Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-12-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
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Project Size(KB) TaxID GenusSpecies
3634494 1600 39766 Thiomicrospira denitrificans
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Thiomicrospira_denitrificans
-------------------------------------------------------------------
Campylobacterales, order, e-proteobacteria
Helicobacteraceae, family, e-proteobacteria
delta/epsilon subdivisions, subphylum, proteobacteria
Thiomicrospira denitrificans, species, e-proteobacteria
Epsilonproteobacteria, class, e-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2175314
# phrap: 2058228
# db:
altered.
1600000
1944514 +/- 248253
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 5557
Number of reads with percent X's >= 20%: 73 = 0.3%
Number of reads with percent X's >= 50%: 50 = 0.2%
Number of reads with percent X's >= 80%: 2 = 0.0%
Total reads in project: 27074
Total bp X'd : 236587
reads >= 20% >= 50% >= 80% screened
Nr with L09136 5197 36 29 1
Nr with pCC1Fos 218 1 0 0
Nr with pMCL200_JGI_XZX+XZK 142 36 21 1
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 8268860
C = 4571536
G = 4531850
T = 8182778
N = 102283
X = 236587
GC fraction = 0.35
Total = 25893894
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634494_fasta.screen.contigs
-------------------------------------------------------------------
A 707011
C 389115
G 363524
T 720524
N 45
fraction GC = 0.35
total bases = 2180219
Libraries and Reads
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Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
-------------------------------------------------------------------
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBF reads.list > grep.reads.list.AIBF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBF 4 500
-------------------------------------------------------------------
#Found 5648 total values totalling 21061382.0000. <3728.998229 +/- 3835.056325>
#Range: [ 1116 - 282391 ]
#Most likely bin: [ 3500 - 4000 ] 2234 counts
#Median bin: [ 3500 - 4000 ] 2234 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 18 0.00 0.00 ]
|X 1500 - 2000 : [ 29 0.01 0.01 ]
|X 2000 - 2500 : [ 79 0.01 0.02 ]
|XX 2500 - 3000 : [ 135 0.02 0.05 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1768 0.31 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2234 0.40 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1282 0.23 0.98 ]
|XX 4500 - 5000 : [ 101 0.02 1.00 ]
#...
| 68000 - 68500 : [ 1 0.00 1.00 ]
#...
| 282000 - 282500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBG reads.list > grep.reads.list.AIBG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBG 4 500
-------------------------------------------------------------------
#Found 5649 total values totalling 51162745.0000. <9056.956098 +/- 2288.752675>
#Range: [ 705 - 88260 ]
#Most likely bin: [ 8500 - 9000 ] 1302 counts
#Median bin: [ 9000 - 9500 ] 1200 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 13 0.00 0.00 ]
| 1500 - 2000 : [ 7 0.00 0.00 ]
| 2000 - 2500 : [ 11 0.00 0.01 ]
|X 2500 - 3000 : [ 17 0.00 0.01 ]
|X 3000 - 3500 : [ 19 0.00 0.01 ]
|X 3500 - 4000 : [ 27 0.00 0.02 ]
|X 4000 - 4500 : [ 32 0.01 0.02 ]
|X 4500 - 5000 : [ 32 0.01 0.03 ]
|X 5000 - 5500 : [ 45 0.01 0.04 ]
|XX 5500 - 6000 : [ 63 0.01 0.05 ]
|XX 6000 - 6500 : [ 62 0.01 0.06 ]
|XX 6500 - 7000 : [ 70 0.01 0.07 ]
|XXX 7000 - 7500 : [ 83 0.01 0.09 ]
|XXXXX 7500 - 8000 : [ 157 0.03 0.11 ]
|XXXXXXXXXXXXXXXX 8000 - 8500 : [ 521 0.09 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 1302 0.23 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 1200 0.21 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 884 0.16 0.80 ]
|XXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 630 0.11 0.92 ]
|XXXXXXXXXXX 10500 - 11000 : [ 349 0.06 0.98 ]
|XXXX 11000 - 11500 : [ 117 0.02 1.00 ]
| 11500 - 12000 : [ 1 0.00 1.00 ]
#...
