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
3634396 1000 NULL Ehrlichia chaffeensis
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Ehrlichia_chaffeensis
-------------------------------------------------------------------
canis group, species group, a-proteobacteria
Alphaproteobacteria, class, a-proteobacteria
Ehrlichia chaffeensis, species, a-proteobacteria
Ehrlichia, genus, a-proteobacteria
Anaplasmataceae, family, a-proteobacteria
Rickettsiales (rickettsias), order, a-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 1115755
# phrap: 1031134
# db:
altered.
1000000
1048963 +/- 48909
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 0
Number of reads with percent X's >= 20%: 0 = 0.0%
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: 7056
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 0
Number of reads with percent X's >= 20%: 0 = 0.0%
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: 819
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 2104238
C = 1080018
G = 1057260
T = 2044822
N = 13389
X = 156367
GC fraction = 0.33
Total = 6456094
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634396_fasta.screen.contigs
-------------------------------------------------------------------
A 405066
C 178780
G 171489
T 397510
N 105
fraction GC = 0.30
total bases = 1152950
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 AHOC reads.list > grep.reads.list.AHOC
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHOC 4 500
-------------------------------------------------------------------
#Found 252 total values totalling 720645.0000. <2859.702381 +/- 704.267363>
#Range: [ 953 - 5144 ]
#Most likely bin: [ 2500 - 3000 ] 79 counts
#Median bin: [ 2500 - 3000 ] 79 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 1 0.00 0.00 ]
|X 1000 - 1500 : [ 1 0.00 0.01 ]
|XXXXXXXXXXX 1500 - 2000 : [ 21 0.08 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 2500 : [ 63 0.25 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 79 0.31 0.65 ]
|XXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 37 0.15 0.80 ]
|XXXXXXXXXXXXXXXX 3500 - 4000 : [ 32 0.13 0.93 ]
|XXXXXXX 4000 - 4500 : [ 13 0.05 0.98 ]
|XX 4500 - 5000 : [ 4 0.02 1.00 ]
|X 5000 - 5500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHOF reads.list > grep.reads.list.AHOF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHOF 4 500
-------------------------------------------------------------------
#Found 183 total values totalling 1099828.0000. <6009.989071 +/- 1558.860828>
#Range: [ 1263 - 8335 ]
#Most likely bin: [ 6500 - 7000 ] 42 counts
#Median bin: [ 6000 - 6500 ] 32 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 1000 - 1500 : [ 4 0.02 0.02 ]
|XXXXX 1500 - 2000 : [ 5 0.03 0.05 ]
|XX 2000 - 2500 : [ 2 0.01 0.06 ]
|XXX 2500 - 3000 : [ 3 0.02 0.08 ]
|XXXX 3000 - 3500 : [ 4 0.02 0.10 ]
|XXXX 3500 - 4000 : [ 4 0.02 0.12 ]
|XXX 4000 - 4500 : [ 3 0.02 0.14 ]
|XXXXXXX 4500 - 5000 : [ 7 0.04 0.17 ]
|XXXXXXXXXX 5000 - 5500 : [ 10 0.05 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 26 0.14 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 32 0.17 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 42 0.23 0.78 ]
|XXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 21 0.11 0.89 ]
|XXXXXXXXXXX 7500 - 8000 : [ 12 0.07 0.96 ]
|XXXXXXXX 8000 - 8500 : [ 8 0.04 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHOG reads.list > grep.reads.list.AHOG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHOG 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
