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
3436094 9000 1172 Anabaena variabilis
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Anabaena_variabilis
-------------------------------------------------------------------
Anabaena variabilis, species, cyanobacteria
Anabaena, genus, cyanobacteria
Nostocaceae, family, cyanobacteria
Nostocales, order, cyanobacteria
Cyanobacteria (blue-green algae), phylum, cyanobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 7072653
# phrap: 6650410
# db:
altered.
9000000
7574354 +/- 1022715
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 75694
Number of reads with percent X's >= 20%: 255 = 0.2%
Number of reads with percent X's >= 50%: 63 = 0.1%
Number of reads with percent X's >= 80%: 9 = 0.0%
Total reads in project: 115816
Total bp X'd : 4729900
reads >= 20% >= 50% >= 80% screened
Nr with L09136 22862 142 43 9
Nr with LRS 1 1 0 0
Nr with pCC1Fos 3781 1 0 0
Nr with pMCL200_JGI_XZX+XZK 49050 111 20 0
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 74
Number of reads with percent X's >= 20%: 3 = 2.4%
Number of reads with percent X's >= 50%: 2 = 1.6%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 126
Total bp X'd : 5894
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3 0 0 0
Nr with pCC1Fos 18 1 0 0
Nr with pMCL200_JGI_XZX+XZK 53 2 2 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 29787433
C = 21642158
G = 21703288
T = 29433252
N = 532744
X = 4729900
GC fraction = 0.40
Total = 107828775
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436094_fasta.screen.contigs
-------------------------------------------------------------------
A 2077371
C 1465308
G 1469191
T 2073766
N 335
fraction GC = 0.41
total bases = 7085971
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 AAWX reads.list > grep.reads.list.AAWX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAWX 4 500
-------------------------------------------------------------------
#Found 21623 total values totalling 83180556.0000. <3846.855478 +/- 4522.405940>
#Range: [ 907 - 449755 ]
#Most likely bin: [ 3500 - 4000 ] 5092 counts
#Median bin: [ 3500 - 4000 ] 5092 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 15 0.00 0.00 ]
|X 1000 - 1500 : [ 126 0.01 0.01 ]
|XX 1500 - 2000 : [ 197 0.01 0.02 ]
|XXX 2000 - 2500 : [ 324 0.01 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2781 0.13 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4974 0.23 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 5092 0.24 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 4145 0.19 0.82 ]
|XXXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 2487 0.12 0.93 ]
|XXXXXXXXX 5000 - 5500 : [ 1148 0.05 0.98 ]
|XX 5500 - 6000 : [ 292 0.01 1.00 ]
| 6000 - 6500 : [ 29 0.00 1.00 ]
#...
| 12000 - 12500 : [ 1 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
#...
| 42500 - 43000 : [ 1 0.00 1.00 ]
#...
| 43500 - 44000 : [ 1 0.00 1.00 ]
#...
| 55500 - 56000 : [ 1 0.00 1.00 ]
#...
| 57000 - 57500 : [ 1 0.00 1.00 ]
#...
| 75500 - 76000 : [ 1 0.00 1.00 ]
#...
| 122500 - 123000 : [ 1 0.00 1.00 ]
#...
| 131500 - 132000 : [ 1 0.00 1.00 ]
#...
| 144000 - 144500 : [ 1 0.00 1.00 ]
#...
| 196000 - 196500 : [ 1 0.00 1.00 ]
#...
| 362000 - 362500 : [ 1 0.00 1.00 ]
#...
