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 Rubrobacter_xylanophilus
-------------------------------------------------------------------
Rubrobacterineae, suborder, high GC Gram+
Actinobacteria, phylum, actinobacteria
Rubrobacteraceae, family, high GC Gram+
Rubrobacterales, order, high GC Gram+
Rubrobacteridae, subclass, high GC Gram+
Rubrobacter xylanophilus, species, high GC Gram+
Rubrobacter, genus, high GC Gram+
Actinobacteria (class) (high G+C Gram-positive bacteria), class, high GC Gram+
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3217347
# phrap: 3136904
# db:
altered.
3177125 +/- 40221
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 24746
Number of reads with percent X's >= 20%: 405 = 1.1%
Number of reads with percent X's >= 50%: 190 = 0.5%
Number of reads with percent X's >= 80%: 29 = 0.1%
Total reads in project: 37220
Total bp X'd : 1676513
reads >= 20% >= 50% >= 80% screened
Nr with L09136 7428 222 119 16
Nr with pCC1Fos 1397 2 0 0
Nr with pMCL200_JGI_XZX+XZK 15921 181 71 13
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 36
Number of reads with percent X's >= 20%: 1 = 1.2%
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: 80
Total bp X'd : 1937
reads >= 20% >= 50% >= 80% screened
Nr with L09136 22 1 0 0
Nr with pCC1Fos 8 0 0 0
Nr with pMCL200_JGI_XZX+XZK 6 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 6589701
C = 13930710
G = 13081302
T = 7051377
N = 265561
X = 1676513
GC fraction = 0.63
Total = 42595164
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436081_fasta.screen.contigs
-------------------------------------------------------------------
A 492941
C 1163287
G 1144551
T 498245
N 399
fraction GC = 0.70
total bases = 3299423
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 ACGS reads.list > grep.reads.list.ACGS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACGS 4 500
-------------------------------------------------------------------
#Found 7348 total values totalling 25018889.0000. <3404.856968 +/- 817.484126>
#Range: [ 212 - 15176 ]
#Most likely bin: [ 2500 - 3000 ] 1939 counts
#Median bin: [ 3000 - 3500 ] 1780 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
#...
|XX 1000 - 1500 : [ 81 0.01 0.01 ]
|XX 1500 - 2000 : [ 114 0.02 0.03 ]
|XXXXXXXXX 2000 - 2500 : [ 420 0.06 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 1939 0.26 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1780 0.24 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1316 0.18 0.77 ]
|XXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 924 0.13 0.89 ]
|XXXXXXXXXXX 4500 - 5000 : [ 511 0.07 0.96 ]
|XXXXX 5000 - 5500 : [ 223 0.03 0.99 ]
|X 5500 - 6000 : [ 37 0.01 1.00 ]
#...
| 13500 - 14000 : [ 1 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACGT reads.list > grep.reads.list.ACGT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACGT 4 500
-------------------------------------------------------------------
#Found 5906 total values totalling 37075509.0000. <6277.600576 +/- 1113.029480>
#Range: [ 100 - 17751 ]
#Most likely bin: [ 6000 - 6500 ] 1923 counts
#Median bin: [ 6000 - 6500 ] 1923 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 3 0.00 0.00 ]
| 500 - 1000 : [ 4 0.00 0.00 ]
|X 1000 - 1500 : [ 35 0.01 0.01 ]
|X 1500 - 2000 : [ 61 0.01 0.02 ]
|X 2000 - 2500 : [ 70 0.01 0.03 ]
|X 2500 - 3000 : [ 61 0.01 0.04 ]
|X 3000 - 3500 : [ 47 0.01 0.05 ]
|X 3500 - 4000 : [ 47 0.01 0.06 ]
|X 4000 - 4500 : [ 47 0.01 0.06 ]
|X 4500 - 5000 : [ 54 0.01 0.07 ]
|XX 5000 - 5500 : [ 95 0.02 0.09 ]
|XXXXXXXXXXXXX 5500 - 6000 : [ 618 0.10 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1923 0.33 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1842 0.31 0.83 ]
|XXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 916 0.16 0.99 ]
|XX 7500 - 8000 : [ 78 0.01 1.00 ]
#...