| 37500 - 38000 : [ 1 0.00 1.00 ]
#...
| 49000 - 49500 : [ 1 0.00 1.00 ]
#...
| 50000 - 50500 : [ 1 0.00 1.00 ]
#...
| 66500 - 67000 : [ 1 0.00 1.00 ]
#...
| 77000 - 77500 : [ 1 0.00 1.00 ]
#...
| 88000 - 88500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBH reads.list > grep.reads.list.AIBH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBH 4 500
-------------------------------------------------------------------
#Found 240 total values totalling 8714542.0000. <36310.591667 +/- 4171.956629>
#Range: [ 21558 - 46425 ]
#Most likely bin: [ 36500 - 37000 ] 19 counts
#Median bin: [ 36000 - 36500 ] 10 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 21500 - 22000 : [ 1 0.00 0.00 ]
#...
|XX 24000 - 24500 : [ 1 0.00 0.01 ]
#...
|XX 25500 - 26000 : [ 1 0.00 0.01 ]
#...
|XXXX 26500 - 27000 : [ 2 0.01 0.02 ]
|XXXX 27000 - 27500 : [ 2 0.01 0.03 ]
#...
|XXXXXX 28000 - 28500 : [ 3 0.01 0.04 ]
#...
|XXXXXX 29000 - 29500 : [ 3 0.01 0.05 ]
|XX 29500 - 30000 : [ 1 0.00 0.06 ]
|XXXX 30000 - 30500 : [ 2 0.01 0.07 ]
|XXXXXXXX 30500 - 31000 : [ 4 0.02 0.08 ]
|XXXX 31000 - 31500 : [ 2 0.01 0.09 ]
|XXXXXXXXXXX 31500 - 32000 : [ 5 0.02 0.11 ]
|XXXXXXXXXXXXXXX 32000 - 32500 : [ 7 0.03 0.14 ]
|XXXXXXXXXXXXXXX 32500 - 33000 : [ 7 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 13 0.05 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 14 0.06 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 11 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 13 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 12 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 12 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 10 0.04 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 19 0.08 0.60 ]
|XXXXXXXXXXXXXXXXX 37000 - 37500 : [ 8 0.03 0.64 ]
|XXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 10 0.04 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 13 0.05 0.73 ]
|XXXXXX 38500 - 39000 : [ 3 0.01 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 11 0.05 0.79 ]
|XXXXXXXXXXXXXXXXX 39500 - 40000 : [ 8 0.03 0.82 ]
|XXXXXXXXXXXXX 40000 - 40500 : [ 6 0.03 0.85 ]
|XXXXXXXXXXX 40500 - 41000 : [ 5 0.02 0.87 ]
|XXXXXXXX 41000 - 41500 : [ 4 0.02 0.89 ]
|XXXXXX 41500 - 42000 : [ 3 0.01 0.90 ]
|XXXX 42000 - 42500 : [ 2 0.01 0.91 ]
|XXXXXXXXXXX 42500 - 43000 : [ 5 0.02 0.93 ]
|XXXXXX 43000 - 43500 : [ 3 0.01 0.94 ]
|XXXX 43500 - 44000 : [ 2 0.01 0.95 ]
|XXXXXX 44000 - 44500 : [ 3 0.01 0.96 ]
|XXXXXXXXXXX 44500 - 45000 : [ 5 0.02 0.98 ]
|XX 45000 - 45500 : [ 1 0.00 0.99 ]
|XXXX 45500 - 46000 : [ 2 0.01 1.00 ]
|XX 46000 - 46500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIBG 8932 +- 1458 (n=2620)
# AIBF 3558 +- 508 (n=2789)
# AIBH 36197 +- 4054 (n=108)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634494_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
AIBF 13824 -1 -1 96 723 13728 89 699 92 705
AIBG 18048 -1 -1 95 668 17379 77 655 88 637
AIBH 1536 -1 -1 66 373 1536 60 585 66 560
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIBF 6871 90 697 92 713 6857 88 700 91 696
