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
3634488 3000 NULL Nitrosococcus oceani
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Nitrosococcus_oceani
-------------------------------------------------------------------
Chromatiales, order, g-proteobacteria
Nitrosococcus oceani, species, g-proteobacteria
Nitrosococcus, genus, g-proteobacteria
Chromatiaceae (purple sulfur bacteria), family, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3516338
# phrap: 3290679
# db:
altered.
3000000
3269005 +/- 211350
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 8473
Number of reads with percent X's >= 20%: 234 = 0.5%
Number of reads with percent X's >= 50%: 128 = 0.3%
Number of reads with percent X's >= 80%: 19 = 0.0%
Total reads in project: 51169
Total bp X'd : 411754
reads >= 20% >= 50% >= 80% screened
Nr with L09136 7857 82 35 8
Nr with pCC1Fos 356 3 3 0
Nr with pMCL200_JGI_XZX+XZK 260 149 90 11
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 6
Number of reads with percent X's >= 20%: 2 = 6.7%
Number of reads with percent X's >= 50%: 2 = 6.7%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 30
Total bp X'd : 1555
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3 0 0 0
Nr with pCC1Fos 1 0 0 0
Nr with pMCL200_JGI_XZX+XZK 2 2 2 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 12282681
C = 12329987
G = 12373876
T = 12048657
N = 213926
X = 411754
GC fraction = 0.50
Total = 49660881
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634488_fasta.screen.contigs
-------------------------------------------------------------------
A 885811
C 907884
G 865332
T 862884
N 884
fraction GC = 0.50
total bases = 3522795
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 AIAF reads.list > grep.reads.list.AIAF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAF 4 500
-------------------------------------------------------------------
#Found 8546 total values totalling 25247218.0000. <2954.273110 +/- 7373.348004>
#Range: [ 945 - 467999 ]
#Most likely bin: [ 2500 - 3000 ] 4572 counts
#Median bin: [ 2500 - 3000 ] 4572 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 34 0.00 0.00 ]
|X 1500 - 2000 : [ 71 0.01 0.01 ]
|XXXXXXXXXXXXXXX 2000 - 2500 : [ 1743 0.20 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 4572 0.53 0.75 ]
|XXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2108 0.25 1.00 ]
| 3500 - 4000 : [ 6 0.00 1.00 ]
#...
| 24500 - 25000 : [ 1 0.00 1.00 ]
#...
| 37500 - 38000 : [ 1 0.00 1.00 ]
#...
| 42500 - 43000 : [ 1 0.00 1.00 ]
#...
| 47500 - 48000 : [ 1 0.00 1.00 ]
#...
| 70500 - 71000 : [ 1 0.00 1.00 ]
#...
| 84500 - 85000 : [ 1 0.00 1.00 ]
#...
| 108000 - 108500 : [ 1 0.00 1.00 ]
#...
| 230500 - 231000 : [ 1 0.00 1.00 ]
#...
| 274500 - 275000 : [ 1 0.00 1.00 ]
#...
| 309000 - 309500 : [ 1 0.00 1.00 ]
#...
| 467500 - 468000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAG reads.list > grep.reads.list.AIAG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAG 4 500
-------------------------------------------------------------------
#Found 12354 total values totalling 96636109.0000. <7822.252631 +/- 9012.747753>
#Range: [ 804 - 600121 ]
#Most likely bin: [ 7500 - 8000 ] 3051 counts
#Median bin: [ 7500 - 8000 ] 3051 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 5 0.00 0.00 ]
|X 1000 - 1500 : [ 41 0.00 0.00 ]
|X 1500 - 2000 : [ 39 0.00 0.01 ]
|X 2000 - 2500 : [ 51 0.00 0.01 ]
|X 2500 - 3000 : [ 76 0.01 0.02 ]
|X 3000 - 3500 : [ 75 0.01 0.02 ]
|X 3500 - 4000 : [ 82 0.01 0.03 ]
|XX 4000 - 4500 : [ 123 0.01 0.04 ]
|XX 4500 - 5000 : [ 160 0.01 0.05 ]
|XX 5000 - 5500 : [ 180 0.01 0.07 ]
|XXX 5500 - 6000 : [ 259 0.02 0.09 ]
|XXXX 6000 - 6500 : [ 326 0.03 0.11 ]
|XXXXXXXX 6500 - 7000 : [ 621 0.05 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 2019 0.16 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 3051 0.25 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 2821 0.23 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 1859 0.15 0.95 ]
|XXXXXXX 9000 - 9500 : [ 516 0.04 1.00 ]
| 9500 - 10000 : [ 38 0.00 1.00 ]
#...