| 8500 - 9000 : [ 2 0.00 1.00 ]
#...
| 16000 - 16500 : [ 1 0.00 1.00 ]
#...
| 17000 - 17500 : [ 1 0.00 1.00 ]
| 17500 - 18000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACGU reads.list > grep.reads.list.ACGU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACGU 4 500
-------------------------------------------------------------------
#Found 298 total values totalling 11352623.0000. <38096.050336 +/- 2685.051376>
#Range: [ 29517 - 46123 ]
#Most likely bin: [ 38500 - 39000 ] 31 counts
#Median bin: [ 38000 - 38500 ] 23 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 29500 - 30000 : [ 1 0.00 0.00 ]
#...
|X 30500 - 31000 : [ 1 0.00 0.01 ]
#...
|XXX 31500 - 32000 : [ 2 0.01 0.01 ]
|XXX 32000 - 32500 : [ 2 0.01 0.02 ]
|XXX 32500 - 33000 : [ 2 0.01 0.03 ]
|XXXXX 33000 - 33500 : [ 4 0.01 0.04 ]
|XXXXX 33500 - 34000 : [ 4 0.01 0.05 ]
|XXXXX 34000 - 34500 : [ 4 0.01 0.07 ]
|XXXXXXXXX 34500 - 35000 : [ 7 0.02 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 21 0.07 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 18 0.06 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 19 0.06 0.29 ]
|XXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 16 0.05 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 30 0.10 0.44 ]
|XXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 15 0.05 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 23 0.08 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 31 0.10 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 19 0.06 0.73 ]
|XXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 15 0.05 0.79 ]
|XXXXXXXXXXXX 40000 - 40500 : [ 9 0.03 0.82 ]
|XXXXXXXXXXXXXX 40500 - 41000 : [ 11 0.04 0.85 ]
|XXXXXXXXXXXXXXX 41000 - 41500 : [ 12 0.04 0.89 ]
|XXXXXXXX 41500 - 42000 : [ 6 0.02 0.91 ]
|XXXX 42000 - 42500 : [ 3 0.01 0.92 ]
|XXXXXXXXXXXXX 42500 - 43000 : [ 10 0.03 0.96 ]
|XXXXXX 43000 - 43500 : [ 5 0.02 0.97 ]
|XXXX 43500 - 44000 : [ 3 0.01 0.98 ]
|XXX 44000 - 44500 : [ 2 0.01 0.99 ]
|X 44500 - 45000 : [ 1 0.00 0.99 ]
#...
|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
-------------------------------------------------------------------
# ACGS 3268 +- 873 (n=3696)
# ACGU 37988 +- 2598 (n=145)
# ACGT 6003 +- 1307 (n=2887)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436081_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
ACGS 19296 -1 -1 97 658 18030 99 683 100 689
ACGT 19200 -1 -1 97 652 16198 99 596 100 652
ACGU 3840 -1 -1 81 506 2992 98 630 100 642
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
ACGS 8984 99 682 100 696 9046 99 685 100 681
ACGT 8049 98 583 100 647 8149 99 610 100 657
ACGU 1410 97 618 100 613 1582 99 641 100 667
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436081_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 37220 19326 87.85 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 3436081_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 37220 total values totalling 23619967.0000. <634.604164 +/- 177.596397>
#Range: [ 15 - 921 ]
#Most likely bin: [ 700 - 750 ] 7199 counts