AIBG 9088 70 665 83 628 8291 85 647 93 645
AIBH 768 50 568 57 544 768 69 597 76 572
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634494_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
72 12307 6593 91.57 95.38 AIBF @
92 13817 7817 84.97 88.51 AIBG @
8 950 567 70.88 73.83 AIBH @
] 27074 14977 87.08 cumulative total@@
LIBRARY PLATE ID COUNT [ AIBF 72 AIBG 92 AIBH 8 ] for 172 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 3634494_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 32643 total values totalling 17894884.0000. <548.199737 +/- 305.943593>
#Range: [ 0 - 914 ]
#Most likely bin: [ 750 - 800 ] 6020 counts
#Median bin: [ 650 - 700 ] 2357 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 5506 0.17 0.17 ]
|XXXX 50 - 100 : [ 675 0.02 0.19 ]
|XXX 100 - 150 : [ 480 0.01 0.20 ]
|XXX 150 - 200 : [ 480 0.01 0.22 ]
|XXX 200 - 250 : [ 482 0.01 0.23 ]
|XXX 250 - 300 : [ 471 0.01 0.25 ]
|XXX 300 - 350 : [ 512 0.02 0.26 ]
|XXXX 350 - 400 : [ 553 0.02 0.28 ]
|XXXX 400 - 450 : [ 565 0.02 0.30 ]
|XXXX 450 - 500 : [ 673 0.02 0.32 ]
|XXXXXX 500 - 550 : [ 868 0.03 0.35 ]
|XXXXXXXX 550 - 600 : [ 1172 0.04 0.38 ]
|XXXXXXXXXXX 600 - 650 : [ 1598 0.05 0.43 ]
|XXXXXXXXXXXXXXXX 650 - 700 : [ 2357 0.07 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3714 0.11 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6020 0.18 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5475 0.17 0.97 ]
|XXXXXXX 850 - 900 : [ 1031 0.03 1.00 ]
| 900 - 950 : [ 11 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBF 3634494_fasta.screen.trimQ15.SaF > reads.trim15.AIBF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBF.rl 2 50
-------------------------------------------------------------------
#Found 13728 total values totalling 8536879.0000. <621.858902 +/- 261.716025>
#Range: [ 0 - 914 ]
#Most likely bin: [ 750 - 800 ] 3165 counts
#Median bin: [ 700 - 750 ] 2020 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXX 0 - 50 : [ 1364 0.10 0.10 ]
|XX 50 - 100 : [ 174 0.01 0.11 ]
|XX 100 - 150 : [ 155 0.01 0.12 ]
|XX 150 - 200 : [ 127 0.01 0.13 ]
|XX 200 - 250 : [ 131 0.01 0.14 ]
|XX 250 - 300 : [ 140 0.01 0.15 ]
|XX 300 - 350 : [ 157 0.01 0.16 ]
|XX 350 - 400 : [ 182 0.01 0.18 ]
|XX 400 - 450 : [ 176 0.01 0.19 ]
|XXX 450 - 500 : [ 245 0.02 0.21 ]
|XXX 500 - 550 : [ 270 0.02 0.23 ]
|XXXXX 550 - 600 : [ 429 0.03 0.26 ]
|XXXXXXXXX 600 - 650 : [ 731 0.05 0.31 ]
|XXXXXXXXXXXXXXXX 650 - 700 : [ 1301 0.09 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2020 0.15 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3165 0.23 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2559 0.19 0.97 ]
|XXXXX 850 - 900 : [ 398 0.03 1.00 ]
| 900 - 950 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBG 3634494_fasta.screen.trimQ15.SaF > reads.trim15.AIBG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBG.rl 2 50
-------------------------------------------------------------------
#Found 17379 total values totalling 8814225.0000. <507.176765 +/- 321.964430>
