ 94 0.00 0.01 ]
|X 0.395 - 0.4 : [ 83 0.00 0.01 ]
|X 0.4 - 0.405 : [ 71 0.00 0.02 ]
|X 0.405 - 0.41 : [ 108 0.00 0.02 ]
|X 0.41 - 0.415 : [ 99 0.00 0.02 ]
|X 0.415 - 0.42 : [ 120 0.00 0.02 ]
|XX 0.42 - 0.425 : [ 144 0.00 0.02 ]
|XX 0.425 - 0.43 : [ 147 0.00 0.03 ]
|XX 0.43 - 0.435 : [ 166 0.00 0.03 ]
|XX 0.435 - 0.44 : [ 189 0.00 0.03 ]
|XXX 0.44 - 0.445 : [ 219 0.00 0.04 ]
|XXX 0.445 - 0.45 : [ 215 0.00 0.04 ]
|XXX 0.45 - 0.455 : [ 253 0.00 0.04 ]
|XXXX 0.455 - 0.46 : [ 289 0.01 0.05 ]
|XXXX 0.46 - 0.465 : [ 333 0.01 0.06 ]
|XXXX 0.465 - 0.47 : [ 356 0.01 0.06 ]
|XXXXXX 0.47 - 0.475 : [ 483 0.01 0.07 ]
|XXXXXXX 0.475 - 0.48 : [ 572 0.01 0.08 ]
|XXXXXXXXX 0.48 - 0.485 : [ 729 0.01 0.09 ]
|XXXXXXXXXXX 0.485 - 0.49 : [ 862 0.01 0.11 ]
|XXXXXXXXXXXX 0.49 - 0.495 : [ 981 0.02 0.12 ]
|XXXXXXXXXXXX 0.495 - 0.5 : [ 991 0.02 0.14 ]
|XXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1569 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1631 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1919 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 2252 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 2500 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 2658 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 2810 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 2981 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 3041 0.05 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 3216 0.06 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 3278 0.06 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 3197 0.06 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 2988 0.05 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 2779 0.05 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 2518 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 2167 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1861 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1486 0.03 0.92 ]
|XXXXXXXXXXXXXX 0.59 - 0.595 : [ 1184 0.02 0.94 ]
|XXXXXXXXXXX 0.595 - 0.6 : [ 903 0.02 0.96 ]
|XXXXXXXXX 0.6 - 0.605 : [ 739 0.01 0.97 ]
|XXXXXX 0.605 - 0.61 : [ 517 0.01 0.98 ]
|XXXX 0.61 - 0.615 : [ 316 0.01 0.98 ]
|XXX 0.615 - 0.62 : [ 255 0.00 0.99 ]
|XX 0.62 - 0.625 : [ 196 0.00 0.99 ]
|XX 0.625 - 0.63 : [ 158 0.00 0.99 ]
|XX 0.63 - 0.635 : [ 131 0.00 1.00 ]
|X 0.635 - 0.64 : [ 69 0.00 1.00 ]
| 0.64 - 0.645 : [ 37 0.00 1.00 ]
| 0.645 - 0.65 : [ 23 0.00 1.00 ]
| 0.65 - 0.655 : [ 27 0.00 1.00 ]
| 0.655 - 0.66 : [ 18 0.00 1.00 ]
| 0.66 - 0.665 : [ 12 0.00 1.00 ]
| 0.665 - 0.67 : [ 16 0.00 1.00 ]
| 0.67 - 0.675 : [ 4 0.00 1.00 ]
| 0.675 - 0.68 : [ 6 0.00 1.00 ]
| 0.68 - 0.685 : [ 8 0.00 1.00 ]
| 0.685 - 0.69 : [ 3 0.00 1.00 ]
| 0.69 - 0.695 : [ 4 0.00 1.00 ]
| 0.695 - 0.7 : [ 1 0.00 1.00 ]
| 0.7 - 0.705 : [ 3 0.00 1.00 ]
| 0.705 - 0.71 : [ 2 0.00 1.00 ]
#...