#Median bin: [ 650 - 700 ] 5633 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 95 0.00 0.00 ]
|XX 50 - 100 : [ 351 0.01 0.01 ]
|XXX 100 - 150 : [ 535 0.01 0.03 ]
|XXX 150 - 200 : [ 579 0.02 0.04 ]
|XXXX 200 - 250 : [ 659 0.02 0.06 ]
|XXXX 250 - 300 : [ 717 0.02 0.08 ]
|XXXX 300 - 350 : [ 768 0.02 0.10 ]
|XXXXX 350 - 400 : [ 879 0.02 0.12 ]
|XXXXXX 400 - 450 : [ 1007 0.03 0.15 ]
|XXXXXX 450 - 500 : [ 1095 0.03 0.18 ]
|XXXXXXXXX 500 - 550 : [ 1538 0.04 0.22 ]
|XXXXXXXXXXXX 550 - 600 : [ 2242 0.06 0.28 ]
|XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3611 0.10 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5633 0.15 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7199 0.19 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6648 0.18 0.90 ]
|XXXXXXXXXXXXXXXXXX 800 - 850 : [ 3294 0.09 0.99 ]
|XX 850 - 900 : [ 365 0.01 1.00 ]
| 900 - 950 : [ 5 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHSU
trimt JAZZ trim 15 readlength histogram for BGAA
trimt JAZZ trim 15 readlength histogram for ACGS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACGS 3436081_fasta.screen.trimQ15.SaF > reads.trim15.ACGS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACGS.rl 2 50
-------------------------------------------------------------------
#Found 18030 total values totalling 12234531.0000. <678.565225 +/- 174.458452>
#Range: [ 21 - 921 ]
#Most likely bin: [ 750 - 800 ] 5027 counts
#Median bin: [ 700 - 750 ] 3316 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 35 0.00 0.00 ]
|X 50 - 100 : [ 109 0.01 0.01 ]
|XX 100 - 150 : [ 201 0.01 0.02 ]
|XX 150 - 200 : [ 235 0.01 0.03 ]
|XX 200 - 250 : [ 271 0.02 0.05 ]
|XX 250 - 300 : [ 300 0.02 0.06 ]
|XXX 300 - 350 : [ 319 0.02 0.08 ]
|XXX 350 - 400 : [ 378 0.02 0.10 ]
|XXX 400 - 450 : [ 368 0.02 0.12 ]
|XXX 450 - 500 : [ 392 0.02 0.14 ]
|XXXX 500 - 550 : [ 516 0.03 0.17 ]
|XXXXX 550 - 600 : [ 660 0.04 0.21 ]
|XXXXXXX 600 - 650 : [ 891 0.05 0.26 ]
|XXXXXXXXXXXX 650 - 700 : [ 1494 0.08 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3316 0.18 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5027 0.28 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3150 0.17 0.98 ]
|XXX 850 - 900 : [ 363 0.02 1.00 ]
| 900 - 950 : [ 5 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACGT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACGT 3436081_fasta.screen.trimQ15.SaF > reads.trim15.ACGT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACGT.rl 2 50
-------------------------------------------------------------------
#Found 16198 total values totalling 9539755.0000. <588.946475 +/- 167.575631>
#Range: [ 15 - 841 ]
#Most likely bin: [ 650 - 700 ] 3595 counts
#Median bin: [ 600 - 650 ] 2437 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 43 0.00 0.00 ]
|XX 50 - 100 : [ 188 0.01 0.01 ]
|XXX 100 - 150 : [ 277 0.02 0.03 ]
|XXX 150 - 200 : [ 299 0.02 0.05 ]
|XXXX 200 - 250 : [ 332 0.02 0.07 ]
|XXXX 250 - 300 : [ 349 0.02 0.09 ]
|XXXX 300 - 350 : [ 372 0.02 0.11 ]
|XXXXX 350 - 400 : [ 439 0.03 0.14 ]
