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
3634493 2000 39765 Thiomicrospira crunogena
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Thiomicrospira_crunogena
-------------------------------------------------------------------
Piscirickettsiaceae, family, g-proteobacteria
Thiotrichales, order, g-proteobacteria
Thiomicrospira crunogena, species, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Thiomicrospira, genus, g-proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2396877
# phrap: 2287771
# db:
altered.
2000000
2228216 +/- 167407
-------------------------------------------------------------------
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: 45759
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: 16
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 12215106
C = 9286804
G = 9367032
T = 12052418
N = 179578
X = 503612
GC fraction = 0.43
Total = 43604550
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634493_fasta.screen.contigs
-------------------------------------------------------------------
A 681884
C 517190
G 519103
T 684572
N 142
fraction GC = 0.43
total bases = 2402891
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 AIBA reads.list > grep.reads.list.AIBA
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBA 4 500
-------------------------------------------------------------------
#Found 145 total values totalling 533162.0000. <3676.979310 +/- 562.661575>
#Range: [ 1684 - 5038 ]
#Most likely bin: [ 3000 - 3500 ] 54 counts
#Median bin: [ 3500 - 4000 ] 42 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1500 - 2000 : [ 1 0.01 0.01 ]
|X 2000 - 2500 : [ 2 0.01 0.02 ]
|XXX 2500 - 3000 : [ 4 0.03 0.05 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 54 0.37 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 42 0.29 0.71 ]
|XXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 29 0.20 0.91 ]
|XXXXXXXXX 4500 - 5000 : [ 12 0.08 0.99 ]
|X 5000 - 5500 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBB reads.list > grep.reads.list.AIBB
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBB 4 500
-------------------------------------------------------------------
#Found 134 total values totalling 830797.0000. <6199.977612 +/- 1057.573656>
#Range: [ 967 - 8017 ]
#Most likely bin: [ 6000 - 6500 ] 38 counts
#Median bin: [ 6000 - 6500 ] 38 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 1 0.01 0.01 ]
#...
|XX 2000 - 2500 : [ 2 0.01 0.02 ]
#...
|X 3000 - 3500 : [ 1 0.01 0.03 ]
#...
|XXXXXXX 4000 - 4500 : [ 7 0.05 0.08 ]
|XX 4500 - 5000 : [ 2 0.01 0.10 ]
|XXXXXX 5000 - 5500 : [ 6 0.04 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 21 0.16 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 38 0.28 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 31 0.23 0.81 ]
|XXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 18 0.13 0.95 ]
|XXXXXX 7500 - 8000 : [ 6 0.04 0.99 ]
|X 8000 - 8500 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBC reads.list > grep.reads.list.AIBC
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBC 4 500
-------------------------------------------------------------------
#Found 12 total values totalling 420818.0000. <35068.166667 +/- 2705.235721>
#Range: [ 30404 - 40914 ]
#Most likely bin: [ 36500 - 37000 ] 2 counts
#Median bin: [ 34000 - 34500 ] 1 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 30000 - 30500 : [ 1 0.08 0.08 ]
#...
|XXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 1 0.08 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 2 0.17 0.33 ]
|XXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 1 0.08 0.42 ]
|XXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 1 0.08 0.50 ]
|XXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 1 0.08 0.58 ]
#...
|XXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 1 0.08 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 2 0.17 0.83 ]
#...
|XXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 1 0.08 0.92 ]
#...
|XXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 1 0.08 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIBC 35542 +- 3373 (n=375)
# AIBA 3608 +- 827 (n=4718)
# AIBB 6266 +- 1268 (n=4931)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634493_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
AIBA 22272 -1 -1 98 719 20686 99 667 100 674
AIBB 26112 -1 -1 95 692 22861 100 733 100 730
AIBC 3072 -1 -1 90 583 2212 99 701 100 718
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIBA 10455 99 653 100 667 10231 99 681 100 682
AIBB 11391 100 730 100 728 11470 100 735 100 732
AIBC 1106 99 723 100 720 1106 99 678 100 716
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634493_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 45759 22459 89.12 cumulative total @@
LIBRARY PLATE ID COUNT [ AIBA 112 AIBB 128 AIBC 12 ] for 252 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 3634493_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 45759 total values totalling 31930601.0000. <697.799362 +/- 137.602474>
#Range: [ 14 - 905 ]
#Most likely bin: [ 750 - 800 ] 13297 counts
#Median bin: [ 700 - 750 ] 10497 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 54 0.00 0.00 ]
|X 50 - 100 : [ 205 0.00 0.01 ]
|X 100 - 150 : [ 285 0.01 0.01 ]
|X 150 - 200 : [ 322 0.01 0.02 ]
|X 200 - 250 : [ 283 0.01 0.03 ]
|X 250 - 300 : [ 339 0.01 0.03 ]
|X 300 - 350 : [ 410 0.01 0.04 ]
|X 350 - 400 : [ 469 0.01 0.05 ]
|XX 400 - 450 : [ 627 0.01 0.07 ]
|XX 450 - 500 : [ 721 0.02 0.08 ]
|XXX 500 - 550 : [ 1032 0.02 0.10 ]
|XXXXX 550 - 600 : [ 1783 0.04 0.14 ]
|XXXXXXXXX 600 - 650 : [ 3114 0.07 0.21 ]
|XXXXXXXXXXXXXXXXX 650 - 700 : [ 5638 0.12 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 10497 0.23 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 13297 0.29 0.85 ]
|XXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6182 0.14 0.99 ]
|XX 850 - 900 : [ 500 0.01 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOUX
trimt JAZZ trim 15 readlength histogram for AIBA
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBA 3634493_fasta.screen.trimQ15.SaF > reads.trim15.AIBA.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBA.rl 2 50
-------------------------------------------------------------------
#Found 20686 total values totalling 13694495.0000. <662.017548 +/- 146.114930>
#Range: [ 26 - 905 ]
#Most likely bin: [ 700 - 750 ] 4636 counts
#Median bin: [ 700 - 750 ] 4636 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 23 0.00 0.00 ]
|X 50 - 100 : [ 138 0.01 0.01 ]
|X 100 - 150 : [ 161 0.01 0.02 ]
|XX 150 - 200 : [ 176 0.01 0.02 ]
|X 200 - 250 : [ 156 0.01 0.03 ]
|XX 250 - 300 : [ 196 0.01 0.04 ]
|XX 300 - 350 : [ 263 0.01 0.05 ]
|XX 350 - 400 : [ 288 0.01 0.07 ]
|XXXX 400 - 450 : [ 421 0.02 0.09 ]
|XXXX 450 - 500 : [ 517 0.02 0.11 ]
|XXXXXX 500 - 550 : [ 731 0.04 0.15 ]
|XXXXXXXXXXXX 550 - 600 : [ 1338 0.06 0.21 ]
|XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2298 0.11 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3538 0.17 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4636 0.22 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4043 0.20 0.91 ]
|XXXXXXXXXXXXXX 800 - 850 : [ 1619 0.08 0.99 ]
|X 850 - 900 : [ 143 0.01 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBB
