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: 12-12-2005
Runby: Kerrie Barry
Description: analysis of libraries in progress (or initial analysis of completed)
-------------------------------------------------------------------
-------------------------------------------------------------------
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
-------------------------------------------------------------------
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 24527558
# phrap: 14223733
# db:
altered.
10000000
16250430 +/- 6101535
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 39119
Number of reads with percent X's >= 20%: 4651 = 3.4%
Number of reads with percent X's >= 50%: 3350 = 2.4%
Number of reads with percent X's >= 80%: 2520 = 1.8%
Total reads in project: 137220
Total bp X'd : 4642791
reads >= 20% >= 50% >= 80% screened
Nr with L09136 32299 2322 1174 693
Nr with LRS 187 187 178 165
Nr with pCC1Fos 4451 55 32 11
Nr with pMCL200_JGI_XZX+XZK 2182 2087 1966 1651
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 8566
Number of reads with percent X's >= 20%: 2697 = 9.3%
Number of reads with percent X's >= 50%: 2551 = 8.8%
Number of reads with percent X's >= 80%: 2278 = 7.8%
Total reads in project: 29088
Total bp X'd : 2592601
reads >= 20% >= 50% >= 80% screened
Nr with L09136 5723 724 691 622
Nr with LRS 187 187 178 165
Nr with pCC1Fos 865 36 20 9
Nr with pMCL200_JGI_XZX+XZK 1791 1750 1662 1482
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 25638624
C = 37757497
G = 37682521
T = 24907150
N = 1051664
X = 4642791
GC fraction = 0.57
Total = 131680247
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3635729_fasta.screen.contigs
-------------------------------------------------------------------
A 5583932
C 8491601
G 8484240
T 5556305
N 537572
fraction GC = 0.59
total bases = 28653650
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 APZO reads.list > grep.reads.list.APZO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APZO 4 500
-------------------------------------------------------------------
#Found 13717 total values totalling 43785448.0000. <3192.057155 +/- 657.163358>
#Range: [ 675 - 5831 ]
#Most likely bin: [ 3000 - 3500 ] 4995 counts
#Median bin: [ 3000 - 3500 ] 4995 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 14 0.00 0.00 ]
|XX 1000 - 1500 : [ 246 0.02 0.02 ]
|XXXXXX 1500 - 2000 : [ 730 0.05 0.07 ]
|XXXXXXX 2000 - 2500 : [ 848 0.06 0.13 ]
|XXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2426 0.18 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4995 0.36 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3214 0.23 0.91 ]
|XXXXXXXXXX 4000 - 4500 : [ 1210 0.09 1.00 ]
| 4500 - 5000 : [ 33 0.00 1.00 ]
#...
| 5500 - 6000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APZP reads.list > grep.reads.list.APZP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APZP 4 500
-------------------------------------------------------------------
#Found 7021 total values totalling 48402335.0000. <6893.937473 +/- 920.310765>
#Range: [ 924 - 9521 ]
#Most likely bin: [ 6500 - 7000 ] 1862 counts
#Median bin: [ 6500 - 7000 ] 1862 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 15 0.00 0.00 ]
| 1500 - 2000 : [ 23 0.00 0.01 ]
| 2000 - 2500 : [ 15 0.00 0.01 ]
|X 2500 - 3000 : [ 38 0.01 0.01 ]
|X 3000 - 3500 : [ 28 0.00 0.02 ]
|X 3500 - 4000 : [ 38 0.01 0.02 ]
| 4000 - 4500 : [ 20 0.00 0.03 ]
| 4500 - 5000 : [ 20 0.00 0.03 ]
| 5000 - 5500 : [ 15 0.00 0.03 ]
|XXXXXX 5500 - 6000 : [ 263 0.04 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1452 0.21 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1862 0.27 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1487 0.21 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1297 0.18 0.94 ]
|XXXXXXXXXX 8000 - 8500 : [ 443 0.06 1.00 ]
| 8500 - 9000 : [ 2 0.00 1.00 ]
| 9000 - 9500 : [ 1 0.00 1.00 ]
| 9500 - 10000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APZS reads.list > grep.reads.list.APZS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APZS 4 500
-------------------------------------------------------------------
#Found 410 total values totalling 13400058.0000. <32683.068293 +/- 8663.403852>
#Range: [ 1110 - 47006 ]
#Most likely bin: [ 32500 - 33000 ] 34 counts
#Median bin: [ 34000 - 34500 ] 23 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 1000 - 1500 : [ 4 0.01 0.01 ]
|XXXXXXXXXXXX 1500 - 2000 : [ 10 0.02 0.03 ]
|XXXXXXXX 2000 - 2500 : [ 7 0.02 0.05 ]
|XXXXX 2500 - 3000 : [ 4 0.01 0.06 ]
|X 3000 - 3500 : [ 1 0.00 0.06 ]
#...
|X 21000 - 21500 : [ 1 0.00 0.07 ]
#...
|X 25000 - 25500 : [ 1 0.00 0.07 ]
#...
