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
3634606 4500 56812 Shewanella frigidimarina
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Shewanella_frigidimarina
-------------------------------------------------------------------
Shewanellaceae, family, g-proteobacteria
Alteromonadales, order, g-proteobacteria
Shewanella frigidimarina, species, g-proteobacteria
Shewanella, genus, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4770085
# phrap: 4429007
# db:
altered.
4500000
4566364 +/- 146939
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 12673
Number of reads with percent X's >= 20%: 250 = 0.4%
Number of reads with percent X's >= 50%: 158 = 0.3%
Number of reads with percent X's >= 80%: 47 = 0.1%
Total reads in project: 58580
Total bp X'd : 588125
reads >= 20% >= 50% >= 80% screened
Nr with L09136 11168 54 32 2
Nr with pCC1Fos 1225 6 4 0
Nr with pMCL200_JGI_XZX+XZK 280 190 122 45
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 13
Number of reads with percent X's >= 20%: 2 = 2.7%
Number of reads with percent X's >= 50%: 2 = 2.7%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 74
Total bp X'd : 1759
reads >= 20% >= 50% >= 80% screened
Nr with L09136 5 0 0 0
Nr with pCC1Fos 6 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 = 16369948
C = 11969795
G = 11922526
T = 16265662
N = 193034
X = 588125
GC fraction = 0.42
Total = 57309090
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634606_fasta.screen.contigs
-------------------------------------------------------------------
A 1408344
C 1001729
G 986319
T 1386005
N 30
fraction GC = 0.42
total bases = 4782427
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 AIOH reads.list > grep.reads.list.AIOH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOH 4 500
-------------------------------------------------------------------
#Found 10671 total values totalling 40204643.0000. <3767.654672 +/- 5621.889019>
#Range: [ 915 - 361969 ]
#Most likely bin: [ 3000 - 3500 ] 3795 counts
#Median bin: [ 3500 - 4000 ] 3193 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 3 0.00 0.00 ]
| 1000 - 1500 : [ 22 0.00 0.00 ]
| 1500 - 2000 : [ 46 0.00 0.01 ]
|XX 2000 - 2500 : [ 185 0.02 0.02 ]
|XXXXXXXXX 2500 - 3000 : [ 814 0.08 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3795 0.36 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3193 0.30 0.76 ]
|XXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1801 0.17 0.92 ]
|XXXXXXX 4500 - 5000 : [ 631 0.06 0.98 ]
|XX 5000 - 5500 : [ 162 0.02 1.00 ]
| 5500 - 6000 : [ 8 0.00 1.00 ]
#...
| 21500 - 22000 : [ 1 0.00 1.00 ]
#...
| 54500 - 55000 : [ 1 0.00 1.00 ]
#...
| 77500 - 78000 : [ 1 0.00 1.00 ]
#...
| 82000 - 82500 : [ 1 0.00 1.00 ]
#...
| 117500 - 118000 : [ 1 0.00 1.00 ]
#...
| 137500 - 138000 : [ 1 0.00 1.00 ]
#...
| 138500 - 139000 : [ 1 0.00 1.00 ]
| 139000 - 139500 : [ 1 0.00 1.00 ]
#...
| 221500 - 222000 : [ 1 0.00 1.00 ]
#...
| 278000 - 278500 : [ 1 0.00 1.00 ]
#...
| 361500 - 362000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOI reads.list > grep.reads.list.AIOI
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOI 4 500
-------------------------------------------------------------------
#Found 13075 total values totalling 88338248.0000. <6756.271358 +/- 5611.678543>
#Range: [ 958 - 281546 ]
#Most likely bin: [ 6000 - 6500 ] 3455 counts
#Median bin: [ 6500 - 7000 ] 3305 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 35 0.00 0.00 ]
| 1500 - 2000 : [ 36 0.00 0.01 ]
| 2000 - 2500 : [ 33 0.00 0.01 ]
| 2500 - 3000 : [ 35 0.00 0.01 ]
|X 3000 - 3500 : [ 57 0.00 0.02 ]
|X 3500 - 4000 : [ 44 0.00 0.02 ]
| 4000 - 4500 : [ 41 0.00 0.02 ]
|X 4500 - 5000 : [ 106 0.01 0.03 ]
|XX 5000 - 5500 : [ 185 0.01 0.04 ]
|XXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1464 0.11 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 3455 0.26 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 3305 0.25 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 2710 0.21 0.88 ]
|XXXXXXXXXXXXXXXX 7500 - 8000 : [ 1422 0.11 0.99 ]
|X 8000 - 8500 : [ 123 0.01 1.00 ]
| 8500 - 9000 : [ 5 0.00 1.00 ]
| 9000 - 9500 : [ 1 0.00 1.00 ]
| 9500 - 10000 : [ 3 0.00 1.00 ]
| 10000 - 10500 : [ 1 0.00 1.00 ]
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 11500 - 12000 : [ 1 0.00 1.00 ]
#...
