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
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Project Size(KB) TaxID GenusSpecies
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Prochlorococcus_marinus
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Prochlorococcus marinus, species, cyanobacteria
Prochlorococcus, genus, cyanobacteria
Prochlorococcaceae, family, cyanobacteria
Prochlorales (prochlorophytes), order, cyanobacteria
Cyanobacteria (blue-green algae), phylum, cyanobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 1718670
# phrap: 1648034
# db:
altered.
1683352 +/- 35318
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 1339
Number of reads with percent X's >= 20%: 320 = 1.4%
Number of reads with percent X's >= 50%: 215 = 0.9%
Number of reads with percent X's >= 80%: 31 = 0.1%
Total reads in project: 23088
Total bp X'd : 216252
reads >= 20% >= 50% >= 80% screened
Nr with pCC1Fos 946 0 0 0
Nr with pMCL200_JGI_XZX+XZK 393 320 215 31
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 162
Number of reads with percent X's >= 20%: 4 = 0.6%
Number of reads with percent X's >= 50%: 3 = 0.4%
Number of reads with percent X's >= 80%: 1 = 0.1%
Total reads in project: 668
Total bp X'd : 8662
reads >= 20% >= 50% >= 80% screened
Nr with pCC1Fos 158 0 0 0
Nr with pMCL200_JGI_XZX+XZK 4 4 3 1
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 7282247
C = 3645139
G = 3651872
T = 7313803
N = 106147
X = 216252
GC fraction = 0.33
Total = 22215460
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436089_fasta.screen.contigs
-------------------------------------------------------------------
A 584265
C 265608
G 273395
T 596215
N 7
fraction GC = 0.31
total bases = 1719490
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 ACCW reads.list > grep.reads.list.ACCW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACCW 4 500
-------------------------------------------------------------------
#Found 4488 total values totalling 19735408.0000. <4397.372549 +/- 20846.253850>
#Range: [ 861 - 691109 ]
#Most likely bin: [ 3000 - 3500 ] 1880 counts
#Median bin: [ 3000 - 3500 ] 1880 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 8 0.00 0.00 ]
|X 1000 - 1500 : [ 67 0.01 0.02 ]
|XX 1500 - 2000 : [ 77 0.02 0.03 ]
|XX 2000 - 2500 : [ 108 0.02 0.06 ]
|XXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 1001 0.22 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1880 0.42 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1135 0.25 0.95 ]
|XXXX 4000 - 4500 : [ 192 0.04 1.00 ]
#...
| 14000 - 14500 : [ 1 0.00 1.00 ]
#...
| 37000 - 37500 : [ 1 0.00 1.00 ]
#...
| 52500 - 53000 : [ 1 0.00 1.00 ]
#...
| 133500 - 134000 : [ 1 0.00 1.00 ]
#...
| 142000 - 142500 : [ 1 0.00 1.00 ]
#...
| 182000 - 182500 : [ 1 0.00 1.00 ]
#...
| 185500 - 186000 : [ 1 0.00 1.00 ]
#...
| 196000 - 196500 : [ 1 0.00 1.00 ]
#...
| 199000 - 199500 : [ 1 0.00 1.00 ]
#...
| 202500 - 203000 : [ 1 0.00 1.00 ]
#...
| 224500 - 225000 : [ 1 0.00 1.00 ]
#...
| 263000 - 263500 : [ 1 0.00 1.00 ]
#...
| 282000 - 282500 : [ 1 0.00 1.00 ]
#...
| 301000 - 301500 : [ 1 0.00 1.00 ]
#...
| 342000 - 342500 : [ 1 0.00 1.00 ]
#...
| 407500 - 408000 : [ 1 0.00 1.00 ]
#...
| 417500 - 418000 : [ 1 0.00 1.00 ]
#...
| 493500 - 494000 : [ 1 0.00 1.00 ]
#...
| 538500 - 539000 : [ 1 0.00 1.00 ]
#...