-------------------------------------------------------------------
# PON 2838 +- 654 (n=727)
# NOO 1060 +- 265 (n=60)
# AHOC 2729 +- 777 (n=132)
# AHOF 5902 +- 1634 (n=87)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634396_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
AHOC 8448 -1 -1 98 739 987 99 688 100 714
AHOF 6912 -1 -1 98 698 970 99 731 100 729
AHOG 1536 -1 -1 94 596 91 89 577 100 566
NOO 1536 -1 -1 86 560 273 99 582 100 614
PON 20352 -1 -1 94 556 14190 98 522 100 544
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHOC 551 99 675 100 712 436 100 705 100 718
AHOF 482 100 731 100 731 488 99 731 100 727
AHOG 40 85 530 100 524 51 92 611 100 600
NOO 138 99 579 100 614 135 99 584 100 613
PON 6975 98 487 100 519 7215 98 556 100 568
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634396_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
36 964 575 15.97 16.64 AHOF @
8 91 69 8.62 8.98 AHOG @
100 4761 2595 25.95 27.03 PON @
40 975 550 13.75 14.32 AHOC @
8 265 143 17.88 18.62 NOO @
] 7056 3932 20.48 cumulative total@@
LIBRARY PLATE ID COUNT [ AHOF 36 AHOG 8 PON 100 AHOC 40 NOO 8 ] for 192 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 3634396_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 16511 total values totalling 8870874.0000. <537.270547 +/- 167.643951>
#Range: [ 15 - 996 ]
#Most likely bin: [ 600 - 650 ] 3413 counts
#Median bin: [ 550 - 600 ] 2463 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 62 0.00 0.00 ]
|XXX 50 - 100 : [ 243 0.01 0.02 ]
|XXXX 100 - 150 : [ 330 0.02 0.04 ]
|XXXX 150 - 200 : [ 363 0.02 0.06 ]
|XXXXX 200 - 250 : [ 411 0.02 0.09 ]
|XXXXX 250 - 300 : [ 469 0.03 0.11 ]
|XXXXXX 300 - 350 : [ 533 0.03 0.15 ]
|XXXXXXXX 350 - 400 : [ 714 0.04 0.19 ]
|XXXXXXXXXX 400 - 450 : [ 813 0.05 0.24 ]
|XXXXXXXXXXXXXX 450 - 500 : [ 1173 0.07 0.31 ]
|XXXXXXXXXXXXXXXXXXX 500 - 550 : [ 1640 0.10 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 2463 0.15 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3413 0.21 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2209 0.13 0.90 ]
|XXXXXXXX 700 - 750 : [ 661 0.04 0.94 ]
|XXXXXXX 750 - 800 : [ 624 0.04 0.98 ]
|XXXX 800 - 850 : [ 318 0.02 1.00 ]
|X 850 - 900 : [ 56 0.00 1.00 ]
| 900 - 950 : [ 14 0.00 1.00 ]
| 950 - 1000 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHOC
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHOC 3634396_fasta.screen.trimQ15.SaF > reads.trim15.AHOC.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHOC.rl 2 50
-------------------------------------------------------------------
#Found 987 total values totalling 675409.0000. <684.304965 +/- 177.995700>
#Range: [ 30 - 996 ]
#Most likely bin: [ 750 - 800 ] 260 counts
#Median bin: [ 700 - 750 ] 174 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 2 0.00 0.00 ]
|X 50 - 100 : [ 4 0.00 0.01 ]
|XX 100 - 150 : [ 13 0.01 0.02 ]
|XX 150 - 200 : [ 14 0.01 0.03 ]
|XX 200 - 250 : [ 11 0.01 0.04 ]
|XXX 250 - 300 : [ 17 0.02 0.06 ]
|XXX 300 - 350 : [ 17 0.02 0.08 ]
|XXXXX 350 - 400 : [ 31 0.03 0.11 ]
|XX 400 - 450 : [ 11 0.01 0.12 ]
|XXXX 450 - 500 : [ 24 0.02 0.15 ]
|XXXX 500 - 550 : [ 26 0.03 0.17 ]
|XXXXX 550 - 600 : [ 30 0.03 0.20 ]
|XXXXXXX 600 - 650 : [ 47 0.05 0.25 ]
|XXXXXXXXXXXXXXX 650 - 700 : [ 95 0.10 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 174 0.18 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 260 0.26 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 147 0.15 0.94 ]
|XXXXXXX 850 - 900 : [ 48 0.05 0.98 ]
