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
3633862 1000 NULL Ehrlichia canis
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Ehrlichia_canis
-------------------------------------------------------------------
canis group, species group, a-proteobacteria
Alphaproteobacteria, class, a-proteobacteria
Ehrlichia canis, 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: 1545271
# phrap: 1776816
# db:
altered.
1000000
1440695 +/- 325640
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 14010
Number of reads with percent X's >= 20%: 67 = 0.3%
Number of reads with percent X's >= 50%: 38 = 0.1%
Number of reads with percent X's >= 80%: 4 = 0.0%
Total reads in project: 26782
Total bp X'd : 733478
reads >= 20% >= 50% >= 80% screened
Nr with L09136 8730 61 36 4
Nr with pCC1Fos 288 0 0 0
Nr with pMCL200_JGI_XZX+XZK 4992 6 2 0
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 589
Number of reads with percent X's >= 20%: 4 = 0.3%
Number of reads with percent X's >= 50%: 3 = 0.2%
Number of reads with percent X's >= 80%: 1 = 0.1%
Total reads in project: 1248
Total bp X'd : 29468
reads >= 20% >= 50% >= 80% screened
Nr with L09136 377 3 3 1
Nr with pCC1Fos 69 0 0 0
Nr with pMCL200_JGI_XZX+XZK 143 1 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 8548556
C = 4031267
G = 3879634
T = 8316846
N = 126672
X = 733478
GC fraction = 0.31
Total = 25636453
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3633862_fasta.screen.contigs
-------------------------------------------------------------------
A 594505
C 264956
G 190236
T 532865
N 244
fraction GC = 0.29
total bases = 1582806
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 PXH reads.list > grep.reads.list.PXH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.PXH 4 500
-------------------------------------------------------------------
#Found 7 total values totalling 261403.0000. <37343.285714 +/- 4086.584732>
#Range: [ 30291 - 43670 ]
#Most likely bin: [ 35000 - 35500 ] 2 counts
#Median bin: [ 36500 - 37000 ] 1 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 30000 - 30500 : [ 1 0.14 0.14 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 2 0.29 0.43 ]
#...
|XXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 1 0.14 0.57 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 2 0.29 0.86 ]
#...
|XXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 1 0.14 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep POO reads.list > grep.reads.list.POO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.POO 4 500
-------------------------------------------------------------------
#Found 4553 total values totalling 16048607.0000. <3524.842302 +/- 8200.066863>
#Range: [ 779 - 374248 ]
#Most likely bin: [ 3000 - 3500 ] 1665 counts
#Median bin: [ 3000 - 3500 ] 1665 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 3 0.00 0.00 ]
| 1000 - 1500 : [ 14 0.00 0.00 ]
| 1500 - 2000 : [ 16 0.00 0.01 ]
|XX 2000 - 2500 : [ 89 0.02 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 1465 0.32 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1665 0.37 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 990 0.22 0.93 ]
|XXXXXXX 4000 - 4500 : [ 304 0.07 1.00 ]
#...
| 82000 - 82500 : [ 1 0.00 1.00 ]
#...
| 123500 - 124000 : [ 1 0.00 1.00 ]
#...
| 145500 - 146000 : [ 1 0.00 1.00 ]
#...
| 176000 - 176500 : [ 1 0.00 1.00 ]
#...
| 177000 - 177500 : [ 1 0.00 1.00 ]
#...
| 261000 - 261500 : [ 1 0.00 1.00 ]
#...
| 374000 - 374500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACYN reads.list > grep.reads.list.ACYN
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACYN 4 500
-------------------------------------------------------------------
#Found 3055 total values totalling 12112782.0000. <3964.904092 +/- 11402.172086>
#Range: [ 1194 - 371634 ]
#Most likely bin: [ 3000 - 3500 ] 1101 counts
#Median bin: [ 3000 - 3500 ] 1101 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 9 0.00 0.00 ]
| 1500 - 2000 : [ 13 0.00 0.01 ]
|XX 2000 - 2500 : [ 60 0.02 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 643 0.21 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1101 0.36 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 859 0.28 0.88 ]
|XXXXXXXXXXXX 4000 - 4500 : [ 329 0.11 0.99 ]
|X 4500 - 5000 : [ 28 0.01 1.00 ]
| 5000 - 5500 : [ 1 0.00 1.00 ]
#...
| 27500 - 28000 : [ 1 0.00 1.00 ]
#...
| 40500 - 41000 : [ 1 0.00 1.00 ]
#...
| 53500 - 54000 : [ 1 0.00 1.00 ]
#...
| 78500 - 79000 : [ 1 0.00 1.00 ]
#...
| 111500 - 112000 : [ 1 0.00 1.00 ]
#...
| 134000 - 134500 : [ 1 0.00 1.00 ]
#...
| 140000 - 140500 : [ 1 0.00 1.00 ]
#...