| 691000 - 691500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACCX reads.list > grep.reads.list.ACCX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACCX 4 500
-------------------------------------------------------------------
#Found 4721 total values totalling 29671676.0000. <6285.040458 +/- 18131.073682>
#Range: [ 146 - 692597 ]
#Most likely bin: [ 5000 - 5500 ] 1391 counts
#Median bin: [ 5000 - 5500 ] 1391 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 7 0.00 0.00 ]
| 500 - 1000 : [ 2 0.00 0.00 ]
| 1000 - 1500 : [ 9 0.00 0.00 ]
|X 1500 - 2000 : [ 20 0.00 0.01 ]
| 2000 - 2500 : [ 16 0.00 0.01 ]
|X 2500 - 3000 : [ 35 0.01 0.02 ]
|X 3000 - 3500 : [ 22 0.00 0.02 ]
|XX 3500 - 4000 : [ 84 0.02 0.04 ]
|XXXXXXX 4000 - 4500 : [ 228 0.05 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 970 0.21 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5000 - 5500 : [ 1391 0.29 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1045 0.22 0.81 ]
|XXXXXXXXXXXXXXXX 6000 - 6500 : [ 540 0.11 0.93 ]
|XXXXXXXX 6500 - 7000 : [ 274 0.06 0.98 ]
|X 7000 - 7500 : [ 51 0.01 0.99 ]
| 7500 - 8000 : [ 6 0.00 1.00 ]
| 8000 - 8500 : [ 3 0.00 1.00 ]
#...
| 17500 - 18000 : [ 1 0.00 1.00 ]
#...
| 52000 - 52500 : [ 1 0.00 1.00 ]
#...
| 74000 - 74500 : [ 1 0.00 1.00 ]
#...
| 134500 - 135000 : [ 1 0.00 1.00 ]
#...
| 159000 - 159500 : [ 1 0.00 1.00 ]
#...
| 181500 - 182000 : [ 1 0.00 1.00 ]
#...
| 209000 - 209500 : [ 1 0.00 1.00 ]
#...
| 212500 - 213000 : [ 1 0.00 1.00 ]
#...
| 215500 - 216000 : [ 1 0.00 1.00 ]
#...
| 224000 - 224500 : [ 1 0.00 1.00 ]
#...
| 253000 - 253500 : [ 1 0.00 1.00 ]
#...
| 261500 - 262000 : [ 1 0.00 1.00 ]
#...
| 333000 - 333500 : [ 1 0.00 1.00 ]
#...
| 334000 - 334500 : [ 1 0.00 1.00 ]
#...
| 342000 - 342500 : [ 1 0.00 1.00 ]
#...
| 356000 - 356500 : [ 1 0.00 1.00 ]
#...
| 501000 - 501500 : [ 1 0.00 1.00 ]
#...
| 692500 - 693000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACCY reads.list > grep.reads.list.ACCY
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACCY 4 500
-------------------------------------------------------------------
#Found 818 total values totalling 30503032.0000. <37289.770171 +/- 3089.874734>
#Range: [ 26152 - 46098 ]
#Most likely bin: [ 37000 - 37500 ] 58 counts
#Median bin: [ 37000 - 37500 ] 58 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 26000 - 26500 : [ 1 0.00 0.00 ]
#...