| 48000 - 48500 : [ 1 0.00 1.00 ]
#...
| 102000 - 102500 : [ 1 0.00 1.00 ]
#...
| 140000 - 140500 : [ 2 0.00 1.00 ]
| 140500 - 141000 : [ 3 0.00 1.00 ]
#...
| 280000 - 280500 : [ 1 0.00 1.00 ]
#...
| 281000 - 281500 : [ 2 0.00 1.00 ]
| 281500 - 282000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOK reads.list > grep.reads.list.AIOK
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOK 4 500
-------------------------------------------------------------------
#Found 1202 total values totalling 43361954.0000. <36074.836938 +/- 4767.397583>
#Range: [ 27696 - 170407 ]
#Most likely bin: [ 35500 - 36000 ] 103 counts
#Median bin: [ 35500 - 36000 ] 103 counts
#Histogram Bins Count Fraction Cum_Fraction
| 27500 - 28000 : [ 1 0.00 0.00 ]
|X 28000 - 28500 : [ 2 0.00 0.00 ]
|X 28500 - 29000 : [ 2 0.00 0.00 ]
|XX 29000 - 29500 : [ 6 0.00 0.01 ]
|X 29500 - 30000 : [ 3 0.00 0.01 ]
|XX 30000 - 30500 : [ 6 0.00 0.02 ]
|XXXXXX 30500 - 31000 : [ 16 0.01 0.03 ]
|XXXXX 31000 - 31500 : [ 14 0.01 0.04 ]
|XXXXXXXXXX 31500 - 32000 : [ 27 0.02 0.06 ]
|XXXXXXXXXXXXXX 32000 - 32500 : [ 35 0.03 0.09 ]
|XXXXXXXXXXXXXXXXX 32500 - 33000 : [ 43 0.04 0.13 ]
|XXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 53 0.04 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 78 0.06 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 89 0.07 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 81 0.07 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 91 0.08 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 103 0.09 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 79 0.07 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 75 0.06 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 76 0.06 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 60 0.05 0.78 ]
|XXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 54 0.04 0.83 ]
|XXXXXXXXXXXXXXXXX 38500 - 39000 : [ 43 0.04 0.86 ]
|XXXXXXXXXXXXXXXX 39000 - 39500 : [ 42 0.03 0.90 ]
|XXXXXXX 39500 - 40000 : [ 18 0.01 0.91 ]
|XXXXXXXXX 40000 - 40500 : [ 24 0.02 0.93 ]
|XXXXXXX 40500 - 41000 : [ 18 0.01 0.95 ]
|XXXXXXX 41000 - 41500 : [ 18 0.01 0.96 ]
|XXXX 41500 - 42000 : [ 11 0.01 0.97 ]
|XXXX 42000 - 42500 : [ 11 0.01 0.98 ]
|XXXX 42500 - 43000 : [ 10 0.01 0.99 ]
|XX 43000 - 43500 : [ 4 0.00 0.99 ]
|XX 43500 - 44000 : [ 4 0.00 1.00 ]
|X 44000 - 44500 : [ 2 0.00 1.00 ]
|X 44500 - 45000 : [ 2 0.00 1.00 ]
#...