|XXXXXX 400 - 450 : [ 583 0.04 0.18 ]
|XXXXXXX 450 - 500 : [ 644 0.04 0.22 ]
|XXXXXXXXXX 500 - 550 : [ 917 0.06 0.27 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 1405 0.09 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2437 0.15 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3595 0.22 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3093 0.19 0.92 ]
|XXXXXXXXXXXXX 750 - 800 : [ 1146 0.07 1.00 ]
|X 800 - 850 : [ 79 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACGU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACGU 3436081_fasta.screen.trimQ15.SaF > reads.trim15.ACGU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACGU.rl 2 50
-------------------------------------------------------------------
#Found 2992 total values totalling 1845681.0000. <616.871992 +/- 183.513867>
#Range: [ 28 - 872 ]
#Most likely bin: [ 700 - 750 ] 790 counts
#Median bin: [ 650 - 700 ] 544 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 17 0.01 0.01 ]
|XXX 50 - 100 : [ 54 0.02 0.02 ]
|XXX 100 - 150 : [ 57 0.02 0.04 ]
|XX 150 - 200 : [ 45 0.02 0.06 ]
|XXX 200 - 250 : [ 56 0.02 0.08 ]
|XXX 250 - 300 : [ 68 0.02 0.10 ]
|XXXX 300 - 350 : [ 77 0.03 0.12 ]
|XXX 350 - 400 : [ 62 0.02 0.15 ]
|XXX 400 - 450 : [ 56 0.02 0.16 ]
|XXX 450 - 500 : [ 59 0.02 0.18 ]
|XXXXX 500 - 550 : [ 105 0.04 0.22 ]
|XXXXXXXXX 550 - 600 : [ 177 0.06 0.28 ]
|XXXXXXXXXXXXXX 600 - 650 : [ 283 0.09 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 544 0.18 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 790 0.26 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 475 0.16 0.98 ]
|XXX 800 - 850 : [ 65 0.02 1.00 ]
| 850 - 900 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436081
-------------------------------------------------------------------
ACGS.000001.000100 pUC18.fa pUC18.fa LRS.fasta
ACGS.000101.000200 pUC18.fa pUC18.fa LRS.fasta
ACGT.000001.000100 pMCL200.fa.4 LRS.fasta
ACGT.000101.000200 pMCL200.fa.4 LRS.fasta
ACGU.000001.000100 pCC1Fos.fa.4 LRS.fasta
ACGS.000001.000100 pUC18.fa pUC18.fa LRS.fasta
ACGS.000101.000200 pUC18.fa pUC18.fa LRS.fasta
ACGT.000001.000100 pMCL200.fa.4 LRS.fasta
ACGT.000101.000200 pMCL200.fa.4 LRS.fasta
ACGU.000001.000100 pCC1Fos.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436081_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436081_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 37127 total values totalling 25946.0677. <0.698846 +/- 0.053878>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.705 - 0.71 ] 1873 counts
#Median bin: [ 0.705 - 0.71 ] 1873 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.12 - 0.125 : [ 1 0.00 0.00 ]
#...
| 0.315 - 0.32 : [ 1 0.00 0.00 ]
#...
| 0.325 - 0.33 : [ 1 0.00 0.00 ]
| 0.33 - 0.335 : [ 1 0.00 0.00 ]
#...
| 0.365 - 0.37 : [ 1 0.00 0.00 ]
| 0.37 - 0.375 : [ 1 0.00 0.00 ]
| 0.375 - 0.38 : [ 3 0.00 0.00 ]
#...
| 0.39 - 0.395 : [ 1 0.00 0.00 ]
#...
| 0.4 - 0.405 : [ 4 0.00 0.00 ]
| 0.405 - 0.41 : [ 1 0.00 0.00 ]
| 0.41 - 0.415 : [ 2 0.00 0.00 ]
| 0.415 - 0.42 : [ 5 0.00 0.00 ]
#...