|X 27000 - 27500 : [ 1 0.00 0.00 ]
|X 27500 - 28000 : [ 2 0.00 0.00 ]
|X 28000 - 28500 : [ 1 0.00 0.01 ]
|X 28500 - 29000 : [ 1 0.00 0.01 ]
|X 29000 - 29500 : [ 2 0.00 0.01 ]
|X 29500 - 30000 : [ 1 0.00 0.01 ]
|XXX 30000 - 30500 : [ 4 0.00 0.02 ]
|X 30500 - 31000 : [ 2 0.00 0.02 ]
|X 31000 - 31500 : [ 2 0.00 0.02 ]
|XXXXX 31500 - 32000 : [ 7 0.01 0.03 ]
|XXXXXXXXXXX 32000 - 32500 : [ 16 0.02 0.05 ]
|XXXXXXXXXXX 32500 - 33000 : [ 16 0.02 0.07 ]
|XXXXXXXXXXXXXXXX 33000 - 33500 : [ 23 0.03 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 36 0.04 0.14 ]
|XXXXXXXXXXXXXXXX 34000 - 34500 : [ 23 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 48 0.06 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 53 0.06 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 49 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 55 0.07 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 40 0.05 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 58 0.07 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 55 0.07 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 56 0.07 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 38 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 30 0.04 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 41 0.05 0.81 ]
|XXXXXXXXXXXXXXXXX 40000 - 40500 : [ 24 0.03 0.84 ]
|XXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 29 0.04 0.87 ]
|XXXXXXXXXXXXXX 41000 - 41500 : [ 21 0.03 0.90 ]
|XXXXXXXXXXXXXXXXX 41500 - 42000 : [ 25 0.03 0.93 ]
|XXXXXXXXXX 42000 - 42500 : [ 15 0.02 0.95 ]
|XXXXXXXX 42500 - 43000 : [ 12 0.01 0.96 ]
|XXXXXXXX 43000 - 43500 : [ 11 0.01 0.98 ]
|XXXXXX 43500 - 44000 : [ 8 0.01 0.99 ]
|XXXXX 44000 - 44500 : [ 7 0.01 0.99 ]
|X 44500 - 45000 : [ 2 0.00 1.00 ]
|X 45000 - 45500 : [ 1 0.00 1.00 ]
|X 45500 - 46000 : [ 1 0.00 1.00 ]
|X 46000 - 46500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# ACCW 3100 +- 1013 (n=2310)
# ACCX 5282 +- 863 (n=2371)
# ACCY 37264 +- 3142 (n=411)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436089_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
ACCW 11520 -1 -1 97 748 10188 100 748 100 754
ACCX 13824 -1 -1 97 750 10352 100 757 100 758
ACCY 2688 -1 -1 99 718 2548 99 724 100 735
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
ACCW 5256 100 738 100 744 4932 100 759 100 765
ACCX 5258 99 752 100 754 5094 100 761 100 762
ACCY 1455 99 733 100 730 1093 99 711 100 742
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436089_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 23088 12199 82.43 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 3436089_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 23088 total values totalling 17224958.0000. <746.056739 +/- 127.258062>
#Range: [ 22 - 923 ]
#Most likely bin: [ 800 - 850 ] 7407 counts
#Median bin: [ 750 - 800 ] 7068 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 27 0.00 0.00 ]
| 50 - 100 : [ 85 0.00 0.00 ]
|X 100 - 150 : [ 114 0.00 0.01 ]
|X 150 - 200 : [ 94 0.00 0.01 ]
|X 200 - 250 : [ 96 0.00 0.02 ]
|X 250 - 300 : [ 127 0.01 0.02 ]
|X 300 - 350 : [ 142 0.01 0.03 ]
|X 350 - 400 : [ 157 0.01 0.04 ]