#Range: [ 0 - 912 ]
#Most likely bin: [ 0 - 50 ] 3572 counts
#Median bin: [ 650 - 700 ] 901 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 3572 0.21 0.21 ]
|XXXXX 50 - 100 : [ 453 0.03 0.23 ]
|XXX 100 - 150 : [ 300 0.02 0.25 ]
|XXXX 150 - 200 : [ 325 0.02 0.27 ]
|XXXX 200 - 250 : [ 326 0.02 0.29 ]
|XXX 250 - 300 : [ 301 0.02 0.30 ]
|XXXX 300 - 350 : [ 328 0.02 0.32 ]
|XXXX 350 - 400 : [ 346 0.02 0.34 ]
|XXXX 400 - 450 : [ 355 0.02 0.36 ]
|XXXX 450 - 500 : [ 394 0.02 0.39 ]
|XXXXXX 500 - 550 : [ 538 0.03 0.42 ]
|XXXXXXXX 550 - 600 : [ 671 0.04 0.46 ]
|XXXXXXXXX 600 - 650 : [ 772 0.04 0.50 ]
|XXXXXXXXXX 650 - 700 : [ 901 0.05 0.55 ]
|XXXXXXXXXXXXXXXXX 700 - 750 : [ 1506 0.09 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2757 0.16 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2894 0.17 0.96 ]
|XXXXXXX 850 - 900 : [ 633 0.04 1.00 ]
| 900 - 950 : [ 7 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBH 3634494_fasta.screen.trimQ15.SaF > reads.trim15.AIBH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBH.rl 2 50
-------------------------------------------------------------------
#Found 1536 total values totalling 543780.0000. <354.023438 +/- 314.534392>
#Range: [ 0 - 846 ]
#Most likely bin: [ 0 - 50 ] 570 counts
#Median bin: [ 350 - 400 ] 25 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 570 0.37 0.37 ]
|XXX 50 - 100 : [ 48 0.03 0.40 ]
|XX 100 - 150 : [ 25 0.02 0.42 ]
|XX 150 - 200 : [ 28 0.02 0.44 ]
|XX 200 - 250 : [ 25 0.02 0.45 ]
|XX 250 - 300 : [ 30 0.02 0.47 ]
|XX 300 - 350 : [ 27 0.02 0.49 ]
|XX 350 - 400 : [ 25 0.02 0.51 ]
|XX 400 - 450 : [ 34 0.02 0.53 ]
|XX 450 - 500 : [ 34 0.02 0.55 ]
|XXXX 500 - 550 : [ 60 0.04 0.59 ]
|XXXXX 550 - 600 : [ 72 0.05 0.64 ]
|XXXXXXX 600 - 650 : [ 95 0.06 0.70 ]
|XXXXXXXXXXX 650 - 700 : [ 155 0.10 0.80 ]
|XXXXXXXXXXXXX 700 - 750 : [ 188 0.12 0.92 ]
|XXXXXXX 750 - 800 : [ 98 0.06 0.99 ]
|XX 800 - 850 : [ 22 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATTA
trimt JAZZ trim 15 readlength histogram for ATTB
trimt JAZZ trim 15 readlength histogram for ATTC
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634494
-------------------------------------------------------------------
AIBF.000001.000100 pUC18.fa LRS.fasta
AIBG.000001.000100 pMCL200.fa LRS.fasta
AIBG.000101.000200 pMCL200.fa LRS.fasta
AIBH.000001.000100 pCC1Fos.fa LRS.fasta
ATTB.000001.000100 LRS.fasta
ATTC.000001.000100
AIBF.000001.000100 pUC18.fa LRS.fasta
AIBG.000001.000100 pMCL200.fa LRS.fasta
AIBG.000101.000200 pMCL200.fa LRS.fasta
AIBH.000001.000100 pCC1Fos.fa LRS.fasta
ATTB.000001.000100 LRS.fasta
ATTC.000001.000100
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634494_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634494_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 26901 total values totalling 9300.4767. <0.345730 +/- 0.041784>
#Range: [ 0.0882 - 0.7027 ]
#Most likely bin: [ 0.35 - 0.355 ] 1518 counts
#Median bin: [ 0.345 - 0.35 ] 1472 counts
| 0.085 - 0.09 : [ 1 0.00 0.00 ]
#...