| 449500 - 450000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAWY reads.list > grep.reads.list.AAWY
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAWY 4 500
-------------------------------------------------------------------
#Found 18534 total values totalling 175227993.0000. <9454.407737 +/- 2240.743948>
#Range: [ 971 - 193854 ]
#Most likely bin: [ 9500 - 10000 ] 2938 counts
#Median bin: [ 9500 - 10000 ] 2938 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 24 0.00 0.00 ]
|X 1500 - 2000 : [ 56 0.00 0.00 ]
|X 2000 - 2500 : [ 69 0.00 0.01 ]
|X 2500 - 3000 : [ 94 0.01 0.01 ]
|X 3000 - 3500 : [ 92 0.00 0.02 ]
|X 3500 - 4000 : [ 97 0.01 0.02 ]
|X 4000 - 4500 : [ 109 0.01 0.03 ]
|XX 4500 - 5000 : [ 141 0.01 0.04 ]
|XX 5000 - 5500 : [ 126 0.01 0.04 ]
|XX 5500 - 6000 : [ 133 0.01 0.05 ]
|XX 6000 - 6500 : [ 144 0.01 0.06 ]
|XXX 6500 - 7000 : [ 189 0.01 0.07 ]
|XXXXX 7000 - 7500 : [ 348 0.02 0.09 ]
|XXXXXXXXX 7500 - 8000 : [ 664 0.04 0.12 ]
|XXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1265 0.07 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 2125 0.11 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 2893 0.16 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 2938 0.16 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 2581 0.14 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXX 10500 - 11000 : [ 1726 0.09 0.85 ]
|XXXXXXXXXXXXXXXX 11000 - 11500 : [ 1164 0.06 0.92 ]
|XXXXXXXXXXX 11500 - 12000 : [ 796 0.04 0.96 ]
|XXXXXX 12000 - 12500 : [ 439 0.02 0.98 ]
|XXX 12500 - 13000 : [ 220 0.01 0.99 ]
|X 13000 - 13500 : [ 77 0.00 1.00 ]
| 13500 - 14000 : [ 14 0.00 1.00 ]
| 14000 - 14500 : [ 4 0.00 1.00 ]
| 14500 - 15000 : [ 4 0.00 1.00 ]
#...
| 193500 - 194000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAWZ reads.list > grep.reads.list.AAWZ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAWZ 4 500
-------------------------------------------------------------------
#Found 2480 total values totalling 84771846.0000. <34182.195968 +/- 3614.411626>
#Range: [ 19955 - 44921 ]
#Most likely bin: [ 34000 - 34500 ] 169 counts
#Median bin: [ 34000 - 34500 ] 169 counts
#Histogram Bins Count Fraction Cum_Fraction
| 19500 - 20000 : [ 1 0.00 0.00 ]
| 20000 - 20500 : [ 1 0.00 0.00 ]
#...
| 21000 - 21500 : [ 1 0.00 0.00 ]
#...
| 22000 - 22500 : [ 1 0.00 0.00 ]
| 22500 - 23000 : [ 2 0.00 0.00 ]
#...
| 23500 - 24000 : [ 2 0.00 0.00 ]
|X 24000 - 24500 : [ 5 0.00 0.01 ]
|XX 24500 - 25000 : [ 8 0.00 0.01 ]
|XXX 25000 - 25500 : [ 13 0.01 0.01 ]
|XXX 25500 - 26000 : [ 14 0.01 0.02 ]
|XXXXX 26000 - 26500 : [ 20 0.01 0.03 ]
|XXXXXXX 26500 - 27000 : [ 29 0.01 0.04 ]
|XXXXX 27000 - 27500 : [ 20 0.01 0.05 ]
|XXXXX 27500 - 28000 : [ 23 0.01 0.06 ]
|XXXXXXXX 28000 - 28500 : [ 32 0.01 0.07 ]
|XXXXXXXXX 28500 - 29000 : [ 39 0.02 0.09 ]
|XXXXXXXXXXX 29000 - 29500 : [ 45 0.02 0.10 ]
|XXXXXXXXXXXXXX 29500 - 30000 : [ 58 0.02 0.13 ]
|XXXXXXXXXXXXX 30000 - 30500 : [ 57 0.02 0.15 ]