|X 400 - 450 : [ 163 0.01 0.04 ]
|X 450 - 500 : [ 195 0.01 0.05 ]
|XX 500 - 550 : [ 288 0.01 0.06 ]
|XX 550 - 600 : [ 406 0.02 0.08 ]
|XXXX 600 - 650 : [ 747 0.03 0.11 ]
|XXXXXXXXX 650 - 700 : [ 1595 0.07 0.18 ]
|XXXXXXXXXXXXXXXXX 700 - 750 : [ 3124 0.14 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 7068 0.31 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7407 0.32 0.95 ]
|XXXXXXX 850 - 900 : [ 1237 0.05 1.00 ]
| 900 - 950 : [ 16 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ANNH
trimt JAZZ trim 15 readlength histogram for ACCW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACCW 3436089_fasta.screen.trimQ15.SaF > reads.trim15.ACCW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACCW.rl 2 50
-------------------------------------------------------------------
#Found 10188 total values totalling 7594934.0000. <745.478406 +/- 126.054703>
#Range: [ 27 - 911 ]
#Most likely bin: [ 750 - 800 ] 3304 counts
#Median bin: [ 750 - 800 ] 3304 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 10 0.00 0.00 ]
| 50 - 100 : [ 32 0.00 0.00 ]
|X 100 - 150 : [ 49 0.00 0.01 ]
|X 150 - 200 : [ 43 0.00 0.01 ]
|X 200 - 250 : [ 48 0.00 0.02 ]
|X 250 - 300 : [ 51 0.01 0.02 ]
|X 300 - 350 : [ 62 0.01 0.03 ]
|X 350 - 400 : [ 68 0.01 0.04 ]
|X 400 - 450 : [ 73 0.01 0.04 ]
|X 450 - 500 : [ 99 0.01 0.05 ]
|XX 500 - 550 : [ 141 0.01 0.07 ]
|XX 550 - 600 : [ 186 0.02 0.08 ]
|XXXX 600 - 650 : [ 327 0.03 0.12 ]
|XXXXXXXX 650 - 700 : [ 671 0.07 0.18 ]
|XXXXXXXXXXXXXXXX 700 - 750 : [ 1312 0.13 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3304 0.32 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3256 0.32 0.96 ]
|XXXXX 850 - 900 : [ 452 0.04 1.00 ]
| 900 - 950 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACCX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACCX 3436089_fasta.screen.trimQ15.SaF > reads.trim15.ACCX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACCX.rl 2 50
-------------------------------------------------------------------
#Found 10352 total values totalling 7799632.0000. <753.442040 +/- 130.721868>
#Range: [ 22 - 923 ]
#Most likely bin: [ 800 - 850 ] 3916 counts
#Median bin: [ 750 - 800 ] 2867 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 7 0.00 0.00 ]
| 50 - 100 : [ 43 0.00 0.00 ]
|X 100 - 150 : [ 56 0.01 0.01 ]
| 150 - 200 : [ 43 0.00 0.01 ]
| 200 - 250 : [ 40 0.00 0.02 ]
|X 250 - 300 : [ 64 0.01 0.02 ]
|X 300 - 350 : [ 69 0.01 0.03 ]
|X 350 - 400 : [ 70 0.01 0.04 ]
|X 400 - 450 : [ 77 0.01 0.05 ]
|X 450 - 500 : [ 87 0.01 0.05 ]
|X 500 - 550 : [ 127 0.01 0.07 ]
|XX 550 - 600 : [ 189 0.02 0.08 ]
|XXX 600 - 650 : [ 314 0.03 0.11 ]
|XXXXXX 650 - 700 : [ 614 0.06 0.17 ]
|XXXXXXXXXX 700 - 750 : [ 985 0.10 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2867 0.28 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3916 0.38 0.92 ]
|XXXXXXXX 850 - 900 : [ 772 0.07 1.00 ]
| 900 - 950 : [ 12 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACCY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACCY 3436089_fasta.screen.trimQ15.SaF > reads.trim15.ACCY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACCY.rl 2 50