| 170000 - 170500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIOH 3548 +- 647 (n=5356)
# AIOK 35904 +- 2657 (n=588)
# AIOI 6529 +- 1111 (n=6590)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634606_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
AIOH 26112 -1 -1 98 750 26112 97 764 98 766
AIOI 37632 -1 -1 92 689 37450 78 720 90 713
AIOK 4608 -1 -1 88 499 4608 82 562 88 566
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIOH 13056 97 754 98 767 13056 96 775 98 765
AIOI 18787 76 718 89 707 18663 80 723 91 719
AIOK 2304 82 554 87 567 2304 83 569 89 565
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634606_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
24 3919 2087 86.96 90.58 AIOK @
136 25269 12817 94.24 98.17 AIOH @
196 29392 15411 78.63 81.90 AIOI @
] 58580 30315 85.15 cumulative total@@
LIBRARY PLATE ID COUNT [ AIOK 24 AIOH 136 AIOI 196 ] for 356 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 3634606_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 68170 total values totalling 42526065.0000. <623.823749 +/- 288.270038>
#Range: [ 0 - 937 ]
#Most likely bin: [ 800 - 850 ] 16389 counts
#Median bin: [ 750 - 800 ] 15382 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 9369 0.14 0.14 ]
|X 50 - 100 : [ 599 0.01 0.15 ]
|X 100 - 150 : [ 463 0.01 0.15 ]
|X 150 - 200 : [ 437 0.01 0.16 ]
|X 200 - 250 : [ 493 0.01 0.17 ]
|XX 250 - 300 : [ 646 0.01 0.18 ]
|X 300 - 350 : [ 589 0.01 0.18 ]
|XX 350 - 400 : [ 617 0.01 0.19 ]
|XX 400 - 450 : [ 709 0.01 0.20 ]
|XX 450 - 500 : [ 811 0.01 0.22 ]
|XXX 500 - 550 : [ 1114 0.02 0.23 ]
|XXXX 550 - 600 : [ 1589 0.02 0.26 ]
|XXXXXX 600 - 650 : [ 2344 0.03 0.29 ]
|XXXXXXXXXX 650 - 700 : [ 3987 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8122 0.12 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 15382 0.23 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 16389 0.24 0.93 ]
|XXXXXXXXXXX 850 - 900 : [ 4390 0.06 1.00 ]
| 900 - 950 : [ 120 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOH 3634606_fasta.screen.trimQ15.SaF > reads.trim15.AIOH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOH.rl 2 50
-------------------------------------------------------------------
#Found 26112 total values totalling 19312440.0000. <739.600184 +/- 164.165538>
#Range: [ 0 - 937 ]
#Most likely bin: [ 750 - 800 ] 8227 counts
#Median bin: [ 750 - 800 ] 8227 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 0 - 50 : [ 803 0.03 0.03 ]
| 50 - 100 : [ 61 0.00 0.03 ]
| 100 - 150 : [ 50 0.00 0.04 ]
| 150 - 200 : [ 63 0.00 0.04 ]
| 200 - 250 : [ 71 0.00 0.04 ]
| 250 - 300 : [ 97 0.00 0.04 ]
| 300 - 350 : [ 79 0.00 0.05 ]
| 350 - 400 : [ 92 0.00 0.05 ]
|X 400 - 450 : [ 127 0.00 0.06 ]
|X 450 - 500 : [ 124 0.00 0.06 ]
|X 500 - 550 : [ 144 0.01 0.07 ]
|X 550 - 600 : [ 192 0.01 0.07 ]
|XX 600 - 650 : [ 481 0.02 0.09 ]
|XXXXXXXX 650 - 700 : [ 1546 0.06 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4511 0.17 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8227 0.32 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7318 0.28 0.92 ]
|XXXXXXXXXX 850 - 900 : [ 2051 0.08 1.00 ]
| 900 - 950 : [ 75 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOI 3634606_fasta.screen.trimQ15.SaF > reads.trim15.AIOI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOI.rl 2 50
-------------------------------------------------------------------