| 0.425 - 0.43 : [ 8 0.00 0.00 ]
| 0.43 - 0.435 : [ 9 0.00 0.00 ]
| 0.435 - 0.44 : [ 6 0.00 0.00 ]
| 0.44 - 0.445 : [ 6 0.00 0.00 ]
| 0.445 - 0.45 : [ 7 0.00 0.00 ]
| 0.45 - 0.455 : [ 11 0.00 0.00 ]
| 0.455 - 0.46 : [ 11 0.00 0.00 ]
| 0.46 - 0.465 : [ 11 0.00 0.00 ]
| 0.465 - 0.47 : [ 9 0.00 0.00 ]
| 0.47 - 0.475 : [ 17 0.00 0.00 ]
| 0.475 - 0.48 : [ 17 0.00 0.00 ]
| 0.48 - 0.485 : [ 15 0.00 0.00 ]
|X 0.485 - 0.49 : [ 24 0.00 0.00 ]
| 0.49 - 0.495 : [ 16 0.00 0.01 ]
| 0.495 - 0.5 : [ 19 0.00 0.01 ]
|X 0.5 - 0.505 : [ 47 0.00 0.01 ]
|X 0.505 - 0.51 : [ 36 0.00 0.01 ]
|X 0.51 - 0.515 : [ 54 0.00 0.01 ]
|X 0.515 - 0.52 : [ 42 0.00 0.01 ]
|X 0.52 - 0.525 : [ 39 0.00 0.01 ]
|X 0.525 - 0.53 : [ 51 0.00 0.01 ]
|X 0.53 - 0.535 : [ 63 0.00 0.01 ]
|X 0.535 - 0.54 : [ 36 0.00 0.02 ]
|X 0.54 - 0.545 : [ 53 0.00 0.02 ]
|X 0.545 - 0.55 : [ 52 0.00 0.02 ]
|XX 0.55 - 0.555 : [ 83 0.00 0.02 ]
|X 0.555 - 0.56 : [ 57 0.00 0.02 ]
|XX 0.56 - 0.565 : [ 91 0.00 0.02 ]
|XX 0.565 - 0.57 : [ 106 0.00 0.03 ]
|XX 0.57 - 0.575 : [ 108 0.00 0.03 ]
|XXX 0.575 - 0.58 : [ 144 0.00 0.03 ]
|XXX 0.58 - 0.585 : [ 154 0.00 0.04 ]
|XXX 0.585 - 0.59 : [ 157 0.00 0.04 ]
|XXXX 0.59 - 0.595 : [ 173 0.00 0.05 ]
|XXXX 0.595 - 0.6 : [ 203 0.01 0.05 ]
|XXXXX 0.6 - 0.605 : [ 225 0.01 0.06 ]
|XXXXX 0.605 - 0.61 : [ 221 0.01 0.06 ]
|XXXXXX 0.61 - 0.615 : [ 260 0.01 0.07 ]
|XXXXXX 0.615 - 0.62 : [ 290 0.01 0.08 ]
|XXXXXX 0.62 - 0.625 : [ 262 0.01 0.09 ]
|XXXXXX 0.625 - 0.63 : [ 304 0.01 0.09 ]
|XXXXXXX 0.63 - 0.635 : [ 317 0.01 0.10 ]
|XXXXXXXX 0.635 - 0.64 : [ 373 0.01 0.11 ]
|XXXXXXXXX 0.64 - 0.645 : [ 408 0.01 0.12 ]
|XXXXXXXXXXX 0.645 - 0.65 : [ 501 0.01 0.14 ]
|XXXXXXXXXXXXX 0.65 - 0.655 : [ 608 0.02 0.15 ]
|XXXXXXXXXXXXXX 0.655 - 0.66 : [ 662 0.02 0.17 ]
|XXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 758 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 925 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 1099 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 1226 0.03 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 1336 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 1522 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 1584 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 1734 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 1837 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 1873 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 1797 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 1775 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 1685 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.725 - 0.73 : [ 1556 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.73 - 0.735 : [ 1520 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.735 - 0.74 : [ 1383 0.04 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.74 - 0.745 : [ 1289 0.03 0.84 ]
|XXXXXXXXXXXXXXXXXXXXX 0.745 - 0.75 : [ 967 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXXXX 0.75 - 0.755 : [ 982 0.03 0.90 ]
|XXXXXXXXXXXXXXXXX 0.755 - 0.76 : [ 798 0.02 0.92 ]
|XXXXXXXXXXXXXX 0.76 - 0.765 : [ 648 0.02 0.93 ]
|XXXXXXXXXX 0.765 - 0.77 : [ 491 0.01 0.95 ]
|XXXXXXXXX 0.77 - 0.775 : [ 422 0.01 0.96 ]
|XXXXXXX 0.775 - 0.78 : [ 334 0.01 0.97 ]
|XXXXX 0.78 - 0.785 : [ 235 0.01 0.97 ]
|XXXX 0.785 - 0.79 : [ 208 0.01 0.98 ]
|XXXX 0.79 - 0.795 : [ 172 0.00 0.98 ]
|XX 0.795 - 0.8 : [ 110 0.00 0.99 ]
|XX 0.8 - 0.805 : [ 106 0.00 0.99 ]
|XX 0.805 - 0.81 : [ 89 0.00 0.99 ]
|X 0.81 - 0.815 : [ 61 0.00 0.99 ]
|X 0.815 - 0.82 : [ 50 0.00 1.00 ]
|X 0.82 - 0.825 : [ 31 0.00 1.00 ]
|X 0.825 - 0.83 : [ 24 0.00 1.00 ]
| 0.83 - 0.835 : [ 20 0.00 1.00 ]
| 0.835 - 0.84 : [ 18 0.00 1.00 ]
| 0.84 - 0.845 : [ 12 0.00 1.00 ]
| 0.845 - 0.85 : [ 10 0.00 1.00 ]
| 0.85 - 0.855 : [ 10 0.00 1.00 ]
| 0.855 - 0.86 : [ 10 0.00 1.00 ]
| 0.86 - 0.865 : [ 5 0.00 1.00 ]
| 0.865 - 0.87 : [ 3 0.00 1.00 ]
| 0.87 - 0.875 : [ 1 0.00 1.00 ]
| 0.875 - 0.88 : [ 6 0.00 1.00 ]
| 0.88 - 0.885 : [ 4 0.00 1.00 ]
| 0.885 - 0.89 : [ 2 0.00 1.00 ]
#...