| 146500 - 147000 : [ 1 0.00 1.00 ]
#...
| 182500 - 183000 : [ 1 0.00 1.00 ]
#...
| 232500 - 233000 : [ 1 0.00 1.00 ]
#...
| 317500 - 318000 : [ 1 0.00 1.00 ]
#...
| 371500 - 372000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACYO reads.list > grep.reads.list.ACYO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACYO 4 500
-------------------------------------------------------------------
#Found 2141 total values totalling 16641491.0000. <7772.765530 +/- 19682.216472>
#Range: [ 1236 - 623655 ]
#Most likely bin: [ 6500 - 7000 ] 567 counts
#Median bin: [ 6500 - 7000 ] 567 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 2 0.00 0.00 ]
| 1500 - 2000 : [ 3 0.00 0.00 ]
|X 2000 - 2500 : [ 9 0.00 0.01 ]
| 2500 - 3000 : [ 6 0.00 0.01 ]
| 3000 - 3500 : [ 3 0.00 0.01 ]
| 3500 - 4000 : [ 7 0.00 0.01 ]
| 4000 - 4500 : [ 7 0.00 0.02 ]
|XX 4500 - 5000 : [ 28 0.01 0.03 ]
|XXX 5000 - 5500 : [ 42 0.02 0.05 ]
|XXXXXXX 5500 - 6000 : [ 106 0.05 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 336 0.16 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 567 0.26 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 502 0.23 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 334 0.16 0.91 ]
|XXXXXXXXXX 8000 - 8500 : [ 144 0.07 0.98 ]
|XXX 8500 - 9000 : [ 38 0.02 1.00 ]
#...
| 9500 - 10000 : [ 1 0.00 1.00 ]
#...
| 35000 - 35500 : [ 1 0.00 1.00 ]
#...
| 79000 - 79500 : [ 1 0.00 1.00 ]
#...
| 327000 - 327500 : [ 1 0.00 1.00 ]
#...
| 335500 - 336000 : [ 1 0.00 1.00 ]
#...
| 488500 - 489000 : [ 1 0.00 1.00 ]
#...
| 623500 - 624000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACYP reads.list > grep.reads.list.ACYP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACYP 4 500
-------------------------------------------------------------------
#Found 179 total values totalling 7121290.0000. <39783.743017 +/- 2278.643758>
#Range: [ 33297 - 45468 ]
#Most likely bin: [ 39000 - 39500 ] 25 counts
#Median bin: [ 39500 - 40000 ] 9 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 33000 - 33500 : [ 1 0.01 0.01 ]
|XX 33500 - 34000 : [ 1 0.01 0.01 ]
|XX 34000 - 34500 : [ 1 0.01 0.02 ]
#...
|XXXXX 35000 - 35500 : [ 3 0.02 0.03 ]
|XXXXX 35500 - 36000 : [ 3 0.02 0.05 ]
|XXXXXXXXXX 36000 - 36500 : [ 6 0.03 0.08 ]
|XXXXXXXXXXX 36500 - 37000 : [ 7 0.04 0.12 ]
|XXXXXXXXXXXXXX 37000 - 37500 : [ 9 0.05 0.17 ]
|XXXXXXXXXX 37500 - 38000 : [ 6 0.03 0.21 ]
|XXXXXXXXXXXXXX 38000 - 38500 : [ 9 0.05 0.26 ]
|XXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 12 0.07 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 25 0.14 0.46 ]
|XXXXXXXXXXXXXX 39500 - 40000 : [ 9 0.05 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 19 0.11 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 16 0.09 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 14 0.08 0.79 ]
|XXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 11 0.06 0.85 ]
|XXXXXXXXXX 42000 - 42500 : [ 6 0.03 0.88 ]
|XXXXXXXXXX 42500 - 43000 : [ 6 0.03 0.92 ]
|XXXXXXXX 43000 - 43500 : [ 5 0.03 0.94 ]
|XXXXXX 43500 - 44000 : [ 4 0.02 0.97 ]
|XXXXX 44000 - 44500 : [ 3 0.02 0.98 ]
|XX 44500 - 45000 : [ 1 0.01 0.99 ]
|XXX 45000 - 45500 : [ 2 0.01 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# POO 3120 +- 482 (n=2349)
# PXH 38430 +- 2873 (n=3)
# ACYO 6688 +- 963 (n=1071)
# ACYN 3282 +- 1213 (n=1703)
# ACYP 39420 +- 2192 (n=88)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3633862_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
ACYN 11520 -1 -1 99 749 8777 99 711 100 726
ACYO 7680 -1 -1 97 651 5196 97 580 100 626
ACYP 1536 -1 -1 98 743 558 99 745 100 761
POO 20736 -1 -1 91 484 12086 96 474 100 492
PXH -1 -1 -1 -1 -1 165 94 424 100 418
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
ACYN 4664 99 716 100 736 4113 99 705 100 714