|XXXXX 26500 - 27000 : [ 4 0.01 0.08 ]
|XXXX 27000 - 27500 : [ 3 0.01 0.09 ]
#...
|XXXX 28000 - 28500 : [ 3 0.01 0.09 ]
|XX 28500 - 29000 : [ 2 0.00 0.10 ]
|XXXXXX 29000 - 29500 : [ 5 0.01 0.11 ]
|XXXXXXX 29500 - 30000 : [ 6 0.01 0.12 ]
|XXXXXX 30000 - 30500 : [ 5 0.01 0.14 ]
|XXXXXXXXXXXXXX 30500 - 31000 : [ 12 0.03 0.17 ]
|XXXXXXXXXXXXXXX 31000 - 31500 : [ 13 0.03 0.20 ]
|XXXXXXXXXXXXXX 31500 - 32000 : [ 12 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 20 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 34 0.08 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 27 0.07 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 24 0.06 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 23 0.06 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 21 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 19 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 22 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 20 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 18 0.04 0.78 ]
|XXXXXXXXX 37000 - 37500 : [ 8 0.02 0.80 ]
|XXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 18 0.04 0.85 ]
|XXXXXXXXXXXXXXXX 38000 - 38500 : [ 14 0.03 0.88 ]
|XXXXXXXXXXXX 38500 - 39000 : [ 10 0.02 0.90 ]
|XXXXXXX 39000 - 39500 : [ 6 0.01 0.92 ]
|XXXXXXXX 39500 - 40000 : [ 7 0.02 0.94 ]
|XXXXX 40000 - 40500 : [ 4 0.01 0.95 ]
|XXXXX 40500 - 41000 : [ 4 0.01 0.96 ]
|XXXXXX 41000 - 41500 : [ 5 0.01 0.97 ]
|XXXX 41500 - 42000 : [ 3 0.01 0.98 ]
|X 42000 - 42500 : [ 1 0.00 0.98 ]
|X 42500 - 43000 : [ 1 0.00 0.98 ]
|X 43000 - 43500 : [ 1 0.00 0.98 ]
|XXXXX 43500 - 44000 : [ 4 0.01 0.99 ]
#...
|XX 46500 - 47000 : [ 2 0.00 1.00 ]
|X 47000 - 47500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# APZP 6875 +- 1082 (n=7203)
# APZO 3134 +- 764 (n=14405)
# APZS 29229 +- 12913 (n=492)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3635729_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
APZO 81792 94 694 97 692 81444 93 644 95 653
APZP 46848 92 752 97 718 45024 92 755 97 744
APZS 10752 85 607 91 575 10752 84 613 91 627
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
APZO 40920 93 640 96 653 40524 93 649 95 654
APZP 22560 92 755 98 744 22464 91 755 95 744
APZS 5376 84 618 91 617 5376 85 608 92 638
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3635729_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
236 45024 22656 96.00 100.00 APZP @
400 81444 38356 95.89 99.89 APZO @
56 10752 5376 96.00 100.00 APZS @
] 137220 66388 95.94 cumulative total@@
LIBRARY PLATE ID COUNT [ APZP 236 APZO 400 APZS 56 ] for 692 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 3635729_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 137220 total values totalling 85489295.0000. <623.009000 +/- 241.361603>
#Range: [ 0 - 990 ]
#Most likely bin: [ 750 - 800 ] 25621 counts
#Median bin: [ 700 - 750 ] 20532 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXX 0 - 50 : [ 9930 0.07 0.07 ]
|XX 50 - 100 : [ 1548 0.01 0.08 ]
|XX 100 - 150 : [ 1320 0.01 0.09 ]
|XX 150 - 200 : [ 1420 0.01 0.10 ]
|XXX 200 - 250 : [ 1629 0.01 0.12 ]
|XXX 250 - 300 : [ 1837 0.01 0.13 ]
|XXX 300 - 350 : [ 2179 0.02 0.14 ]
|XXXX 350 - 400 : [ 2327 0.02 0.16 ]
|XXXX 400 - 450 : [ 2824 0.02 0.18 ]
|XXXXX 450 - 500 : [ 3390 0.02 0.21 ]
|XXXXXXX 500 - 550 : [ 4395 0.03 0.24 ]
|XXXXXXXXXX 550 - 600 : [ 6427 0.05 0.29 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 9884 0.07 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 14476 0.11 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 20532 0.15 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 25621 0.19 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 21299 0.16 0.95 ]
|XXXXXXXXX 850 - 900 : [ 5789 0.04 1.00 ]
|X 900 - 950 : [ 374 0.00 1.00 ]
| 950 - 1000 : [ 19 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APZO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APZO 3635729_fasta.screen.trimQ15.SaF > reads.trim15.APZO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APZO.rl 2 50
-------------------------------------------------------------------
#Found 81444 total values totalling 48704058.0000. <598.006704 +/- 228.541137>
#Range: [ 0 - 990 ]
#Most likely bin: [ 700 - 750 ] 13758 counts
#Median bin: [ 650 - 700 ] 11123 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 0 - 50 : [ 5044 0.06 0.06 ]
|XXX 50 - 100 : [ 978 0.01 0.07 ]
|XXX 100 - 150 : [ 931 0.01 0.09 ]
|XXX 150 - 200 : [ 1015 0.01 0.10 ]
|XXXX 200 - 250 : [ 1207 0.01 0.11 ]
|XXXX 250 - 300 : [ 1272 0.02 0.13 ]
|XXXX 300 - 350 : [ 1532 0.02 0.15 ]
|XXXXX 350 - 400 : [ 1749 0.02 0.17 ]
|XXXXXX 400 - 450 : [ 2210 0.03 0.20 ]
|XXXXXXXX 450 - 500 : [ 2723 0.03 0.23 ]