#Found 37450 total values totalling 21063226.0000. <562.435941 +/- 329.137055>
#Range: [ 0 - 923 ]
#Most likely bin: [ 800 - 850 ] 9047 counts
#Median bin: [ 700 - 750 ] 3068 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 7877 0.21 0.21 ]
|XX 50 - 100 : [ 420 0.01 0.22 ]
|X 100 - 150 : [ 339 0.01 0.23 ]
|X 150 - 200 : [ 301 0.01 0.24 ]
|X 200 - 250 : [ 321 0.01 0.25 ]
|XX 250 - 300 : [ 340 0.01 0.26 ]
|XX 300 - 350 : [ 374 0.01 0.27 ]
|XX 350 - 400 : [ 406 0.01 0.28 ]
|XX 400 - 450 : [ 443 0.01 0.29 ]
|XX 450 - 500 : [ 512 0.01 0.30 ]
|XXX 500 - 550 : [ 698 0.02 0.32 ]
|XXXX 550 - 600 : [ 946 0.03 0.35 ]
|XXXXX 600 - 650 : [ 1243 0.03 0.38 ]
|XXXXXXXX 650 - 700 : [ 1737 0.05 0.43 ]
|XXXXXXXXXXXXXX 700 - 750 : [ 3068 0.08 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6994 0.19 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 9047 0.24 0.94 ]
|XXXXXXXXXX 850 - 900 : [ 2339 0.06 1.00 ]
| 900 - 950 : [ 45 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOK
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOK 3634606_fasta.screen.trimQ15.SaF > reads.trim15.AIOK.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOK.rl 2 50
-------------------------------------------------------------------
#Found 4608 total values totalling 2150399.0000. <466.666450 +/- 254.823759>
#Range: [ 0 - 836 ]
#Most likely bin: [ 650 - 700 ] 704 counts
#Median bin: [ 550 - 600 ] 451 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 689 0.15 0.15 ]
|XXXXXXX 50 - 100 : [ 118 0.03 0.18 ]
|XXXX 100 - 150 : [ 74 0.02 0.19 ]
|XXXX 150 - 200 : [ 73 0.02 0.21 ]
|XXXXXX 200 - 250 : [ 101 0.02 0.23 ]
|XXXXXXXXXXXX 250 - 300 : [ 209 0.05 0.27 ]
|XXXXXXXX 300 - 350 : [ 136 0.03 0.30 ]
|XXXXXXX 350 - 400 : [ 119 0.03 0.33 ]
|XXXXXXXX 400 - 450 : [ 139 0.03 0.36 ]
|XXXXXXXXXX 450 - 500 : [ 175 0.04 0.40 ]
|XXXXXXXXXXXXXXX 500 - 550 : [ 272 0.06 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 451 0.10 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 620 0.13 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 704 0.15 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 543 0.12 0.96 ]
|XXXXXXXXX 750 - 800 : [ 161 0.03 0.99 ]
|X 800 - 850 : [ 24 0.01 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634606
-------------------------------------------------------------------
AIOH.000001.000100 pUC18.fa LRS.fasta
AIOH.000101.000200 pUC18.fa LRS.fasta
AIOI.000001.000100 pMCL200.fa LRS.fasta
AIOI.000101.000200 pMCL200.fa LRS.fasta
AIOI.000201.000300 pMCL200.fa LRS.fasta
AIOK.000001.000100 pCC1Fos.fa LRS.fasta
AIOH.000001.000100 pUC18.fa LRS.fasta
AIOH.000101.000200 pUC18.fa LRS.fasta
AIOI.000001.000100 pMCL200.fa LRS.fasta
AIOI.000101.000200 pMCL200.fa LRS.fasta
AIOI.000201.000300 pMCL200.fa LRS.fasta
AIOK.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634606_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634606_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 58427 total values totalling 24367.4837. <0.417059 +/- 0.039125>
#Range: [ 0.0769 - 0.9259 ]
#Most likely bin: [ 0.425 - 0.43 ] 3573 counts
#Median bin: [ 0.415 - 0.42 ] 3513 counts
| 0.075 - 0.08 : [ 1 0.00 0.00 ]
#...
| 0.135 - 0.14 : [ 1 0.00 0.00 ]
#...
| 0.15 - 0.155 : [ 1 0.00 0.00 ]
| 0.155 - 0.16 : [ 1 0.00 0.00 ]
#...
| 0.18 - 0.185 : [ 2 0.00 0.00 ]
| 0.185 - 0.19 : [ 1 0.00 0.00 ]
| 0.19 - 0.195 : [ 1 0.00 0.00 ]
#...