| 0.135 - 0.14 : [ 1 0.00 0.00 ]
| 0.14 - 0.145 : [ 1 0.00 0.00 ]
| 0.145 - 0.15 : [ 2 0.00 0.00 ]
| 0.15 - 0.155 : [ 1 0.00 0.00 ]
| 0.155 - 0.16 : [ 2 0.00 0.00 ]
| 0.16 - 0.165 : [ 2 0.00 0.00 ]
| 0.165 - 0.17 : [ 2 0.00 0.00 ]
| 0.17 - 0.175 : [ 3 0.00 0.00 ]
| 0.175 - 0.18 : [ 3 0.00 0.00 ]
| 0.18 - 0.185 : [ 5 0.00 0.00 ]
| 0.185 - 0.19 : [ 3 0.00 0.00 ]
| 0.19 - 0.195 : [ 5 0.00 0.00 ]
| 0.195 - 0.2 : [ 7 0.00 0.00 ]
| 0.2 - 0.205 : [ 13 0.00 0.00 ]
| 0.205 - 0.21 : [ 9 0.00 0.00 ]
| 0.21 - 0.215 : [ 14 0.00 0.00 ]
| 0.215 - 0.22 : [ 16 0.00 0.00 ]
|X 0.22 - 0.225 : [ 19 0.00 0.00 ]
|X 0.225 - 0.23 : [ 25 0.00 0.00 ]
|X 0.23 - 0.235 : [ 24 0.00 0.01 ]
|X 0.235 - 0.24 : [ 37 0.00 0.01 ]
|XX 0.24 - 0.245 : [ 69 0.00 0.01 ]
|XX 0.245 - 0.25 : [ 68 0.00 0.01 ]
|XX 0.25 - 0.255 : [ 92 0.00 0.02 ]
|XXX 0.255 - 0.26 : [ 107 0.00 0.02 ]
|XXX 0.26 - 0.265 : [ 130 0.00 0.02 ]
|XXXX 0.265 - 0.27 : [ 142 0.01 0.03 ]
|XXXXX 0.27 - 0.275 : [ 202 0.01 0.04 ]
|XXXXXX 0.275 - 0.28 : [ 228 0.01 0.05 ]
|XXXXXXXX 0.28 - 0.285 : [ 289 0.01 0.06 ]
|XXXXXXXXXX 0.285 - 0.29 : [ 398 0.01 0.07 ]
|XXXXXXXXXXXXX 0.29 - 0.295 : [ 481 0.02 0.09 ]
|XXXXXXXXXXXXXXX 0.295 - 0.3 : [ 574 0.02 0.11 ]
|XXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 703 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 842 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 960 0.04 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 1112 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 1187 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 1255 0.05 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 1423 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 1493 0.06 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 1478 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 1472 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 1518 0.06 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 1310 0.05 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 1303 0.05 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 1228 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 1089 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 996 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 902 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 717 0.03 0.89 ]
|XXXXXXXXXXXXXXX 0.39 - 0.395 : [ 573 0.02 0.91 ]
|XXXXXXXXXXXX 0.395 - 0.4 : [ 446 0.02 0.93 ]
|XXXXXXXXXX 0.4 - 0.405 : [ 388 0.01 0.94 ]
|XXXXXXXX 0.405 - 0.41 : [ 288 0.01 0.95 ]
|XXXXXX 0.41 - 0.415 : [ 235 0.01 0.96 ]
|XXXX 0.415 - 0.42 : [ 170 0.01 0.97 ]
|XXX 0.42 - 0.425 : [ 112 0.00 0.97 ]
|XX 0.425 - 0.43 : [ 85 0.00 0.98 ]
|XX 0.43 - 0.435 : [ 67 0.00 0.98 ]
|XX 0.435 - 0.44 : [ 65 0.00 0.98 ]