|XXXXXXXXXX 500 - 550 : [ 3595 0.04 0.27 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 5244 0.06 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 7927 0.10 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 11123 0.14 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 13758 0.17 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 11772 0.14 0.89 ]
|XXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6793 0.08 0.97 ]
|XXXXXXX 850 - 900 : [ 2263 0.03 1.00 ]
|X 900 - 950 : [ 289 0.00 1.00 ]
| 950 - 1000 : [ 19 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APZP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APZP 3635729_fasta.screen.trimQ15.SaF > reads.trim15.APZP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APZP.rl 2 50
-------------------------------------------------------------------
#Found 45024 total values totalling 31183791.0000. <692.603745 +/- 237.621338>
#Range: [ 0 - 938 ]
#Most likely bin: [ 800 - 850 ] 13681 counts
#Median bin: [ 750 - 800 ] 12519 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 0 - 50 : [ 3525 0.08 0.08 ]
|X 50 - 100 : [ 250 0.01 0.08 ]
|X 100 - 150 : [ 211 0.00 0.09 ]
|X 150 - 200 : [ 224 0.00 0.09 ]
|X 200 - 250 : [ 206 0.00 0.10 ]
|X 250 - 300 : [ 243 0.01 0.10 ]
|X 300 - 350 : [ 253 0.01 0.11 ]
|X 350 - 400 : [ 288 0.01 0.12 ]
|X 400 - 450 : [ 287 0.01 0.12 ]
|X 450 - 500 : [ 395 0.01 0.13 ]
|X 500 - 550 : [ 428 0.01 0.14 ]
|XX 550 - 600 : [ 628 0.01 0.15 ]
|XXX 600 - 650 : [ 1002 0.02 0.18 ]
|XXXXXX 650 - 700 : [ 2135 0.05 0.22 ]
|XXXXXXXXXXXXXXXX 700 - 750 : [ 5363 0.12 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 12519 0.28 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 13681 0.30 0.92 ]
|XXXXXXXXXX 850 - 900 : [ 3311 0.07 1.00 ]
| 900 - 950 : [ 75 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APZS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APZS 3635729_fasta.screen.trimQ15.SaF > reads.trim15.APZS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APZS.rl 2 50
-------------------------------------------------------------------
#Found 10752 total values totalling 5601446.0000. <520.967820 +/- 275.610841>
#Range: [ 0 - 932 ]
#Most likely bin: [ 700 - 750 ] 1411 counts
#Median bin: [ 600 - 650 ] 955 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1361 0.13 0.13 ]
|XXXXXXXXX 50 - 100 : [ 320 0.03 0.16 ]
|XXXXX 100 - 150 : [ 178 0.02 0.17 ]
|XXXXX 150 - 200 : [ 181 0.02 0.19 ]
|XXXXXX 200 - 250 : [ 216 0.02 0.21 ]
|XXXXXXXXX 250 - 300 : [ 322 0.03 0.24 ]
|XXXXXXXXXXX 300 - 350 : [ 394 0.04 0.28 ]
|XXXXXXXX 350 - 400 : [ 290 0.03 0.30 ]
|XXXXXXXXX 400 - 450 : [ 327 0.03 0.33 ]
|XXXXXXXX 450 - 500 : [ 272 0.03 0.36 ]
|XXXXXXXXXXX 500 - 550 : [ 372 0.03 0.39 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 555 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 955 0.09 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1218 0.11 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1411 0.13 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1330 0.12 0.90 ]
|XXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 825 0.08 0.98 ]
|XXXXXX 850 - 900 : [ 215 0.02 1.00 ]
| 900 - 950 : [ 10 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AZYA
trimt JAZZ trim 15 readlength histogram for AZYB
trimt JAZZ trim 15 readlength histogram for AZYC
trimt JAZZ trim 15 readlength histogram for SBXG
trimt JAZZ trim 15 readlength histogram for BIXY
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3635729
-------------------------------------------------------------------
APZO.000001.000100 pUC18.fa pUC18.fa LRS.fasta
APZO.000101.000200 pUC18.fa pUC18.fa LRS.fasta
APZO.000201.000300 pUC18.fa pUC18.fa LRS.fasta
APZO.000301.000400 pUC18.fa pUC18.fa LRS.fasta
APZO.000401.000500 pUC18.fa pUC18.fa LRS.fasta
APZP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
APZP.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
APZP.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
APZS.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
BIXY.000001.000100 pSMART-HCKan.fa pSMART-HCKan.fa LRS.fasta
APZO.000001.000100 pUC18.fa pUC18.fa LRS.fasta
APZO.000101.000200 pUC18.fa pUC18.fa LRS.fasta
APZO.000201.000300 pUC18.fa pUC18.fa LRS.fasta
APZO.000301.000400 pUC18.fa pUC18.fa LRS.fasta
APZO.000401.000500 pUC18.fa pUC18.fa LRS.fasta
APZP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
APZP.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
APZP.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
APZS.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
BIXY.000001.000100 pSMART-HCKan.fa pSMART-HCKan.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3635729_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3635729_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 127465 total values totalling 77826.9056. <0.610575 +/- 0.096567>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.64 - 0.645 ] 5608 counts
#Median bin: [ 0.635 - 0.64 ] 5556 counts
| 0 - 0.005 : [ 5 0.00 0.00 ]
#...