ACYO 2638 98 575 100 625 2558 97 584 100 627
ACYP 282 99 727 100 729 276 99 763 100 793
POO 6068 96 473 100 491 6018 96 475 100 492
PXH 84 94 443 100 435 81 94 405 100 401
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3633862_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 26782 13589 67.94 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 3633862_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 26782 total values totalling 15155023.0000. <565.865992 +/- 200.244242>
#Range: [ 17 - 995 ]
#Most likely bin: [ 650 - 700 ] 3079 counts
#Median bin: [ 600 - 650 ] 2984 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 50 : [ 124 0.00 0.00 ]
|XXXXXXX 50 - 100 : [ 566 0.02 0.03 ]
|XXXXXXXX 100 - 150 : [ 644 0.02 0.05 ]
|XXXXXXXXX 150 - 200 : [ 666 0.02 0.07 ]
|XXXXXXXXXX 200 - 250 : [ 750 0.03 0.10 ]
|XXXXXXXXXX 250 - 300 : [ 767 0.03 0.13 ]
|XXXXXXXXXXX 300 - 350 : [ 830 0.03 0.16 ]
|XXXXXXXXXXXXX 350 - 400 : [ 1036 0.04 0.20 ]
|XXXXXXXXXXXXXXXX 400 - 450 : [ 1218 0.05 0.25 ]
|XXXXXXXXXXXXXXXXXXXXX 450 - 500 : [ 1580 0.06 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 1996 0.07 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 2585 0.10 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2984 0.11 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3079 0.11 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3032 0.11 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2928 0.11 0.93 ]
|XXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1571 0.06 0.98 ]
|XXXX 850 - 900 : [ 340 0.01 1.00 ]
|X 900 - 950 : [ 74 0.00 1.00 ]
| 950 - 1000 : [ 12 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for PXH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep PXH 3633862_fasta.screen.trimQ15.SaF > reads.trim15.PXH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.PXH.rl 2 50
-------------------------------------------------------------------
#Found 165 total values totalling 66553.0000. <403.351515 +/- 185.086313>
#Range: [ 37 - 729 ]
#Most likely bin: [ 550 - 600 ] 28 counts
#Median bin: [ 400 - 450 ] 12 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 1 0.01 0.01 ]
|XXXXXXXXXXXXX 50 - 100 : [ 9 0.05 0.06 ]
|XXXXXXXXXXXXXXXXX 100 - 150 : [ 12 0.07 0.13 ]
|XXXXXXXXXXXXX 150 - 200 : [ 9 0.05 0.19 ]
|XXXXXXXXXXXXXX 200 - 250 : [ 10 0.06 0.25 ]
|XXXXXXXXXXXXXXXXXXX 250 - 300 : [ 13 0.08 0.33 ]
|XXXXXXXXXXX 300 - 350 : [ 8 0.05 0.38 ]
|XXXXXXXXXXXXXXXX 350 - 400 : [ 11 0.07 0.44 ]
|XXXXXXXXXXXXXXXXX 400 - 450 : [ 12 0.07 0.52 ]
|XXXXXXXXXXXXXXXXXXXX 450 - 500 : [ 14 0.08 0.60 ]
|XXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 14 0.08 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 28 0.17 0.85 ]
|XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 15 0.09 0.95 ]
|XXXXXXXXXXX 650 - 700 : [ 8 0.05 0.99 ]
|X 700 - 750 : [ 1 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for XHR
trimt JAZZ trim 15 readlength histogram for PPQ
trimt JAZZ trim 15 readlength histogram for POO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep POO 3633862_fasta.screen.trimQ15.SaF > reads.trim15.POO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.POO.rl 2 50
-------------------------------------------------------------------
#Found 12086 total values totalling 5532163.0000. <457.733162 +/- 175.525244>
#Range: [ 25 - 781 ]
#Most likely bin: [ 550 - 600 ] 1717 counts
#Median bin: [ 500 - 550 ] 1507 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 50 : [ 72 0.01 0.01 ]
|XXXXXXXXXX 50 - 100 : [ 410 0.03 0.04 ]
|XXXXXXXXXXX 100 - 150 : [ 482 0.04 0.08 ]
|XXXXXXXXXXX 150 - 200 : [ 481 0.04 0.12 ]
|XXXXXXXXXXXXX 200 - 250 : [ 541 0.04 0.16 ]
|XXXXXXXXXXXXX 250 - 300 : [ 561 0.05 0.21 ]
|XXXXXXXXXXXXXX 300 - 350 : [ 613 0.05 0.26 ]
|XXXXXXXXXXXXXXXXXX 350 - 400 : [ 755 0.06 0.32 ]
