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 in progress (or initial analysis of completed)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3640420 2600 NULL Marinobacter aquaeolei
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Marinobacter_aquaeolei
-------------------------------------------------------------------
Alteromonadales, order, g-proteobacteria
Alteromonadaceae, family, g-proteobacteria
Marinobacter hydrocarbonoclasticus, species, g-proteobacteria
Marinobacter, genus, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3908789
# phrap: 2929695
# db:
altered.
2600000
3146161 +/- 555802
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 3282
Number of reads with percent X's >= 20%: 608 = 4.0%
Number of reads with percent X's >= 50%: 574 = 3.8%
Number of reads with percent X's >= 80%: 520 = 3.4%
Total reads in project: 15207
Total bp X'd : 588847
reads >= 20% >= 50% >= 80% screened
Nr with L09136 2991 321 303 264
Nr with LRS 20 20 20 20
Nr with pMCL200_JGI_XZX+XZK 271 267 251 236
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 607
Number of reads with percent X's >= 20%: 547 = 37.7%
Number of reads with percent X's >= 50%: 537 = 37.0%
Number of reads with percent X's >= 80%: 507 = 34.9%
Total reads in project: 1452
Total bp X'd : 458097
reads >= 20% >= 50% >= 80% screened
Nr with L09136 353 293 287 264
Nr with LRS 20 20 20 20
Nr with pMCL200_JGI_XZX+XZK 234 234 230 223
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 2947873
C = 3764096
G = 3788519
T = 2874300
N = 87592
X = 588847
GC fraction = 0.54
Total = 14051227
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3640420_fasta.screen.contigs
-------------------------------------------------------------------
A 869462
C 1157519
G 1156035
T 873544
N 1362
fraction GC = 0.57
total bases = 4057922
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 ATST reads.list > grep.reads.list.ATST
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ATST 4 500
-------------------------------------------------------------------
#Found 1610 total values totalling 5035039.0000. <3127.353416 +/- 301.784580>
#Range: [ 638 - 3825 ]
#Most likely bin: [ 3000 - 3500 ] 1090 counts
#Median bin: [ 3000 - 3500 ] 1090 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 6 0.00 0.00 ]
| 1000 - 1500 : [ 8 0.00 0.01 ]
| 1500 - 2000 : [ 5 0.00 0.01 ]
| 2000 - 2500 : [ 4 0.00 0.01 ]
|XXXXXXXXXXXXXXX 2500 - 3000 : [ 396 0.25 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1090 0.68 0.94 ]
|XXXX 3500 - 4000 : [ 101 0.06 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ATSU reads.list > grep.reads.list.ATSU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ATSU 4 500
-------------------------------------------------------------------
#Found 798 total values totalling 4121066.0000. <5164.243108 +/- 728.212252>
#Range: [ 994 - 6288 ]
#Most likely bin: [ 5000 - 5500 ] 302 counts
#Median bin: [ 5000 - 5500 ] 302 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
|X 1000 - 1500 : [ 7 0.01 0.01 ]
|X 1500 - 2000 : [ 9 0.01 0.02 ]
| 2000 - 2500 : [ 1 0.00 0.02 ]
|X 2500 - 3000 : [ 6 0.01 0.03 ]
| 3000 - 3500 : [ 1 0.00 0.03 ]
| 3500 - 4000 : [ 1 0.00 0.03 ]
| 4000 - 4500 : [ 3 0.00 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 229 0.29 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5000 - 5500 : [ 302 0.38 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 201 0.25 0.95 ]
|XXXXX 6000 - 6500 : [ 37 0.05 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ATSW reads.list > grep.reads.list.ATSW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ATSW 4 500