| 0.035 - 0.04 : [ 1 0.00 0.00 ]
#...
| 0.11 - 0.115 : [ 1 0.00 0.00 ]
#...
| 0.135 - 0.14 : [ 1 0.00 0.00 ]
| 0.14 - 0.145 : [ 2 0.00 0.00 ]
#...
| 0.155 - 0.16 : [ 1 0.00 0.00 ]
| 0.16 - 0.165 : [ 1 0.00 0.00 ]
#...
| 0.17 - 0.175 : [ 1 0.00 0.00 ]
| 0.175 - 0.18 : [ 2 0.00 0.00 ]
#...
| 0.185 - 0.19 : [ 1 0.00 0.00 ]
| 0.19 - 0.195 : [ 2 0.00 0.00 ]
| 0.195 - 0.2 : [ 1 0.00 0.00 ]
| 0.2 - 0.205 : [ 4 0.00 0.00 ]
| 0.205 - 0.21 : [ 5 0.00 0.00 ]
| 0.21 - 0.215 : [ 4 0.00 0.00 ]
| 0.215 - 0.22 : [ 7 0.00 0.00 ]
| 0.22 - 0.225 : [ 10 0.00 0.00 ]
| 0.225 - 0.23 : [ 9 0.00 0.00 ]
| 0.23 - 0.235 : [ 16 0.00 0.00 ]
| 0.235 - 0.24 : [ 13 0.00 0.00 ]
| 0.24 - 0.245 : [ 25 0.00 0.00 ]
| 0.245 - 0.25 : [ 27 0.00 0.00 ]
| 0.25 - 0.255 : [ 43 0.00 0.00 ]
| 0.255 - 0.26 : [ 51 0.00 0.00 ]
| 0.26 - 0.265 : [ 49 0.00 0.00 ]
| 0.265 - 0.27 : [ 66 0.00 0.00 ]
|X 0.27 - 0.275 : [ 82 0.00 0.00 ]
|X 0.275 - 0.28 : [ 75 0.00 0.00 ]
|X 0.28 - 0.285 : [ 104 0.00 0.00 ]
|X 0.285 - 0.29 : [ 127 0.00 0.01 ]
|X 0.29 - 0.295 : [ 135 0.00 0.01 ]
|X 0.295 - 0.3 : [ 153 0.00 0.01 ]
|X 0.3 - 0.305 : [ 191 0.00 0.01 ]
|X 0.305 - 0.31 : [ 199 0.00 0.01 ]
|XX 0.31 - 0.315 : [ 223 0.00 0.01 ]
|XX 0.315 - 0.32 : [ 231 0.00 0.01 ]
|XX 0.32 - 0.325 : [ 274 0.00 0.02 ]
|XXX 0.325 - 0.33 : [ 359 0.00 0.02 ]
|XXX 0.33 - 0.335 : [ 387 0.00 0.02 ]
|XXX 0.335 - 0.34 : [ 430 0.00 0.03 ]
|XXX 0.34 - 0.345 : [ 462 0.00 0.03 ]
|XXX 0.345 - 0.35 : [ 449 0.00 0.03 ]
|XXXX 0.35 - 0.355 : [ 509 0.00 0.04 ]
|XXXX 0.355 - 0.36 : [ 592 0.00 0.04 ]
|XXXX 0.36 - 0.365 : [ 620 0.00 0.05 ]
|XXXX 0.365 - 0.37 : [ 614 0.00 0.05 ]
|XXXX 0.37 - 0.375 : [ 560 0.00 0.06 ]
|XXXX 0.375 - 0.38 : [ 543 0.00 0.06 ]
|XXXX 0.38 - 0.385 : [ 530 0.00 0.06 ]
|XXXX 0.385 - 0.39 : [ 528 0.00 0.07 ]
|XXXX 0.39 - 0.395 : [ 526 0.00 0.07 ]
|XXX 0.395 - 0.4 : [ 393 0.00 0.08 ]
|XXX 0.4 - 0.405 : [ 410 0.00 0.08 ]
|XXX 0.405 - 0.41 : [ 396 0.00 0.08 ]
|XX 0.41 - 0.415 : [ 334 0.00 0.08 ]
|XXX 0.415 - 0.42 : [ 363 0.00 0.09 ]
|XX 0.42 - 0.425 : [ 319 0.00 0.09 ]
|XX 0.425 - 0.43 : [ 327 0.00 0.09 ]
|XX 0.43 - 0.435 : [ 279 0.00 0.09 ]
|XX 0.435 - 0.44 : [ 287 0.00 0.10 ]
|XX 0.44 - 0.445 : [ 294 0.00 0.10 ]
|XX 0.445 - 0.45 : [ 286 0.00 0.10 ]
|XX 0.45 - 0.455 : [ 303 0.00 0.10 ]
|XX 0.455 - 0.46 : [ 277 0.00 0.11 ]
|XX 0.46 - 0.465 : [ 295 0.00 0.11 ]
|XX 0.465 - 0.47 : [ 265 0.00 0.11 ]
|XX 0.47 - 0.475 : [ 282 0.00 0.11 ]
|XX 0.475 - 0.48 : [ 301 0.00 0.12 ]
|XX 0.48 - 0.485 : [ 305 0.00 0.12 ]
|XX 0.485 - 0.49 : [ 304 0.00 0.12 ]
|XX 0.49 - 0.495 : [ 319 0.00 0.12 ]
|XX 0.495 - 0.5 : [ 238 0.00 0.12 ]
|XXX 0.5 - 0.505 : [ 359 0.00 0.13 ]
|XX 0.505 - 0.51 : [ 296 0.00 0.13 ]
|XX 0.51 - 0.515 : [ 322 0.00 0.13 ]
|XX 0.515 - 0.52 : [ 316 0.00 0.13 ]
|XX 0.52 - 0.525 : [ 350 0.00 0.14 ]
|XXX 0.525 - 0.53 : [ 448 0.00 0.14 ]
|XXXX 0.53 - 0.535 : [ 527 0.00 0.14 ]
|XXXX 0.535 - 0.54 : [ 500 0.00 0.15 ]
|XXXX 0.54 - 0.545 : [ 575 0.00 0.15 ]
|XXXX 0.545 - 0.55 : [ 581 0.00 0.16 ]