|X 0.44 - 0.445 : [ 49 0.00 0.98 ]
|X 0.445 - 0.45 : [ 28 0.00 0.98 ]
|X 0.45 - 0.455 : [ 32 0.00 0.99 ]
|X 0.455 - 0.46 : [ 34 0.00 0.99 ]
| 0.46 - 0.465 : [ 16 0.00 0.99 ]
|X 0.465 - 0.47 : [ 26 0.00 0.99 ]
|X 0.47 - 0.475 : [ 22 0.00 0.99 ]
|X 0.475 - 0.48 : [ 27 0.00 0.99 ]
|X 0.48 - 0.485 : [ 28 0.00 0.99 ]
|X 0.485 - 0.49 : [ 27 0.00 0.99 ]
|X 0.49 - 0.495 : [ 29 0.00 0.99 ]
|X 0.495 - 0.5 : [ 27 0.00 0.99 ]
|X 0.5 - 0.505 : [ 37 0.00 1.00 ]
| 0.505 - 0.51 : [ 17 0.00 1.00 ]
| 0.51 - 0.515 : [ 9 0.00 1.00 ]
| 0.515 - 0.52 : [ 18 0.00 1.00 ]
| 0.52 - 0.525 : [ 16 0.00 1.00 ]
| 0.525 - 0.53 : [ 3 0.00 1.00 ]
| 0.53 - 0.535 : [ 2 0.00 1.00 ]
| 0.535 - 0.54 : [ 4 0.00 1.00 ]
| 0.54 - 0.545 : [ 8 0.00 1.00 ]
| 0.545 - 0.55 : [ 11 0.00 1.00 ]
| 0.55 - 0.555 : [ 7 0.00 1.00 ]
| 0.555 - 0.56 : [ 3 0.00 1.00 ]
| 0.56 - 0.565 : [ 10 0.00 1.00 ]
| 0.565 - 0.57 : [ 7 0.00 1.00 ]
| 0.57 - 0.575 : [ 2 0.00 1.00 ]
| 0.575 - 0.58 : [ 1 0.00 1.00 ]
| 0.58 - 0.585 : [ 2 0.00 1.00 ]
| 0.585 - 0.59 : [ 1 0.00 1.00 ]
| 0.59 - 0.595 : [ 1 0.00 1.00 ]
| 0.595 - 0.6 : [ 1 0.00 1.00 ]
#...
| 0.605 - 0.61 : [ 1 0.00 1.00 ]
#...
| 0.62 - 0.625 : [ 1 0.00 1.00 ]
#...
| 0.63 - 0.635 : [ 1 0.00 1.00 ]
#...
| 0.7 - 0.705 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 8. 65 reads; 7657 bp (untrimmed), 7452 (trimmed).
Contig 9. 67 reads; 6291 bp (untrimmed), 6079 (trimmed).
Contig 10. 86 reads; 8363 bp (untrimmed), 8260 (trimmed).
Contig 11. 104 reads; 8248 bp (untrimmed), 8163 (trimmed).
Contig 12. 139 reads; 15714 bp (untrimmed), 15691 (trimmed).
Contig 13. 141 reads; 17662 bp (untrimmed), 17655 (trimmed).
Contig 14. 254 reads; 21047 bp (untrimmed), 20996 (trimmed).
Contig 15. 269 reads; 33191 bp (untrimmed), 32965 (trimmed).
Contig 16. 420 reads; 46134 bp (untrimmed), 45872 (trimmed).
Contig 17. 465 reads; 38596 bp (untrimmed), 38369 (trimmed).
Contig 18. 469 reads; 41629 bp (untrimmed), 41451 (trimmed).
Contig 19. 653 reads; 62893 bp (untrimmed), 62599 (trimmed).
Contig 20. 663 reads; 54081 bp (untrimmed), 53922 (trimmed).
Contig 21. 713 reads; 61629 bp (untrimmed), 61485 (trimmed).
Contig 22. 726 reads; 58883 bp (untrimmed), 58551 (trimmed).
Contig 23. 763 reads; 61700 bp (untrimmed), 61071 (trimmed).
Contig 24. 803 reads; 62151 bp (untrimmed), 62099 (trimmed).
Contig 25. 1036 reads; 83589 bp (untrimmed), 83549 (trimmed).
Contig 26. 1110 reads; 85480 bp (untrimmed), 85431 (trimmed).
Contig 27. 1292 reads; 115206 bp (untrimmed), 115122 (trimmed).
Contig 28. 1307 reads; 106360 bp (untrimmed), 106280 (trimmed).
Contig 29. 1308 reads; 117501 bp (untrimmed), 117297 (trimmed).
Contig 30. 1371 reads; 109843 bp (untrimmed), 109743 (trimmed).