-------------------------------------------------------------------
#Found -1 total values totalling 0.0000. <-0.000000 +/- 0.000000>
#Range: [ - ]
#Most likely bin: [ 0 - 500 ] 1 counts
#Median bin: [ 0 - 500 ] counts
#Histogram Bins Count Fraction Cum_Fraction
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# ATSU 5057 +- 987 (n=391)
# ATST 3005 +- 395 (n=806)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3640420_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
ATST 23808 89 717 95 760 7623 89 614 94 617
ATSU 23808 93 759 97 727 7296 93 796 97 788
ATSW 3072 89 642 95 632 288 96 633 100 655
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
ATST 3820 88 607 94 613 3803 89 621 94 622
ATSU 3456 93 797 98 787 3840 93 796 97 788
ATSW 288 96 633 100 655 0 0 0 0 0
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3640420_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
40 7623 3838 95.95 99.95 ATST @
40 7296 3840 96.00 100.00 ATSU @
3 288 288 96.00 100.00 ATSW @
] 15207 7966 95.98 cumulative total@@
LIBRARY PLATE ID COUNT [ ATST 40 ATSU 40 ATSW 3 ] for 83 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 3640420_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 15207 total values totalling 9759176.0000. <641.755507 +/- 241.640686>
#Range: [ 0 - 929 ]
#Most likely bin: [ 800 - 850 ] 3336 counts
#Median bin: [ 700 - 750 ] 1738 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 0 - 50 : [ 1267 0.08 0.08 ]
|X 50 - 100 : [ 96 0.01 0.09 ]
|X 100 - 150 : [ 90 0.01 0.10 ]
|X 150 - 200 : [ 87 0.01 0.10 ]
|X 200 - 250 : [ 85 0.01 0.11 ]
|X 250 - 300 : [ 102 0.01 0.11 ]
|X 300 - 350 : [ 121 0.01 0.12 ]
|XX 350 - 400 : [ 184 0.01 0.13 ]
|XXX 400 - 450 : [ 232 0.02 0.15 ]
|XXXX 450 - 500 : [ 330 0.02 0.17 ]
|XXXXX 500 - 550 : [ 441 0.03 0.20 ]
|XXXXXXXXX 550 - 600 : [ 756 0.05 0.25 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 1319 0.09 0.34 ]
|XXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1673 0.11 0.45 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1738 0.11 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2452 0.16 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3336 0.22 0.94 ]
|XXXXXXXXXXX 850 - 900 : [ 882 0.06 1.00 ]
| 900 - 950 : [ 16 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATST
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ATST 3640420_fasta.screen.trimQ15.SaF > reads.trim15.ATST.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ATST.rl 2 50
-------------------------------------------------------------------
#Found 7623 total values totalling 4167622.0000. <546.716778 +/- 227.162498>
#Range: [ 0 - 841 ]
#Most likely bin: [ 650 - 700 ] 1579 counts
#Median bin: [ 600 - 650 ] 1260 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 782 0.10 0.10 ]
|XX 50 - 100 : [ 70 0.01 0.11 ]
|XX 100 - 150 : [ 69 0.01 0.12 ]
|XX 150 - 200 : [ 63 0.01 0.13 ]
|XX 200 - 250 : [ 67 0.01 0.14 ]
|XX 250 - 300 : [ 77 0.01 0.15 ]
|XX 300 - 350 : [ 98 0.01 0.16 ]
|XXXX 350 - 400 : [ 159 0.02 0.18 ]
|XXXXX 400 - 450 : [ 202 0.03 0.21 ]
|XXXXXXXX 450 - 500 : [ 304 0.04 0.25 ]
|XXXXXXXXXX 500 - 550 : [ 410 0.05 0.30 ]
|XXXXXXXXXXXXXXXXXX 550 - 600 : [ 713 0.09 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1260 0.17 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1579 0.21 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1308 0.17 0.94 ]
|XXXXXXXXXXX 750 - 800 : [ 431 0.06 1.00 ]