|XXXX 0.55 - 0.555 : [ 603 0.00 0.16 ]
|XXXXX 0.555 - 0.56 : [ 652 0.01 0.17 ]
|XXXXX 0.56 - 0.565 : [ 765 0.01 0.17 ]
|XXXXXX 0.565 - 0.57 : [ 882 0.01 0.18 ]
|XXXXXXX 0.57 - 0.575 : [ 1029 0.01 0.19 ]
|XXXXXXXXX 0.575 - 0.58 : [ 1287 0.01 0.20 ]
|XXXXXXXXXXX 0.58 - 0.585 : [ 1487 0.01 0.21 ]
|XXXXXXXXXXXX 0.585 - 0.59 : [ 1707 0.01 0.22 ]
|XXXXXXXXXXXXXXX 0.59 - 0.595 : [ 2041 0.02 0.24 ]
|XXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 2295 0.02 0.26 ]
|XXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 2851 0.02 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 3271 0.03 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 3682 0.03 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 4191 0.03 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 4366 0.03 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 4849 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 5157 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 5556 0.04 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 5608 0.04 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 5532 0.04 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 5439 0.04 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 5142 0.04 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 5065 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 4746 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 4242 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 3878 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 3418 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 3171 0.02 0.89 ]
|XXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 2659 0.02 0.91 ]
|XXXXXXXXXXXXXXX 0.695 - 0.7 : [ 2146 0.02 0.92 ]
|XXXXXXXXXXXXX 0.7 - 0.705 : [ 1867 0.01 0.94 ]
|XXXXXXXXXXX 0.705 - 0.71 : [ 1552 0.01 0.95 ]
|XXXXXXXXX 0.71 - 0.715 : [ 1225 0.01 0.96 ]
|XXXXXXXX 0.715 - 0.72 : [ 1081 0.01 0.97 ]
|XXXXXX 0.72 - 0.725 : [ 832 0.01 0.98 ]
|XXXXX 0.725 - 0.73 : [ 727 0.01 0.98 ]
|XXXX 0.73 - 0.735 : [ 564 0.00 0.99 ]
|XXX 0.735 - 0.74 : [ 434 0.00 0.99 ]
|XX 0.74 - 0.745 : [ 322 0.00 0.99 ]
|X 0.745 - 0.75 : [ 196 0.00 0.99 ]
|XX 0.75 - 0.755 : [ 216 0.00 1.00 ]
|X 0.755 - 0.76 : [ 135 0.00 1.00 ]
|X 0.76 - 0.765 : [ 116 0.00 1.00 ]
|X 0.765 - 0.77 : [ 88 0.00 1.00 ]
| 0.77 - 0.775 : [ 43 0.00 1.00 ]
| 0.775 - 0.78 : [ 44 0.00 1.00 ]
| 0.78 - 0.785 : [ 39 0.00 1.00 ]
| 0.785 - 0.79 : [ 26 0.00 1.00 ]
| 0.79 - 0.795 : [ 23 0.00 1.00 ]
| 0.795 - 0.8 : [ 7 0.00 1.00 ]
| 0.8 - 0.805 : [ 26 0.00 1.00 ]
| 0.805 - 0.81 : [ 15 0.00 1.00 ]
| 0.81 - 0.815 : [ 16 0.00 1.00 ]
| 0.815 - 0.82 : [ 10 0.00 1.00 ]
| 0.82 - 0.825 : [ 4 0.00 1.00 ]
| 0.825 - 0.83 : [ 10 0.00 1.00 ]
| 0.83 - 0.835 : [ 3 0.00 1.00 ]
| 0.835 - 0.84 : [ 3 0.00 1.00 ]
| 0.84 - 0.845 : [ 1 0.00 1.00 ]
| 0.845 - 0.85 : [ 1 0.00 1.00 ]
| 0.85 - 0.855 : [ 3 0.00 1.00 ]
| 0.855 - 0.86 : [ 4 0.00 1.00 ]
| 0.86 - 0.865 : [ 6 0.00 1.00 ]
| 0.865 - 0.87 : [ 1 0.00 1.00 ]
#...