| 0.205 - 0.21 : [ 2 0.00 0.00 ]
| 0.21 - 0.215 : [ 1 0.00 0.00 ]
| 0.215 - 0.22 : [ 2 0.00 0.00 ]
| 0.22 - 0.225 : [ 1 0.00 0.00 ]
| 0.225 - 0.23 : [ 3 0.00 0.00 ]
| 0.23 - 0.235 : [ 5 0.00 0.00 ]
| 0.235 - 0.24 : [ 4 0.00 0.00 ]
| 0.24 - 0.245 : [ 7 0.00 0.00 ]
| 0.245 - 0.25 : [ 5 0.00 0.00 ]
| 0.25 - 0.255 : [ 7 0.00 0.00 ]
| 0.255 - 0.26 : [ 8 0.00 0.00 ]
| 0.26 - 0.265 : [ 24 0.00 0.00 ]
| 0.265 - 0.27 : [ 21 0.00 0.00 ]
| 0.27 - 0.275 : [ 22 0.00 0.00 ]
| 0.275 - 0.28 : [ 16 0.00 0.00 ]
| 0.28 - 0.285 : [ 26 0.00 0.00 ]
| 0.285 - 0.29 : [ 37 0.00 0.00 ]
|X 0.29 - 0.295 : [ 58 0.00 0.00 ]
|X 0.295 - 0.3 : [ 68 0.00 0.01 ]
|X 0.3 - 0.305 : [ 69 0.00 0.01 ]
|X 0.305 - 0.31 : [ 82 0.00 0.01 ]
|X 0.31 - 0.315 : [ 95 0.00 0.01 ]
|XX 0.315 - 0.32 : [ 138 0.00 0.01 ]
|XX 0.32 - 0.325 : [ 164 0.00 0.01 ]
|XX 0.325 - 0.33 : [ 188 0.00 0.02 ]
|XXX 0.33 - 0.335 : [ 238 0.00 0.02 ]
|XXX 0.335 - 0.34 : [ 266 0.00 0.03 ]
|XXXX 0.34 - 0.345 : [ 381 0.01 0.03 ]
|XXXXX 0.345 - 0.35 : [ 472 0.01 0.04 ]
|XXXXXXX 0.35 - 0.355 : [ 597 0.01 0.05 ]
|XXXXXXXX 0.355 - 0.36 : [ 720 0.01 0.06 ]
|XXXXXXXXXX 0.36 - 0.365 : [ 860 0.01 0.08 ]
|XXXXXXXXXXXX 0.365 - 0.37 : [ 1034 0.02 0.10 ]
|XXXXXXXXXXXXXX 0.37 - 0.375 : [ 1281 0.02 0.12 ]
|XXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 1523 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 1730 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 2131 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 2394 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 2682 0.05 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 3028 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 3122 0.05 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 3351 0.06 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 3513 0.06 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 3537 0.06 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 3573 0.06 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 3285 0.06 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 3088 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 2742 0.05 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 2427 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 2004 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 1741 0.03 0.90 ]
|XXXXXXXXXXXXXX 0.46 - 0.465 : [ 1221 0.02 0.92 ]
|XXXXXXXXXXX 0.465 - 0.47 : [ 1010 0.02 0.94 ]
|XXXXXXXXX 0.47 - 0.475 : [ 814 0.01 0.96 ]
|XXXXXX 0.475 - 0.48 : [ 555 0.01 0.96 ]
|XXXX 0.48 - 0.485 : [ 395 0.01 0.97 ]
|XXX 0.485 - 0.49 : [ 309 0.01 0.98 ]
|XX 0.49 - 0.495 : [ 206 0.00 0.98 ]
|XX 0.495 - 0.5 : [ 148 0.00 0.98 ]
|XX 0.5 - 0.505 : [ 164 0.00 0.99 ]
|X 0.505 - 0.51 : [ 78 0.00 0.99 ]