| 47500 - 48000 : [ 1 0.00 1.00 ]
#...
| 69500 - 70000 : [ 1 0.00 1.00 ]
#...
| 71500 - 72000 : [ 1 0.00 1.00 ]
#...
| 122000 - 122500 : [ 1 0.00 1.00 ]
#...
| 142500 - 143000 : [ 1 0.00 1.00 ]
#...
| 144000 - 144500 : [ 1 0.00 1.00 ]
#...
| 158000 - 158500 : [ 1 0.00 1.00 ]
#...
| 219500 - 220000 : [ 1 0.00 1.00 ]
#...
| 228000 - 228500 : [ 1 0.00 1.00 ]
#...
| 474000 - 474500 : [ 1 0.00 1.00 ]
#...
| 496500 - 497000 : [ 1 0.00 1.00 ]
#...
| 600000 - 600500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAH reads.list > grep.reads.list.AIAH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAH 4 500
-------------------------------------------------------------------
#Found 703 total values totalling 27362212.0000. <38922.065434 +/- 2996.580494>
#Range: [ 29577 - 46677 ]
#Most likely bin: [ 39500 - 40000 ] 54 counts
#Median bin: [ 38500 - 39000 ] 43 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 29500 - 30000 : [ 1 0.00 0.00 ]
#...
|X 30500 - 31000 : [ 1 0.00 0.00 ]
#...
|XX 31500 - 32000 : [ 3 0.00 0.01 ]
|XXXX 32000 - 32500 : [ 5 0.01 0.01 ]
|X 32500 - 33000 : [ 1 0.00 0.02 ]
|XXXXXXXX 33000 - 33500 : [ 11 0.02 0.03 ]
|XXXXXXX 33500 - 34000 : [ 10 0.01 0.05 ]
|XXXXXXXXXXXXX 34000 - 34500 : [ 17 0.02 0.07 ]
|XXXXXXXXXXXXXX 34500 - 35000 : [ 19 0.03 0.10 ]
|XXXXXXXXXXXXXXXX 35000 - 35500 : [ 21 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 33 0.05 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 31 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 42 0.06 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 43 0.06 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 49 0.07 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 38 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 43 0.06 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 31 0.04 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 54 0.08 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 42 0.06 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 31 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 31 0.04 0.79 ]
|XXXXXXXXXXXXXXXX 41500 - 42000 : [ 22 0.03 0.82 ]
|XXXXXXXXXXXXXXX 42000 - 42500 : [ 20 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 30 0.04 0.89 ]
|XXXXXXXXXXXXXXX 43000 - 43500 : [ 20 0.03 0.92 ]
|XXXXXXXXXXXXXXXXX 43500 - 44000 : [ 23 0.03 0.96 ]
|XXXXXXXXXX 44000 - 44500 : [ 13 0.02 0.97 ]
|XXXXXX 44500 - 45000 : [ 8 0.01 0.99 ]
|XXX 45000 - 45500 : [ 4 0.01 0.99 ]
|XXXX 45500 - 46000 : [ 5 0.01 1.00 ]
#...