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBB 3634493_fasta.screen.trimQ15.SaF > reads.trim15.AIBB.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBB.rl 2 50
-------------------------------------------------------------------
#Found 22861 total values totalling 16700367.0000. <730.517781 +/- 119.932767>
#Range: [ 14 - 899 ]
#Most likely bin: [ 750 - 800 ] 8571 counts
#Median bin: [ 750 - 800 ] 8571 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 22 0.00 0.00 ]
| 50 - 100 : [ 54 0.00 0.00 ]
|X 100 - 150 : [ 110 0.00 0.01 ]
|X 150 - 200 : [ 138 0.01 0.01 ]
|X 200 - 250 : [ 119 0.01 0.02 ]
|X 250 - 300 : [ 118 0.01 0.02 ]
|X 300 - 350 : [ 122 0.01 0.03 ]
|X 350 - 400 : [ 148 0.01 0.04 ]
|X 400 - 450 : [ 172 0.01 0.04 ]
|X 450 - 500 : [ 182 0.01 0.05 ]
|X 500 - 550 : [ 246 0.01 0.06 ]
|XX 550 - 600 : [ 373 0.02 0.08 ]
|XXX 600 - 650 : [ 666 0.03 0.11 ]
|XXXXXXXXX 650 - 700 : [ 1842 0.08 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5334 0.23 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8571 0.37 0.80 ]
|XXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4302 0.19 0.99 ]
|XX 850 - 900 : [ 342 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBC
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBC 3634493_fasta.screen.trimQ15.SaF > reads.trim15.AIBC.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBC.rl 2 50
-------------------------------------------------------------------
#Found 2212 total values totalling 1535739.0000. <694.276221 +/- 142.581895>
#Range: [ 21 - 880 ]
#Most likely bin: [ 750 - 800 ] 683 counts
#Median bin: [ 700 - 750 ] 527 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 9 0.00 0.00 ]
|X 50 - 100 : [ 13 0.01 0.01 ]
|X 100 - 150 : [ 14 0.01 0.02 ]
| 150 - 200 : [ 8 0.00 0.02 ]
| 200 - 250 : [ 8 0.00 0.02 ]
|X 250 - 300 : [ 25 0.01 0.03 ]
|X 300 - 350 : [ 25 0.01 0.05 ]
|XX 350 - 400 : [ 33 0.01 0.06 ]
|XX 400 - 450 : [ 34 0.02 0.08 ]
|X 450 - 500 : [ 22 0.01 0.09 ]
|XXX 500 - 550 : [ 55 0.02 0.11 ]
|XXXX 550 - 600 : [ 72 0.03 0.14 ]
|XXXXXXXXX 600 - 650 : [ 150 0.07 0.21 ]
|XXXXXXXXXXXXXXX 650 - 700 : [ 258 0.12 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 527 0.24 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 683 0.31 0.88 ]
|XXXXXXXXXXXXXXX 800 - 850 : [ 261 0.12 0.99 ]
|X 850 - 900 : [ 15 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOPA
trimt JAZZ trim 15 readlength histogram for APZA
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634493
-------------------------------------------------------------------
AIBA.000001.000100 pUC18.fa LRS.fasta
AIBA.000101.000200 pUC18.fa LRS.fasta
AIBB.000001.000100 pMCL200.fa LRS.fasta
AIBB.000101.000200 pMCL200.fa LRS.fasta
AIBC.000001.000100
AIBA.000001.000100 pUC18.fa LRS.fasta
AIBA.000101.000200 pUC18.fa LRS.fasta
AIBB.000001.000100 pMCL200.fa LRS.fasta
AIBB.000101.000200 pMCL200.fa LRS.fasta
AIBC.000001.000100
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634493_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634493_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 45696 total values totalling 19614.4782. <0.429238 +/- 0.040970>
#Range: [ 0.098 - 0.6382 ]
#Most likely bin: [ 0.435 - 0.44 ] 2537 counts
#Median bin: [ 0.43 - 0.435 ] 2399 counts
| 0.095 - 0.1 : [ 1 0.00 0.00 ]
#...
| 0.125 - 0.13 : [ 1 0.00 0.00 ]
#...
| 0.14 - 0.145 : [ 1 0.00 0.00 ]
#...
| 0.2 - 0.205 : [ 1 0.00 0.00 ]
#...
| 0.22 - 0.225 : [ 2 0.00 0.00 ]
#...
