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
3634504 3000 68909 Deinococcus geothermalis
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Deinococcus_geothermalis
-------------------------------------------------------------------
Deinococci, class, eubacteria
Deinococcaceae, family, eubacteria
Deinococcales (radio-resistant micrococci), order, eubacteria
Deinococcus geothermalis, species, eubacteria
Deinococcus, genus, eubacteria
Deinococcus-Thermus, phylum, eubacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3150337
# phrap: 2870349
# db:
altered.
3000000
3006895 +/- 114408
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 0
Number of reads with percent X's >= 20%: 0 = 0.0%
Number of reads with percent X's >= 50%: 0 = 0.0%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 34919
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 0
Number of reads with percent X's >= 20%: 0 = 0.0%
Number of reads with percent X's >= 50%: 0 = 0.0%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 59
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 5610556
C = 10938887
G = 10928493
T = 5701045
N = 145942
X = 372419
GC fraction = 0.65
Total = 33697342
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634504_fasta.screen.contigs
-------------------------------------------------------------------
A 527423
C 1051876
G 1049776
T 534928
N 82
fraction GC = 0.66
total bases = 3164085
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 AICX reads.list > grep.reads.list.AICX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICX 4 500
-------------------------------------------------------------------
#Found 7069 total values totalling 26027449.0000. <3681.913849 +/- 2540.202997>
#Range: [ 845 - 164214 ]
#Most likely bin: [ 3000 - 3500 ] 2646 counts
#Median bin: [ 3500 - 4000 ] 2550 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
| 1000 - 1500 : [ 20 0.00 0.00 ]
| 1500 - 2000 : [ 19 0.00 0.01 ]
|X 2000 - 2500 : [ 59 0.01 0.01 ]
|XXX 2500 - 3000 : [ 188 0.03 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2646 0.37 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2550 0.36 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1430 0.20 0.98 ]
|XX 4500 - 5000 : [ 150 0.02 1.00 ]
| 5000 - 5500 : [ 1 0.00 1.00 ]
#...
| 30000 - 30500 : [ 1 0.00 1.00 ]
#...
| 44500 - 45000 : [ 1 0.00 1.00 ]
#...
| 129500 - 130000 : [ 1 0.00 1.00 ]
#...
| 164000 - 164500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICY reads.list > grep.reads.list.AICY
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICY 4 500
-------------------------------------------------------------------
#Found 5394 total values totalling 38046278.0000. <7053.444197 +/- 10048.699877>
#Range: [ 1013 - 364883 ]
#Most likely bin: [ 6000 - 6500 ] 1270 counts
#Median bin: [ 6500 - 7000 ] 1170 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 7 0.00 0.00 ]
| 1500 - 2000 : [ 8 0.00 0.00 ]
| 2000 - 2500 : [ 12 0.00 0.01 ]
|X 2500 - 3000 : [ 20 0.00 0.01 ]
|X 3000 - 3500 : [ 18 0.00 0.01 ]
|X 3500 - 4000 : [ 20 0.00 0.02 ]
|X 4000 - 4500 : [ 29 0.01 0.02 ]
|X 4500 - 5000 : [ 37 0.01 0.03 ]
|XXXXXXXXX 5000 - 5500 : [ 297 0.06 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 955 0.18 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1270 0.24 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1170 0.22 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 870 0.16 0.87 ]
|XXXXXXXXXXXXXXX 7500 - 8000 : [ 484 0.09 0.96 ]
|XXXXX 8000 - 8500 : [ 157 0.03 0.99 ]
| 8500 - 9000 : [ 2 0.00 0.99 ]
| 9000 - 9500 : [ 4 0.00 0.99 ]
#...
| 11000 - 11500 : [ 2 0.00 0.99 ]
| 11500 - 12000 : [ 1 0.00 0.99 ]
#...
| 12500 - 13000 : [ 1 0.00 0.99 ]
#...
| 14000 - 14500 : [ 1 0.00 0.99 ]
#...