-------------------------------------------------------------------
#Found 2548 total values totalling 1830392.0000. <718.364207 +/- 113.106797>
#Range: [ 26 - 878 ]
#Most likely bin: [ 750 - 800 ] 897 counts
#Median bin: [ 700 - 750 ] 827 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 10 0.00 0.00 ]
| 50 - 100 : [ 10 0.00 0.01 ]
| 100 - 150 : [ 9 0.00 0.01 ]
| 150 - 200 : [ 8 0.00 0.01 ]
| 200 - 250 : [ 8 0.00 0.02 ]
|X 250 - 300 : [ 12 0.00 0.02 ]
| 300 - 350 : [ 11 0.00 0.03 ]
|X 350 - 400 : [ 19 0.01 0.03 ]
|X 400 - 450 : [ 13 0.01 0.04 ]
| 450 - 500 : [ 9 0.00 0.04 ]
|X 500 - 550 : [ 20 0.01 0.05 ]
|X 550 - 600 : [ 31 0.01 0.06 ]
|XXXXX 600 - 650 : [ 106 0.04 0.10 ]
|XXXXXXXXXXXXXX 650 - 700 : [ 310 0.12 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 827 0.32 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 897 0.35 0.90 ]
|XXXXXXXXXX 800 - 850 : [ 235 0.09 0.99 ]
|X 850 - 900 : [ 13 0.01 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436089
-------------------------------------------------------------------
ACCW.000001.000100 pMCL200.fa LRS.fasta
ACCX.000001.000100 pMCL200.fa LRS.fasta
ACCY.000001.000100 pCC1Fos.fa.4 LRS.fasta
ACCW.000001.000100 pMCL200.fa LRS.fasta
ACCX.000001.000100 pMCL200.fa LRS.fasta
ACCY.000001.000100 pCC1Fos.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436089_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436089_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 23053 total values totalling 7498.1103. <0.325255 +/- 0.062591>
#Range: [ 0.1428 - 0.7575 ]
#Most likely bin: [ 0.32 - 0.325 ] 1131 counts
#Median bin: [ 0.315 - 0.32 ] 1041 counts
| 0.14 - 0.145 : [ 2 0.00 0.00 ]
| 0.145 - 0.15 : [ 1 0.00 0.00 ]
| 0.15 - 0.155 : [ 2 0.00 0.00 ]
| 0.155 - 0.16 : [ 1 0.00 0.00 ]
| 0.16 - 0.165 : [ 1 0.00 0.00 ]
| 0.165 - 0.17 : [ 1 0.00 0.00 ]
| 0.17 - 0.175 : [ 3 0.00 0.00 ]
| 0.175 - 0.18 : [ 4 0.00 0.00 ]
| 0.18 - 0.185 : [ 7 0.00 0.00 ]
| 0.185 - 0.19 : [ 10 0.00 0.00 ]
| 0.19 - 0.195 : [ 9 0.00 0.00 ]
|X 0.195 - 0.2 : [ 15 0.00 0.00 ]
|X 0.2 - 0.205 : [ 20 0.00 0.00 ]
|X 0.205 - 0.21 : [ 37 0.00 0.00 ]
|XX 0.21 - 0.215 : [ 48 0.00 0.01 ]
|XXX 0.215 - 0.22 : [ 71 0.00 0.01 ]
|XXX 0.22 - 0.225 : [ 90 0.00 0.01 ]
|XXXX 0.225 - 0.23 : [ 114 0.00 0.02 ]
|XXXXX 0.23 - 0.235 : [ 140 0.01 0.02 ]
|XXXXXXX 0.235 - 0.24 : [ 186 0.01 0.03 ]
|XXXXXXX 0.24 - 0.245 : [ 187 0.01 0.04 ]
|XXXXXXXX 0.245 - 0.25 : [ 214 0.01 0.05 ]
|XXXXXXXXXXX 0.25 - 0.255 : [ 322 0.01 0.06 ]
|XXXXXXXXXXXXX 0.255 - 0.26 : [ 375 0.02 0.08 ]
|XXXXXXXXXXXXXXXX 0.26 - 0.265 : [ 460 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXX 0.265 - 0.27 : [ 537 0.02 0.12 ]