|XXXXXXXXXXXXXXXX 30500 - 31000 : [ 66 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXX 31000 - 31500 : [ 84 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXX 31500 - 32000 : [ 81 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 112 0.05 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 117 0.05 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 138 0.06 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 152 0.06 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 169 0.07 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 147 0.06 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 159 0.06 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 141 0.06 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 129 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 118 0.05 0.80 ]
|XXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 89 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 78 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 77 0.03 0.90 ]
|XXXXXXXXXXXXXXX 38500 - 39000 : [ 63 0.03 0.92 ]
|XXXXXXXXXXX 39000 - 39500 : [ 45 0.02 0.94 ]
|XXXXXXXX 39500 - 40000 : [ 33 0.01 0.96 ]
|XXX 40000 - 40500 : [ 14 0.01 0.96 ]
|XXXXX 40500 - 41000 : [ 20 0.01 0.97 ]
|XXXX 41000 - 41500 : [ 16 0.01 0.98 ]
|XXXX 41500 - 42000 : [ 17 0.01 0.98 ]
|XXXX 42000 - 42500 : [ 16 0.01 0.99 ]
|X 42500 - 43000 : [ 5 0.00 0.99 ]
|XX 43000 - 43500 : [ 9 0.00 0.99 ]
|X 43500 - 44000 : [ 6 0.00 1.00 ]
|X 44000 - 44500 : [ 6 0.00 1.00 ]
| 44500 - 45000 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AAWZ 34088 +- 3606 (n=1210)
# AAWX 3690 +- 967 (n=10809)
# AAWY 9235 +- 1803 (n=9443)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436094_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
AAWX 62592 -1 -1 96 668 55994 99 664 100 673
AAWY 65280 -1 -1 92 589 51819 97 522 100 571
AAWZ 9984 -1 -1 90 584 8003 98 645 100 656
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AAWX 25661 100 670 100 687 30333 99 658 100 661
AAWY 25360 96 520 100 570 26459 97 524 100 571
AAWZ 4026 98 656 100 653 3977 99 633 100 660
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436094_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 115816 63187 90.79 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 3436094_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 115816 total values totalling 68343052.0000. <590.100262 +/- 174.244113>
#Range: [ 16 - 936 ]
#Most likely bin: [ 650 - 700 ] 21306 counts
#Median bin: [ 600 - 650 ] 17310 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 443 0.00 0.00 ]
|XXX 50 - 100 : [ 1692 0.01 0.02 ]
|XXXX 100 - 150 : [ 1970 0.02 0.04 ]
|XXXX 150 - 200 : [ 2150 0.02 0.05 ]
|XXXX 200 - 250 : [ 2193 0.02 0.07 ]
|XXXXX 250 - 300 : [ 2412 0.02 0.09 ]
|XXXXX 300 - 350 : [ 2650 0.02 0.12 ]
|XXXXXX 350 - 400 : [ 3269 0.03 0.14 ]
|XXXXXXX 400 - 450 : [ 3809 0.03 0.18 ]
|XXXXXXXXX 450 - 500 : [ 4900 0.04 0.22 ]
|XXXXXXXXXXXXX 500 - 550 : [ 6987 0.06 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 11473 0.10 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 17310 0.15 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 21306 0.18 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 20216 0.17 0.89 ]
|XXXXXXXXXXXXXXXXX 750 - 800 : [ 9247 0.08 0.97 ]
|XXXXXX 800 - 850 : [ 3142 0.03 0.99 ]
|X 850 - 900 : [ 637 0.01 1.00 ]
| 900 - 950 : [ 10 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHST
trimt JAZZ trim 15 readlength histogram for AAWX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAWX 3436094_fasta.screen.trimQ15.SaF > reads.trim15.AAWX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAWX.rl 2 50
-------------------------------------------------------------------
#Found 55994 total values totalling 36944682.0000. <659.797157 +/- 133.049098>
#Range: [ 16 - 915 ]
#Most likely bin: [ 700 - 750 ] 16119 counts
#Median bin: [ 650 - 700 ] 12793 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 90 0.00 0.00 ]
|X 50 - 100 : [ 274 0.00 0.01 ]
|X 100 - 150 : [ 350 0.01 0.01 ]
|X 150 - 200 : [ 427 0.01 0.02 ]
|X 200 - 250 : [ 431 0.01 0.03 ]
|X 250 - 300 : [ 470 0.01 0.04 ]
|X 300 - 350 : [ 544 0.01 0.05 ]
|XX 350 - 400 : [ 727 0.01 0.06 ]
|XX 400 - 450 : [ 902 0.02 0.08 ]
|XXX 450 - 500 : [ 1152 0.02 0.10 ]
|XXXX 500 - 550 : [ 1632 0.03 0.12 ]
|XXXXXXXX 550 - 600 : [ 3226 0.06 0.18 ]
|XXXXXXXXXXXXXXXXX 600 - 650 : [ 6894 0.12 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 12793 0.23 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 16119 0.29 0.82 ]
|XXXXXXXXXXXXXXXXXX 750 - 800 : [ 7197 0.13 0.95 ]
|XXXXXX 800 - 850 : [ 2287 0.04 0.99 ]
|X 850 - 900 : [ 473 0.01 1.00 ]
| 900 - 950 : [ 6 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAWY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAWY 3436094_fasta.screen.trimQ15.SaF > reads.trim15.AAWY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAWY.rl 2 50
-------------------------------------------------------------------
#Found 51819 total values totalling 26308659.0000. <507.702947 +/- 176.298469>
#Range: [ 22 - 854 ]
#Most likely bin: [ 600 - 650 ] 9637 counts
#Median bin: [ 550 - 600 ] 7944 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 314 0.01 0.01 ]
|XXXXXX 50 - 100 : [ 1334 0.03 0.03 ]
|XXXXXX 100 - 150 : [ 1509 0.03 0.06 ]
|XXXXXXX 150 - 200 : [ 1570 0.03 0.09 ]
|XXXXXXX 200 - 250 : [ 1591 0.03 0.12 ]
|XXXXXXX 250 - 300 : [ 1774 0.03 0.16 ]
|XXXXXXXX 300 - 350 : [ 1906 0.04 0.19 ]
|XXXXXXXXXX 350 - 400 : [ 2330 0.04 0.24 ]
|XXXXXXXXXXX 400 - 450 : [ 2730 0.05 0.29 ]
|XXXXXXXXXXXXXXX 450 - 500 : [ 3621 0.07 0.36 ]
|XXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 5161 0.10 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 7944 0.15 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 9637 0.19 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 7022 0.14 0.93 ]
|XXXXXXXXXX 700 - 750 : [ 2435 0.05 0.98 ]
|XXX 750 - 800 : [ 805 0.02 1.00 ]
|X 800 - 850 : [ 135 0.00 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAWZ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAWZ 3436094_fasta.screen.trimQ15.SaF > reads.trim15.AAWZ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAWZ.rl 2 50
-------------------------------------------------------------------
#Found 8003 total values totalling 5089711.0000. <635.975384 +/- 184.975317>
#Range: [ 18 - 936 ]
#Most likely bin: [ 700 - 750 ] 1662 counts
#Median bin: [ 650 - 700 ] 1491 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 39 0.00 0.00 ]
|XX 50 - 100 : [ 84 0.01 0.02 ]
|XXX 100 - 150 : [ 111 0.01 0.03 ]
|XXXX 150 - 200 : [ 153 0.02 0.05 ]
|XXXX 200 - 250 : [ 171 0.02 0.07 ]
|XXXX 250 - 300 : [ 168 0.02 0.09 ]
|XXXXX 300 - 350 : [ 200 0.02 0.12 ]
|XXXXX 350 - 400 : [ 212 0.03 0.14 ]