|XXXXXXXXXXXXXXXXXXXXX 400 - 450 : [ 885 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 450 - 500 : [ 1149 0.10 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 1507 0.12 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1717 0.14 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1580 0.13 0.89 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1068 0.09 0.98 ]
|XXXXXX 700 - 750 : [ 258 0.02 1.00 ]
| 750 - 800 : [ 7 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ASNW
trimt JAZZ trim 15 readlength histogram for ACYN
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACYN 3633862_fasta.screen.trimQ15.SaF > reads.trim15.ACYN.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACYN.rl 2 50
-------------------------------------------------------------------
#Found 8777 total values totalling 6200687.0000. <706.469978 +/- 148.039949>
#Range: [ 26 - 995 ]
#Most likely bin: [ 750 - 800 ] 2491 counts
#Median bin: [ 700 - 750 ] 1848 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 20 0.00 0.00 ]
|X 50 - 100 : [ 40 0.00 0.01 ]
|X 100 - 150 : [ 47 0.01 0.01 ]
|X 150 - 200 : [ 63 0.01 0.02 ]
|X 200 - 250 : [ 67 0.01 0.03 ]
|X 250 - 300 : [ 77 0.01 0.04 ]
|X 300 - 350 : [ 86 0.01 0.05 ]
|XX 350 - 400 : [ 118 0.01 0.06 ]
|XX 400 - 450 : [ 141 0.02 0.08 ]
|XXX 450 - 500 : [ 176 0.02 0.10 ]
|XXX 500 - 550 : [ 159 0.02 0.11 ]
|XXXX 550 - 600 : [ 232 0.03 0.14 ]
|XXXXXXX 600 - 650 : [ 463 0.05 0.19 ]
|XXXXXXXXXXXXXXX 650 - 700 : [ 914 0.10 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1848 0.21 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2491 0.28 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1423 0.16 0.95 ]
|XXXXX 850 - 900 : [ 326 0.04 0.99 ]
|X 900 - 950 : [ 74 0.01 1.00 ]
| 950 - 1000 : [ 12 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACYO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACYO 3633862_fasta.screen.trimQ15.SaF > reads.trim15.ACYO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACYO.rl 2 50
-------------------------------------------------------------------
#Found 5196 total values totalling 2943170.0000. <566.429946 +/- 175.175846>
#Range: [ 23 - 825 ]
#Most likely bin: [ 650 - 700 ] 1031 counts
#Median bin: [ 600 - 650 ] 911 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 29 0.01 0.01 ]
|XXXX 50 - 100 : [ 104 0.02 0.03 ]
|XXXX 100 - 150 : [ 102 0.02 0.05 ]
|XXXX 150 - 200 : [ 110 0.02 0.07 ]
|XXXXX 200 - 250 : [ 129 0.02 0.09 ]
|XXXX 250 - 300 : [ 113 0.02 0.11 ]
|XXXXX 300 - 350 : [ 122 0.02 0.14 ]
|XXXXXX 350 - 400 : [ 148 0.03 0.16 ]
|XXXXXXX 400 - 450 : [ 180 0.03 0.20 ]
|XXXXXXXXX 450 - 500 : [ 238 0.05 0.25 ]
|XXXXXXXXXXXX 500 - 550 : [ 312 0.06 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 601 0.12 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 911 0.18 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1031 0.20 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 820 0.16 0.95 ]
|XXXXXXXXX 750 - 800 : [ 232 0.04 1.00 ]
|X 800 - 850 : [ 14 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACYP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACYP 3633862_fasta.screen.trimQ15.SaF > reads.trim15.ACYP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACYP.rl 2 50
-------------------------------------------------------------------
#Found 558 total values totalling 412450.0000. <739.157706 +/- 120.728866>
#Range: [ 17 - 875 ]
#Most likely bin: [ 750 - 800 ] 198 counts
#Median bin: [ 750 - 800 ] 198 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 2 0.00 0.00 ]
|X 50 - 100 : [ 3 0.01 0.01 ]
| 100 - 150 : [ 1 0.00 0.01 ]
|X 150 - 200 : [ 3 0.01 0.02 ]
|X 200 - 250 : [ 3 0.01 0.02 ]
|X 250 - 300 : [ 3 0.01 0.03 ]
| 300 - 350 : [ 1 0.00 0.03 ]
|X 350 - 400 : [ 4 0.01 0.04 ]
#...