|X 800 - 850 : [ 31 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATSU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ATSU 3640420_fasta.screen.trimQ15.SaF > reads.trim15.ATSU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ATSU.rl 2 50
-------------------------------------------------------------------
#Found 7296 total values totalling 5415755.0000. <742.290981 +/- 214.655065>
#Range: [ 0 - 929 ]
#Most likely bin: [ 800 - 850 ] 3261 counts
#Median bin: [ 800 - 850 ] 3261 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 0 - 50 : [ 478 0.07 0.07 ]
| 50 - 100 : [ 22 0.00 0.07 ]
| 100 - 150 : [ 15 0.00 0.07 ]
| 150 - 200 : [ 20 0.00 0.07 ]
| 200 - 250 : [ 9 0.00 0.07 ]
| 250 - 300 : [ 10 0.00 0.08 ]
| 300 - 350 : [ 13 0.00 0.08 ]
| 350 - 400 : [ 17 0.00 0.08 ]
| 400 - 450 : [ 19 0.00 0.08 ]
| 450 - 500 : [ 20 0.00 0.09 ]
| 500 - 550 : [ 24 0.00 0.09 ]
| 550 - 600 : [ 31 0.00 0.09 ]
|X 600 - 650 : [ 46 0.01 0.10 ]
|X 650 - 700 : [ 71 0.01 0.11 ]
|XXXXX 700 - 750 : [ 387 0.05 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1967 0.27 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3261 0.45 0.88 ]
|XXXXXXXXXXX 850 - 900 : [ 870 0.12 1.00 ]
| 900 - 950 : [ 16 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATSW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ATSW 3640420_fasta.screen.trimQ15.SaF > reads.trim15.ATSW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ATSW.rl 2 50
-------------------------------------------------------------------
#Found 288 total values totalling 175799.0000. <610.413194 +/- 232.106760>
#Range: [ 0 - 887 ]
#Most likely bin: [ 750 - 800 ] 54 counts
#Median bin: [ 700 - 750 ] 43 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 0 - 50 : [ 7 0.02 0.02 ]
|XXX 50 - 100 : [ 4 0.01 0.04 ]
|XXXX 100 - 150 : [ 6 0.02 0.06 ]
|XXX 150 - 200 : [ 4 0.01 0.07 ]
|XXXXXXX 200 - 250 : [ 9 0.03 0.10 ]
|XXXXXXXXXXX 250 - 300 : [ 15 0.05 0.16 ]
|XXXXXXX 300 - 350 : [ 10 0.03 0.19 ]
|XXXXXX 350 - 400 : [ 8 0.03 0.22 ]
|XXXXXXXX 400 - 450 : [ 11 0.04 0.26 ]
|XXXX 450 - 500 : [ 6 0.02 0.28 ]
|XXXXX 500 - 550 : [ 7 0.02 0.30 ]
|XXXXXXXXX 550 - 600 : [ 12 0.04 0.34 ]
|XXXXXXXXXX 600 - 650 : [ 13 0.05 0.39 ]
|XXXXXXXXXXXXXXXXX 650 - 700 : [ 23 0.08 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 43 0.15 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 54 0.19 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 44 0.15 0.96 ]
|XXXXXXXXX 850 - 900 : [ 12 0.04 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3640420
-------------------------------------------------------------------
ATST.000001.000100 pUC18.fa pUC18.fa LRS.fasta
ATST.000101.000200 pUC18.fa pUC18.fa LRS.fasta
ATSU.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
ATSU.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
ATSW.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
ATST.000001.000100 pUC18.fa pUC18.fa LRS.fasta
ATST.000101.000200 pUC18.fa pUC18.fa LRS.fasta
ATSU.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
ATSU.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
ATSW.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3640420_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3640420_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 13955 total values totalling 7946.1537. <0.569413 +/- 0.041384>
#Range: [ 0.2667 - 0.7917 ]
#Most likely bin: [ 0.585 - 0.59 ] 790 counts
#Median bin: [ 0.57 - 0.575 ] 783 counts
#Entropy = 5.0343 bits
| 0.265 - 0.27 : [ 1 0.00 0.00 ]
#...
| 0.3 - 0.305 : [ 1 0.00 0.00 ]
#...
| 0.32 - 0.325 : [ 1 0.00 0.00 ]
#...
| 0.33 - 0.335 : [ 1 0.00 0.00 ]
#...
| 0.36 - 0.365 : [ 2 0.00 0.00 ]
| 0.365 - 0.37 : [ 1 0.00 0.00 ]
#...