|XXXX 400 - 450 : [ 177 0.02 0.16 ]
|XXX 450 - 500 : [ 127 0.02 0.18 ]
|XXXXX 500 - 550 : [ 194 0.02 0.20 ]
|XXXXXXX 550 - 600 : [ 303 0.04 0.24 ]
|XXXXXXXXXXXXXXXXXXX 600 - 650 : [ 779 0.10 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1491 0.19 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1662 0.21 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1245 0.16 0.89 ]
|XXXXXXXXXXXXXXXXX 800 - 850 : [ 720 0.09 0.98 ]
|XXXX 850 - 900 : [ 163 0.02 1.00 ]
| 900 - 950 : [ 4 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436094
-------------------------------------------------------------------
AAWX.000001.000100 pUC18.fa.4 LRS.fasta
AAWX.000101.000200 pUC18.fa.4 LRS.fasta
AAWX.000201.000300 pUC18.fa.4 LRS.fasta
AAWX.000301.000400 pUC18.fa.4 LRS.fasta
AAWY.000001.000100 pMCL200.fa.4 LRS.fasta
AAWY.000101.000200 pMCL200.fa LRS.fasta
AAWY.000201.000300 pMCL200.fa.4 LRS.fasta
AAWY.000301.000400 pMCL200.fa.4 LRS.fasta
AAWZ.000001.000100 pCC1Fos.fa.4 LRS.fasta
AAWX.000001.000100 pUC18.fa.4 LRS.fasta
AAWX.000101.000200 pUC18.fa.4 LRS.fasta
AAWX.000201.000300 pUC18.fa.4 LRS.fasta
AAWX.000301.000400 pUC18.fa.4 LRS.fasta
AAWY.000001.000100 pMCL200.fa.4 LRS.fasta
AAWY.000101.000200 pMCL200.fa LRS.fasta
AAWY.000201.000300 pMCL200.fa.4 LRS.fasta
AAWY.000301.000400 pMCL200.fa.4 LRS.fasta
AAWZ.000001.000100 pCC1Fos.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436094_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436094_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 115377 total values totalling 47705.2848. <0.413473 +/- 0.050454>
#Range: [ 0.0435 - 1 ]
#Most likely bin: [ 0.435 - 0.44 ] 5084 counts
#Median bin: [ 0.415 - 0.42 ] 4633 counts
| 0.04 - 0.045 : [ 1 0.00 0.00 ]
#...
| 0.08 - 0.085 : [ 1 0.00 0.00 ]
#...
| 0.09 - 0.095 : [ 1 0.00 0.00 ]
#...
| 0.1 - 0.105 : [ 1 0.00 0.00 ]
| 0.105 - 0.11 : [ 2 0.00 0.00 ]
#...
| 0.12 - 0.125 : [ 1 0.00 0.00 ]
#...
| 0.13 - 0.135 : [ 1 0.00 0.00 ]
#...
| 0.14 - 0.145 : [ 1 0.00 0.00 ]
| 0.145 - 0.15 : [ 2 0.00 0.00 ]
| 0.15 - 0.155 : [ 2 0.00 0.00 ]
#...
| 0.16 - 0.165 : [ 2 0.00 0.00 ]
| 0.165 - 0.17 : [ 2 0.00 0.00 ]
| 0.17 - 0.175 : [ 6 0.00 0.00 ]
#...
| 0.18 - 0.185 : [ 3 0.00 0.00 ]
| 0.185 - 0.19 : [ 9 0.00 0.00 ]
| 0.19 - 0.195 : [ 7 0.00 0.00 ]
| 0.195 - 0.2 : [ 3 0.00 0.00 ]
| 0.2 - 0.205 : [ 6 0.00 0.00 ]
| 0.205 - 0.21 : [ 10 0.00 0.00 ]
| 0.21 - 0.215 : [ 16 0.00 0.00 ]
| 0.215 - 0.22 : [ 16 0.00 0.00 ]
| 0.22 - 0.225 : [ 11 0.00 0.00 ]
| 0.225 - 0.23 : [ 27 0.00 0.00 ]
| 0.23 - 0.235 : [ 26 0.00 0.00 ]
| 0.235 - 0.24 : [ 23 0.00 0.00 ]
| 0.24 - 0.245 : [ 27 0.00 0.00 ]
| 0.245 - 0.25 : [ 20 0.00 0.00 ]
| 0.25 - 0.255 : [ 49 0.00 0.00 ]
|X 0.255 - 0.26 : [ 64 0.00 0.00 ]
|X 0.26 - 0.265 : [ 78 0.00 0.00 ]
|X 0.265 - 0.27 : [ 101 0.00 0.00 ]
|X 0.27 - 0.275 : [ 137 0.00 0.01 ]
|X 0.275 - 0.28 : [ 173 0.00 0.01 ]
|XX 0.28 - 0.285 : [ 240 0.00 0.01 ]
|XX 0.285 - 0.29 : [ 231 0.00 0.01 ]
|XX 0.29 - 0.295 : [ 278 0.00 0.01 ]
|XXX 0.295 - 0.3 : [ 379 0.00 0.02 ]
|XXXX 0.3 - 0.305 : [ 464 0.00 0.02 ]
|XXXX 0.305 - 0.31 : [ 569 0.00 0.03 ]
|XXXXX 0.31 - 0.315 : [ 681 0.01 0.03 ]
|XXXXXX 0.315 - 0.32 : [ 767 0.01 0.04 ]
|XXXXXXXX 0.32 - 0.325 : [ 958 0.01 0.05 ]