|X 0.51 - 0.515 : [ 66 0.00 0.99 ]
|X 0.515 - 0.52 : [ 48 0.00 0.99 ]
|X 0.52 - 0.525 : [ 49 0.00 0.99 ]
| 0.525 - 0.53 : [ 40 0.00 0.99 ]
| 0.53 - 0.535 : [ 41 0.00 0.99 ]
| 0.535 - 0.54 : [ 24 0.00 0.99 ]
| 0.54 - 0.545 : [ 27 0.00 0.99 ]
| 0.545 - 0.55 : [ 21 0.00 0.99 ]
| 0.55 - 0.555 : [ 25 0.00 0.99 ]
|X 0.555 - 0.56 : [ 46 0.00 0.99 ]
|X 0.56 - 0.565 : [ 92 0.00 1.00 ]
|X 0.565 - 0.57 : [ 55 0.00 1.00 ]
| 0.57 - 0.575 : [ 21 0.00 1.00 ]
| 0.575 - 0.58 : [ 14 0.00 1.00 ]
| 0.58 - 0.585 : [ 19 0.00 1.00 ]
| 0.585 - 0.59 : [ 12 0.00 1.00 ]
| 0.59 - 0.595 : [ 11 0.00 1.00 ]
| 0.595 - 0.6 : [ 8 0.00 1.00 ]
| 0.6 - 0.605 : [ 13 0.00 1.00 ]
| 0.605 - 0.61 : [ 9 0.00 1.00 ]
| 0.61 - 0.615 : [ 21 0.00 1.00 ]
| 0.615 - 0.62 : [ 12 0.00 1.00 ]
| 0.62 - 0.625 : [ 13 0.00 1.00 ]
| 0.625 - 0.63 : [ 11 0.00 1.00 ]
| 0.63 - 0.635 : [ 15 0.00 1.00 ]
| 0.635 - 0.64 : [ 10 0.00 1.00 ]
| 0.64 - 0.645 : [ 10 0.00 1.00 ]
| 0.645 - 0.65 : [ 2 0.00 1.00 ]
| 0.65 - 0.655 : [ 2 0.00 1.00 ]
#...
| 0.66 - 0.665 : [ 1 0.00 1.00 ]
#...
| 0.67 - 0.675 : [ 2 0.00 1.00 ]
| 0.675 - 0.68 : [ 1 0.00 1.00 ]
#...
| 0.685 - 0.69 : [ 1 0.00 1.00 ]
| 0.69 - 0.695 : [ 1 0.00 1.00 ]
#...
| 0.705 - 0.71 : [ 2 0.00 1.00 ]
#...
| 0.925 - 0.93 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 64. 636 reads; 61624 bp (untrimmed), 61605 (trimmed).
Contig 65. 641 reads; 60929 bp (untrimmed), 60811 (trimmed).
Contig 66. 648 reads; 56769 bp (untrimmed), 56615 (trimmed).
Contig 67. 650 reads; 57626 bp (untrimmed), 57151 (trimmed).
Contig 68. 676 reads; 62970 bp (untrimmed), 62727 (trimmed).
Contig 69. 683 reads; 57256 bp (untrimmed), 57201 (trimmed).
Contig 70. 687 reads; 61758 bp (untrimmed), 61664 (trimmed).
Contig 71. 746 reads; 62343 bp (untrimmed), 62178 (trimmed).
Contig 72. 762 reads; 58562 bp (untrimmed), 58460 (trimmed).
Contig 73. 776 reads; 61761 bp (untrimmed), 61727 (trimmed).
Contig 74. 818 reads; 73133 bp (untrimmed), 73085 (trimmed).
Contig 75. 931 reads; 91082 bp (untrimmed), 91057 (trimmed).
Contig 76. 968 reads; 83615 bp (untrimmed), 83492 (trimmed).
Contig 77. 1286 reads; 101078 bp (untrimmed), 100848 (trimmed).
Contig 78. 1345 reads; 97882 bp (untrimmed), 97866 (trimmed).
Contig 79. 2042 reads; 172744 bp (untrimmed), 172724 (trimmed).
Contig 80. 2080 reads; 148647 bp (untrimmed), 148603 (trimmed).
Contig 81. 2118 reads; 169292 bp (untrimmed), 169244 (trimmed).
Contig 82. 2405 reads; 200925 bp (untrimmed), 200892 (trimmed).
Contig 83. 2574 reads; 208417 bp (untrimmed), 208399 (trimmed).
Contig 84. 2588 reads; 172006 bp (untrimmed), 171922 (trimmed).
Contig 85. 2769 reads; 210670 bp (untrimmed), 210626 (trimmed).
Contig 86. 2809 reads; 226823 bp (untrimmed), 226791 (trimmed).