| 15000 - 15500 : [ 2 0.00 0.99 ]
#...
| 23000 - 23500 : [ 1 0.00 1.00 ]
#...
| 28500 - 29000 : [ 2 0.00 1.00 ]
#...
| 30500 - 31000 : [ 2 0.00 1.00 ]
#...
| 35000 - 35500 : [ 1 0.00 1.00 ]
#...
| 42000 - 42500 : [ 1 0.00 1.00 ]
#...
| 52000 - 52500 : [ 1 0.00 1.00 ]
#...
| 64000 - 64500 : [ 1 0.00 1.00 ]
#...
| 65500 - 66000 : [ 1 0.00 1.00 ]
#...
| 70000 - 70500 : [ 1 0.00 1.00 ]
#...
| 73000 - 73500 : [ 1 0.00 1.00 ]
#...
| 82000 - 82500 : [ 1 0.00 1.00 ]
#...
| 84000 - 84500 : [ 2 0.00 1.00 ]
#...
| 99500 - 100000 : [ 1 0.00 1.00 ]
#...
| 124000 - 124500 : [ 1 0.00 1.00 ]
#...
| 133500 - 134000 : [ 1 0.00 1.00 ]
#...
| 140500 - 141000 : [ 1 0.00 1.00 ]
#...
| 144500 - 145000 : [ 1 0.00 1.00 ]
#...
| 162000 - 162500 : [ 1 0.00 1.00 ]
#...
| 179500 - 180000 : [ 1 0.00 1.00 ]
#...
| 203000 - 203500 : [ 1 0.00 1.00 ]
#...
| 208500 - 209000 : [ 1 0.00 1.00 ]
#...
| 232500 - 233000 : [ 1 0.00 1.00 ]
#...
| 341500 - 342000 : [ 1 0.00 1.00 ]
#...
| 364500 - 365000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICZ reads.list > grep.reads.list.AICZ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICZ 4 500
-------------------------------------------------------------------
#Found 805 total values totalling 31527311.0000. <39164.361491 +/- 3130.295765>
#Range: [ 29169 - 55017 ]
#Most likely bin: [ 39000 - 39500 ] 61 counts
#Median bin: [ 39000 - 39500 ] 61 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 29000 - 29500 : [ 2 0.00 0.00 ]
#...
|X 30000 - 30500 : [ 1 0.00 0.00 ]
|X 30500 - 31000 : [ 1 0.00 0.00 ]
|X 31000 - 31500 : [ 1 0.00 0.01 ]
|XXX 31500 - 32000 : [ 4 0.00 0.01 ]
|XXXX 32000 - 32500 : [ 6 0.01 0.02 ]
|XXX 32500 - 33000 : [ 5 0.01 0.02 ]
|XXXX 33000 - 33500 : [ 6 0.01 0.03 ]
|XXXXXXXX 33500 - 34000 : [ 12 0.01 0.05 ]
|XXXXXXXXXXXXX 34000 - 34500 : [ 20 0.02 0.07 ]
|XXXXXXXXXX 34500 - 35000 : [ 15 0.02 0.09 ]
|XXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 27 0.03 0.12 ]
|XXXXXXXXXXXXXXX 35500 - 36000 : [ 23 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 30 0.04 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 47 0.06 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 48 0.06 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 45 0.06 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 36 0.04 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 55 0.07 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 61 0.08 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 42 0.05 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 50 0.06 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 41 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 39 0.05 0.77 ]
|XXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 28 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 39 0.05 0.85 ]
|XXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 30 0.04 0.89 ]
|XXXXXXXXXX 43000 - 43500 : [ 16 0.02 0.91 ]
|XXXXXXXXXXXXXX 43500 - 44000 : [ 22 0.03 0.93 ]
|XXXXXXXXXXXXX 44000 - 44500 : [ 20 0.02 0.96 ]
|XXXXXXXXX 44500 - 45000 : [ 13 0.02 0.98 ]
|XXXXXXX 45000 - 45500 : [ 10 0.01 0.99 ]
|XXXXX 45500 - 46000 : [ 7 0.01 1.00 ]
|X 46000 - 46500 : [ 1 0.00 1.00 ]
#...