|X 450 - 500 : [ 3 0.01 0.04 ]
|X 500 - 550 : [ 4 0.01 0.05 ]
|X 550 - 600 : [ 7 0.01 0.06 ]
|XXX 600 - 650 : [ 15 0.03 0.09 ]
|XXXXXXXXXXXX 650 - 700 : [ 58 0.10 0.19 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 105 0.19 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 198 0.35 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 134 0.24 0.97 ]
|XXX 850 - 900 : [ 14 0.03 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACUB
trimt JAZZ trim 15 readlength histogram for ACUC
trimt JAZZ trim 15 readlength histogram for ACUF
trimt JAZZ trim 15 readlength histogram for AHWW
trimt JAZZ trim 15 readlength histogram for TRO
trimt JAZZ trim 15 readlength histogram for AOOZ
trimt JAZZ trim 15 readlength histogram for ATGX
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3633862
-------------------------------------------------------------------
ACYN.000001.000100 pUC18.fa LRS.fasta
ACYO.000001.000100 pMCL200.fa LRS.fasta
ACYP.000001.000100 pCC1Fos.fa.4 LRS.fasta
POO.000001.000100 pUC18.fa LRS.fasta
POO.000101.000200 pUC18.fa LRS.fasta
PXH.000001.000100 pCC1Fos.fa.4 LRS.fasta
ACYN.000001.000100 pUC18.fa LRS.fasta
ACYO.000001.000100 pMCL200.fa LRS.fasta
ACYP.000001.000100 pCC1Fos.fa.4 LRS.fasta
POO.000001.000100 pUC18.fa LRS.fasta
POO.000101.000200 pUC18.fa LRS.fasta
PXH.000001.000100 pCC1Fos.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3633862_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3633862_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 26669 total values totalling 7884.5195. <0.295644 +/- 0.058020>
#Range: [ 0.0312 - 0.8411 ]
#Most likely bin: [ 0.29 - 0.295 ] 1173 counts
#Median bin: [ 0.29 - 0.295 ] 1173 counts
| 0.03 - 0.035 : [ 1 0.00 0.00 ]
#...
| 0.08 - 0.085 : [ 2 0.00 0.00 ]
| 0.085 - 0.09 : [ 1 0.00 0.00 ]
| 0.09 - 0.095 : [ 1 0.00 0.00 ]
| 0.095 - 0.1 : [ 2 0.00 0.00 ]
| 0.1 - 0.105 : [ 2 0.00 0.00 ]
| 0.105 - 0.11 : [ 1 0.00 0.00 ]
#...
| 0.115 - 0.12 : [ 5 0.00 0.00 ]
| 0.12 - 0.125 : [ 3 0.00 0.00 ]
| 0.125 - 0.13 : [ 3 0.00 0.00 ]
| 0.13 - 0.135 : [ 2 0.00 0.00 ]
| 0.135 - 0.14 : [ 3 0.00 0.00 ]
| 0.14 - 0.145 : [ 7 0.00 0.00 ]
| 0.145 - 0.15 : [ 7 0.00 0.00 ]
| 0.15 - 0.155 : [ 10 0.00 0.00 ]
| 0.155 - 0.16 : [ 11 0.00 0.00 ]
|X 0.16 - 0.165 : [ 20 0.00 0.00 ]
|X 0.165 - 0.17 : [ 25 0.00 0.00 ]
|X 0.17 - 0.175 : [ 28 0.00 0.01 ]
|X 0.175 - 0.18 : [ 25 0.00 0.01 ]
|X 0.18 - 0.185 : [ 40 0.00 0.01 ]
|XXX 0.185 - 0.19 : [ 79 0.00 0.01 ]
|XX 0.19 - 0.195 : [ 67 0.00 0.01 ]
|XXXX 0.195 - 0.2 : [ 105 0.00 0.02 ]
|XXXXX 0.2 - 0.205 : [ 153 0.01 0.02 ]
|XXXXXX 0.205 - 0.21 : [ 187 0.01 0.03 ]
|XXXXXXXX 0.21 - 0.215 : [ 241 0.01 0.04 ]
|XXXXXXXXXXX 0.215 - 0.22 : [ 317 0.01 0.05 ]
|XXXXXXXXXXXXX 0.22 - 0.225 : [ 371 0.01 0.06 ]
|XXXXXXXXXXXXXXX 0.225 - 0.23 : [ 437 0.02 0.08 ]
|XXXXXXXXXXXXXXXX 0.23 - 0.235 : [ 470 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.235 - 0.24 : [ 670 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.24 - 0.245 : [ 722 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.245 - 0.25 : [ 746 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.25 - 0.255 : [ 885 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.255 - 0.26 : [ 907 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.26 - 0.265 : [ 1008 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.265 - 0.27 : [ 1006 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.27 - 0.275 : [ 1144 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.275 - 0.28 : [ 1153 0.04 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.28 - 0.285 : [ 1169 0.04 