Contig 87. 3365 reads; 238599 bp (untrimmed), 238576 (trimmed).
Contig 88. 4104 reads; 300947 bp (untrimmed), 300643 (trimmed).
Contig 89. 5251 reads; 414092 bp (untrimmed), 413818 (trimmed).
Contig 90. 5631 reads; 423697 bp (untrimmed), 423656 (trimmed).
--------------------------------------------------------------
Totals 58506 reads; 4782427 bp (untrimmed), 4770085 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4781939 bases = 11.31 +- 4.63 = 0.21 +- 4.12
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 88 total values totalling 699.2100. <7.945568 +/- 3.577961>
#Range: [ 1.25 - 13.96 ]
#Most likely bin: [ 9.5 - 10 ] 9 counts
#Median bin: [ 8.5 - 9 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 1 - 1.5 : [ 2 0.02 0.02 ]
|XXXXXXXXXXXXX 1.5 - 2 : [ 3 0.03 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 7 0.08 0.14 ]
|XXXXXXXXX 2.5 - 3 : [ 2 0.02 0.16 ]
|XXXXXXXXX 3 - 3.5 : [ 2 0.02 0.18 ]
|XXXXXXXXXXXXX 3.5 - 4 : [ 3 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 4 0.05 0.26 ]
|XXXX 4.5 - 5 : [ 1 0.01 0.27 ]
|XXXXXXXXX 5 - 5.5 : [ 2 0.02 0.30 ]
#...
|XXXX 6 - 6.5 : [ 1 0.01 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 6 0.07 0.38 ]
|XXXXXXXXX 7 - 7.5 : [ 2 0.02 0.40 ]
|XXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 4 0.05 0.44 ]
|XXXXXXXXX 8 - 8.5 : [ 2 0.02 0.47 ]
|XXXXXXXXXXXXX 8.5 - 9 : [ 3 0.03 0.50 ]
|XXXXXXXXX 9 - 9.5 : [ 2 0.02 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 9 0.10 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 7 0.08 0.70 ]
|XXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 4 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 7 0.08 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.08 0.91 ]
|XXXXXXXXXXXXX 12 - 12.5 : [ 3 0.03 0.94 ]
|XXXXXXXXXXXXX 12.5 - 13 : [ 3 0.03 0.98 ]
|XXXX 13 - 13.5 : [ 1 0.01 0.99 ]
|XXXX 13.5 - 14 : [ 1 0.01 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 67 total values totalling 637.1500. <9.509701 +/- 2.443984>
#Range: [ 3.44 - 13.96 ]
#Most likely bin: [ 9.5 - 10 ] 9 counts
#Median bin: [ 9.5 - 10 ] 9 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 3 - 3.5 : [ 2 0.03 0.03 ]
|XXXX 3.5 - 4 : [ 1 0.01 0.04 ]
|XXXX 4 - 4.5 : [ 1 0.01 0.06 ]
|XXXX 4.5 - 5 : [ 1 0.01 0.07 ]
|XXXX 5 - 5.5 : [ 1 0.01 0.09 ]
#...