|X 47000 - 47500 : [ 1 0.00 1.00 ]
#...
|X 55000 - 55500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AICY 6451 +- 1135 (n=2766)
# AICZ 39039 +- 3052 (n=397)
# AICX 3560 +- 961 (n=3550)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634504_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
AICX 16128 -1 -1 98 760 15517 100 769 100 775
AICY 18624 -1 -1 95 702 16442 99 763 100 753
AICZ 3072 -1 -1 99 699 2960 99 691 100 720
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AICX 7760 100 754 100 770 7757 100 785 100 779
AICY 8151 99 768 100 758 8291 99 758 100 749
AICZ 1498 99 705 100 725 1462 98 677 100 716
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634504_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 34919 17493 90.64 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 3634504_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 34919 total values totalling 26361187.0000. <754.923881 +/- 131.141972>
#Range: [ 19 - 933 ]
#Most likely bin: [ 800 - 850 ] 11867 counts
#Median bin: [ 750 - 800 ] 10735 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 80 0.00 0.00 ]
|X 50 - 100 : [ 156 0.00 0.01 ]
|X 100 - 150 : [ 161 0.00 0.01 ]
|X 150 - 200 : [ 218 0.01 0.02 ]
| 200 - 250 : [ 137 0.00 0.02 ]
|X 250 - 300 : [ 183 0.01 0.03 ]
|X 300 - 350 : [ 224 0.01 0.03 ]
|X 350 - 400 : [ 238 0.01 0.04 ]
|X 400 - 450 : [ 233 0.01 0.05 ]
|X 450 - 500 : [ 231 0.01 0.05 ]
|X 500 - 550 : [ 262 0.01 0.06 ]
|X 550 - 600 : [ 413 0.01 0.07 ]
|XX 600 - 650 : [ 674 0.02 0.09 ]
|XXXXXX 650 - 700 : [ 1685 0.05 0.14 ]
|XXXXXXXXXXXXXXX 700 - 750 : [ 4586 0.13 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 10735 0.31 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 11867 0.34 0.92 ]
|XXXXXXXXX 850 - 900 : [ 2784 0.08 1.00 ]
| 900 - 950 : [ 52 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICX 3634504_fasta.screen.trimQ15.SaF > reads.trim15.AICX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICX.rl 2 50
-------------------------------------------------------------------
#Found 15517 total values totalling 11911043.0000. <767.612490 +/- 114.233757>
#Range: [ 26 - 933 ]
#Most likely bin: [ 800 - 850 ] 5579 counts
#Median bin: [ 750 - 800 ] 4948 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 18 0.00 0.00 ]
| 50 - 100 : [ 21 0.00 0.00 ]
| 100 - 150 : [ 40 0.00 0.01 ]
|X 150 - 200 : [ 131 0.01 0.01 ]
| 200 - 250 : [ 47 0.00 0.02 ]
| 250 - 300 : [ 46 0.00 0.02 ]
| 300 - 350 : [ 61 0.00 0.02 ]
| 350 - 400 : [ 67 0.00 0.03 ]
|X 400 - 450 : [ 84 0.01 0.03 ]
|X 450 - 500 : [ 91 0.01 0.04 ]
|X 500 - 550 : [ 101 0.01 0.05 ]
|X 550 - 600 : [ 142 0.01 0.05 ]
|XX 600 - 650 : [ 219 0.01 0.07 ]
|XXXX 650 - 700 : [ 583 0.04 0.11 ]
|XXXXXXXXXXXXXX 700 - 750 : [ 1907 0.12 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4948 0.32 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5579 0.36 0.91 ]
|XXXXXXXXXX 850 - 900 : [ 1395 0.09 1.00 ]
| 900 - 950 : [ 37 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICY 3634504_fasta.screen.trimQ15.SaF > reads.trim15.AICY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICY.rl 2 50