| 0.23 - 0.235 : [ 1 0.00 0.00 ]
| 0.235 - 0.24 : [ 3 0.00 0.00 ]
| 0.24 - 0.245 : [ 3 0.00 0.00 ]
| 0.245 - 0.25 : [ 4 0.00 0.00 ]
| 0.25 - 0.255 : [ 7 0.00 0.00 ]
| 0.255 - 0.26 : [ 15 0.00 0.00 ]
| 0.26 - 0.265 : [ 10 0.00 0.00 ]
| 0.265 - 0.27 : [ 12 0.00 0.00 ]
| 0.27 - 0.275 : [ 8 0.00 0.00 ]
| 0.275 - 0.28 : [ 15 0.00 0.00 ]
| 0.28 - 0.285 : [ 29 0.00 0.00 ]
| 0.285 - 0.29 : [ 27 0.00 0.00 ]
| 0.29 - 0.295 : [ 31 0.00 0.00 ]
|X 0.295 - 0.3 : [ 47 0.00 0.00 ]
|X 0.3 - 0.305 : [ 45 0.00 0.01 ]
|X 0.305 - 0.31 : [ 64 0.00 0.01 ]
|X 0.31 - 0.315 : [ 95 0.00 0.01 ]
|XX 0.315 - 0.32 : [ 100 0.00 0.01 ]
|XX 0.32 - 0.325 : [ 107 0.00 0.01 ]
|XX 0.325 - 0.33 : [ 138 0.00 0.02 ]
|XX 0.33 - 0.335 : [ 142 0.00 0.02 ]
|XXX 0.335 - 0.34 : [ 213 0.00 0.02 ]
|XXXX 0.34 - 0.345 : [ 241 0.01 0.03 ]
|XXXXX 0.345 - 0.35 : [ 305 0.01 0.04 ]
|XXXXXX 0.35 - 0.355 : [ 404 0.01 0.05 ]
|XXXXXXX 0.355 - 0.36 : [ 454 0.01 0.06 ]
|XXXXXXXXXX 0.36 - 0.365 : [ 605 0.01 0.07 ]
|XXXXXXXXX 0.365 - 0.37 : [ 596 0.01 0.08 ]
|XXXXXXXXXXXXX 0.37 - 0.375 : [ 795 0.02 0.10 ]
|XXXXXXXXXXXX 0.375 - 0.38 : [ 762 0.02 0.12 ]
|XXXXXXXXXXXXXXX 0.38 - 0.385 : [ 959 0.02 0.14 ]
|XXXXXXXXXXXXXXX 0.385 - 0.39 : [ 957 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 1128 0.02 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 1366 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 1589 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 1714 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 1858 0.04 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 2067 0.05 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 2243 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 2494 0.05 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 2399 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 2537 0.06 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 2494 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 2321 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 2240 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 2057 0.05 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 1811 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 1687 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 1434 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 1182 0.03 0.92 ]
|XXXXXXXXXXXXXX 0.48 - 0.485 : [ 898 0.02 0.93 ]
|XXXXXXXXXXXX 0.485 - 0.49 : [ 774 0.02 0.95 ]
|XXXXXXXXX 0.49 - 0.495 : [ 565 0.01 0.96 ]
|XXXXXX 0.495 - 0.5 : [ 388 0.01 0.97 ]
|XXXXXX 0.5 - 0.505 : [ 366 0.01 0.98 ]
|XXX 0.505 - 0.51 : [ 213 0.00 0.99 ]
|XXX 0.51 - 0.515 : [ 163 0.00 0.99 ]
|XX 0.515 - 0.52 : [ 133 0.00 0.99 ]
|X 0.52 - 0.525 : [ 85 0.00 0.99 ]
|X 0.525 - 0.53 : [ 48 0.00 0.99 ]
|X 0.53 - 0.535 : [ 34 0.00 1.00 ]
| 0.535 - 0.54 : [ 30 0.00 1.00 ]
| 0.54 - 0.545 : [ 16 0.00 1.00 ]
| 0.545 - 0.55 : [ 11 0.00 1.00 ]
| 0.55 - 0.555 : [ 10 0.00 1.00 ]
| 0.555 - 0.56 : [ 28 0.00 1.00 ]
|X 0.56 - 0.565 : [ 70 0.00 1.00 ]
| 0.565 - 0.57 : [ 24 0.00 1.00 ]
| 0.57 - 0.575 : [ 5 0.00 1.00 ]
| 0.575 - 0.58 : [ 1 0.00 1.00 ]
| 0.58 - 0.585 : [ 4 0.00 1.00 ]
#...