|XX 900 - 950 : [ 14 0.01 1.00 ]
| 950 - 1000 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHOF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHOF 3634396_fasta.screen.trimQ15.SaF > reads.trim15.AHOF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHOF.rl 2 50
-------------------------------------------------------------------
#Found 970 total values totalling 705961.0000. <727.794845 +/- 116.189687>
#Range: [ 32 - 877 ]
#Most likely bin: [ 750 - 800 ] 350 counts
#Median bin: [ 750 - 800 ] 350 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 1 0.00 0.00 ]
| 50 - 100 : [ 4 0.00 0.01 ]
|X 100 - 150 : [ 5 0.01 0.01 ]
| 150 - 200 : [ 2 0.00 0.01 ]
|X 200 - 250 : [ 5 0.01 0.02 ]
| 250 - 300 : [ 1 0.00 0.02 ]
|X 300 - 350 : [ 7 0.01 0.03 ]
|X 350 - 400 : [ 9 0.01 0.04 ]
|X 400 - 450 : [ 7 0.01 0.04 ]
| 450 - 500 : [ 3 0.00 0.05 ]
|XX 500 - 550 : [ 14 0.01 0.06 ]
|XX 550 - 600 : [ 15 0.02 0.08 ]
|XXXX 600 - 650 : [ 39 0.04 0.12 ]
|XXXXXXXXX 650 - 700 : [ 83 0.09 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 247 0.25 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 350 0.36 0.82 ]
|XXXXXXXXXXXXXXXXXXX 800 - 850 : [ 170 0.18 0.99 ]
|X 850 - 900 : [ 8 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHOG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHOG 3634396_fasta.screen.trimQ15.SaF > reads.trim15.AHOG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHOG.rl 2 50
-------------------------------------------------------------------
#Found 91 total values totalling 47354.0000. <520.373626 +/- 234.583177>
#Range: [ 15 - 810 ]
#Most likely bin: [ 700 - 750 ] 14 counts
#Median bin: [ 600 - 650 ] 10 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 0 - 50 : [ 4 0.04 0.04 ]
|XXXXXXXXXXXXXXXXX 50 - 100 : [ 6 0.07 0.11 ]
|XXX 100 - 150 : [ 1 0.01 0.12 ]
|XXXXXXXXX 150 - 200 : [ 3 0.03 0.15 ]
|XXXXXX 200 - 250 : [ 2 0.02 0.18 ]
|XXXXXXXXX 250 - 300 : [ 3 0.03 0.21 ]
|XXXXXX 300 - 350 : [ 2 0.02 0.23 ]
|XXXXXXXXXXXXXX 350 - 400 : [ 5 0.05 0.29 ]
|XXXXXXXXXXX 400 - 450 : [ 4 0.04 0.33 ]
|XXXXXXXXX 450 - 500 : [ 3 0.03 0.36 ]
|XXXXXXXXXXXXXXXXX 500 - 550 : [ 6 0.07 0.43 ]
|XXXXXXXXXXXXXX 550 - 600 : [ 5 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 10 0.11 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 10 0.11 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 14 0.15 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 12 0.13 0.99 ]
|XXX 800 - 850 : [ 1 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for BFUH
trimt JAZZ trim 15 readlength histogram for BFUI
trimt JAZZ trim 15 readlength histogram for BFUN
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634396
-------------------------------------------------------------------
AHOC.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHOF.000001.000100 pMCL200.fa LRS.fasta
AHOG.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
BFUH.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AHOC.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHOF.000001.000100 pMCL200.fa LRS.fasta
AHOG.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
BFUH.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634396_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634396_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 7034 total values totalling 2271.4533. <0.322925 +/- 0.087152>
#Range: [ 0.1509 - 0.9131 ]
#Most likely bin: [ 0.3 - 0.305 ] 344 counts
#Median bin: [ 0.3 - 0.305 ] 344 counts
| 0.15 - 0.155 : [ 2 0.00 0.00 ]
| 0.155 - 0.16 : [ 3 0.00 0.00 ]
#...