-------------------------------------------------------------------
#Found 16442 total values totalling 12428911.0000. <755.924523 +/- 134.412325>
#Range: [ 19 - 916 ]
#Most likely bin: [ 800 - 850 ] 5898 counts
#Median bin: [ 750 - 800 ] 4871 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 50 0.00 0.00 ]
|X 50 - 100 : [ 107 0.01 0.01 ]
|X 100 - 150 : [ 95 0.01 0.02 ]
|X 150 - 200 : [ 77 0.00 0.02 ]
| 200 - 250 : [ 70 0.00 0.02 ]
|X 250 - 300 : [ 88 0.01 0.03 ]
|X 300 - 350 : [ 83 0.01 0.03 ]
| 350 - 400 : [ 71 0.00 0.04 ]
|X 400 - 450 : [ 92 0.01 0.04 ]
|X 450 - 500 : [ 108 0.01 0.05 ]
|X 500 - 550 : [ 129 0.01 0.06 ]
|X 550 - 600 : [ 211 0.01 0.07 ]
|XX 600 - 650 : [ 336 0.02 0.09 ]
|XXXXX 650 - 700 : [ 791 0.05 0.14 ]
|XXXXXXXXXXXXXX 700 - 750 : [ 2003 0.12 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4871 0.30 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5898 0.36 0.92 ]
|XXXXXXXXX 850 - 900 : [ 1347 0.08 1.00 ]
| 900 - 950 : [ 15 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICZ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICZ 3634504_fasta.screen.trimQ15.SaF > reads.trim15.AICZ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICZ.rl 2 50
-------------------------------------------------------------------
#Found 2960 total values totalling 2021233.0000. <682.848986 +/- 167.568281>
#Range: [ 27 - 886 ]
#Most likely bin: [ 750 - 800 ] 916 counts
#Median bin: [ 700 - 750 ] 676 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 12 0.00 0.00 ]
|X 50 - 100 : [ 28 0.01 0.01 ]
|X 100 - 150 : [ 26 0.01 0.02 ]
| 150 - 200 : [ 10 0.00 0.03 ]
|X 200 - 250 : [ 20 0.01 0.03 ]
|XX 250 - 300 : [ 49 0.02 0.05 ]
|XXX 300 - 350 : [ 80 0.03 0.08 ]
|XXXX 350 - 400 : [ 100 0.03 0.11 ]
|XX 400 - 450 : [ 57 0.02 0.13 ]
|X 450 - 500 : [ 32 0.01 0.14 ]
|X 500 - 550 : [ 32 0.01 0.15 ]
|XXX 550 - 600 : [ 60 0.02 0.17 ]
|XXXXX 600 - 650 : [ 119 0.04 0.21 ]
|XXXXXXXXXXXXXX 650 - 700 : [ 311 0.11 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 676 0.23 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 916 0.31 0.85 ]
|XXXXXXXXXXXXXXXXX 800 - 850 : [ 390 0.13 0.99 ]
|XX 850 - 900 : [ 42 0.01 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634504
-------------------------------------------------------------------
AICX.000001.000100 pUC18.fa.4 LRS.fasta
AICY.000001.000100 pMCL200.fa.4 LRS.fasta
AICY.000101.000200 pMCL200.fa.4 LRS.fasta
AICZ.000001.000100 pCC1Fos.fa.4 LRS.fasta
AICX.000001.000100 pUC18.fa.4 LRS.fasta
AICY.000001.000100 pMCL200.fa.4 LRS.fasta
AICY.000101.000200 pMCL200.fa.4 LRS.fasta
AICZ.000001.000100 pCC1Fos.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634504_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634504_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 34807 total values totalling 23104.0795. <0.663777 +/- 0.038602>
#Range: [ 0.3913 - 0.8824 ]
#Most likely bin: [ 0.67 - 0.675 ] 2032 counts
#Median bin: [ 0.665 - 0.67 ] 1993 counts
| 0.39 - 0.395 : [ 3 0.00 0.00 ]
#...