| 0.375 - 0.38 : [ 1 0.00 0.00 ]
| 0.38 - 0.385 : [ 2 0.00 0.00 ]
| 0.385 - 0.39 : [ 3 0.00 0.00 ]
| 0.39 - 0.395 : [ 6 0.00 0.00 ]
| 0.395 - 0.4 : [ 1 0.00 0.00 ]
| 0.4 - 0.405 : [ 5 0.00 0.00 ]
|X 0.405 - 0.41 : [ 10 0.00 0.00 ]
| 0.41 - 0.415 : [ 6 0.00 0.00 ]
| 0.415 - 0.42 : [ 4 0.00 0.00 ]
| 0.42 - 0.425 : [ 9 0.00 0.00 ]
|X 0.425 - 0.43 : [ 13 0.00 0.00 ]
|X 0.43 - 0.435 : [ 10 0.00 0.01 ]
|X 0.435 - 0.44 : [ 17 0.00 0.01 ]
|X 0.44 - 0.445 : [ 19 0.00 0.01 ]
|X 0.445 - 0.45 : [ 14 0.00 0.01 ]
|X 0.45 - 0.455 : [ 26 0.00 0.01 ]
|XX 0.455 - 0.46 : [ 33 0.00 0.01 ]
|XX 0.46 - 0.465 : [ 37 0.00 0.02 ]
|XX 0.465 - 0.47 : [ 48 0.00 0.02 ]
|XXX 0.47 - 0.475 : [ 58 0.00 0.02 ]
|XXX 0.475 - 0.48 : [ 63 0.00 0.03 ]
|XXXX 0.48 - 0.485 : [ 86 0.01 0.03 ]
|XXXXX 0.485 - 0.49 : [ 103 0.01 0.04 ]
|XXXXXX 0.49 - 0.495 : [ 111 0.01 0.05 ]
|XXXXXXX 0.495 - 0.5 : [ 142 0.01 0.06 ]
|XXXXXXXXXX 0.5 - 0.505 : [ 198 0.01 0.07 ]
|XXXXXXXXXX 0.505 - 0.51 : [ 202 0.01 0.09 ]
|XXXXXXXXXX 0.51 - 0.515 : [ 206 0.01 0.10 ]
|XXXXXXXXXXXXX 0.515 - 0.52 : [ 247 0.02 0.12 ]
|XXXXXXXXXXXXXX 0.52 - 0.525 : [ 273 0.02 0.14 ]
|XXXXXXXXXXXXXXX 0.525 - 0.53 : [ 302 0.02 0.16 ]
|XXXXXXXXXXXXXXX 0.53 - 0.535 : [ 292 0.02 0.18 ]
|XXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 381 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 404 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 480 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 551 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 583 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 645 0.05 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 701 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 783 0.06 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 777 0.06 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 772 0.06 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 790 0.06 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 707 0.05 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 625 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 654 0.05 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 524 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 464 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 392 0.03 0.92 ]
|XXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 316 0.02 0.94 ]
|XXXXXXXXXXXX 0.625 - 0.63 : [ 239 0.02 0.96 ]
|XXXXXXXXX 0.63 - 0.635 : [ 179 0.01 0.97 ]
|XXXXXX 0.635 - 0.64 : [ 123 0.01 0.98 ]
|XXXXX 0.64 - 0.645 : [ 95 0.01 0.98 ]
|XXXX 0.645 - 0.65 : [ 78 0.01 0.99 ]
|XX 0.65 - 0.655 : [ 47 0.00 0.99 ]
|X 0.655 - 0.66 : [ 27 0.00 1.00 ]
|X 0.66 - 0.665 : [ 21 0.00 1.00 ]
|X 0.665 - 0.67 : [ 16 0.00 1.00 ]
| 0.67 - 0.675 : [ 8 0.00 1.00 ]
| 0.675 - 0.68 : [ 3 0.00 1.00 ]
| 0.68 - 0.685 : [ 5 0.00 1.00 ]
| 0.685 - 0.69 : [ 3 0.00 1.00 ]
| 0.69 - 0.695 : [ 3 0.00 1.00 ]
| 0.695 - 0.7 : [ 2 0.00 1.00 ]
| 0.7 - 0.705 : [ 1 0.00 1.00 ]
| 0.705 - 0.71 : [ 1 0.00 1.00 ]
#...
| 0.79 - 0.795 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 1218. 50 reads; 13688 bp (untrimmed), 13662 (trimmed).
Contig 1219. 51 reads; 10888 bp (untrimmed), 10789 (trimmed).
Contig 1220. 52 reads; 12418 bp (untrimmed), 12376 (trimmed).
Contig 1221. 52 reads; 13566 bp (untrimmed), 13529 (trimmed).
Contig 1222. 54 reads; 10400 bp (untrimmed), 10239 (trimmed).
Contig 1223. 54 reads; 13297 bp (untrimmed), 13248 (trimmed).
Contig 1224. 55 reads; 14606 bp (untrimmed), 14498 (trimmed).