| 0.165 - 0.17 : [ 1 0.00 0.00 ]
| 0.17 - 0.175 : [ 3 0.00 0.00 ]
| 0.175 - 0.18 : [ 4 0.00 0.00 ]
|X 0.18 - 0.185 : [ 5 0.00 0.00 ]
|X 0.185 - 0.19 : [ 11 0.00 0.00 ]
|X 0.19 - 0.195 : [ 11 0.00 0.01 ]
|XX 0.195 - 0.2 : [ 13 0.00 0.01 ]
|XX 0.2 - 0.205 : [ 20 0.00 0.01 ]
|XX 0.205 - 0.21 : [ 21 0.00 0.01 ]
|XXX 0.21 - 0.215 : [ 26 0.00 0.02 ]
|XXXXX 0.215 - 0.22 : [ 40 0.01 0.02 ]
|XXXXX 0.22 - 0.225 : [ 43 0.01 0.03 ]
|XXXXXXXX 0.225 - 0.23 : [ 67 0.01 0.04 ]
|XXXXXXXXX 0.23 - 0.235 : [ 78 0.01 0.05 ]
|XXXXXXXXXXX 0.235 - 0.24 : [ 94 0.01 0.06 ]
|XXXXXXXXXXXXX 0.24 - 0.245 : [ 116 0.02 0.08 ]
|XXXXXXXXXX 0.245 - 0.25 : [ 90 0.01 0.09 ]
|XXXXXXXXXXXXXXXXXXXXX 0.25 - 0.255 : [ 179 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXXXX 0.255 - 0.26 : [ 175 0.02 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.26 - 0.265 : [ 231 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.265 - 0.27 : [ 239 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.27 - 0.275 : [ 265 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.275 - 0.28 : [ 250 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.28 - 0.285 : [ 263 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.285 - 0.29 : [ 329 0.05 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 326 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.295 - 0.3 : [ 278 0.04 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 344 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 318 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 288 0.04 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 291 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 311 0.04 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 239 0.03 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 222 0.03 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 207 0.03 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 186 0.03 0.79 ]
|XXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 151 0.02 0.82 ]
|XXXXXXXXXXXXXX 0.35 - 0.355 : [ 117 0.02 0.83 ]
|XXXXXXXXXXXX 0.355 - 0.36 : [ 99 0.01 0.85 ]
|XXXXXXXXX 0.36 - 0.365 : [ 77 0.01 0.86 ]
|XXXXXXXXX 0.365 - 0.37 : [ 75 0.01 0.87 ]
|XXXXXXX 0.37 - 0.375 : [ 62 0.01 0.88 ]
|XXXX 0.375 - 0.38 : [ 35 0.00 0.88 ]
|XXXXX 0.38 - 0.385 : [ 43 0.01 0.89 ]
|XXXX 0.385 - 0.39 : [ 32 0.00 0.89 ]
|XXXX 0.39 - 0.395 : [ 32 0.00 0.90 ]
|XXX 0.395 - 0.4 : [ 26 0.00 0.90 ]
|XXXX 0.4 - 0.405 : [ 32 0.00 0.91 ]
|XX 0.405 - 0.41 : [ 21 0.00 0.91 ]
|XX 0.41 - 0.415 : [ 13 0.00 0.91 ]
|XX 0.415 - 0.42 : [ 21 0.00 0.91 ]
|XX 0.42 - 0.425 : [ 14 0.00 0.92 ]
|XX 0.425 - 0.43 : [ 16 0.00 0.92 ]
|X 0.43 - 0.435 : [ 11 0.00 0.92 ]