| 0.715 - 0.72 : [ 2 0.00 1.00 ]
| 0.72 - 0.725 : [ 2 0.00 1.00 ]
#...
| 0.73 - 0.735 : [ 2 0.00 1.00 ]
| 0.735 - 0.74 : [ 1 0.00 1.00 ]
| 0.74 - 0.745 : [ 1 0.00 1.00 ]
#...
| 0.75 - 0.755 : [ 1 0.00 1.00 ]
#...
| 0.77 - 0.775 : [ 1 0.00 1.00 ]
#...
| 0.79 - 0.795 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 77. 424 reads; 34993 bp (untrimmed), 34841 (trimmed).
Contig 78. 441 reads; 38634 bp (untrimmed), 38614 (trimmed).
Contig 79. 447 reads; 37430 bp (untrimmed), 37329 (trimmed).
Contig 80. 486 reads; 51222 bp (untrimmed), 51187 (trimmed).
Contig 81. 501 reads; 40361 bp (untrimmed), 40323 (trimmed).
Contig 82. 515 reads; 56631 bp (untrimmed), 56577 (trimmed).
Contig 83. 525 reads; 38318 bp (untrimmed), 38164 (trimmed).
Contig 84. 528 reads; 51908 bp (untrimmed), 51665 (trimmed).
Contig 85. 578 reads; 41853 bp (untrimmed), 41456 (trimmed).
Contig 86. 686 reads; 59678 bp (untrimmed), 59657 (trimmed).
Contig 87. 695 reads; 59132 bp (untrimmed), 59087 (trimmed).
Contig 88. 752 reads; 69475 bp (untrimmed), 69393 (trimmed).
Contig 89. 839 reads; 66572 bp (untrimmed), 66560 (trimmed).
Contig 90. 928 reads; 73255 bp (untrimmed), 72747 (trimmed).
Contig 91. 1154 reads; 85849 bp (untrimmed), 85734 (trimmed).
Contig 92. 1343 reads; 91375 bp (untrimmed), 91320 (trimmed).
Contig 93. 1387 reads; 113743 bp (untrimmed), 113468 (trimmed).
Contig 94. 1432 reads; 106951 bp (untrimmed), 106664 (trimmed).
Contig 95. 1715 reads; 108606 bp (untrimmed), 108436 (trimmed).
Contig 96. 1982 reads; 136578 bp (untrimmed), 136421 (trimmed).
Contig 97. 2012 reads; 128803 bp (untrimmed), 128731 (trimmed).
Contig 98. 2688 reads; 177631 bp (untrimmed), 177625 (trimmed).
Contig 99. 3355 reads; 206973 bp (untrimmed), 206895 (trimmed).
Contig 100. 4373 reads; 295660 bp (untrimmed), 295385 (trimmed).
Contig 101. 4612 reads; 345928 bp (untrimmed), 345904 (trimmed).
Contig 102. 6659 reads; 417779 bp (untrimmed), 417734 (trimmed).
Contig 103. 9068 reads; 542652 bp (untrimmed), 542619 (trimmed).