| 0.59 - 0.595 : [ 1 0.00 1.00 ]
| 0.595 - 0.6 : [ 4 0.00 1.00 ]
#...
| 0.605 - 0.61 : [ 2 0.00 1.00 ]
#...
| 0.615 - 0.62 : [ 1 0.00 1.00 ]
#...
| 0.635 - 0.64 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 14. 163 reads; 13986 bp (untrimmed), 13888 (trimmed).
Contig 15. 185 reads; 15556 bp (untrimmed), 15529 (trimmed).
Contig 16. 217 reads; 12714 bp (untrimmed), 12550 (trimmed).
Contig 17. 427 reads; 28082 bp (untrimmed), 28034 (trimmed).
Contig 18. 531 reads; 33724 bp (untrimmed), 33722 (trimmed).
Contig 19. 549 reads; 33103 bp (untrimmed), 32939 (trimmed).
Contig 20. 550 reads; 30255 bp (untrimmed), 30114 (trimmed).
Contig 21. 647 reads; 34629 bp (untrimmed), 34605 (trimmed).
Contig 22. 814 reads; 44150 bp (untrimmed), 44097 (trimmed).
Contig 23. 814 reads; 38291 bp (untrimmed), 38271 (trimmed).
Contig 24. 823 reads; 54716 bp (untrimmed), 54699 (trimmed).
Contig 25. 880 reads; 48973 bp (untrimmed), 48953 (trimmed).
Contig 26. 905 reads; 40515 bp (untrimmed), 40386 (trimmed).
Contig 27. 1089 reads; 61816 bp (untrimmed), 61787 (trimmed).
Contig 28. 1129 reads; 68489 bp (untrimmed), 68312 (trimmed).
Contig 29. 1232 reads; 62369 bp (untrimmed), 62315 (trimmed).
Contig 30. 1727 reads; 102351 bp (untrimmed), 102267 (trimmed).
Contig 31. 1923 reads; 103721 bp (untrimmed), 103543 (trimmed).
Contig 32. 2160 reads; 116966 bp (untrimmed), 116658 (trimmed).
Contig 33. 2195 reads; 117713 bp (untrimmed), 117685 (trimmed).
Contig 34. 2363 reads; 124896 bp (untrimmed), 124714 (trimmed).
Contig 35. 2388 reads; 124304 bp (untrimmed), 123898 (trimmed).
Contig 36. 3325 reads; 176690 bp (untrimmed), 176667 (trimmed).
Contig 37. 3960 reads; 197985 bp (untrimmed), 197860 (trimmed).
Contig 38. 4143 reads; 229168 bp (untrimmed), 228882 (trimmed).
Contig 39. 4236 reads; 200705 bp (untrimmed), 200681 (trimmed).
Contig 40. 6217 reads; 260640 bp (untrimmed), 260416 (trimmed).
--------------------------------------------------------------
Totals 45743 reads; 2402891 bp (untrimmed), 2396877 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2410695 bases = 17.02 +- 7.62 = 0.24 +- 6.39
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 45 total values totalling 509.0500. <11.312222 +/- 6.699508>
#Range: [ 1.44 - 21.31 ]
#Most likely bin: [ 16.5 - 17 ] 6 counts
#Median bin: [ 14.5 - 15 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXX 1 - 1.5 : [ 2 0.04 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 6 0.13 0.18 ]
|XXXXXXX 2 - 2.5 : [ 1 0.02 0.20 ]
|XXXXXXX 2.5 - 3 : [ 1 0.02 0.22 ]
#...
|XXXXXXXXXXXXX 3.5 - 4 : [ 2 0.04 0.27 ]
|XXXXXXX 4 - 4.5 : [ 1 0.02 0.29 ]
#...