| 0.4 - 0.405 : [ 1 0.00 0.00 ]
#...
| 0.41 - 0.415 : [ 1 0.00 0.00 ]
| 0.415 - 0.42 : [ 4 0.00 0.00 ]
| 0.42 - 0.425 : [ 4 0.00 0.00 ]
| 0.425 - 0.43 : [ 6 0.00 0.00 ]
| 0.43 - 0.435 : [ 4 0.00 0.00 ]
| 0.435 - 0.44 : [ 4 0.00 0.00 ]
| 0.44 - 0.445 : [ 1 0.00 0.00 ]
| 0.445 - 0.45 : [ 2 0.00 0.00 ]
| 0.45 - 0.455 : [ 3 0.00 0.00 ]
| 0.455 - 0.46 : [ 2 0.00 0.00 ]
| 0.46 - 0.465 : [ 5 0.00 0.00 ]
| 0.465 - 0.47 : [ 3 0.00 0.00 ]
| 0.47 - 0.475 : [ 2 0.00 0.00 ]
| 0.475 - 0.48 : [ 6 0.00 0.00 ]
| 0.48 - 0.485 : [ 11 0.00 0.00 ]
| 0.485 - 0.49 : [ 13 0.00 0.00 ]
| 0.49 - 0.495 : [ 11 0.00 0.00 ]
| 0.495 - 0.5 : [ 13 0.00 0.00 ]
| 0.5 - 0.505 : [ 24 0.00 0.00 ]
| 0.505 - 0.51 : [ 16 0.00 0.00 ]
| 0.51 - 0.515 : [ 25 0.00 0.00 ]
| 0.515 - 0.52 : [ 22 0.00 0.01 ]
| 0.52 - 0.525 : [ 21 0.00 0.01 ]
|X 0.525 - 0.53 : [ 30 0.00 0.01 ]
|X 0.53 - 0.535 : [ 29 0.00 0.01 ]
|X 0.535 - 0.54 : [ 28 0.00 0.01 ]
|X 0.54 - 0.545 : [ 41 0.00 0.01 ]
|X 0.545 - 0.55 : [ 31 0.00 0.01 ]
|X 0.55 - 0.555 : [ 43 0.00 0.01 ]
|X 0.555 - 0.56 : [ 75 0.00 0.01 ]
|X 0.56 - 0.565 : [ 67 0.00 0.02 ]
|XX 0.565 - 0.57 : [ 108 0.00 0.02 ]
|XX 0.57 - 0.575 : [ 125 0.00 0.02 ]
|XX 0.575 - 0.58 : [ 122 0.00 0.03 ]
|XXX 0.58 - 0.585 : [ 147 0.00 0.03 ]
|XXXX 0.585 - 0.59 : [ 187 0.01 0.04 ]
|XXXXX 0.59 - 0.595 : [ 238 0.01 0.04 ]
|XXXXX 0.595 - 0.6 : [ 276 0.01 0.05 ]
|XXXXXXX 0.6 - 0.605 : [ 363 0.01 0.06 ]
|XXXXXXXXX 0.605 - 0.61 : [ 442 0.01 0.07 ]
|XXXXXXXXXXX 0.61 - 0.615 : [ 550 0.02 0.09 ]
|XXXXXXXXXXXXXX 0.615 - 0.62 : [ 690 0.02 0.11 ]
|XXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 796 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 1018 0.03 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 1103 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 1322 0.04 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 1526 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 1638 0.05 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 1772 0.05 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 1846 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 1927 0.06 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 1993 0.06 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 2032 0.06 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 1962 0.06 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 1874 0.05 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 1728 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 1548 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 1437 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 1235 0.04 0.88 ]
|XXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 1084 0.03 0.91 ]
|XXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 839 0.02 0.93 ]
|XXXXXXXXXXXXX 0.715 - 0.72 : [ 670 0.02 0.95 ]
|XXXXXXXXXX 0.72 - 0.725 : [ 533 0.02 0.97 ]
|XXXXXXX 0.725 - 0.73 : [ 335 0.01 0.98 ]
|XXXX 0.73 - 0.735 : [ 204 0.01 0.98 ]
|XXX 0.735 - 0.74 : [ 172 0.00 0.99 ]
|XX 0.74 - 0.745 : [ 118 0.00 0.99 ]
|XX 0.745 - 0.75 : [ 94 0.00 0.99 ]
|X 0.75 - 0.755 : [ 56 0.00 1.00 ]
|X 0.755 - 0.76 : [ 42 0.00 1.00 ]
| 0.76 - 0.765 : [ 25 0.00 1.00 ]
| 0.765 - 0.77 : [ 23 0.00 1.00 ]
| 0.77 - 0.775 : [ 11 0.00 1.00 ]
| 0.775 - 0.78 : [ 12 0.00 1.00 ]
| 0.78 - 0.785 : [ 11 0.00 1.00 ]
| 0.785 - 0.79 : [ 4 0.00 1.00 ]
| 0.79 - 0.795 : [ 4 0.00 1.00 ]
| 0.795 - 0.8 : [ 2 0.00 1.00 ]
| 0.8 - 0.805 : [ 2 0.00 1.00 ]
| 0.805 - 0.81 : [ 3 0.00 1.00 ]
| 0.81 - 0.815 : [ 2 0.00 1.00 ]
| 0.815 - 0.82 : [ 1 0.00 1.00 ]
| 0.82 - 0.825 : [ 2 0.00 1.00 ]
#...
| 0.83 - 0.835 : [ 1 0.00 1.00 ]
#...
| 0.88 - 0.885 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 86. 139 reads; 22692 bp (untrimmed), 22439 (trimmed).
Contig 87. 143 reads; 21932 bp (untrimmed), 21368 (trimmed).
Contig 88. 170 reads; 30336 bp (untrimmed), 30188 (trimmed).
Contig 89. 199 reads; 34649 bp (untrimmed), 34376 (trimmed).
Contig 90. 228 reads; 29841 bp (untrimmed), 29802 (trimmed).
Contig 91. 236 reads; 36046 bp (untrimmed), 35805 (trimmed).
Contig 92. 237 reads; 21339 bp (untrimmed), 21289 (trimmed).
Contig 93. 245 reads; 38936 bp (untrimmed), 38928 (trimmed).
Contig 94. 270 reads; 30022 bp (untrimmed), 29877 (trimmed).
Contig 95. 300 reads; 29308 bp (untrimmed), 29285 (trimmed).
Contig 96. 311 reads; 50708 bp (untrimmed), 50688 (trimmed).
Contig 97. 341 reads; 32048 bp (untrimmed), 31891 (trimmed).
Contig 98. 344 reads; 34052 bp (untrimmed), 34011 (trimmed).
Contig 99. 388 reads; 40071 bp (untrimmed), 40051 (trimmed).
Contig 100. 499 reads; 70582 bp (untrimmed), 70524 (trimmed).
Contig 101. 751 reads; 64298 bp (untrimmed), 64178 (trimmed).
Contig 102. 937 reads; 89222 bp (untrimmed), 89202 (trimmed).
Contig 103. 992 reads; 72583 bp (untrimmed), 72530 (trimmed).
Contig 104. 1390 reads; 110817 bp (untrimmed), 110792 (trimmed).
Contig 105. 1520 reads; 117209 bp (untrimmed), 117175 (trimmed).
Contig 106. 2102 reads; 158365 bp (untrimmed), 158245 (trimmed).
Contig 107. 2628 reads; 175822 bp (untrimmed), 175814 (trimmed).
Contig 108. 2794 reads; 228710 bp (untrimmed), 228684 (trimmed).