Contig 1225. 55 reads; 12965 bp (untrimmed), 12965 (trimmed).
Contig 1226. 56 reads; 11763 bp (untrimmed), 11681 (trimmed).
Contig 1227. 59 reads; 10699 bp (untrimmed), 10631 (trimmed).
Contig 1228. 59 reads; 11348 bp (untrimmed), 11270 (trimmed).
Contig 1229. 60 reads; 16925 bp (untrimmed), 16708 (trimmed).
Contig 1230. 62 reads; 14427 bp (untrimmed), 14372 (trimmed).
Contig 1231. 68 reads; 14313 bp (untrimmed), 14256 (trimmed).
Contig 1232. 68 reads; 14814 bp (untrimmed), 14717 (trimmed).
Contig 1233. 71 reads; 16439 bp (untrimmed), 16408 (trimmed).
Contig 1234. 72 reads; 15122 bp (untrimmed), 15057 (trimmed).
Contig 1235. 73 reads; 11200 bp (untrimmed), 11160 (trimmed).
Contig 1236. 74 reads; 19012 bp (untrimmed), 18813 (trimmed).
Contig 1237. 77 reads; 16465 bp (untrimmed), 16302 (trimmed).
Contig 1238. 84 reads; 24153 bp (untrimmed), 23680 (trimmed).
Contig 1239. 87 reads; 20317 bp (untrimmed), 20235 (trimmed).
Contig 1240. 87 reads; 17793 bp (untrimmed), 17764 (trimmed).
Contig 1241. 88 reads; 21404 bp (untrimmed), 21196 (trimmed).
Contig 1242. 91 reads; 17252 bp (untrimmed), 17167 (trimmed).
Contig 1243. 94 reads; 21332 bp (untrimmed), 21320 (trimmed).
Contig 1244. 161 reads; 25610 bp (untrimmed), 25026 (trimmed).
--------------------------------------------------------------
Totals 13755 reads; 4057922 bp (untrimmed), 3908789 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4050666 bases = 2.88 +- 1.58 = 0.58 +- 1.70
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 1233 total values totalling 3133.8800. <2.541671 +/- 0.797834>
#Range: [ 1.05 - 5.82 ]
#Most likely bin: [ 1.5 - 2 ] 266 counts
#Median bin: [ 2 - 2.5 ] 262 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXX 1 - 1.5 : [ 92 0.07 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 266 0.22 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 262 0.21 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 263 0.21 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 194 0.16 0.87 ]
|XXXXXXXXXXXXXXXX 3.5 - 4 : [ 105 0.09 0.96 ]
|XXXXX 4 - 4.5 : [ 36 0.03 0.99 ]
|X 4.5 - 5 : [ 9 0.01 1.00 ]
|X 5 - 5.5 : [ 5 0.00 1.00 ]
| 5.5 - 6 : [ 1 0.00 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 447 total values totalling 1414.4200. <3.164251 +/- 0.630734>
#Range: [ 2.03 - 5.82 ]
#Most likely bin: [ 2.5 - 3 ] 133 counts
#Median bin: [ 3 - 3.5 ] 124 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 62 0.14 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 133 0.30 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 124 0.28 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 85 0.19 0.90 ]
|XXXXXXXXXX 4 - 4.5 : [ 32 0.07 0.98 ]
|XX 4.5 - 5 : [ 6 0.01 0.99 ]
|X 5 - 5.5 : [ 4 0.01 1.00 ]
| 5.5 - 6 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 163 2 reads 1601 bases = 1.05 +- 0.22 = 0.15 +- 0.96
Contig 23 2 reads 1059 bases = 1.07 +- 0.26 = 0.05 +- 0.96
Contig 270 3 reads 2306 bases = 1.07 +- 0.25 = 0.39 +- 0.88
Contig 135 2 reads 1742 bases = 1.09 +- 0.29 = 1.09 +- 0.29