|XXXXXXX 5 - 5.5 : [ 1 0.02 0.31 ]
|XXXXXXX 5.5 - 6 : [ 1 0.02 0.33 ]
|XXXXXXX 6 - 6.5 : [ 1 0.02 0.36 ]
#...
|XXXXXXX 7 - 7.5 : [ 1 0.02 0.38 ]
#...
|XXXXXXXXXXXXX 10.5 - 11 : [ 2 0.04 0.42 ]
#...
|XXXXXXX 13 - 13.5 : [ 1 0.02 0.44 ]
|XXXXXXXXXXXXX 13.5 - 14 : [ 2 0.04 0.49 ]
#...
|XXXXXXXXXXXXX 14.5 - 15 : [ 2 0.04 0.53 ]
|XXXXXXXXXXXXX 15 - 15.5 : [ 2 0.04 0.58 ]
|XXXXXXX 15.5 - 16 : [ 1 0.02 0.60 ]
|XXXXXXXXXXXXXXXXXXXX 16 - 16.5 : [ 3 0.07 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 16.5 - 17 : [ 6 0.13 0.80 ]
|XXXXXXXXXXXXX 17 - 17.5 : [ 2 0.04 0.84 ]
|XXXXXXXXXXXXX 17.5 - 18 : [ 2 0.04 0.89 ]
#...
|XXXXXXX 18.5 - 19 : [ 1 0.02 0.91 ]
|XXXXXXXXXXXXX 19 - 19.5 : [ 2 0.04 0.96 ]
|XXXXXXX 19.5 - 20 : [ 1 0.02 0.98 ]
#...
|XXXXXXX 21 - 21.5 : [ 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 31 total values totalling 458.5500. <14.791935 +/- 4.173604>
#Range: [ 4.12 - 21.31 ]
#Most likely bin: [ 16.5 - 17 ] 6 counts
#Median bin: [ 16 - 16.5 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 4 - 4.5 : [ 1 0.03 0.03 ]
#...
|XXXXXXX 5 - 5.5 : [ 1 0.03 0.06 ]
#...
|XXXXXXX 6 - 6.5 : [ 1 0.03 0.10 ]
#...
|XXXXXXX 7 - 7.5 : [ 1 0.03 0.13 ]
#...
|XXXXXXXXXXXXX 10.5 - 11 : [ 2 0.06 0.19 ]
#...
|XXXXXXX 13 - 13.5 : [ 1 0.03 0.23 ]
|XXXXXXXXXXXXX 13.5 - 14 : [ 2 0.06 0.29 ]
#...
|XXXXXXXXXXXXX 14.5 - 15 : [ 2 0.06 0.35 ]
|XXXXXXXXXXXXX 15 - 15.5 : [ 2 0.06 0.42 ]
|XXXXXXX 15.5 - 16 : [ 1 0.03 0.45 ]
|XXXXXXXXXXXXXXXXXXXX 16 - 16.5 : [ 3 0.10 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 16.5 - 17 : [ 6 0.19 0.74 ]
|XXXXXXXXXXXXX 17 - 17.5 : [ 2 0.06 0.81 ]
|XXXXXXXXXXXXX 17.5 - 18 : [ 2 0.06 0.87 ]
#...
|XXXXXXX 18.5 - 19 : [ 1 0.03 0.90 ]
|XXXXXXX 19 - 19.5 : [ 1 0.03 0.94 ]
|XXXXXXX 19.5 - 20 : [ 1 0.03 0.97 ]
#...