|X 46500 - 47000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIAG 7463 +- 1372 (n=6112)
# AIAF 2705 +- 878 (n=4353)
# AIAH 38842 +- 3087 (n=347)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634488_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
AIAF 19200 -1 -1 98 756 19200 95 771 98 775
AIAG 38400 -1 -1 93 657 37747 80 610 88 619
AIAH 3072 -1 -1 83 472 3072 77 576 83 567
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIAF 9600 95 754 98 768 9600 96 788 98 781
AIAG 19039 74 592 84 597 18708 86 627 93 639
AIAH 1536 75 590 81 573 1536 79 563 86 562
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634488_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
200 30345 16801 84.00 87.51 AIAG @
16 2470 1347 84.19 87.70 AIAH @
100 18354 9223 92.23 96.07 AIAF @
] 51169 27371 86.62 cumulative total@@
LIBRARY PLATE ID COUNT [ AIAG 200 AIAH 16 AIAF 100 ] for 316 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 3634488_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 60019 total values totalling 34009999.0000. <566.653876 +/- 288.661182>
#Range: [ 0 - 931 ]
#Most likely bin: [ 750 - 800 ] 10935 counts
#Median bin: [ 650 - 700 ] 4396 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 7947 0.13 0.13 ]
|XXXXX 50 - 100 : [ 1298 0.02 0.15 ]
|XXX 100 - 150 : [ 904 0.02 0.17 ]
|XXX 150 - 200 : [ 928 0.02 0.18 ]
|XXX 200 - 250 : [ 855 0.01 0.20 ]
|XXX 250 - 300 : [ 947 0.02 0.21 ]
|XXXX 300 - 350 : [ 982 0.02 0.23 ]
|XXXX 350 - 400 : [ 992 0.02 0.25 ]
|XXXXX 400 - 450 : [ 1251 0.02 0.27 ]
|XXXXX 450 - 500 : [ 1496 0.02 0.29 ]
|XXXXXXXX 500 - 550 : [ 2122 0.04 0.33 ]
|XXXXXXXXXX 550 - 600 : [ 2614 0.04 0.37 ]
|XXXXXXXXXXXXX 600 - 650 : [ 3422 0.06 0.43 ]
|XXXXXXXXXXXXXXXX 650 - 700 : [ 4396 0.07 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6998 0.12 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 10935 0.18 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 9776 0.16 0.96 ]
|XXXXXXXX 850 - 900 : [ 2121 0.04 1.00 ]
| 900 - 950 : [ 35 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ASBI
trimt JAZZ trim 15 readlength histogram for ASNY
trimt JAZZ trim 15 readlength histogram for AIAF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAF 3634488_fasta.screen.trimQ15.SaF > reads.trim15.AIAF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAF.rl 2 50
-------------------------------------------------------------------
#Found 19200 total values totalling 14143623.0000. <736.647031 +/- 177.314955>
#Range: [ 0 - 927 ]
#Most likely bin: [ 750 - 800 ] 6235 counts
#Median bin: [ 750 - 800 ] 6235 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 0 - 50 : [ 839 0.04 0.04 ]
| 50 - 100 : [ 26 0.00 0.05 ]
| 100 - 150 : [ 24 0.00 0.05 ]
| 150 - 200 : [ 34 0.00 0.05 ]
| 200 - 250 : [ 37 0.00 0.05 ]
| 250 - 300 : [ 33 0.00 0.05 ]
| 300 - 350 : [ 29 0.00 0.05 ]
| 350 - 400 : [ 42 0.00 0.06 ]
| 400 - 450 : [ 36 0.00 0.06 ]
| 450 - 500 : [ 51 0.00 0.06 ]
|X 500 - 550 : [ 78 0.00 0.06 ]
|X 550 - 600 : [ 119 0.01 0.07 ]
|XX 600 - 650 : [ 328 0.02 0.09 ]
|XXXXXXX 650 - 700 : [ 1056 0.06 0.14 ]
|XXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3144 0.16 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6235 0.32 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5794 0.30 0.93 ]
|XXXXXXXX 850 - 900 : [ 1276 0.07 1.00 ]
| 900 - 950 : [ 19 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAG 3634488_fasta.screen.trimQ15.SaF > reads.trim15.AIAG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAG.rl 2 50
-------------------------------------------------------------------
#Found 37747 total values totalling 18489513.0000. <489.827351 +/- 296.622833>
#Range: [ 0 - 931 ]