Contig 158 2 reads 1580 bases = 1.09 +- 0.29 = 1.09 +- 0.29
Contig 25 2 reads 1614 bases = 1.09 +- 0.28 = -0.11 +- 0.95
Contig 82 2 reads 1416 bases = 1.09 +- 0.28 = 1.09 +- 0.28
Contig 160 2 reads 1671 bases = 1.11 +- 0.32 = 0.01 +- 0.94
Contig 98 2 reads 1609 bases = 1.12 +- 0.32 = -0.04 +- 0.94
Contig 18 2 reads 1334 bases = 1.13 +- 0.33 = -0.33 +- 0.87
Contig 111 2 reads 954 bases = 1.14 +- 0.35 = 1.14 +- 0.35
Contig 113 2 reads 1425 bases = 1.14 +- 0.35 = -0.31 +- 0.87
Contig 260 3 reads 2115 bases = 1.14 +- 0.35 = 1.14 +- 0.35
Contig 14 2 reads 1481 bases = 1.15 +- 0.36 = 1.15 +- 0.36
Contig 190 3 reads 2185 bases = 1.15 +- 0.36 = 0.54 +- 0.91
Contig 143 2 reads 1259 bases = 1.16 +- 0.36 = 1.16 +- 0.36
Contig 35 2 reads 1620 bases = 1.17 +- 0.38 = -0.02 +- 0.91
Contig 90 2 reads 1475 bases = 1.17 +- 0.38 = -0.17 +- 0.89
Contig 169 2 reads 1266 bases = 1.18 +- 0.38 = 1.18 +- 0.38
Contig 75 2 reads 974 bases = 1.18 +- 0.38 = 1.18 +- 0.38
Contig 1212 46 reads 8890 bases = 4.44 +- 2.00 = 0.20 +- 2.21
Contig 1228 59 reads 11348 bases = 4.44 +- 1.98 = 0.41 +- 2.90
Contig 1093 22 reads 4266 bases = 4.46 +- 1.41 = 1.10 +- 2.46
Contig 1158 30 reads 5584 bases = 4.47 +- 2.92 = 1.53 +- 2.19
Contig 1215 47 reads 8575 bases = 4.49 +- 2.56 = 0.57 +- 2.23
Contig 598 7 reads 1398 bases = 4.57 +- 2.22 = 2.10 +- 1.46
Contig 838 10 reads 1990 bases = 4.57 +- 3.02 = 0.11 +- 0.79
Contig 1216 47 reads 8563 bases = 4.61 +- 2.32 = 0.16 +- 2.32
Contig 635 7 reads 1405 bases = 4.61 +- 1.99 = 0.60 +- 0.58
Contig 1112 23 reads 4324 bases = 4.63 +- 1.59 = 0.83 +- 2.11
Contig 1200 41 reads 7504 bases = 4.70 +- 1.89 = 0.24 +- 2.24
Contig 1098 22 reads 3732 bases = 4.74 +- 1.97 = 0.05 +- 2.71
Contig 1085 21 reads 3698 bases = 4.78 +- 1.86 = 0.02 +- 1.96
Contig 915 12 reads 2052 bases = 4.91 +- 2.23 = 1.51 +- 0.92
Contig 666 8 reads 1410 bases = 5.02 +- 2.29 = 1.58 +- 1.78
Contig 1102 22 reads 3645 bases = 5.12 +- 2.13 = 0.68 +- 2.53
Contig 911 12 reads 2031 bases = 5.22 +- 2.34 = 2.78 +- 2.21
Contig 1244 161 reads 25610 bases = 5.28 +- 2.40 = 0.30 +- 2.30
Contig 1235 73 reads 11200 bases = 5.44 +- 2.69 = 0.28 +- 2.49
Contig 1209 46 reads 6841 bases = 5.82 +- 3.07 = 0.27 +- 2.55
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 358
HQ Discrepant reads = 184
Chimeric reads = 28
Suspect alignments = 67
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 3.57 SUN/Ultra-2/3
Equivalent to Phil Green's version 0.990329
Score matrix (set by value of penalty: -2)
A C G T N X
A 1 -2 -2 -2 0 -3
C -2 1 -2 -2 0 -3
G -2 -2 1 -2 0 -3
T -2 -2 -2 1 0 -3
N 0 0 0 0 0 0
X -3 -3 -3 -3 0 -3
gap_init: -4
gap_ext: -3
ins_gap_ext: -3
del_gap_ext: -3
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 30
maxmatch: 55
max_group_size: 20
minscore: 55
bandwidth: 14
indexwordsize: 10
vector_bound: 20
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 13
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -5
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/microbe4/3640420/edit_dir.30Nov04.QC