--------------------------------------------------------------
Totals 57888 reads; 4264533 bp (untrimmed), 4252489 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4264297 bases = 11.66 +- 5.24 = 0.20 +- 4.28
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 102 total values totalling 780.8000. <7.654902 +/- 4.123532>
#Range: [ 1.25 - 20.88 ]
#Most likely bin: [ 2.5 - 3 ] 8 counts
#Median bin: [ 8 - 8.5 ] 5 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 1 - 1.5 : [ 2 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 4 0.04 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 7 0.07 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 8 0.08 0.21 ]
|XXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 4 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 4 0.04 0.28 ]
|XXXXXXXXXXXXXXX 4 - 4.5 : [ 3 0.03 0.31 ]
|XXXXX 4.5 - 5 : [ 1 0.01 0.32 ]
|XXXXXXXXXXXXXXX 5 - 5.5 : [ 3 0.03 0.35 ]
|XXXXXXXXXXXXXXX 5.5 - 6 : [ 3 0.03 0.38 ]
|XXXXXXXXXX 6 - 6.5 : [ 2 0.02 0.40 ]
|XXXXXXXXXX 6.5 - 7 : [ 2 0.02 0.42 ]
|XXXXXXXXXX 7 - 7.5 : [ 2 0.02 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 5 0.05 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 5 0.05 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 6 0.06 0.60 ]
|XXXXX 9 - 9.5 : [ 1 0.01 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 6 0.06 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 7 0.07 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 5 0.05 0.78 ]
|XXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 4 0.04 0.86 ]
|XXXXXXXXXX 12 - 12.5 : [ 2 0.02 0.88 ]
|XXXXXXXXXXXXXXX 12.5 - 13 : [ 3 0.03 0.91 ]
|XXXXXXXXXX 13 - 13.5 : [ 2 0.02 0.93 ]
|XXXXXXXXXX 13.5 - 14 : [ 2 0.02 0.95 ]
|XXXXXXXXXX 14 - 14.5 : [ 2 0.02 0.97 ]
|XXXXX 14.5 - 15 : [ 1 0.01 0.98 ]
#...
|XXXXX 16.5 - 17 : [ 1 0.01 0.99 ]
#...
|XXXXX 20.5 - 21 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Histogram of Major Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000
-------------------------------------------------------------------
#Found 74 total values totalling 663.3600. <8.964324 +/- 3.183214>
#Range: [ 2.24 - 16.71 ]
#Most likely bin: [ 10 - 10.5 ] 7 counts
#Median bin: [ 9 - 9.5 ] 1 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 2 - 2.5 : [ 1 0.01 0.01 ]
#...
|XXXXXXXXXXXXXXXXX 3 - 3.5 : [ 3 0.04 0.05 ]
|XXXXXXXXXXXXXXXXX 3.5 - 4 : [ 3 0.04 0.09 ]
|XXXXXXXXXXXXXXXXX 4 - 4.5 : [ 3 0.04 0.14 ]
#...
|XXXXXXXXXXXXXXXXX 5 - 5.5 : [ 3 0.04 0.18 ]
|XXXXXXXXXXXXXXXXX 5.5 - 6 : [ 3 0.04 0.22 ]
|XXXXXXXXXXX 6 - 6.5 : [ 2 0.03 0.24 ]
|XXXXXXXXXXX 6.5 - 7 : [ 2 0.03 0.27 ]
|XXXXXXXXXXX 7 - 7.5 : [ 2 0.03 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 4 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 4 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 6 0.08 0.49 ]
|XXXXXX 9 - 9.5 : [ 1 0.01 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 5 0.07 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 7 0.09 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 5 0.07 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.05 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 4 0.05 0.84 ]
|XXXXXXXXXXX 12 - 12.5 : [ 2 0.03 0.86 ]
|XXXXXXXXXXXXXXXXX 12.5 - 13 : [ 3 0.04 0.91 ]
|XXXXXXXXXXX 13 - 13.5 : [ 2 0.03 0.93 ]
|XXXXXXXXXXX 13.5 - 14 : [ 2 0.03 0.96 ]
|XXXXXXXXXXX 14 - 14.5 : [ 2 0.03 0.99 ]
#...