#Most likely bin: [ 0 - 50 ] 6505 counts
#Median bin: [ 550 - 600 ] 2290 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 6505 0.17 0.17 ]
|XXXXXXX 50 - 100 : [ 1171 0.03 0.20 ]
|XXXXX 100 - 150 : [ 811 0.02 0.22 ]
|XXXXX 150 - 200 : [ 823 0.02 0.25 ]
|XXXXX 200 - 250 : [ 750 0.02 0.27 ]
|XXXXX 250 - 300 : [ 819 0.02 0.29 ]
|XXXXX 300 - 350 : [ 865 0.02 0.31 ]
|XXXXX 350 - 400 : [ 870 0.02 0.33 ]
|XXXXXXX 400 - 450 : [ 1110 0.03 0.36 ]
|XXXXXXXX 450 - 500 : [ 1349 0.04 0.40 ]
|XXXXXXXXXXXX 500 - 550 : [ 1898 0.05 0.45 ]
|XXXXXXXXXXXXXX 550 - 600 : [ 2290 0.06 0.51 ]
|XXXXXXXXXXXXXXXXX 600 - 650 : [ 2837 0.08 0.59 ]
|XXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3026 0.08 0.67 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3493 0.09 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4394 0.12 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3886 0.10 0.98 ]
|XXXXX 850 - 900 : [ 835 0.02 1.00 ]
| 900 - 950 : [ 15 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAH 3634488_fasta.screen.trimQ15.SaF > reads.trim15.AIAH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAH.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 1376863.0000. <448.197591 +/- 288.410423>
#Range: [ 0 - 919 ]
#Most likely bin: [ 0 - 50 ] 603 counts
#Median bin: [ 550 - 600 ] 205 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 603 0.20 0.20 ]
|XXXXXXX 50 - 100 : [ 101 0.03 0.23 ]
|XXXXX 100 - 150 : [ 69 0.02 0.25 ]
|XXXXX 150 - 200 : [ 71 0.02 0.27 ]
|XXXXX 200 - 250 : [ 68 0.02 0.30 ]
|XXXXXX 250 - 300 : [ 95 0.03 0.33 ]
|XXXXXX 300 - 350 : [ 88 0.03 0.36 ]
|XXXXX 350 - 400 : [ 80 0.03 0.38 ]
|XXXXXXX 400 - 450 : [ 105 0.03 0.42 ]
|XXXXXX 450 - 500 : [ 96 0.03 0.45 ]
|XXXXXXXXXX 500 - 550 : [ 146 0.05 0.50 ]
|XXXXXXXXXXXXXX 550 - 600 : [ 205 0.07 0.56 ]
|XXXXXXXXXXXXXXXXX 600 - 650 : [ 257 0.08 0.65 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 314 0.10 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 361 0.12 0.87 ]
|XXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 306 0.10 0.97 ]
|XXXXXX 800 - 850 : [ 96 0.03 1.00 ]
|X 850 - 900 : [ 10 0.00 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APYY
trimt JAZZ trim 15 readlength histogram for AZWF
trimt JAZZ trim 15 readlength histogram for AZWG
trimt JAZZ trim 15 readlength histogram for AZWH
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634488
-------------------------------------------------------------------
AIAF.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIAF.000101.000200 pUC18.fa LRS.fasta
AIAG.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIAG.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AIAG.000201.000300 pMCL200.fa LRS.fasta
AIAH.000001.000100 pCC1Fos.fa LRS.fasta
AIAF.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIAF.000101.000200 pUC18.fa LRS.fasta
AIAG.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIAG.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AIAG.000201.000300 pMCL200.fa LRS.fasta
AIAH.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634488_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634488_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 51007 total values totalling 25627.7327. <0.502436 +/- 0.052771>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.5 - 0.505 ] 2466 counts
#Median bin: [ 0.5 - 0.505 ] 2466 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.1 - 0.105 : [ 1 0.00 0.00 ]
#...
| 0.13 - 0.135 : [ 1 0.00 0.00 ]
#...
| 0.165 - 0.17 : [ 1 0.00 0.00 ]
#...
| 0.2 - 0.205 : [ 2 0.00 0.00 ]
| 0.205 - 0.21 : [ 1 0.00 0.00 ]
| 0.21 - 0.215 : [ 2 0.00 0.00 ]
| 0.215 - 0.22 : [ 1 0.00 0.00 ]
| 0.22 - 0.225 : [ 1 0.00 0.00 ]
#...