|XXXXXXXXXXXXXXXXXXXXX 0.27 - 0.275 : [ 594 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.275 - 0.28 : [ 692 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.28 - 0.285 : [ 837 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.285 - 0.29 : [ 857 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 927 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.295 - 0.3 : [ 962 0.04 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 1010 0.04 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 1022 0.04 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 1007 0.04 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 1041 0.05 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 1131 0.05 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 1063 0.05 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 999 0.04 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 941 0.04 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 975 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 793 0.03 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 673 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 632 0.03 0.82 ]
|XXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 565 0.02 0.85 ]
|XXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 522 0.02 0.87 ]
|XXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 451 0.02 0.89 ]
|XXXXXXXXXXXXX 0.375 - 0.38 : [ 354 0.02 0.91 ]
|XXXXXXXXX 0.38 - 0.385 : [ 266 0.01 0.92 ]
|XXXXXXXX 0.385 - 0.39 : [ 223 0.01 0.93 ]
|XXXXXXX 0.39 - 0.395 : [ 196 0.01 0.94 ]
|XXXX 0.395 - 0.4 : [ 127 0.01 0.94 ]
|XXXX 0.4 - 0.405 : [ 115 0.00 0.95 ]
|XXX 0.405 - 0.41 : [ 88 0.00 0.95 ]
|XXX 0.41 - 0.415 : [ 84 0.00 0.95 ]
|XXX 0.415 - 0.42 : [ 72 0.00 0.96 ]
|X 0.42 - 0.425 : [ 40 0.00 0.96 ]
|X 0.425 - 0.43 : [ 22 0.00 0.96 ]
|X 0.43 - 0.435 : [ 28 0.00 0.96 ]
|X 0.435 - 0.44 : [ 17 0.00 0.96 ]
|X 0.44 - 0.445 : [ 28 0.00 0.96 ]
|X 0.445 - 0.45 : [ 17 0.00 0.96 ]
|X 0.45 - 0.455 : [ 17 0.00 0.96 ]
| 0.455 - 0.46 : [ 11 0.00 0.97 ]
|X 0.46 - 0.465 : [ 17 0.00 0.97 ]
| 0.465 - 0.47 : [ 13 0.00 0.97 ]
|X 0.47 - 0.475 : [ 18 0.00 0.97 ]
| 0.475 - 0.48 : [ 11 0.00 0.97 ]
| 0.48 - 0.485 : [ 4 0.00 0.97 ]
| 0.485 - 0.49 : [ 9 0.00 0.97 ]
|X 0.49 - 0.495 : [ 15 0.00 0.97 ]
| 0.495 - 0.5 : [ 8 0.00 0.97 ]
|X 0.5 - 0.505 : [ 16 0.00 0.97 ]
| 0.505 - 0.51 : [ 13 0.00 0.97 ]
| 0.51 - 0.515 : [ 14 0.00 0.97 ]
|X 0.515 - 0.52 : [ 17 0.00 0.97 ]
|X 0.52 - 0.525 : [ 19 0.00 0.97 ]
|X 0.525 - 0.53 : [ 23 0.00 0.97 ]
|X 0.53 - 0.535 : [ 22 0.00 0.97 ]
| 0.535 - 0.54 : [ 13 0.00 0.98 ]
|X 0.54 - 0.545 : [ 19 0.00 0.98 ]
|X 0.545 - 0.55 : [ 28 0.00 0.98 ]
| 0.55 - 0.555 : [ 14 0.00 0.98 ]
| 0.555 - 0.56 : [ 14 0.00 0.98 ]
|X 0.56 - 0.565 : [ 20 0.00 0.98 ]
|X 0.565 - 0.57 : [ 18 0.00 0.98 ]
|X 0.57 - 0.575 : [ 20 0.00 0.98 ]
|X 0.575 - 0.58 : [ 29 0.00 0.98 ]
|XX 0.58 - 0.585 : [ 48 0.00 0.98 ]
|X 0.585 - 0.59 : [ 30 0.00 0.99 ]
|X 0.59 - 0.595 : [ 34 0.00 0.99 ]
|X 0.595 - 0.6 : [ 31 0.00 0.99 ]
|X 0.6 - 0.605 : [ 33 0.00 0.99 ]
|X 0.605 - 0.61 : [ 29 0.00 0.99 ]
|X 0.61 - 0.615 : [ 35 0.00 0.99 ]
|X 0.615 - 0.62 : [ 28 0.00 0.99 ]
|X 0.62 - 0.625 : [ 23 0.00 1.00 ]
|X 0.625 - 0.63 : [ 20 0.00 1.00 ]
|X 0.63 - 0.635 : [ 21 0.00 1.00 ]
|X 0.635 - 0.64 : [ 17 0.00 1.00 ]
| 0.64 - 0.645 : [ 13 0.00 1.00 ]
| 0.645 - 0.65 : [ 9 0.00 1.00 ]
| 0.65 - 0.655 : [ 6 0.00 1.00 ]
| 0.655 - 0.66 : [ 7 0.00 1.00 ]
| 0.66 - 0.665 : [ 6 0.00 1.00 ]
| 0.665 - 0.67 : [ 3 0.00 1.00 ]
| 0.67 - 0.675 : [ 2 0.00 1.00 ]
| 0.675 - 0.68 : [ 3 0.00 1.00 ]
| 0.68 - 0.685 : [ 2 0.00 1.00 ]
#...