| 0.875 - 0.88 : [ 2 0.00 1.00 ]
#...
| 0.89 - 0.895 : [ 1 0.00 1.00 ]
| 0.895 - 0.9 : [ 1 0.00 1.00 ]
#...
| 0.905 - 0.91 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 16017. 633 reads; 58289 bp (untrimmed), 58118 (trimmed).
Contig 16018. 638 reads; 53211 bp (untrimmed), 53094 (trimmed).
Contig 16019. 639 reads; 54916 bp (untrimmed), 54709 (trimmed).
Contig 16020. 641 reads; 59102 bp (untrimmed), 58850 (trimmed).
Contig 16021. 665 reads; 62508 bp (untrimmed), 62396 (trimmed).
Contig 16022. 671 reads; 60365 bp (untrimmed), 59969 (trimmed).
Contig 16023. 693 reads; 63232 bp (untrimmed), 62990 (trimmed).
Contig 16024. 711 reads; 52699 bp (untrimmed), 52215 (trimmed).
Contig 16025. 732 reads; 66298 bp (untrimmed), 66257 (trimmed).
Contig 16026. 737 reads; 65102 bp (untrimmed), 64954 (trimmed).
Contig 16027. 738 reads; 49554 bp (untrimmed), 49443 (trimmed).
Contig 16028. 763 reads; 61895 bp (untrimmed), 61681 (trimmed).
Contig 16029. 765 reads; 65443 bp (untrimmed), 65392 (trimmed).
Contig 16030. 782 reads; 73736 bp (untrimmed), 73513 (trimmed).
Contig 16031. 798 reads; 57242 bp (untrimmed), 56997 (trimmed).
Contig 16032. 806 reads; 82305 bp (untrimmed), 82034 (trimmed).
Contig 16033. 856 reads; 83681 bp (untrimmed), 83606 (trimmed).
Contig 16034. 902 reads; 75158 bp (untrimmed), 75117 (trimmed).
Contig 16035. 955 reads; 83536 bp (untrimmed), 83500 (trimmed).
Contig 16036. 964 reads; 66559 bp (untrimmed), 66464 (trimmed).
Contig 16037. 964 reads; 90070 bp (untrimmed), 89953 (trimmed).
Contig 16038. 1012 reads; 52710 bp (untrimmed), 52631 (trimmed).
Contig 16039. 1031 reads; 83546 bp (untrimmed), 83212 (trimmed).
Contig 16040. 1076 reads; 84111 bp (untrimmed), 84001 (trimmed).
Contig 16041. 1224 reads; 101063 bp (untrimmed), 100995 (trimmed).
Contig 16042. 1382 reads; 122807 bp (untrimmed), 122687 (trimmed).
Contig 16043. 1465 reads; 139686 bp (untrimmed), 139548 (trimmed).