| 0.235 - 0.24 : [ 1 0.00 0.00 ]
#...
| 0.245 - 0.25 : [ 1 0.00 0.00 ]
| 0.25 - 0.255 : [ 3 0.00 0.00 ]
| 0.255 - 0.26 : [ 2 0.00 0.00 ]
| 0.26 - 0.265 : [ 1 0.00 0.00 ]
| 0.265 - 0.27 : [ 3 0.00 0.00 ]
| 0.27 - 0.275 : [ 5 0.00 0.00 ]
| 0.275 - 0.28 : [ 7 0.00 0.00 ]
| 0.28 - 0.285 : [ 6 0.00 0.00 ]
| 0.285 - 0.29 : [ 4 0.00 0.00 ]
| 0.29 - 0.295 : [ 10 0.00 0.00 ]
| 0.295 - 0.3 : [ 10 0.00 0.00 ]
| 0.3 - 0.305 : [ 12 0.00 0.00 ]
| 0.305 - 0.31 : [ 13 0.00 0.00 ]
| 0.31 - 0.315 : [ 16 0.00 0.00 ]
| 0.315 - 0.32 : [ 18 0.00 0.00 ]
| 0.32 - 0.325 : [ 25 0.00 0.00 ]
| 0.325 - 0.33 : [ 22 0.00 0.00 ]
|X 0.33 - 0.335 : [ 35 0.00 0.00 ]
| 0.335 - 0.34 : [ 27 0.00 0.00 ]
|X 0.34 - 0.345 : [ 35 0.00 0.01 ]
|X 0.345 - 0.35 : [ 53 0.00 0.01 ]
|X 0.35 - 0.355 : [ 48 0.00 0.01 ]
|X 0.355 - 0.36 : [ 66 0.00 0.01 ]
|X 0.36 - 0.365 : [ 90 0.00 0.01 ]
|XX 0.365 - 0.37 : [ 98 0.00 0.01 ]
|XX 0.37 - 0.375 : [ 102 0.00 0.01 ]
|XX 0.375 - 0.38 : [ 133 0.00 0.02 ]
|XXX 0.38 - 0.385 : [ 170 0.00 0.02 ]
|XXX 0.385 - 0.39 : [ 206 0.00 0.02 ]
|XXX 0.39 - 0.395 : [ 211 0.00 0.03 ]
|XXXX 0.395 - 0.4 : [ 241 0.00 0.03 ]
|XXXXXX 0.4 - 0.405 : [ 352 0.01 0.04 ]
|XXXXXX 0.405 - 0.41 : [ 350 0.01 0.05 ]
|XXXXXXX 0.41 - 0.415 : [ 403 0.01 0.05 ]
|XXXXXXXX 0.415 - 0.42 : [ 468 0.01 0.06 ]
|XXXXXXXXX 0.42 - 0.425 : [ 537 0.01 0.07 ]
|XXXXXXXXXX 0.425 - 0.43 : [ 624 0.01 0.09 ]
|XXXXXXXXXXX 0.43 - 0.435 : [ 680 0.01 0.10 ]
|XXXXXXXXXXXX 0.435 - 0.44 : [ 724 0.01 0.11 ]
|XXXXXXXXXXXXX 0.44 - 0.445 : [ 791 0.02 0.13 ]
|XXXXXXXXXXXXXX 0.445 - 0.45 : [ 889 0.02 0.15 ]
|XXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 1001 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 1152 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 1264 0.02 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 1458 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 1553 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 1674 0.03 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 1729 0.03 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1872 0.04 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1997 0.04 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1951 0.04 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 2466 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 2214 0.04 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 2172 0.04 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 2138 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1999 0.04 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1883 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1743 0.03 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1678 0.03 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1538 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1405 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1245 0.02 0.86 ]
|XXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1167 0.02 0.88 ]
|XXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 991 0.02 0.90 ]
|XXXXXXXXXXXXXX 0.565 - 0.57 : [ 862 0.02 0.91 ]
|XXXXXXXXXXXX 0.57 - 0.575 : [ 735 0.01 0.93 ]
|XXXXXXXXXX 0.575 - 0.58 : [ 595 0.01 0.94 ]
|XXXXXXXXX 0.58 - 0.585 : [ 539 0.01 0.95 ]
|XXXXXXX 0.585 - 0.59 : [ 443 0.01 0.96 ]
|XXXXXX 0.59 - 0.595 : [ 368 0.01 0.97 ]
|XXXXX 0.595 - 0.6 : [ 301 0.01 0.97 ]
|XXXX 0.6 - 0.605 : [ 269 0.01 0.98 ]
|XXX 0.605 - 0.61 : [ 181 0.00 0.98 ]
|XXX 0.61 - 0.615 : [ 178 0.00 0.99 ]
|XX 0.615 - 0.62 : [ 153 0.00 0.99 ]
|XX 0.62 - 0.625 : [ 125 0.00 0.99 ]
|X 0.625 - 0.63 : [ 91 0.00 0.99 ]
|X 0.63 - 0.635 : [ 75 0.00 0.99 ]
|X 0.635 - 0.64 : [ 69 0.00 1.00 ]
|X 0.64 - 0.645 : [ 41 0.00 1.00 ]
|X 0.645 - 0.65 : [ 33 0.00 1.00 ]
|X 0.65 - 0.655 : [ 31 0.00 1.00 ]
| 0.655 - 0.66 : [ 26 0.00 1.00 ]
| 0.66 - 0.665 : [ 13 0.00 1.00 ]
| 0.665 - 0.67 : [ 21 0.00 1.00 ]
| 0.67 - 0.675 : [ 9 0.00 1.00 ]
| 0.675 - 0.68 : [ 14 0.00 1.00 ]
| 0.68 - 0.685 : [ 10 0.00 1.00 ]
| 0.685 - 0.69 : [ 6 0.00 1.00 ]
| 0.69 - 0.695 : [ 4 0.00 1.00 ]
| 0.695 - 0.7 : [ 1 0.00 1.00 ]
| 0.7 - 0.705 : [ 1 0.00 1.00 ]
| 0.705 - 0.71 : [ 1 0.00 1.00 ]
| 0.71 - 0.715 : [ 2 0.00 1.00 ]
#...
| 0.72 - 0.725 : [ 4 0.00 1.00 ]
| 0.725 - 0.73 : [ 4 0.00 1.00 ]
| 0.73 - 0.735 : [ 3 0.00 1.00 ]
| 0.735 - 0.74 : [ 2 0.00 1.00 ]
#...
| 0.75 - 0.755 : [ 2 0.00 1.00 ]
#...
| 0.865 - 0.87 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 10. 17 reads; 1069 bp (untrimmed), 977 (trimmed).
Contig 11. 22 reads; 3947 bp (untrimmed), 3928 (trimmed).
Contig 12. 28 reads; 967 bp (untrimmed), 917 (trimmed).
Contig 13. 120 reads; 11924 bp (untrimmed), 11819 (trimmed).
Contig 14. 137 reads; 16791 bp (untrimmed), 16728 (trimmed).
Contig 15. 192 reads; 17180 bp (untrimmed), 17164 (trimmed).
Contig 16. 380 reads; 31711 bp (untrimmed), 31524 (trimmed).
Contig 17. 382 reads; 31498 bp (untrimmed), 31365 (trimmed).
Contig 18. 470 reads; 41142 bp (untrimmed), 40892 (trimmed).
Contig 19. 563 reads; 42667 bp (untrimmed), 42587 (trimmed).
Contig 20. 569 reads; 41630 bp (untrimmed), 41569 (trimmed).
Contig 21. 748 reads; 51885 bp (untrimmed), 51885 (trimmed).
Contig 22. 860 reads; 63928 bp (untrimmed), 63485 (trimmed).
Contig 23. 1225 reads; 87909 bp (untrimmed), 87871 (trimmed).
Contig 24. 1262 reads; 88852 bp (untrimmed), 88815 (trimmed).
Contig 25. 1396 reads; 101559 bp (untrimmed), 101502 (trimmed).