|XXXXXX 16.5 - 17 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 1 3 reads 1950 bases = 1.25 +- 0.43 = 0.59 +- 0.95
Contig 4 3 reads 1894 bases = 1.33 +- 0.47 = 1.33 +- 0.47
Contig 12 4 reads 1985 bases = 1.80 +- 0.72 = 0.01 +- 1.44
Contig 22 7 reads 2267 bases = 1.85 +- 1.17 = 0.88 +- 1.38
Contig 2 3 reads 962 bases = 1.89 +- 0.97 = 0.97 +- 0.30
Contig 10 4 reads 1956 bases = 1.96 +- 0.82 = 1.11 +- 0.71
Contig 9 3 reads 1451 bases = 2.09 +- 0.88 = 2.09 +- 0.88
Contig 14 4 reads 1693 bases = 2.13 +- 0.92 = 2.13 +- 0.92
Contig 11 4 reads 1812 bases = 2.16 +- 1.16 = -0.14 +- 0.88
Contig 28 11 reads 3452 bases = 2.24 +- 1.04 = 0.11 +- 1.70
Contig 20 6 reads 2491 bases = 2.32 +- 1.00 = 0.70 +- 1.81
Contig 3 3 reads 1082 bases = 2.34 +- 0.81 = 2.34 +- 0.81
Contig 19 6 reads 2254 bases = 2.44 +- 0.81 = -0.13 +- 1.33
Contig 5 3 reads 1198 bases = 2.50 +- 0.87 = 2.50 +- 0.87
Contig 7 3 reads 1028 bases = 2.61 +- 0.54 = 2.61 +- 0.54
Contig 18 6 reads 2037 bases = 2.62 +- 1.25 = 1.70 +- 0.64
Contig 17 5 reads 1715 bases = 2.71 +- 1.28 = 2.71 +- 1.28
Contig 21 7 reads 1994 bases = 2.76 +- 1.00 = 2.76 +- 1.00
Contig 8 3 reads 644 bases = 2.78 +- 0.58 = 1.04 +- 0.22
Contig 15 4 reads 1274 bases = 2.79 +- 1.18 = 1.84 +- 0.42
Contig 101 4612 reads 345928 bases = 11.44 +- 4.17 = 0.04 +- 4.21
Contig 59 219 reads 16702 bases = 11.48 +- 5.16 = 0.11 +- 5.14
Contig 94 1432 reads 106951 bases = 11.54 +- 4.81 = 0.07 +- 4.14
Contig 91 1154 reads 85849 bases = 11.69 +- 4.12 = 0.03 +- 3.67
Contig 83 525 reads 38318 bases = 11.76 +- 4.35 = 0.15 +- 4.35
Contig 85 578 reads 41853 bases = 11.81 +- 4.32 = 0.38 +- 3.84
Contig 76 423 reads 29178 bases = 12.40 +- 6.09 = 0.90 +- 5.07
Contig 96 1982 reads 136578 bases = 12.43 +- 4.58 = 0.14 +- 3.97
Contig 92 1343 reads 91375 bases = 12.72 +- 5.21 = 0.10 +- 3.92
Contig 57 182 reads 12311 bases = 12.73 +- 4.93 = 0.90 +- 5.65
Contig 100 4373 reads 295660 bases = 12.74 +- 4.87 = 0.12 +- 4.53
Contig 98 2688 reads 177631 bases = 13.04 +- 5.09 = 0.20 +- 4.24
Contig 97 2012 reads 128803 bases = 13.49 +- 4.92 = 0.09 +- 4.52
Contig 95 1715 reads 108606 bases = 13.60 +- 4.85 = 0.26 +- 4.13
Contig 102 6659 reads 417779 bases = 13.67 +- 4.75 = 0.08 +- 4.54
Contig 99 3355 reads 206973 bases = 14.12 +- 4.85 = 0.17 +- 4.62
Contig 103 9068 reads 542652 bases = 14.37 +- 5.73 = 0.02 +- 4.82
Contig 38 22 reads 1350 bases = 14.51 +- 6.87 = 0.67 +- 1.32
Contig 45 60 reads 3004 bases = 16.71 +- 9.31 = 14.22 +- 9.86
Contig 43 42 reads 545 bases = 20.88 +- 5.78 = 20.83 +- 5.82
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 42
Chimeric reads = 198
Suspect alignments = 311
-------------------------------------------------------------------
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/microbe3/3634604/edit_dir.08Oct04.QD