|XXXXXXXXX 0.325 - 0.33 : [ 1122 0.01 0.06 ]
|XXXXXXXXXX 0.33 - 0.335 : [ 1264 0.01 0.07 ]
|XXXXXXXXXXX 0.335 - 0.34 : [ 1423 0.01 0.08 ]
|XXXXXXXXXXXXX 0.34 - 0.345 : [ 1713 0.01 0.09 ]
|XXXXXXXXXXXXXX 0.345 - 0.35 : [ 1821 0.02 0.11 ]
|XXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 2019 0.02 0.13 ]
|XXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 2136 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 2461 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 2707 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 2756 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 3110 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 3383 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 3586 0.03 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 3622 0.03 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 3638 0.03 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 4132 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 4241 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 4466 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 4633 0.04 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 4799 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 4982 0.04 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 4904 0.04 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 5084 0.04 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 4761 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 4386 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 4216 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 3747 0.03 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 3450 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 2878 0.02 0.89 ]
|XXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 2448 0.02 0.91 ]
|XXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 2078 0.02 0.93 ]
|XXXXXXXXXXXXX 0.48 - 0.485 : [ 1667 0.01 0.94 ]
|XXXXXXXXXX 0.485 - 0.49 : [ 1322 0.01 0.96 ]
|XXXXXXXXX 0.49 - 0.495 : [ 1081 0.01 0.97 ]
|XXXXX 0.495 - 0.5 : [ 667 0.01 0.97 ]
|XXXXXX 0.5 - 0.505 : [ 787 0.01 0.98 ]
|XXXX 0.505 - 0.51 : [ 448 0.00 0.98 ]
|XXX 0.51 - 0.515 : [ 388 0.00 0.99 ]
|XX 0.515 - 0.52 : [ 299 0.00 0.99 ]
|XX 0.52 - 0.525 : [ 231 0.00 0.99 ]
|X 0.525 - 0.53 : [ 186 0.00 0.99 ]
|X 0.53 - 0.535 : [ 150 0.00 0.99 ]
|X 0.535 - 0.54 : [ 124 0.00 0.99 ]
|X 0.54 - 0.545 : [ 86 0.00 0.99 ]
|X 0.545 - 0.55 : [ 75 0.00 1.00 ]
| 0.55 - 0.555 : [ 63 0.00 1.00 ]
| 0.555 - 0.56 : [ 49 0.00 1.00 ]
| 0.56 - 0.565 : [ 54 0.00 1.00 ]
| 0.565 - 0.57 : [ 32 0.00 1.00 ]
| 0.57 - 0.575 : [ 35 0.00 1.00 ]
| 0.575 - 0.58 : [ 22 0.00 1.00 ]
| 0.58 - 0.585 : [ 36 0.00 1.00 ]
| 0.585 - 0.59 : [ 19 0.00 1.00 ]
| 0.59 - 0.595 : [ 17 0.00 1.00 ]
| 0.595 - 0.6 : [ 20 0.00 1.00 ]
| 0.6 - 0.605 : [ 16 0.00 1.00 ]
| 0.605 - 0.61 : [ 15 0.00 1.00 ]
| 0.61 - 0.615 : [ 12 0.00 1.00 ]
| 0.615 - 0.62 : [ 15 0.00 1.00 ]
| 0.62 - 0.625 : [ 8 0.00 1.00 ]
| 0.625 - 0.63 : [ 9 0.00 1.00 ]
| 0.63 - 0.635 : [ 6 0.00 1.00 ]
| 0.635 - 0.64 : [ 8 0.00 1.00 ]
| 0.64 - 0.645 : [ 8 0.00 1.00 ]
| 0.645 - 0.65 : [ 5 0.00 1.00 ]
| 0.65 - 0.655 : [ 4 0.00 1.00 ]
| 0.655 - 0.66 : [ 4 0.00 1.00 ]
| 0.66 - 0.665 : [ 5 0.00 1.00 ]
| 0.665 - 0.67 : [ 3 0.00 1.00 ]
#...