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.285 - 0.29 : [ 1171 0.04 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 1173 0.04 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.295 - 0.3 : [ 1096 0.04 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 1107 0.04 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 1054 0.04 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 1021 0.04 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 1008 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 919 0.03 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 863 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 761 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 549 0.02 0.85 ]
|XXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 483 0.02 0.87 ]
|XXXXXXXXXXXXXXX 0.345 - 0.35 : [ 433 0.02 0.89 ]
|XXXXXXXXXXXXXX 0.35 - 0.355 : [ 403 0.02 0.90 ]
|XXXXXXXXXXXX 0.355 - 0.36 : [ 349 0.01 0.92 ]
|XXXXXXXXXX 0.36 - 0.365 : [ 296 0.01 0.93 ]
|XXXXXXX 0.365 - 0.37 : [ 215 0.01 0.94 ]
|XXXXXXX 0.37 - 0.375 : [ 213 0.01 0.94 ]
|XXXXXX 0.375 - 0.38 : [ 188 0.01 0.95 ]
|XXXX 0.38 - 0.385 : [ 127 0.00 0.95 ]
|XXXX 0.385 - 0.39 : [ 103 0.00 0.96 ]
|XXX 0.39 - 0.395 : [ 93 0.00 0.96 ]
|XX 0.395 - 0.4 : [ 53 0.00 0.96 ]
|XX 0.4 - 0.405 : [ 56 0.00 0.97 ]
|XX 0.405 - 0.41 : [ 62 0.00 0.97 ]
|XX 0.41 - 0.415 : [ 53 0.00 0.97 ]
|X 0.415 - 0.42 : [ 41 0.00 0.97 ]
|XX 0.42 - 0.425 : [ 46 0.00 0.97 ]
|X 0.425 - 0.43 : [ 33 0.00 0.98 ]
|X 0.43 - 0.435 : [ 40 0.00 0.98 ]
|X 0.435 - 0.44 : [ 22 0.00 0.98 ]
|X 0.44 - 0.445 : [ 27 0.00 0.98 ]
|X 0.445 - 0.45 : [ 27 0.00 0.98 ]
|X 0.45 - 0.455 : [ 22 0.00 0.98 ]
|X 0.455 - 0.46 : [ 23 0.00 0.98 ]
|X 0.46 - 0.465 : [ 25 0.00 0.98 ]
|X 0.465 - 0.47 : [ 20 0.00 0.98 ]
| 0.47 - 0.475 : [ 8 0.00 0.98 ]
|X 0.475 - 0.48 : [ 28 0.00 0.98 ]
|X 0.48 - 0.485 : [ 20 0.00 0.98 ]
|X 0.485 - 0.49 : [ 20 0.00 0.99 ]
| 0.49 - 0.495 : [ 13 0.00 0.99 ]
| 0.495 - 0.5 : [ 12 0.00 0.99 ]
|X 0.5 - 0.505 : [ 21 0.00 0.99 ]
| 0.505 - 0.51 : [ 12 0.00 0.99 ]
| 0.51 - 0.515 : [ 11 0.00 0.99 ]
|X 0.515 - 0.52 : [ 15 0.00 0.99 ]
| 0.52 - 0.525 : [ 12 0.00 0.99 ]
| 0.525 - 0.53 : [ 11 0.00 0.99 ]
| 0.53 - 0.535 : [ 9 0.00 0.99 ]
|X 0.535 - 0.54 : [ 17 0.00 0.99 ]
|X 0.54 - 0.545 : [ 16 0.00 0.99 ]
| 0.545 - 0.55 : [ 12 0.00 0.99 ]
|X 0.55 - 0.555 : [ 21 0.00 0.99 ]
| 0.555 - 0.56 : [ 9 0.00 0.99 ]
| 0.56 - 0.565 : [ 14 0.00 0.99 ]
| 0.565 - 0.57 : [ 14 0.00 0.99 ]
| 0.57 - 0.575 : [ 11 0.00 0.99 ]
|X 0.575 - 0.58 : [ 20 0.00 1.00 ]
|X 0.58 - 0.585 : [ 17 0.00 1.00 ]
| 0.585 - 0.59 : [ 13 0.00 1.00 ]
| 0.59 - 0.595 : [ 10 0.00 1.00 ]
| 0.595 - 0.6 : [ 7 0.00 1.00 ]
| 0.6 - 0.605 : [ 11 0.00 1.00 ]
| 0.605 - 0.61 : [ 3 0.00 1.00 ]
| 0.61 - 0.615 : [ 8 0.00 1.00 ]
| 0.615 - 0.62 : [ 6 0.00 1.00 ]
| 0.62 - 0.625 : [ 6 0.00 1.00 ]
| 0.625 - 0.63 : [ 5 0.00 1.00 ]
| 0.63 - 0.635 : [ 3 0.00 1.00 ]
| 0.635 - 0.64 : [ 2 0.00 1.00 ]
| 0.64 - 0.645 : [ 6 0.00 1.00 ]
| 0.645 - 0.65 : [ 2 0.00 1.00 ]
| 0.65 - 0.655 : [ 4 0.00 1.00 ]
#...
| 0.66 - 0.665 : [ 2 0.00 1.00 ]
#...
| 0.675 - 0.68 : [ 2 0.00 1.00 ]
| 0.68 - 0.685 : [ 2 0.00 1.00 ]
| 0.685 - 0.69 : [ 1 0.00 1.00 ]
| 0.69 - 0.695 : [ 1 0.00 1.00 ]
| 0.695 - 0.7 : [ 1 0.00 1.00 ]
| 0.7 - 0.705 : [ 4 0.00 1.00 ]
| 0.705 - 0.71 : [ 5 0.00 1.00 ]
| 0.71 - 0.715 : [ 2 0.00 1.00 ]
#...
| 0.725 - 0.73 : [ 1 0.00 1.00 ]
| 0.73 - 0.735 : [ 2 0.00 1.00 ]
#...
| 0.785 - 0.79 : [ 2 0.00 1.00 ]
| 0.79 - 0.795 : [ 2 0.00 1.00 ]
#...
| 0.83 - 0.835 : [ 1 0.00 1.00 ]
#...
| 0.84 - 0.845 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 131. 7 reads; 2347 bp (untrimmed), 2006 (trimmed).