|XXXXXXX 21 - 21.5 : [ 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 40 2 reads 1240 bases = 1.44 +- 0.50 = -0.07 +- 0.75
Contig 31 2 reads 1240 bases = 1.49 +- 0.50 = 1.49 +- 0.50
Contig 21 2 reads 1126 bases = 1.71 +- 0.45 = 1.71 +- 0.45
Contig 17 2 reads 1006 bases = 1.74 +- 0.44 = 1.74 +- 0.44
Contig 43 3 reads 1503 bases = 1.77 +- 0.85 = 1.77 +- 0.85
Contig 42 2 reads 654 bases = 1.96 +- 0.19 = -0.04 +- 0.19
Contig 5 2 reads 1003 bases = 1.97 +- 0.18 = 1.97 +- 0.18
Contig 19 2 reads 635 bases = 1.98 +- 0.13 = 0.02 +- 0.13
Contig 13 2 reads 709 bases = 2.00 +- 0.00 = 0.00 +- 0.00
Contig 49 6 reads 2027 bases = 2.63 +- 1.25 = 0.98 +- 2.09
Contig 48 6 reads 1454 bases = 3.52 +- 1.92 = 2.16 +- 2.01
Contig 50 8 reads 2011 bases = 3.55 +- 1.45 = 0.04 +- 2.45
Contig 54 13 reads 2621 bases = 4.12 +- 1.93 = 2.67 +- 1.13
Contig 55 14 reads 2459 bases = 5.01 +- 2.70 = 4.34 +- 2.61
Contig 53 9 reads 1450 bases = 5.72 +- 3.25 = 1.77 +- 1.69
Contig 56 32 reads 4374 bases = 6.33 +- 3.15 = 5.17 +- 3.25
Contig 57 53 reads 6275 bases = 7.24 +- 2.15 = 1.61 +- 6.03
Contig 59 167 reads 13986 bases = 10.53 +- 4.72 = 0.77 +- 6.29
Contig 60 189 reads 15556 bases = 10.69 +- 5.01 = 0.90 +- 5.57
Contig 69 831 reads 54716 bases = 13.48 +- 6.96 = 0.50 +- 6.18
Contig 75 1749 reads 102351 bases = 15.15 +- 5.92 = 0.28 +- 6.73
Contig 72 1104 reads 61816 bases = 15.76 +- 6.79 = 0.65 +- 6.74
Contig 70 890 reads 48973 bases = 16.15 +- 6.66 = 0.39 +- 6.47
Contig 83 4224 reads 229168 bases = 16.22 +- 6.27 = 0.08 +- 6.08
Contig 64 560 reads 30255 bases = 16.31 +- 6.59 = 0.34 +- 6.28
Contig 76 1941 reads 103721 bases = 16.54 +- 7.03 = 0.01 +- 6.81
Contig 77 2191 reads 116966 bases = 16.57 +- 7.52 = 0.28 +- 6.06
Contig 68 828 reads 44150 bases = 16.67 +- 6.28 = 0.44 +- 6.91
Contig 78 2223 reads 117713 bases = 16.71 +- 6.96 = 0.16 +- 7.28
Contig 65 660 reads 34629 bases = 16.83 +- 6.99 = 0.26 +- 6.70
Contig 81 3360 reads 176690 bases = 16.89 +- 6.67 = 0.25 +- 5.70
Contig 79 2396 reads 124896 bases = 17.01 +- 6.07 = -0.05 +- 6.22
Contig 80 2411 reads 124304 bases = 17.28 +- 6.61 = 0.12 +- 6.60
Contig 74 1316 reads 63026 bases = 17.90 +- 7.53 = 0.05 +- 7.19
Contig 82 4010 reads 197985 bases = 17.90 +- 9.45 = 0.23 +- 6.08
Contig 84 4279 reads 200705 bases = 18.88 +- 6.72 = 0.13 +- 5.91
Contig 58 165 reads 1744 bases = 19.02 +- 49.05 = 0.47 +- 6.89
Contig 67 822 reads 38291 bases = 19.07 +- 6.71 = 0.23 +- 6.24
Contig 71 915 reads 40515 bases = 19.86 +- 6.23 = 0.35 +- 4.62
Contig 85 6284 reads 260640 bases = 21.31 +- 7.92 = 0.01 +- 6.82
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 2
Chimeric reads = 65
Suspect alignments = 382
-------------------------------------------------------------------
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/microbe4/3634493/edit_dir.26Apr04.QD