| 0.675 - 0.68 : [ 5 0.00 1.00 ]
| 0.68 - 0.685 : [ 6 0.00 1.00 ]
| 0.685 - 0.69 : [ 2 0.00 1.00 ]
| 0.69 - 0.695 : [ 3 0.00 1.00 ]
| 0.695 - 0.7 : [ 3 0.00 1.00 ]
| 0.7 - 0.705 : [ 3 0.00 1.00 ]
#...
| 0.71 - 0.715 : [ 7 0.00 1.00 ]
| 0.715 - 0.72 : [ 4 0.00 1.00 ]
| 0.72 - 0.725 : [ 1 0.00 1.00 ]
#...
| 0.735 - 0.74 : [ 2 0.00 1.00 ]
#...
| 0.745 - 0.75 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 2 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 62. 1460 reads; 82065 bp (untrimmed), 82065 (trimmed).
Contig 63. 1487 reads; 90124 bp (untrimmed), 89947 (trimmed).
Contig 64. 1501 reads; 101340 bp (untrimmed), 101175 (trimmed).
Contig 65. 1531 reads; 94976 bp (untrimmed), 94976 (trimmed).
Contig 66. 1703 reads; 101596 bp (untrimmed), 101291 (trimmed).
Contig 67. 1817 reads; 116357 bp (untrimmed), 116123 (trimmed).
Contig 68. 1888 reads; 115370 bp (untrimmed), 115370 (trimmed).
Contig 69. 1912 reads; 118558 bp (untrimmed), 118518 (trimmed).
Contig 70. 1999 reads; 128424 bp (untrimmed), 128060 (trimmed).
Contig 71. 2116 reads; 126658 bp (untrimmed), 126538 (trimmed).
Contig 72. 2199 reads; 134315 bp (untrimmed), 133798 (trimmed).
Contig 73. 2380 reads; 134866 bp (untrimmed), 134832 (trimmed).
Contig 74. 2948 reads; 180441 bp (untrimmed), 180397 (trimmed).
Contig 75. 3078 reads; 174647 bp (untrimmed), 174632 (trimmed).
Contig 76. 3224 reads; 205788 bp (untrimmed), 205684 (trimmed).
Contig 77. 3355 reads; 217981 bp (untrimmed), 217704 (trimmed).
Contig 78. 3365 reads; 206420 bp (untrimmed), 206168 (trimmed).
Contig 79. 3696 reads; 236978 bp (untrimmed), 236862 (trimmed).
Contig 80. 3965 reads; 231083 bp (untrimmed), 231081 (trimmed).
Contig 81. 4282 reads; 252923 bp (untrimmed), 252894 (trimmed).
Contig 82. 4338 reads; 273420 bp (untrimmed), 273195 (trimmed).
Contig 83. 4581 reads; 290165 bp (untrimmed), 289869 (trimmed).
Contig 84. 5225 reads; 285750 bp (untrimmed), 285750 (trimmed).
Contig 85. 6032 reads; 336516 bp (untrimmed), 336516 (trimmed).
Contig 86. 6098 reads; 349882 bp (untrimmed), 349794 (trimmed).
Contig 87. 8223 reads; 464887 bp (untrimmed), 464868 (trimmed).
Contig 88. 9028 reads; 526235 bp (untrimmed), 526179 (trimmed).