|XX 0.435 - 0.44 : [ 16 0.00 0.92 ]
|X 0.44 - 0.445 : [ 10 0.00 0.92 ]
|X 0.445 - 0.45 : [ 8 0.00 0.92 ]
|XX 0.45 - 0.455 : [ 16 0.00 0.93 ]
|XX 0.455 - 0.46 : [ 15 0.00 0.93 ]
|X 0.46 - 0.465 : [ 6 0.00 0.93 ]
|X 0.465 - 0.47 : [ 11 0.00 0.93 ]
| 0.47 - 0.475 : [ 4 0.00 0.93 ]
|X 0.475 - 0.48 : [ 7 0.00 0.93 ]
|X 0.48 - 0.485 : [ 12 0.00 0.93 ]
|X 0.485 - 0.49 : [ 11 0.00 0.94 ]
|X 0.49 - 0.495 : [ 12 0.00 0.94 ]
|X 0.495 - 0.5 : [ 5 0.00 0.94 ]
|X 0.5 - 0.505 : [ 9 0.00 0.94 ]
|X 0.505 - 0.51 : [ 8 0.00 0.94 ]
|X 0.51 - 0.515 : [ 7 0.00 0.94 ]
|X 0.515 - 0.52 : [ 12 0.00 0.94 ]
|X 0.52 - 0.525 : [ 5 0.00 0.94 ]
|X 0.525 - 0.53 : [ 8 0.00 0.95 ]
|X 0.53 - 0.535 : [ 10 0.00 0.95 ]
|X 0.535 - 0.54 : [ 5 0.00 0.95 ]
|X 0.54 - 0.545 : [ 8 0.00 0.95 ]
|X 0.545 - 0.55 : [ 12 0.00 0.95 ]
|X 0.55 - 0.555 : [ 10 0.00 0.95 ]
|X 0.555 - 0.56 : [ 6 0.00 0.95 ]
|X 0.56 - 0.565 : [ 8 0.00 0.95 ]
|X 0.565 - 0.57 : [ 12 0.00 0.96 ]
|XX 0.57 - 0.575 : [ 21 0.00 0.96 ]
|X 0.575 - 0.58 : [ 12 0.00 0.96 ]
|XX 0.58 - 0.585 : [ 20 0.00 0.96 ]
|XXX 0.585 - 0.59 : [ 22 0.00 0.97 ]
|XX 0.59 - 0.595 : [ 13 0.00 0.97 ]
|XX 0.595 - 0.6 : [ 14 0.00 0.97 ]
|X 0.6 - 0.605 : [ 12 0.00 0.97 ]
|XX 0.605 - 0.61 : [ 17 0.00 0.97 ]
|XX 0.61 - 0.615 : [ 16 0.00 0.98 ]
|XX 0.615 - 0.62 : [ 16 0.00 0.98 ]
|X 0.62 - 0.625 : [ 9 0.00 0.98 ]
|XX 0.625 - 0.63 : [ 15 0.00 0.98 ]
|XX 0.63 - 0.635 : [ 18 0.00 0.98 ]
|XX 0.635 - 0.64 : [ 18 0.00 0.99 ]
|X 0.64 - 0.645 : [ 8 0.00 0.99 ]
|X 0.645 - 0.65 : [ 11 0.00 0.99 ]
|X 0.65 - 0.655 : [ 11 0.00 0.99 ]
|X 0.655 - 0.66 : [ 6 0.00 0.99 ]
|X 0.66 - 0.665 : [ 6 0.00 0.99 ]
|X 0.665 - 0.67 : [ 6 0.00 0.99 ]
|X 0.67 - 0.675 : [ 5 0.00 0.99 ]
| 0.675 - 0.68 : [ 2 0.00 0.99 ]
| 0.68 - 0.685 : [ 3 0.00 1.00 ]
| 0.685 - 0.69 : [ 4 0.00 1.00 ]
| 0.69 - 0.695 : [ 2 0.00 1.00 ]
| 0.695 - 0.7 : [ 4 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 ]
| 0.715 - 0.72 : [ 1 0.00 1.00 ]
#...
| 0.725 - 0.73 : [ 1 0.00 1.00 ]
| 0.73 - 0.735 : [ 1 0.00 1.00 ]
#...
| 0.74 - 0.745 : [ 1 0.00 1.00 ]
| 0.745 - 0.75 : [ 1 0.00 1.00 ]
| 0.75 - 0.755 : [ 1 0.00 1.00 ]
| 0.755 - 0.76 : [ 2 0.00 1.00 ]
#...
| 0.765 - 0.77 : [ 1 0.00 1.00 ]
#...
| 0.775 - 0.78 : [ 1 0.00 1.00 ]
| 0.78 - 0.785 : [ 1 0.00 1.00 ]
#...
| 0.79 - 0.795 : [ 2 0.00 1.00 ]
| 0.795 - 0.8 : [ 1 0.00 1.00 ]
#...
| 0.81 - 0.815 : [ 1 0.00 1.00 ]
#...
| 0.82 - 0.825 : [ 1 0.00 1.00 ]
#...
| 0.86 - 0.865 : [ 1 0.00 1.00 ]
#...
| 0.875 - 0.88 : [ 2 0.00 1.00 ]
#...
| 0.91 - 0.915 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 176. 67 reads; 11021 bp (untrimmed), 10981 (trimmed).
Contig 177. 68 reads; 12556 bp (untrimmed), 12525 (trimmed).