Contig 31. 1585 reads; 120561 bp (untrimmed), 120537 (trimmed).
Contig 32. 2195 reads; 173173 bp (untrimmed), 173173 (trimmed).
Contig 33. 2208 reads; 188434 bp (untrimmed), 188213 (trimmed).
Contig 34. 6753 reads; 458011 bp (untrimmed), 457967 (trimmed).
--------------------------------------------------------------
Totals 27060 reads; 2180219 bp (untrimmed), 2175314 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2179564 bases = 11.00 +- 4.92 = 0.19 +- 3.98
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 33 total values totalling 302.0700. <9.153636 +/- 2.613579>
#Range: [ 2.32 - 13.09 ]
#Most likely bin: [ 10.5 - 11 ] 6 counts
#Median bin: [ 10 - 10.5 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 2 - 2.5 : [ 1 0.03 0.03 ]
#...
|XXXXXXXXXXXXX 3 - 3.5 : [ 2 0.06 0.09 ]
#...
|XXXXXXX 4.5 - 5 : [ 1 0.03 0.12 ]
#...
|XXXXXXX 6 - 6.5 : [ 1 0.03 0.15 ]
#...
|XXXXXXXXXXXXX 7 - 7.5 : [ 2 0.06 0.21 ]
|XXXXXXXXXXXXX 7.5 - 8 : [ 2 0.06 0.27 ]
|XXXXXXX 8 - 8.5 : [ 1 0.03 0.30 ]
|XXXXXXX 8.5 - 9 : [ 1 0.03 0.33 ]
|XXXXXXXXXXXXX 9 - 9.5 : [ 2 0.06 0.39 ]
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 3 0.09 0.48 ]
|XXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 3 0.09 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 6 0.18 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 5 0.15 0.91 ]
|XXXXXXXXXXXXX 11.5 - 12 : [ 2 0.06 0.97 ]
#...
|XXXXXXX 13 - 13.5 : [ 1 0.03 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 31 total values totalling 296.5800. <9.567097 +/- 2.106934>
#Range: [ 3.48 - 13.09 ]
#Most likely bin: [ 10.5 - 11 ] 6 counts
#Median bin: [ 10 - 10.5 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 3 - 3.5 : [ 1 0.03 0.03 ]
#...
|XXXXXXX 4.5 - 5 : [ 1 0.03 0.06 ]
#...
|XXXXXXX 6 - 6.5 : [ 1 0.03 0.10 ]
#...
|XXXXXXXXXXXXX 7 - 7.5 : [ 2 0.06 0.16 ]
|XXXXXXXXXXXXX 7.5 - 8 : [ 2 0.06 0.23 ]
|XXXXXXX 8 - 8.5 : [ 1 0.03 0.26 ]
|XXXXXXX 8.5 - 9 : [ 1 0.03 0.29 ]
|XXXXXXXXXXXXX 9 - 9.5 : [ 2 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 3 0.10 0.45 ]
|XXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 3 0.10 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 6 0.19 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 5 0.16 0.90 ]
|XXXXXXXXXXXXX 11.5 - 12 : [ 2 0.06 0.97 ]
#...