| 0.895 - 0.9 : [ 2 0.00 1.00 ]
| 0.9 - 0.905 : [ 2 0.00 1.00 ]
#...
| 0.91 - 0.915 : [ 2 0.00 1.00 ]
#...
| 0.925 - 0.93 : [ 1 0.00 1.00 ]
#...
| 0.945 - 0.95 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 2 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 152. 356 reads; 25955 bp (untrimmed), 25955 (trimmed).
Contig 153. 362 reads; 34986 bp (untrimmed), 34070 (trimmed).
Contig 154. 363 reads; 24643 bp (untrimmed), 24224 (trimmed).
Contig 155. 372 reads; 34734 bp (untrimmed), 33900 (trimmed).
Contig 156. 383 reads; 37496 bp (untrimmed), 37496 (trimmed).
Contig 157. 435 reads; 40547 bp (untrimmed), 40527 (trimmed).
Contig 158. 462 reads; 35547 bp (untrimmed), 34658 (trimmed).
Contig 159. 477 reads; 40066 bp (untrimmed), 39172 (trimmed).
Contig 160. 481 reads; 35535 bp (untrimmed), 34796 (trimmed).
Contig 161. 518 reads; 38320 bp (untrimmed), 37743 (trimmed).
Contig 162. 524 reads; 48601 bp (untrimmed), 48571 (trimmed).
Contig 163. 524 reads; 43071 bp (untrimmed), 43071 (trimmed).
Contig 164. 580 reads; 56021 bp (untrimmed), 55516 (trimmed).
Contig 165. 587 reads; 66614 bp (untrimmed), 65882 (trimmed).
Contig 166. 621 reads; 59920 bp (untrimmed), 59920 (trimmed).
Contig 167. 727 reads; 60762 bp (untrimmed), 60723 (trimmed).
Contig 168. 733 reads; 61834 bp (untrimmed), 60730 (trimmed).
Contig 169. 740 reads; 49041 bp (untrimmed), 47814 (trimmed).
Contig 170. 790 reads; 54000 bp (untrimmed), 54000 (trimmed).
Contig 171. 1017 reads; 64386 bp (untrimmed), 63765 (trimmed).
Contig 172. 1097 reads; 84407 bp (untrimmed), 84407 (trimmed).
Contig 173. 1200 reads; 78489 bp (untrimmed), 77913 (trimmed).
Contig 174. 1244 reads; 113386 bp (untrimmed), 111958 (trimmed).
Contig 175. 1334 reads; 93897 bp (untrimmed), 93897 (trimmed).
Contig 176. 1496 reads; 112444 bp (untrimmed), 111928 (trimmed).
Contig 177. 1611 reads; 111506 bp (untrimmed), 110529 (trimmed).
Contig 178. 2439 reads; 148676 bp (untrimmed), 148676 (trimmed).