Contig 178. 70 reads; 11439 bp (untrimmed), 11268 (trimmed).
Contig 179. 70 reads; 11062 bp (untrimmed), 10849 (trimmed).
Contig 180. 73 reads; 10706 bp (untrimmed), 10671 (trimmed).
Contig 181. 73 reads; 15082 bp (untrimmed), 15040 (trimmed).
Contig 182. 73 reads; 11778 bp (untrimmed), 11435 (trimmed).
Contig 183. 73 reads; 7446 bp (untrimmed), 7342 (trimmed).
Contig 184. 78 reads; 10944 bp (untrimmed), 10897 (trimmed).
Contig 185. 80 reads; 13461 bp (untrimmed), 13408 (trimmed).
Contig 186. 82 reads; 13096 bp (untrimmed), 13052 (trimmed).
Contig 187. 82 reads; 11816 bp (untrimmed), 11670 (trimmed).
Contig 188. 91 reads; 18249 bp (untrimmed), 17989 (trimmed).
Contig 189. 92 reads; 15009 bp (untrimmed), 15001 (trimmed).
Contig 190. 94 reads; 16459 bp (untrimmed), 15823 (trimmed).
Contig 191. 98 reads; 16055 bp (untrimmed), 15616 (trimmed).
Contig 192. 103 reads; 15648 bp (untrimmed), 15485 (trimmed).
Contig 193. 110 reads; 14950 bp (untrimmed), 14896 (trimmed).
Contig 194. 114 reads; 20120 bp (untrimmed), 20081 (trimmed).
Contig 195. 124 reads; 18110 bp (untrimmed), 17905 (trimmed).
Contig 196. 129 reads; 23886 bp (untrimmed), 23474 (trimmed).
Contig 197. 139 reads; 22847 bp (untrimmed), 22827 (trimmed).
Contig 198. 140 reads; 26407 bp (untrimmed), 26262 (trimmed).
Contig 199. 144 reads; 24222 bp (untrimmed), 24202 (trimmed).
Contig 200. 163 reads; 25220 bp (untrimmed), 25177 (trimmed).
Contig 201. 197 reads; 32409 bp (untrimmed), 32194 (trimmed).
Contig 202. 260 reads; 45018 bp (untrimmed), 44463 (trimmed).
--------------------------------------------------------------
Totals 6237 reads; 1152950 bp (untrimmed), 1115755 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 1152033 bases = 4.29 +- 2.19 = 0.45 +- 2.11
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 200 total values totalling 745.3000. <3.726500 +/- 1.291254>
#Range: [ 1.51 - 9.14 ]
#Most likely bin: [ 3.5 - 4 ] 30 counts
#Median bin: [ 3.5 - 4 ] 30 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 20 0.10 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 20 0.10 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 27 0.14 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 17 0.09 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 30 0.15 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 26 0.13 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 25 0.12 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 23 0.12 0.94 ]
|XXXXXXXXX 5.5 - 6 : [ 7 0.04 0.97 ]
|X 6 - 6.5 : [ 1 0.01 0.98 ]
|X 6.5 - 7 : [ 1 0.01 0.98 ]
|XXX 7 - 7.5 : [ 2 0.01 0.99 ]
#...
|X 9 - 9.5 : [ 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 125 total values totalling 545.9800. <4.367840 +/- 0.985626>
#Range: [ 2.01 - 9.14 ]
#Most likely bin: [ 3.5 - 4 ] 26 counts
#Median bin: [ 4 - 4.5 ] 24 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 2 - 2.5 : [ 2 0.02 0.02 ]
|XXXXXXXXX 2.5 - 3 : [ 6 0.05 0.06 ]
|XXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 12 0.10 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 26 0.21 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 24 0.19 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 22 0.18 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 23 0.18 0.92 ]
|XXXXXXXXXXX 5.5 - 6 : [ 7 0.06 0.98 ]
#...
|XXX 7 - 7.5 : [ 2 0.02 0.99 ]
#...