Contig 132. 7 reads; 2318 bp (untrimmed), 1829 (trimmed).
Contig 133. 8 reads; 1663 bp (untrimmed), 1411 (trimmed).
Contig 134. 8 reads; 1775 bp (untrimmed), 1683 (trimmed).
Contig 135. 8 reads; 3648 bp (untrimmed), 3569 (trimmed).
Contig 136. 9 reads; 1734 bp (untrimmed), 1556 (trimmed).
Contig 137. 9 reads; 2583 bp (untrimmed), 2182 (trimmed).
Contig 138. 10 reads; 2200 bp (untrimmed), 1928 (trimmed).
Contig 139. 10 reads; 1831 bp (untrimmed), 1793 (trimmed).
Contig 140. 10 reads; 1344 bp (untrimmed), 1313 (trimmed).
Contig 141. 11 reads; 2409 bp (untrimmed), 2033 (trimmed).
Contig 142. 12 reads; 2260 bp (untrimmed), 1890 (trimmed).
Contig 143. 13 reads; 3163 bp (untrimmed), 3100 (trimmed).
Contig 144. 13 reads; 2853 bp (untrimmed), 2815 (trimmed).
Contig 145. 13 reads; 4321 bp (untrimmed), 3792 (trimmed).
Contig 146. 14 reads; 2715 bp (untrimmed), 2631 (trimmed).
Contig 147. 15 reads; 2911 bp (untrimmed), 2778 (trimmed).
Contig 148. 18 reads; 4780 bp (untrimmed), 4725 (trimmed).
Contig 149. 22 reads; 2370 bp (untrimmed), 2067 (trimmed).
Contig 150. 22 reads; 2588 bp (untrimmed), 2476 (trimmed).
Contig 151. 35 reads; 9993 bp (untrimmed), 9977 (trimmed).
Contig 152. 45 reads; 4514 bp (untrimmed), 4336 (trimmed).
Contig 153. 356 reads; 22292 bp (untrimmed), 22264 (trimmed).
Contig 154. 2098 reads; 113529 bp (untrimmed), 113523 (trimmed).
Contig 155. 3002 reads; 148276 bp (untrimmed), 147947 (trimmed).
Contig 156. 5440 reads; 307225 bp (untrimmed), 307047 (trimmed).
Contig 157. 13796 reads; 714319 bp (untrimmed), 714285 (trimmed).
--------------------------------------------------------------
Totals 25534 reads; 1582806 bp (untrimmed), 1545271 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 1581421 bases = 13.10 +- 6.73 = 0.62 +- 4.35
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 155 total values totalling 471.2500. <3.040323 +/- 2.413525>
#Range: [ 1.24 - 16.35 ]
#Most likely bin: [ 1.5 - 2 ] 34 counts
#Median bin: [ 2.5 - 3 ] 34 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXX 1 - 1.5 : [ 11 0.07 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 34 0.22 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 31 0.20 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 34 0.22 0.71 ]
|XXXXXXXXXXXXXXXX 3 - 3.5 : [ 14 0.09 0.80 ]
|XXXXXXXXXXXXXX 3.5 - 4 : [ 12 0.08 0.88 ]
|XXXXXX 4 - 4.5 : [ 5 0.03 0.91 ]
|XXXXXXX 4.5 - 5 : [ 6 0.04 0.95 ]
#...
|XXXX 7 - 7.5 : [ 3 0.02 0.97 ]
#...
|X 12.5 - 13 : [ 1 0.01 0.97 ]
#...
|X 14 - 14.5 : [ 1 0.01 0.98 ]
#...
|X 15 - 15.5 : [ 1 0.01 0.99 ]
|X 15.5 - 16 : [ 1 0.01 0.99 ]
|X 16 - 16.5 : [ 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 18 total values totalling 131.6600. <7.314444 +/- 4.928739>
#Range: [ 2.56 - 16.35 ]
#Most likely bin: [ 3.5 - 4 ] 4 counts
#Median bin: [ 4 - 4.5 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 2 0.11 0.11 ]
|XXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 2 0.11 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 4 0.22 0.44 ]
|XXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 2 0.11 0.56 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 3 0.17 0.72 ]
#...