Contig 26. 1724 reads; 114491 bp (untrimmed), 114457 (trimmed).
Contig 27. 1772 reads; 110496 bp (untrimmed), 110434 (trimmed).
Contig 28. 2331 reads; 158488 bp (untrimmed), 157669 (trimmed).
Contig 29. 2435 reads; 164793 bp (untrimmed), 164570 (trimmed).
Contig 30. 2678 reads; 172486 bp (untrimmed), 172465 (trimmed).
Contig 31. 2704 reads; 182093 bp (untrimmed), 181088 (trimmed).
Contig 32. 2920 reads; 202466 bp (untrimmed), 202429 (trimmed).
Contig 33. 3587 reads; 229590 bp (untrimmed), 229471 (trimmed).
Contig 34. 5476 reads; 372187 bp (untrimmed), 371793 (trimmed).
Contig 35. 5990 reads; 427951 bp (untrimmed), 427753 (trimmed).
Contig 36. 11097 reads; 740353 bp (untrimmed), 740306 (trimmed).
--------------------------------------------------------------
Totals 51139 reads; 3522795 bp (untrimmed), 3516338 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3521232 bases = 13.07 +- 4.50 = 0.18 +- 4.18
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 33 total values totalling 341.7100. <10.354848 +/- 3.825823>
#Range: [ 1.61 - 14.39 ]
#Most likely bin: [ 13 - 13.5 ] 6 counts
#Median bin: [ 12 - 12.5 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 1.5 - 2 : [ 1 0.03 0.03 ]
|XXXXXXX 2 - 2.5 : [ 1 0.03 0.06 ]
#...
|XXXXXXX 3 - 3.5 : [ 1 0.03 0.09 ]
|XXXXXXX 3.5 - 4 : [ 1 0.03 0.12 ]
|XXXXXXX 4 - 4.5 : [ 1 0.03 0.15 ]
#...
|XXXXXXX 5 - 5.5 : [ 1 0.03 0.18 ]
|XXXXXXX 5.5 - 6 : [ 1 0.03 0.21 ]
#...
|XXXXXXX 7 - 7.5 : [ 1 0.03 0.24 ]
|XXXXXXX 7.5 - 8 : [ 1 0.03 0.27 ]
#...
|XXXXXXX 9 - 9.5 : [ 1 0.03 0.30 ]
#...
|XXXXXXXXXXXXX 10 - 10.5 : [ 2 0.06 0.36 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 2 0.06 0.42 ]
#...
|XXXXXXX 11.5 - 12 : [ 1 0.03 0.45 ]
|XXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 3 0.09 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.12 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 6 0.18 0.85 ]
|XXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 3 0.09 0.94 ]
|XXXXXXXXXXXXX 14 - 14.5 : [ 2 0.06 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 26 total values totalling 302.8100. <11.646538 +/- 2.633890>
#Range: [ 3.34 - 14.39 ]
#Most likely bin: [ 13 - 13.5 ] 6 counts
#Median bin: [ 12.5 - 13 ] 4 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 3 - 3.5 : [ 1 0.04 0.04 ]
#...
|XXXXXXX 5 - 5.5 : [ 1 0.04 0.08 ]
#...
|XXXXXXX 7.5 - 8 : [ 1 0.04 0.12 ]
#...
|XXXXXXX 9 - 9.5 : [ 1 0.04 0.15 ]
#...
|XXXXXXXXXXXXX 10 - 10.5 : [ 2 0.08 0.23 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 2 0.08 0.31 ]
#...