--------------------------------------------------------------
Totals 108132 reads; 28653650 bp (untrimmed), 24527558 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 24341615 bases = 3.44 +- 4.38 = 0.56 +- 2.93
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 11412 total values totalling 21967.9700. <1.924989 +/- 4.177147>
#Range: [ 1.02 - 299.59 ]
#Most likely bin: [ 1.5 - 2 ] 4511 counts
#Median bin: [ 1.5 - 2 ] 4511 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 4245 0.37 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 4511 0.40 0.77 ]
|XXXXXXXXXXXXX 2 - 2.5 : [ 1484 0.13 0.90 ]
|XXXXX 2.5 - 3 : [ 613 0.05 0.95 ]
|XX 3 - 3.5 : [ 176 0.02 0.97 ]
|X 3.5 - 4 : [ 86 0.01 0.97 ]
| 4 - 4.5 : [ 22 0.00 0.98 ]
| 4.5 - 5 : [ 23 0.00 0.98 ]
| 5 - 5.5 : [ 9 0.00 0.98 ]
| 5.5 - 6 : [ 15 0.00 0.98 ]
| 6 - 6.5 : [ 20 0.00 0.98 ]
| 6.5 - 7 : [ 14 0.00 0.98 ]
| 7 - 7.5 : [ 18 0.00 0.98 ]
| 7.5 - 8 : [ 34 0.00 0.99 ]
| 8 - 8.5 : [ 30 0.00 0.99 ]
| 8.5 - 9 : [ 36 0.00 0.99 ]
| 9 - 9.5 : [ 23 0.00 1.00 ]
| 9.5 - 10 : [ 14 0.00 1.00 ]
| 10 - 10.5 : [ 10 0.00 1.00 ]
| 10.5 - 11 : [ 4 0.00 1.00 ]
| 11 - 11.5 : [ 2 0.00 1.00 ]
| 11.5 - 12 : [ 2 0.00 1.00 ]
| 12 - 12.5 : [ 1 0.00 1.00 ]
| 12.5 - 13 : [ 3 0.00 1.00 ]
| 13 - 13.5 : [ 2 0.00 1.00 ]
| 13.5 - 14 : [ 2 0.00 1.00 ]
| 14 - 14.5 : [ 1 0.00 1.00 ]
#...
| 15 - 15.5 : [ 1 0.00 1.00 ]
| 15.5 - 16 : [ 1 0.00 1.00 ]
| 16 - 16.5 : [ 1 0.00 1.00 ]
#...
| 17.5 - 18 : [ 1 0.00 1.00 ]
#...
| 21.5 - 22 : [ 1 0.00 1.00 ]
#...
| 31.5 - 32 : [ 1 0.00 1.00 ]
#...
| 33.5 - 34 : [ 1 0.00 1.00 ]
#...
| 42 - 42.5 : [ 1 0.00 1.00 ]
#...
| 43.5 - 44 : [ 1 0.00 1.00 ]
#...
| 46 - 46.5 : [ 1 0.00 1.00 ]
#...
| 298.5 - 299 : [ 1 0.00 1.00 ]
#...
| 299.5 - 300 : [ 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 818 total values totalling 3540.0700. <4.327714 +/- 3.022116>
#Range: [ 1.64 - 31.85 ]
#Most likely bin: [ 2 - 2.5 ] 211 counts
#Median bin: [ 2.5 - 3 ] 181 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 1.5 - 2 : [ 52 0.06 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 211 0.26 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 181 0.22 0.54 ]
|XXXXXXXXXXXXXX 3 - 3.5 : [ 75 0.09 0.63 ]
|XXXXXXXX 3.5 - 4 : [ 43 0.05 0.69 ]
|XXX 4 - 4.5 : [ 15 0.02 0.71 ]
|XXX 4.5 - 5 : [ 14 0.02 0.72 ]
|X 5 - 5.5 : [ 5 0.01 0.73 ]
|XX 5.5 - 6 : [ 12 0.01 0.74 ]
|XXX 6 - 6.5 : [ 18 0.02 0.77 ]
|XX 6.5 - 7 : [ 13 0.02 0.78 ]
|XXX 7 - 7.5 : [ 17 0.02 0.80 ]
|XXXXXX 7.5 - 8 : [ 33 0.04 0.84 ]
|XXXXXX 8 - 8.5 : [ 30 0.04 0.88 ]
|XXXXXX 8.5 - 9 : [ 31 0.04 0.92 ]
|XXXX 9 - 9.5 : [ 23 0.03 0.94 ]
|XXX 9.5 - 10 : [ 14 0.02 0.96 ]
|XX 10 - 10.5 : [ 10 0.01 0.97 ]
|X 10.5 - 11 : [ 4 0.00 0.98 ]
| 11 - 11.5 : [ 2 0.00 0.98 ]
| 11.5 - 12 : [ 2 0.00 0.98 ]
| 12 - 12.5 : [ 1 0.00 0.99 ]
| 12.5 - 13 : [ 2 0.00 0.99 ]
| 13 - 13.5 : [ 2 0.00 0.99 ]
| 13.5 - 14 : [ 1 0.00 0.99 ]
| 14 - 14.5 : [ 1 0.00 0.99 ]
#...
| 15 - 15.5 : [ 1 0.00 0.99 ]
| 15.5 - 16 : [ 1 0.00 1.00 ]
| 16 - 16.5 : [ 1 0.00 1.00 ]
#...
| 17.5 - 18 : [ 1 0.00 1.00 ]
#...
| 21.5 - 22 : [ 1 0.00 1.00 ]
#...