| 0.695 - 0.7 : [ 1 0.00 1.00 ]
#...
| 0.715 - 0.72 : [ 1 0.00 1.00 ]
#...
| 0.755 - 0.76 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
--------------------------------------------------------------
Contig 1. 2 reads; 884 bp (untrimmed), 864 (trimmed).
Contig 2. 3 reads; 1803 bp (untrimmed), 1744 (trimmed).
Contig 3. 3 reads; 1758 bp (untrimmed), 1503 (trimmed).
Contig 4. 3 reads; 1970 bp (untrimmed), 1723 (trimmed).
Contig 5. 3 reads; 1674 bp (untrimmed), 1522 (trimmed).
Contig 6. 7 reads; 98 bp (untrimmed), 98 (trimmed).
Contig 7. 13 reads; 146 bp (untrimmed), 146 (trimmed).
Contig 8. 20 reads; 254 bp (untrimmed), 254 (trimmed).
Contig 9. 23 reads; 867 bp (untrimmed), 848 (trimmed).
Contig 10. 10730 reads; 840654 bp (untrimmed), 840598 (trimmed).
Contig 11. 11613 reads; 869382 bp (untrimmed), 869370 (trimmed).
--------------------------------------------------------------
Totals 22420 reads; 1719490 bp (untrimmed), 1718670 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 1796845 bases = 11.38 +- 4.81 = 0.01 +- 3.65
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 65 total values totalling 166.2100. <2.557077 +/- 3.766530>
#Range: [ 1.04 - 23.69 ]
#Most likely bin: [ 1 - 1.5 ] 38 counts
#Median bin: [ 1 - 1.5 ] 38 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 38 0.58 0.58 ]
|XXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 20 0.31 0.89 ]
#...
|X 3.5 - 4 : [ 1 0.02 0.91 ]
#...
|X 7.5 - 8 : [ 1 0.02 0.92 ]
#...
|XX 11.5 - 12 : [ 2 0.03 0.95 ]
|X 12 - 12.5 : [ 1 0.02 0.97 ]
|X 12.5 - 13 : [ 1 0.02 0.98 ]
#...
|X 23.5 - 24 : [ 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 3 total values totalling 36.4300. <12.143333 +/- 0.558231>
#Range: [ 11.57 - 12.90 ]
#Most likely bin: [ 11.5 - 12 ] 2 counts
#Median bin: [ 11.5 - 12 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 2 0.67 0.67 ]
#...
|XXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 1 0.33 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 48 2 reads 1904 bases = 1.04 +- 0.19 = 1.04 +- 0.19
Contig 51 2 reads 1829 bases = 1.04 +- 0.20 = 0.01 +- 0.98
Contig 47 2 reads 1796 bases = 1.06 +- 0.24 = 1.06 +- 0.24
Contig 20 2 reads 1701 bases = 1.08 +- 0.27 = 1.08 +- 0.27
Contig 40 2 reads 1688 bases = 1.09 +- 0.29 = -0.06 +- 0.95
Contig 65 2 reads 1694 bases = 1.10 +- 0.30 = 1.10 +- 0.30
Contig 72 2 reads 1605 bases = 1.10 +- 0.29 = 0.06 +- 0.95
Contig 4 2 reads 1778 bases = 1.11 +- 0.31 = -0.05 +- 0.94
Contig 8 2 reads 1666 bases = 1.13 +- 0.33 = -0.02 +- 0.93
Contig 19 2 reads 1562 bases = 1.14 +- 0.35 = -0.14 +- 0.92
Contig 32 2 reads 1634 bases = 1.14 +- 0.35 = 1.14 +- 0.35
Contig 22 2 reads 1568 bases = 1.15 +- 0.35 = 0.04 +- 0.92
Contig 31 2 reads 1518 bases = 1.20 +- 0.40 = 0.02 +- 0.90
Contig 23 2 reads 1662 bases = 1.21 +- 0.41 = 0.02 +- 0.89
Contig 43 2 reads 1539 bases = 1.22 +- 0.42 = 0.01 +- 0.88
Contig 34 2 reads 1546 bases = 1.23 +- 0.42 = -0.06 +- 0.87
Contig 10 2 reads 1544 bases = 1.25 +- 0.43 = 1.25 +- 0.43
Contig 42 2 reads 1429 bases = 1.25 +- 0.43 = 1.25 +- 0.43
Contig 16 2 reads 1506 bases = 1.31 +- 0.46 = -0.04 +- 0.83
Contig 13 2 reads 1357 bases = 1.32 +- 0.47 = 1.32 +- 0.47
Contig 54 2 reads 1168 bases = 1.61 +- 0.49 = -0.03 +- 0.62
Contig 63 2 reads 1137 bases = 1.63 +- 0.48 = 1.63 +- 0.48
Contig 30 2 reads 1099 bases = 1.65 +- 0.48 = 1.65 +- 0.48
Contig 74 3 reads 1758 bases = 1.70 +- 0.69 = 1.70 +- 0.69
Contig 76 3 reads 1674 bases = 1.71 +- 0.68 = 0.55 +- 0.50
Contig 45 2 reads 1074 bases = 1.74 +- 0.44 = 1.74 +- 0.44
Contig 12 2 reads 1044 bases = 1.80 +- 0.40 = 1.80 +- 0.40
Contig 39 2 reads 1106 bases = 1.80 +- 0.40 = 1.80 +- 0.40
Contig 70 2 reads 1077 bases = 1.86 +- 0.34 = -0.03 +- 0.37
Contig 58 2 reads 959 bases = 1.91 +- 0.29 = 1.91 +- 0.29
Contig 71 2 reads 902 bases = 1.95 +- 0.22 = 1.95 +- 0.22
Contig 36 2 reads 961 bases = 1.96 +- 0.20 = 0.04 +- 0.20
Contig 59 2 reads 1000 bases = 1.98 +- 0.14 = 1.98 +- 0.14
Contig 82 25 reads 1007 bases = 3.57 +- 7.29 = 3.57 +- 7.29
Contig 78 10 reads 997 bases = 7.99 +- 1.83 = 0.23 +- 1.39
Contig 87 11737 reads 840718 bases = 11.57 +- 4.28 = -0.02 +- 3.62
Contig 86 10509 reads 712430 bases = 11.96 +- 4.52 = -0.05 +- 3.86
Contig 83 26 reads 781 bases = 12.04 +- 9.10 = 5.37 +- 1.02
Contig 85 2264 reads 158391 bases = 12.90 +- 3.94 = 0.02 +- 3.59
Contig 81 24 reads 750 bases = 23.69 +- 1.42 = 0.05 +- 1.43
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 442
HQ Discrepant reads = 0
Chimeric reads = 26
Suspect alignments = 166
-------------------------------------------------------------------
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/finished1/microbe/3436089/edit_dir.02Mar04.QD