|XXXX 6 - 6.5 : [ 1 0.01 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 5 0.07 0.18 ]
|XXXXXXXXX 7 - 7.5 : [ 2 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 4 0.06 0.27 ]
|XXXXXXXXX 8 - 8.5 : [ 2 0.03 0.30 ]
|XXXXXXXXXXXXX 8.5 - 9 : [ 3 0.04 0.34 ]
|XXXXXXXXX 9 - 9.5 : [ 2 0.03 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 9 0.13 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 7 0.10 0.61 ]
|XXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 4 0.06 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 7 0.10 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.10 0.88 ]
|XXXXXXXXXXXXX 12 - 12.5 : [ 3 0.04 0.93 ]
|XXXXXXXXXXXXX 12.5 - 13 : [ 3 0.04 0.97 ]
|XXXX 13 - 13.5 : [ 1 0.01 0.99 ]
|XXXX 13.5 - 14 : [ 1 0.01 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 1484 bases = 1.25 +- 0.43 = 1.25 +- 0.43
Contig 7 3 reads 1921 bases = 1.48 +- 0.50 = 1.48 +- 0.50
Contig 9 4 reads 2513 bases = 1.54 +- 0.57 = 0.76 +- 1.05
Contig 10 4 reads 2194 bases = 1.66 +- 0.52 = 0.87 +- 1.18
Contig 11 4 reads 1743 bases = 1.90 +- 0.96 = -0.31 +- 0.65
Contig 3 3 reads 1191 bases = 2.23 +- 0.89 = 2.23 +- 0.89
Contig 17 6 reads 1924 bases = 2.27 +- 1.34 = 0.09 +- 0.83
Contig 12 4 reads 1707 bases = 2.29 +- 1.00 = 1.07 +- 0.69
Contig 6 3 reads 1267 bases = 2.35 +- 0.85 = 0.82 +- 0.59
Contig 13 4 reads 1521 bases = 2.36 +- 0.79 = 2.36 +- 0.79
Contig 8 3 reads 1206 bases = 2.37 +- 0.87 = 0.70 +- 0.64
Contig 5 3 reads 998 bases = 2.41 +- 0.70 = 2.41 +- 0.70
Contig 18 6 reads 1977 bases = 2.87 +- 1.42 = 2.87 +- 1.42
Contig 19 7 reads 2202 bases = 2.92 +- 2.05 = 0.43 +- 1.15
Contig 23 10 reads 2720 bases = 3.44 +- 2.12 = 2.73 +- 2.57
Contig 29 23 reads 6197 bases = 3.44 +- 1.55 = 0.78 +- 3.28
Contig 15 5 reads 1183 bases = 3.67 +- 1.44 = 3.67 +- 1.44
Contig 14 5 reads 1218 bases = 3.81 +- 1.43 = 2.38 +- 1.13
Contig 27 15 reads 3554 bases = 3.98 +- 2.10 = 2.89 +- 1.28
Contig 20 8 reads 1669 bases = 4.01 +- 1.39 = 3.36 +- 1.91
Contig 60 512 reads 42875 bases = 11.12 +- 4.36 = 0.31 +- 4.44
Contig 71 746 reads 62343 bases = 11.12 +- 4.88 = 0.78 +- 5.82
Contig 47 235 reads 19532 bases = 11.18 +- 4.53 = 1.03 +- 3.87
Contig 86 2809 reads 226823 bases = 11.40 +- 4.63 = 0.06 +- 3.55
Contig 83 2574 reads 208417 bases = 11.44 +- 4.63 = 0.04 +- 4.40
Contig 63 613 reads 49035 bases = 11.57 +- 5.13 = 0.12 +- 4.94
Contig 81 2118 reads 169292 bases = 11.61 +- 4.04 = 0.10 +- 4.05
Contig 73 776 reads 61761 bases = 11.62 +- 3.59 = 0.48 +- 3.42
Contig 89 5251 reads 414092 bases = 11.70 +- 4.07 = 0.13 +- 3.81
Contig 77 1286 reads 101078 bases = 11.72 +- 4.28 = -0.01 +- 3.67
Contig 72 762 reads 58562 bases = 11.97 +- 4.57 = 0.01 +- 3.69
Contig 51 314 reads 24256 bases = 11.99 +- 3.87 = 0.53 +- 3.83
Contig 85 2769 reads 210670 bases = 12.17 +- 4.75 = 0.04 +- 4.20
Contig 59 503 reads 38219 bases = 12.24 +- 3.53 = 0.11 +- 4.30
Contig 90 5631 reads 423697 bases = 12.28 +- 4.89 = 0.05 +- 3.90
Contig 88 4104 reads 300947 bases = 12.60 +- 4.25 = 0.12 +- 4.25
Contig 78 1345 reads 97882 bases = 12.69 +- 4.62 = 0.21 +- 3.62
Contig 80 2080 reads 148647 bases = 12.87 +- 5.07 = 0.10 +- 4.16
Contig 87 3365 reads 238599 bases = 13.08 +- 5.32 = 0.32 +- 5.37
Contig 84 2588 reads 172006 bases = 13.96 +- 4.81 = 0.03 +- 4.03
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 2008
HQ Discrepant reads = 42
Chimeric reads = 35
Suspect alignments = 417
-------------------------------------------------------------------
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/microbe3/3634606/edit_dir.26Jul04.QD