| 31.5 - 32 : [ 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 10004 2 reads 1989 bases = 1.02 +- 0.14 = 0.04 +- 0.99
Contig 10047 2 reads 1958 bases = 1.02 +- 0.15 = 1.02 +- 0.15
Contig 5203 2 reads 1766 bases = 1.02 +- 0.16 = 0.07 +- 0.98
Contig 5495 2 reads 1734 bases = 1.02 +- 0.15 = 1.02 +- 0.15
Contig 5937 2 reads 1858 bases = 1.02 +- 0.15 = 0.00 +- 0.99
Contig 6161 2 reads 1451 bases = 1.02 +- 0.16 = 1.02 +- 0.16
Contig 6725 2 reads 1751 bases = 1.02 +- 0.14 = -0.14 +- 0.98
Contig 6766 2 reads 1853 bases = 1.02 +- 0.15 = 1.02 +- 0.15
Contig 6967 2 reads 1848 bases = 1.02 +- 0.14 = 1.02 +- 0.14
Contig 6969 2 reads 1868 bases = 1.02 +- 0.14 = 0.02 +- 0.99
Contig 7135 2 reads 1778 bases = 1.02 +- 0.14 = 1.02 +- 0.14
Contig 7206 2 reads 1682 bases = 1.02 +- 0.16 = 0.15 +- 0.98
Contig 9091 2 reads 1577 bases = 1.02 +- 0.15 = -0.23 +- 0.96
Contig 9478 2 reads 1580 bases = 1.02 +- 0.16 = 0.18 +- 0.97
Contig 9602 2 reads 1594 bases = 1.02 +- 0.15 = 1.02 +- 0.15
Contig 9768 2 reads 1780 bases = 1.02 +- 0.14 = 1.02 +- 0.14
Contig 9805 2 reads 1814 bases = 1.02 +- 0.14 = 0.12 +- 0.98
Contig 9928 2 reads 1560 bases = 1.02 +- 0.16 = 1.02 +- 0.16
Contig 10057 2 reads 1703 bases = 1.03 +- 0.17 = 1.03 +- 0.17
Contig 10065 2 reads 1208 bases = 1.03 +- 0.17 = 1.03 +- 0.17
Contig 15958 249 reads 15908 bases = 12.53 +- 4.85 = -0.05 +- 3.49
Contig 15715 19 reads 1036 bases = 12.58 +- 6.29 = 12.58 +- 6.29
Contig 15882 90 reads 5800 bases = 12.67 +- 9.63 = 3.27 +- 4.05
Contig 15987 364 reads 22668 bases = 13.18 +- 3.73 = 0.23 +- 3.17
Contig 15957 244 reads 15526 bases = 13.43 +- 4.31 = 0.28 +- 4.15
Contig 15692 18 reads 1059 bases = 13.53 +- 6.11 = 13.53 +- 6.11
Contig 15850 58 reads 3391 bases = 13.89 +- 5.61 = -2.74 +- 4.36
Contig 15823 38 reads 2244 bases = 14.08 +- 13.39 = 9.35 +- 11.46
Contig 15936 171 reads 9290 bases = 15.44 +- 10.30 = -1.41 +- 3.00
Contig 16038 1012 reads 52710 bases = 15.98 +- 9.18 = 0.33 +- 3.82
Contig 15868 76 reads 3770 bases = 16.39 +- 6.91 = -1.11 +- 4.09
Contig 15870 77 reads 3779 bases = 17.64 +- 15.65 = 3.47 +- 2.69
Contig 15952 217 reads 6909 bases = 21.67 +- 16.28 = -0.68 +- 3.96
Contig 15911 132 reads 3370 bases = 31.85 +- 38.41 = 2.32 +- 4.88
Contig 15844 50 reads 1028 bases = 33.62 +- 16.33 = 33.62 +- 16.33
Contig 15849 57 reads 1105 bases = 42.29 +- 18.67 = 42.29 +- 18.67
Contig 15853 60 reads 1057 bases = 43.79 +- 19.83 = 43.79 +- 19.83
Contig 15857 66 reads 1056 bases = 46.02 +- 21.42 = 46.02 +- 21.42
Contig 15979 327 reads 672 bases = 298.96 +- 55.90 = 289.92 +- 53.43
Contig 15977 321 reads 635 bases = 299.59 +- 46.24 = 290.88 +- 45.02
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 2582
HQ Discrepant reads = 870
Chimeric reads = 3245
Suspect alignments = 1430
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 4.18 SUN Solaris 7,8
Score matrix /psf/QC/Applications/pphrap/matrix/score_matrix.8
A C G T N X
A 1 -8 -8 -8 0 0
C -8 1 -8 -8 0 0
G -8 -8 1 -8 0 0
T -8 -8 -8 1 0 0
N 0 0 0 0 0 0
X 0 0 0 0 0 0
gap_init: -10
gap_ext: -9
ins_gap_ext: -9
del_gap_ext: -9
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: 20
maxmatch: 45
max_group_size: 20
minscore: 35
bandwidth: 14
indexwordsize: 10
vector_bound: 10
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 19
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -8
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
File generated in /psf/project/assorted1/microbe/community/3635729/edit_dir.25Jul05.QC