--------------------------------------------------------------
Totals 37140 reads; 3299423 bp (untrimmed), 3217347 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3295356 bases = 9.99 +- 4.86 = 0.39 +- 3.72
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 172 total values totalling 1301.6000. <7.567442 +/- 3.125748>
#Range: [ 1.22 - 14.78 ]
#Most likely bin: [ 7.5 - 8 ] 14 counts
#Median bin: [ 7.5 - 8 ] 14 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXX 1 - 1.5 : [ 5 0.03 0.03 ]
|XXXXXXXXXXX 1.5 - 2 : [ 4 0.02 0.05 ]
|XXXXXXXXXXXXXX 2 - 2.5 : [ 5 0.03 0.08 ]
|XXXXXXXXXXXXXX 2.5 - 3 : [ 5 0.03 0.11 ]
|XXXXXXXXXXXXXXXXX 3 - 3.5 : [ 6 0.03 0.15 ]
|XXXXXXXXXXX 3.5 - 4 : [ 4 0.02 0.17 ]
|XXXXXXXXXXX 4 - 4.5 : [ 4 0.02 0.19 ]
|XXXXXXXXX 4.5 - 5 : [ 3 0.02 0.21 ]
|XXXXXXXXXXX 5 - 5.5 : [ 4 0.02 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 10 0.06 0.29 ]
|XXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 7 0.04 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 8 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 11 0.06 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 14 0.08 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 11 0.06 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 13 0.08 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 13 0.08 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 12 0.07 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 8 0.05 0.85 ]
|XXXXXXXXXXXXXXXXX 10.5 - 11 : [ 6 0.03 0.89 ]
|XXXXXXXXX 11 - 11.5 : [ 3 0.02 0.91 ]
|XXXXXX 11.5 - 12 : [ 2 0.01 0.92 ]
|XXXXXXXXXXX 12 - 12.5 : [ 4 0.02 0.94 ]
|XXXXXXXXX 12.5 - 13 : [ 3 0.02 0.96 ]
|XXXXXX 13 - 13.5 : [ 2 0.01 0.97 ]
|XXX 13.5 - 14 : [ 1 0.01 0.98 ]
|XXXXXX 14 - 14.5 : [ 2 0.01 0.99 ]
|XXXXXX 14.5 - 15 : [ 2 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 145 total values totalling 1222.1800. <8.428828 +/- 2.522434>
#Range: [ 2.43 - 14.78 ]
#Most likely bin: [ 8.5 - 9 ] 13 counts
#Median bin: [ 8 - 8.5 ] 11 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 2 - 2.5 : [ 1 0.01 0.01 ]
|XXX 2.5 - 3 : [ 1 0.01 0.01 ]
|XXXXXX 3 - 3.5 : [ 2 0.01 0.03 ]
|XXXXXXXXX 3.5 - 4 : [ 3 0.02 0.05 ]
|XXXXXXXXX 4 - 4.5 : [ 3 0.02 0.07 ]
|XXXXXX 4.5 - 5 : [ 2 0.01 0.08 ]
|XXXXXXXXXXXX 5 - 5.5 : [ 4 0.03 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 9 0.06 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 7 0.05 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 7 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 11 0.08 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 13 0.09 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 11 0.08 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 13 0.09 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 13 0.09 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 12 0.08 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 8 0.06 0.83 ]
|XXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 6 0.04 0.87 ]
|XXXXXXXXX 11 - 11.5 : [ 3 0.02 0.89 ]
|XXXXXX 11.5 - 12 : [ 2 0.01 0.90 ]