Contig 109. 3478 reads; 278606 bp (untrimmed), 278544 (trimmed).
Contig 110. 3697 reads; 289255 bp (untrimmed), 289224 (trimmed).
Contig 111. 3973 reads; 317038 bp (untrimmed), 316875 (trimmed).
Contig 112. 5049 reads; 421330 bp (untrimmed), 421243 (trimmed).
--------------------------------------------------------------
Totals 34860 reads; 3164085 bp (untrimmed), 3150337 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3046604 bases = 10.44 +- 4.61 = 0.15 +- 3.70
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 51 total values totalling 364.2500. <7.142157 +/- 3.056013>
#Range: [ 2.17 - 13.68 ]
#Most likely bin: [ 5.5 - 6 ] 6 counts
#Median bin: [ 5.5 - 6 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 3 0.06 0.06 ]
|XXXXXXX 2.5 - 3 : [ 1 0.02 0.08 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 4 0.08 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 6 0.12 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 6 0.12 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 6 0.12 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 4 0.08 0.59 ]
|XXXXXXX 6.5 - 7 : [ 1 0.02 0.61 ]
|XXXXXXX 7 - 7.5 : [ 1 0.02 0.63 ]
#...
|XXXXXXXXXXXXX 8 - 8.5 : [ 2 0.04 0.67 ]
|XXXXXXX 8.5 - 9 : [ 1 0.02 0.69 ]
|XXXXXXXXXXXXX 9 - 9.5 : [ 2 0.04 0.73 ]
|XXXXXXXXXXXXX 9.5 - 10 : [ 2 0.04 0.76 ]
|XXXXXXX 10 - 10.5 : [ 1 0.02 0.78 ]
|XXXXXXX 10.5 - 11 : [ 1 0.02 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.08 0.88 ]
|XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.06 0.94 ]
|XXXXXXX 12 - 12.5 : [ 1 0.02 0.96 ]
|XXXXXXX 12.5 - 13 : [ 1 0.02 0.98 ]
#...
|XXXXXXX 13.5 - 14 : [ 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 51 total values totalling 364.2500. <7.142157 +/- 3.056013>
#Range: [ 2.17 - 13.68 ]
#Most likely bin: [ 5.5 - 6 ] 6 counts
#Median bin: [ 5.5 - 6 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 3 0.06 0.06 ]
|XXXXXXX 2.5 - 3 : [ 1 0.02 0.08 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 4 0.08 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 6 0.12 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 6 0.12 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 6 0.12 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 4 0.08 0.59 ]
|XXXXXXX 6.5 - 7 : [ 1 0.02 0.61 ]
|XXXXXXX 7 - 7.5 : [ 1 0.02 0.63 ]
#...
|XXXXXXXXXXXXX 8 - 8.5 : [ 2 0.04 0.67 ]
|XXXXXXX 8.5 - 9 : [ 1 0.02 0.69 ]
|XXXXXXXXXXXXX 9 - 9.5 : [ 2 0.04 0.73 ]
|XXXXXXXXXXXXX 9.5 - 10 : [ 2 0.04 0.76 ]
|XXXXXXX 10 - 10.5 : [ 1 0.02 0.78 ]
|XXXXXXX 10.5 - 11 : [ 1 0.02 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.08 0.88 ]
|XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.06 0.94 ]
|XXXXXXX 12 - 12.5 : [ 1 0.02 0.96 ]
|XXXXXXX 12.5 - 13 : [ 1 0.02 0.98 ]
#...