|XXXXXXXXXX 12.5 - 13 : [ 1 0.06 0.78 ]
#...
|XXXXXXXXXX 14 - 14.5 : [ 1 0.06 0.83 ]
#...
|XXXXXXXXXX 15 - 15.5 : [ 1 0.06 0.89 ]
|XXXXXXXXXX 15.5 - 16 : [ 1 0.06 0.94 ]
|XXXXXXXXXX 16 - 16.5 : [ 1 0.06 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 20 3 reads 2382 bases = 1.24 +- 0.43 = 0.32 +- 1.03
Contig 10 3 reads 2300 bases = 1.29 +- 0.45 = 0.40 +- 1.17
Contig 43 3 reads 1977 bases = 1.29 +- 0.45 = 0.54 +- 1.09
Contig 12 3 reads 2386 bases = 1.31 +- 0.46 = 0.42 +- 1.23
Contig 39 3 reads 2198 bases = 1.43 +- 0.52 = 0.41 +- 1.26
Contig 2 2 reads 858 bases = 1.44 +- 0.50 = 0.56 +- 0.50
Contig 40 3 reads 1993 bases = 1.44 +- 0.50 = 0.69 +- 0.59
Contig 14 3 reads 1789 bases = 1.48 +- 0.50 = 0.86 +- 0.68
Contig 18 3 reads 1891 bases = 1.48 +- 0.69 = 0.37 +- 0.78
Contig 51 3 reads 2152 bases = 1.48 +- 0.56 = 0.43 +- 0.76
Contig 75 4 reads 2667 bases = 1.48 +- 0.64 = 1.48 +- 0.64
Contig 15 3 reads 1891 bases = 1.53 +- 0.75 = 0.39 +- 1.05
Contig 24 3 reads 1854 bases = 1.53 +- 0.50 = 0.52 +- 1.10
Contig 29 3 reads 2040 bases = 1.57 +- 0.71 = 0.68 +- 0.47
Contig 60 4 reads 2793 bases = 1.57 +- 0.51 = 0.80 +- 1.18
Contig 25 3 reads 2046 bases = 1.58 +- 0.63 = 0.57 +- 0.49
Contig 110 5 reads 3249 bases = 1.61 +- 0.62 = 0.24 +- 1.22
Contig 48 3 reads 1689 bases = 1.62 +- 0.67 = 0.60 +- 0.49
Contig 79 4 reads 2222 bases = 1.62 +- 0.76 = 0.85 +- 0.61
Contig 47 3 reads 1641 bases = 1.65 +- 0.72 = 0.64 +- 0.48
Contig 109 5 reads 1122 bases = 3.95 +- 1.02 = 2.26 +- 0.99
Contig 133 8 reads 1663 bases = 4.08 +- 2.49 = 1.59 +- 0.80
Contig 134 8 reads 1775 bases = 4.15 +- 1.73 = 3.12 +- 1.28
Contig 146 14 reads 2715 bases = 4.16 +- 2.27 = 0.49 +- 1.46
Contig 141 11 reads 2409 bases = 4.24 +- 2.94 = 0.19 +- 1.73
Contig 118 6 reads 1321 bases = 4.34 +- 1.69 = 1.38 +- 1.71
Contig 105 5 reads 1033 bases = 4.57 +- 0.93 = 0.77 +- 0.65
Contig 139 10 reads 1831 bases = 4.65 +- 2.38 = 1.16 +- 3.30
Contig 126 7 reads 1071 bases = 4.71 +- 1.93 = 0.67 +- 0.54
Contig 140 10 reads 1344 bases = 4.83 +- 2.11 = 1.61 +- 1.06
Contig 127 7 reads 1314 bases = 4.85 +- 2.19 = 0.94 +- 0.74
Contig 136 9 reads 1734 bases = 4.93 +- 2.50 = 4.93 +- 2.50
Contig 149 22 reads 2370 bases = 7.22 +- 5.56 = 4.23 +- 3.40
Contig 150 22 reads 2588 bases = 7.31 +- 4.89 = 3.12 +- 2.14
Contig 152 45 reads 4514 bases = 7.35 +- 4.80 = 3.40 +- 2.58
Contig 153 356 reads 22292 bases = 12.96 +- 6.74 = 0.60 +- 4.97
Contig 156 5440 reads 307225 bases = 14.32 +- 4.73 = 0.62 +- 4.77
Contig 154 2098 reads 113529 bases = 15.13 +- 5.55 = 0.60 +- 5.22
Contig 157 13796 reads 714319 bases = 15.60 +- 5.06 = 0.37 +- 4.61
Contig 155 3002 reads 148276 bases = 16.35 +- 5.20 = 0.54 +- 4.51
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 258
HQ Discrepant reads = 38
Chimeric reads = 50
Suspect alignments = 101
-------------------------------------------------------------------
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/finished2/microbe/3633862/edit_dir.10Nov03.QD