|XXXXXXX 13 - 13.5 : [ 1 0.03 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 2 4 reads 1526 bases = 2.32 +- 1.14 = 2.32 +- 1.14
Contig 3 5 reads 1477 bases = 3.17 +- 1.52 = 3.17 +- 1.52
Contig 4 11 reads 2685 bases = 3.48 +- 2.15 = 3.48 +- 2.15
Contig 5 19 reads 3608 bases = 4.63 +- 2.86 = 0.39 +- 1.87
Contig 6 26 reads 3619 bases = 6.38 +- 2.67 = 1.64 +- 3.61
Contig 13 141 reads 17662 bases = 7.13 +- 2.58 = 1.14 +- 2.91
Contig 15 269 reads 33191 bases = 7.16 +- 3.32 = 0.49 +- 2.94
Contig 8 65 reads 7657 bases = 7.74 +- 3.28 = 1.02 +- 2.50
Contig 12 139 reads 15714 bases = 7.78 +- 2.81 = 0.19 +- 4.52
Contig 16 420 reads 46134 bases = 8.05 +- 3.01 = 0.18 +- 3.66
Contig 10 86 reads 8363 bases = 8.52 +- 3.47 = 4.20 +- 3.42
Contig 19 653 reads 62893 bases = 9.28 +- 4.00 = 0.21 +- 3.93
Contig 9 67 reads 6291 bases = 9.48 +- 3.72 = 0.71 +- 4.31
Contig 7 29 reads 2622 bases = 9.73 +- 8.02 = 9.73 +- 8.02
Contig 29 1308 reads 117501 bases = 9.80 +- 3.92 = 0.41 +- 3.53
Contig 18 469 reads 41629 bases = 9.97 +- 3.70 = 0.02 +- 3.33
Contig 27 1292 reads 115206 bases = 10.03 +- 4.01 = 0.04 +- 3.82
Contig 21 713 reads 61629 bases = 10.24 +- 3.55 = 0.13 +- 4.03
Contig 33 2208 reads 188434 bases = 10.31 +- 3.93 = 0.01 +- 3.74
Contig 17 465 reads 38596 bases = 10.52 +- 4.21 = 0.72 +- 3.55
Contig 7 29 reads 2622 bases = 9.73 +- 8.02 = 9.73 +- 8.02
Contig 29 1308 reads 117501 bases = 9.80 +- 3.92 = 0.41 +- 3.53
Contig 18 469 reads 41629 bases = 9.97 +- 3.70 = 0.02 +- 3.33
Contig 27 1292 reads 115206 bases = 10.03 +- 4.01 = 0.04 +- 3.82
Contig 21 713 reads 61629 bases = 10.24 +- 3.55 = 0.13 +- 4.03
Contig 33 2208 reads 188434 bases = 10.31 +- 3.93 = 0.01 +- 3.74
Contig 17 465 reads 38596 bases = 10.52 +- 4.21 = 0.72 +- 3.55
Contig 20 663 reads 54081 bases = 10.65 +- 4.05 = 0.14 +- 4.04
Contig 14 254 reads 21047 bases = 10.71 +- 4.62 = 0.53 +- 5.19
Contig 28 1307 reads 106360 bases = 10.84 +- 3.94 = 0.05 +- 3.80
Contig 22 726 reads 58883 bases = 10.94 +- 4.20 = 0.44 +- 4.47
Contig 23 763 reads 61700 bases = 10.98 +- 4.00 = -0.04 +- 4.00
Contig 30 1371 reads 109843 bases = 11.03 +- 4.00 = 0.13 +- 3.84
Contig 25 1036 reads 83589 bases = 11.04 +- 3.64 = 0.07 +- 3.91
Contig 11 104 reads 8248 bases = 11.19 +- 4.48 = 0.37 +- 2.50
Contig 32 2195 reads 173173 bases = 11.26 +- 3.92 = 0.03 +- 3.52
Contig 24 803 reads 62151 bases = 11.44 +- 3.77 = 0.44 +- 3.93
Contig 26 1110 reads 85480 bases = 11.51 +- 3.96 = 0.04 +- 4.02
Contig 31 1585 reads 120561 bases = 11.67 +- 5.16 = 0.15 +- 4.19
Contig 34 6753 reads 458011 bases = 13.09 +- 6.72 = 0.08 +- 4.37
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 736
HQ Discrepant reads = 27
Chimeric reads = 73
Suspect alignments = 199
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 3.57 SUN/Ultra-2/3
Equivalent to Phil Green's version 0.990329
Score matrix (set by value of penalty: -2)
A C G T N X
A 1 -2 -2 -2 0 -3
C -2 1 -2 -2 0 -3
G -2 -2 1 -2 0 -3
T -2 -2 -2 1 0 -3
N 0 0 0 0 0 0
X -3 -3 -3 -3 0 -3
gap_init: -4
gap_ext: -3
ins_gap_ext: -3
del_gap_ext: -3
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 30
maxmatch: 55
max_group_size: 20
minscore: 55
bandwidth: 14
indexwordsize: 10
vector_bound: 20
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 13
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -5
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/finished2/microbe/3634494/edit_dir.25Aug04.QD