|XXXXXXX 13.5 - 14 : [ 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 95 11 reads 4808 bases = 2.17 +- 0.84 = 0.17 +- 1.19
Contig 99 14 reads 5538 bases = 2.32 +- 1.20 = 0.32 +- 1.47
Contig 101 19 reads 7128 bases = 2.47 +- 1.00 = 0.11 +- 1.56
Contig 96 12 reads 3807 bases = 2.96 +- 1.08 = 1.07 +- 1.53
Contig 108 31 reads 6827 bases = 4.13 +- 2.22 = -0.01 +- 1.77
Contig 106 29 reads 6085 bases = 4.21 +- 2.03 = 1.28 +- 1.78
Contig 107 30 reads 6369 bases = 4.21 +- 1.80 = 0.21 +- 2.81
Contig 97 13 reads 2773 bases = 4.38 +- 1.72 = 1.65 +- 1.47
Contig 104 26 reads 5205 bases = 4.56 +- 2.72 = 0.48 +- 1.94
Contig 110 41 reads 8048 bases = 4.69 +- 1.32 = 0.53 +- 2.09
Contig 111 45 reads 8418 bases = 4.89 +- 2.10 = 0.93 +- 2.72
Contig 102 21 reads 3877 bases = 4.93 +- 2.13 = 1.18 +- 1.54
Contig 116 77 reads 14018 bases = 4.94 +- 2.43 = 0.30 +- 2.61
Contig 120 110 reads 18477 bases = 4.98 +- 1.91 = 0.35 +- 2.39
Contig 112 45 reads 8076 bases = 5.16 +- 1.74 = 0.30 +- 1.75
Contig 103 25 reads 4291 bases = 5.27 +- 1.91 = 0.23 +- 2.46
Contig 124 171 reads 30277 bases = 5.28 +- 2.63 = 0.06 +- 2.37
Contig 119 91 reads 15814 bases = 5.29 +- 2.32 = 0.59 +- 2.38
Contig 125 199 reads 34649 bases = 5.32 +- 2.23 = 0.27 +- 2.37
Contig 98 14 reads 2447 bases = 5.37 +- 2.26 = 4.62 +- 2.35
Contig 126 229 reads 29841 bases = 7.05 +- 2.96 = 0.64 +- 3.28
Contig 118 89 reads 10163 bases = 8.09 +- 3.55 = 1.42 +- 3.92
Contig 130 274 reads 30022 bases = 8.33 +- 3.40 = 0.42 +- 2.76
Contig 135 390 reads 40071 bases = 8.90 +- 3.29 = 0.64 +- 3.28
Contig 134 347 reads 34052 bases = 9.37 +- 3.62 = 0.16 +- 3.38
Contig 131 304 reads 29308 bases = 9.46 +- 3.90 = 0.22 +- 4.11
Contig 138 943 reads 89222 bases = 9.69 +- 3.65 = 0.34 +- 3.30
Contig 133 344 reads 32048 bases = 9.74 +- 4.49 = 0.37 +- 3.09
Contig 128 239 reads 21339 bases = 10.24 +- 4.07 = 0.70 +- 4.13
Contig 137 760 reads 64298 bases = 10.81 +- 4.59 = 0.28 +- 4.09
Contig 148 5083 reads 421330 bases = 11.07 +- 3.97 = 0.08 +- 3.68
Contig 144 2816 reads 228710 bases = 11.27 +- 4.94 = 0.03 +- 3.85
Contig 140 1397 reads 110817 bases = 11.44 +- 3.58 = 0.09 +- 3.49
Contig 145 3507 reads 278606 bases = 11.44 +- 3.77 = -0.01 +- 4.10
Contig 147 4038 reads 317038 bases = 11.69 +- 4.64 = 0.08 +- 4.07
Contig 146 3733 reads 289255 bases = 11.80 +- 3.89 = 0.09 +- 3.92
Contig 141 1536 reads 117208 bases = 11.97 +- 4.22 = -0.09 +- 3.89
Contig 142 2123 reads 158365 bases = 12.21 +- 4.07 = 0.08 +- 4.25
Contig 139 1000 reads 72583 bases = 12.69 +- 4.56 = 0.22 +- 3.96
Contig 143 2649 reads 175822 bases = 13.68 +- 4.39 = 0.06 +- 4.34
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 39
Chimeric reads = 54
Suspect alignments = 210
-------------------------------------------------------------------
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/microbe4/3634504/edit_dir.07Apr04.QD