|XX 9 - 9.5 : [ 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 11 3 reads 1535 bases = 1.51 +- 0.53 = 0.53 +- 0.50
Contig 29 4 reads 2420 bases = 1.56 +- 0.65 = 1.56 +- 0.65
Contig 6 3 reads 1519 bases = 1.56 +- 0.50 = 1.56 +- 0.50
Contig 26 4 reads 2150 bases = 1.58 +- 0.66 = 0.86 +- 0.61
Contig 31 4 reads 1387 bases = 1.61 +- 1.07 = 1.21 +- 0.41
Contig 23 4 reads 2039 bases = 1.66 +- 0.61 = 0.76 +- 0.68
Contig 19 3 reads 1493 bases = 1.69 +- 0.59 = 0.69 +- 0.76
Contig 10 3 reads 1522 bases = 1.70 +- 0.60 = 0.80 +- 1.04
Contig 8 3 reads 1538 bases = 1.74 +- 0.79 = 0.46 +- 1.01
Contig 5 2 reads 920 bases = 1.76 +- 0.43 = 1.76 +- 0.43
Contig 42 5 reads 2247 bases = 1.83 +- 0.63 = 1.11 +- 1.08
Contig 28 4 reads 1837 bases = 1.86 +- 0.90 = 0.98 +- 0.47
Contig 4 2 reads 906 bases = 1.86 +- 0.34 = 1.86 +- 0.34
Contig 43 5 reads 2170 bases = 1.88 +- 0.88 = 1.13 +- 1.36
Contig 17 3 reads 1337 bases = 1.90 +- 0.80 = 1.90 +- 0.80
Contig 2 2 reads 998 bases = 1.91 +- 0.28 = 1.91 +- 0.28
Contig 1 2 reads 824 bases = 1.92 +- 0.27 = 1.92 +- 0.27
Contig 34 5 reads 1490 bases = 1.95 +- 1.03 = 1.69 +- 0.73
Contig 30 4 reads 1521 bases = 1.96 +- 0.80 = -0.07 +- 0.80
Contig 52 6 reads 2331 bases = 1.98 +- 0.83 = 1.98 +- 0.83
Contig 135 31 reads 4760 bases = 5.28 +- 2.23 = 0.12 +- 1.39
Contig 140 34 reads 5391 bases = 5.29 +- 2.37 = 1.47 +- 3.13
Contig 141 35 reads 5508 bases = 5.29 +- 2.67 = 0.23 +- 1.72
Contig 192 103 reads 15648 bases = 5.29 +- 2.62 = 0.19 +- 2.71
Contig 137 32 reads 4561 bases = 5.32 +- 2.43 = 0.86 +- 1.94
Contig 101 18 reads 2873 bases = 5.45 +- 2.29 = 1.67 +- 1.75
Contig 120 23 reads 3491 bases = 5.47 +- 2.29 = 0.96 +- 2.44
Contig 165 52 reads 7442 bases = 5.47 +- 2.43 = 0.17 +- 1.92
Contig 195 124 reads 18110 bases = 5.55 +- 2.60 = 0.04 +- 2.42
Contig 180 73 reads 10706 bases = 5.59 +- 2.43 = 0.10 +- 2.11
Contig 159 47 reads 6802 bases = 5.64 +- 2.65 = 0.43 +- 2.15
Contig 187 82 reads 11816 bases = 5.64 +- 2.50 = 0.97 +- 2.91
Contig 132 30 reads 4215 bases = 5.75 +- 2.31 = 0.96 +- 1.73
Contig 184 78 reads 10944 bases = 5.84 +- 2.56 = 0.60 +- 2.53
Contig 193 110 reads 14950 bases = 5.90 +- 2.65 = 0.53 +- 2.41
Contig 93 15 reads 1920 bases = 6.42 +- 3.11 = 1.62 +- 1.66
Contig 74 10 reads 1075 bases = 6.83 +- 2.49 = 2.90 +- 2.00
Contig 147 37 reads 3783 bases = 7.11 +- 3.35 = 0.29 +- 1.46
Contig 183 73 reads 7446 bases = 7.24 +- 3.30 = 0.19 +- 1.99
Contig 149 38 reads 3067 bases = 9.14 +- 4.02 = 0.09 +- 1.88
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 38
Chimeric reads = 10
Suspect alignments = 6
-------------------------------------------------------------------
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/microbe3/3634396/edit_dir.16Jun04.QD