|XXXXXXXXXXXX 12 - 12.5 : [ 4 0.03 0.93 ]
|XXXXXXXXX 12.5 - 13 : [ 3 0.02 0.95 ]
|XXXXXX 13 - 13.5 : [ 2 0.01 0.97 ]
|XXX 13.5 - 14 : [ 1 0.01 0.97 ]
|XXXXXX 14 - 14.5 : [ 2 0.01 0.99 ]
|XXXXXX 14.5 - 15 : [ 2 0.01 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 4 2 reads 1299 bases = 1.22 +- 0.41 = 1.22 +- 0.41
Contig 8 3 reads 1921 bases = 1.23 +- 0.42 = 0.59 +- 0.94
Contig 9 3 reads 1439 bases = 1.38 +- 0.74 = 1.38 +- 0.74
Contig 6 3 reads 1264 bases = 1.41 +- 0.65 = 1.41 +- 0.65
Contig 5 2 reads 738 bases = 1.44 +- 0.50 = -0.50 +- 0.56
Contig 13 3 reads 2069 bases = 1.60 +- 0.82 = 0.32 +- 0.85
Contig 14 4 reads 1809 bases = 1.75 +- 0.80 = 1.75 +- 0.80
Contig 24 7 reads 2385 bases = 1.91 +- 1.48 = 1.49 +- 0.84
Contig 18 6 reads 1291 bases = 1.97 +- 0.87 = 1.50 +- 0.85
Contig 17 6 reads 1291 bases = 2.06 +- 1.32 = -0.47 +- 0.97
Contig 25 7 reads 2470 bases = 2.32 +- 1.32 = 1.16 +- 2.29
Contig 22 7 reads 530 bases = 2.39 +- 1.26 = 0.07 +- 0.77
Contig 36 11 reads 3052 bases = 2.43 +- 2.16 = 0.37 +- 1.63
Contig 26 7 reads 2362 bases = 2.45 +- 1.28 = 0.76 +- 1.84
Contig 7 3 reads 894 bases = 2.50 +- 0.63 = 0.65 +- 0.48
Contig 12 3 reads 1232 bases = 2.55 +- 0.79 = 2.55 +- 0.79
Contig 23 7 reads 1431 bases = 2.60 +- 1.98 = -0.23 +- 1.41
Contig 19 6 reads 969 bases = 2.85 +- 0.78 = 0.60 +- 1.03
Contig 41 15 reads 4014 bases = 2.99 +- 1.84 = 0.83 +- 1.49
Contig 20 6 reads 1956 bases = 3.00 +- 1.18 = 2.02 +- 1.71
Contig 168 733 reads 61834 bases = 10.89 +- 4.40 = 0.21 +- 3.74
Contig 158 462 reads 35547 bases = 11.04 +- 4.46 = 0.78 +- 3.83
Contig 130 251 reads 18917 bases = 11.32 +- 4.85 = 1.63 +- 3.96
Contig 161 518 reads 38320 bases = 11.42 +- 4.86 = 0.56 +- 4.29
Contig 167 727 reads 60762 bases = 11.55 +- 4.04 = 0.12 +- 3.51
Contig 176 1496 reads 112444 bases = 11.75 +- 4.43 = 0.02 +- 4.12
Contig 160 481 reads 35535 bases = 12.09 +- 4.46 = 0.11 +- 3.67
Contig 175 1334 reads 93897 bases = 12.24 +- 4.18 = 0.12 +- 3.85
Contig 142 303 reads 22913 bases = 12.34 +- 5.91 = 0.42 +- 3.33
Contig 172 1097 reads 84407 bases = 12.42 +- 4.61 = 0.28 +- 3.96
Contig 152 356 reads 25955 bases = 12.63 +- 4.83 = 0.79 +- 5.13
Contig 170 790 reads 54000 bases = 12.74 +- 4.26 = 0.43 +- 3.63
Contig 177 1611 reads 111506 bases = 12.95 +- 5.40 = 0.14 +- 4.49
Contig 173 1200 reads 78489 bases = 13.02 +- 4.50 = 0.23 +- 4.18
Contig 169 740 reads 49041 bases = 13.41 +- 5.76 = 0.25 +- 4.37
Contig 171 1017 reads 64386 bases = 13.91 +- 5.00 = 0.28 +- 5.31
Contig 154 363 reads 24643 bases = 14.04 +- 4.59 = 0.22 +- 5.01
Contig 140 282 reads 18058 bases = 14.49 +- 4.97 = 1.13 +- 5.26
Contig 141 292 reads 17476 bases = 14.56 +- 3.63 = 1.27 +- 3.93
Contig 178 2439 reads 148676 bases = 14.78 +- 5.53 = 0.05 +- 4.76
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1166
HQ Discrepant reads = 77
Chimeric reads = 123
Suspect alignments = 86
-------------------------------------------------------------------
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/microbe2/3436081/edit_dir.12Nov03.QD