|XXXXXXX 11.5 - 12 : [ 1 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 3 0.12 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.15 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 6 0.23 0.85 ]
|XXXXXXXXXXXXX 13.5 - 14 : [ 2 0.08 0.92 ]
|XXXXXXXXXXXXX 14 - 14.5 : [ 2 0.08 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 2 2 reads 520 bases = 1.61 +- 0.49 = 1.61 +- 0.49
Contig 5 5 reads 1845 bases = 2.39 +- 1.42 = 2.39 +- 1.42
Contig 9 15 reads 4271 bases = 3.34 +- 1.57 = 0.13 +- 2.04
Contig 8 10 reads 1983 bases = 3.98 +- 1.68 = 2.21 +- 0.99
Contig 6 7 reads 1593 bases = 4.18 +- 1.71 = 1.89 +- 1.85
Contig 11 22 reads 3947 bases = 5.37 +- 2.49 = 1.99 +- 3.79
Contig 7 9 reads 967 bases = 5.81 +- 2.35 = 5.81 +- 2.35
Contig 12 28 reads 967 bases = 7.31 +- 9.12 = 2.71 +- 3.94
Contig 14 137 reads 16791 bases = 7.51 +- 2.51 = 0.38 +- 3.08
Contig 13 120 reads 11924 bases = 9.15 +- 3.99 = 1.60 +- 5.01
Contig 15 192 reads 17180 bases = 10.15 +- 3.95 = 0.20 +- 5.17
Contig 18 470 reads 41142 bases = 10.49 +- 4.12 = 0.15 +- 3.98
Contig 16 380 reads 31711 bases = 10.94 +- 4.09 = 0.42 +- 5.15
Contig 17 382 reads 31498 bases = 10.96 +- 5.13 = 0.18 +- 4.48
Contig 19 563 reads 42667 bases = 11.72 +- 4.10 = 0.22 +- 4.33
Contig 22 860 reads 63928 bases = 12.13 +- 4.57 = 0.29 +- 4.16
Contig 23 1225 reads 87909 bases = 12.29 +- 4.27 = 0.33 +- 4.07
Contig 20 569 reads 41630 bases = 12.33 +- 5.21 = 0.30 +- 4.57
Contig 25 1396 reads 101559 bases = 12.51 +- 4.50 = 0.04 +- 4.35
Contig 35 5990 reads 427951 bases = 12.64 +- 4.36 = 0.10 +- 4.47
Contig 17 382 reads 31498 bases = 10.96 +- 5.13 = 0.18 +- 4.48
Contig 19 563 reads 42667 bases = 11.72 +- 4.10 = 0.22 +- 4.33
Contig 22 860 reads 63928 bases = 12.13 +- 4.57 = 0.29 +- 4.16
Contig 23 1225 reads 87909 bases = 12.29 +- 4.27 = 0.33 +- 4.07
Contig 20 569 reads 41630 bases = 12.33 +- 5.21 = 0.30 +- 4.57
Contig 25 1396 reads 101559 bases = 12.51 +- 4.50 = 0.04 +- 4.35
Contig 35 5990 reads 427951 bases = 12.64 +- 4.36 = 0.10 +- 4.47
Contig 24 1262 reads 88852 bases = 12.71 +- 3.93 = 0.42 +- 3.82
Contig 32 2920 reads 202466 bases = 12.96 +- 4.09 = 0.34 +- 3.80
Contig 21 748 reads 51885 bases = 13.01 +- 4.74 = 0.13 +- 4.38
Contig 34 5476 reads 372187 bases = 13.21 +- 4.45 = 0.22 +- 4.11
Contig 28 2331 reads 158488 bases = 13.29 +- 4.37 = 0.36 +- 4.07
Contig 29 2435 reads 164793 bases = 13.30 +- 4.24 = -0.03 +- 4.27
Contig 31 2704 reads 182093 bases = 13.35 +- 4.27 = 0.33 +- 3.86
Contig 36 11097 reads 740353 bases = 13.49 +- 4.42 = 0.01 +- 4.09
Contig 26 1724 reads 114491 bases = 13.54 +- 4.64 = 0.27 +- 4.30
Contig 10 17 reads 1069 bases = 13.62 +- 5.49 = 0.73 +- 1.16
Contig 30 2678 reads 172486 bases = 13.95 +- 4.42 = 0.28 +- 4.18
Contig 33 3587 reads 229590 bases = 14.08 +- 4.43 = 0.21 +- 4.15
Contig 27 1772 reads 110496 bases = 14.39 +- 4.63 = -0.02 +- 4.43
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1045
HQ Discrepant reads = 13
Chimeric reads = 112
Suspect alignments = 361
-------------------------------------------------------------------
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/3634488/edit_dir.12Jul04.QD