--------------------------------------------------------------
Totals 115690 reads; 7085971 bp (untrimmed), 7072653 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 7082485 bases = 13.07 +- 5.50 = 0.24 +- 4.31
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 84 total values totalling 862.2000. <10.264286 +/- 4.036785>
#Range: [ 1.57 - 21.34 ]
#Most likely bin: [ 12.5 - 13 ] 13 counts
#Median bin: [ 12 - 12.5 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 1.5 - 2 : [ 2 0.02 0.02 ]
|XXX 2 - 2.5 : [ 1 0.01 0.04 ]
|XXXXXXXXXXXX 2.5 - 3 : [ 4 0.05 0.08 ]
|XXX 3 - 3.5 : [ 1 0.01 0.10 ]
|XXXXXXXXX 3.5 - 4 : [ 3 0.04 0.13 ]
#...
|XXXXXXXXX 4.5 - 5 : [ 3 0.04 0.17 ]
|XXXXXX 5 - 5.5 : [ 2 0.02 0.19 ]
|XXXXXX 5.5 - 6 : [ 2 0.02 0.21 ]
|XXX 6 - 6.5 : [ 1 0.01 0.23 ]
|XXX 6.5 - 7 : [ 1 0.01 0.24 ]
#...
|XXXXXX 7.5 - 8 : [ 2 0.02 0.26 ]
|XXXXXX 8 - 8.5 : [ 2 0.02 0.29 ]
|XXXXXXXXX 8.5 - 9 : [ 3 0.04 0.32 ]
|XXXXXX 9 - 9.5 : [ 2 0.02 0.35 ]
|XXX 9.5 - 10 : [ 1 0.01 0.36 ]
|XXX 10 - 10.5 : [ 1 0.01 0.37 ]
|XXXXXXXXXXXX 10.5 - 11 : [ 4 0.05 0.42 ]
|XXXXXXXXXXXX 11 - 11.5 : [ 4 0.05 0.46 ]
|XXXXXX 11.5 - 12 : [ 2 0.02 0.49 ]
|XXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 6 0.07 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 13 0.15 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 12 0.14 0.86 ]
|XXXXXXXXXXXXXXX 13.5 - 14 : [ 5 0.06 0.92 ]
|XXXXXXXXXXXX 14 - 14.5 : [ 4 0.05 0.96 ]
|XXXXXX 14.5 - 15 : [ 2 0.02 0.99 ]
#...
|XXX 21 - 21.5 : [ 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 68 total values totalling 799.1600. <11.752353 +/- 2.736588>
#Range: [ 4.59 - 21.34 ]
#Most likely bin: [ 12.5 - 13 ] 13 counts
#Median bin: [ 12.5 - 13 ] 13 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 4.5 - 5 : [ 2 0.03 0.03 ]
|XXX 5 - 5.5 : [ 1 0.01 0.04 ]
|XXX 5.5 - 6 : [ 1 0.01 0.06 ]
|XXX 6 - 6.5 : [ 1 0.01 0.07 ]
|XXX 6.5 - 7 : [ 1 0.01 0.09 ]
#...
|XXXXXX 7.5 - 8 : [ 2 0.03 0.12 ]
|XXX 8 - 8.5 : [ 1 0.01 0.13 ]
|XXXXXX 8.5 - 9 : [ 2 0.03 0.16 ]
|XXXXXX 9 - 9.5 : [ 2 0.03 0.19 ]
|XXX 9.5 - 10 : [ 1 0.01 0.21 ]
|XXX 10 - 10.5 : [ 1 0.01 0.22 ]
|XXXXXXXXXXXX 10.5 - 11 : [ 4 0.06 0.28 ]
|XXXXXXXXXXXX 11 - 11.5 : [ 4 0.06 0.34 ]
|XXXXXX 11.5 - 12 : [ 2 0.03 0.37 ]
|XXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 6 0.09 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 13 0.19 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 12 0.18 0.82 ]
|XXXXXXXXXXXXXXX 13.5 - 14 : [ 5 0.07 0.90 ]
|XXXXXXXXXXXX 14 - 14.5 : [ 4 0.06 0.96 ]
|XXXXXX 14.5 - 15 : [ 2 0.03 0.99 ]
#...
|XXX 21 - 21.5 : [ 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 6 3 reads 1842 bases = 1.57 +- 0.68 = 0.28 +- 0.93
Contig 5 2 reads 1431 bases = 1.59 +- 0.49 = 1.59 +- 0.49
Contig 10 3 reads 1242 bases = 2.22 +- 0.74 = 0.60 +- 0.49
Contig 7 3 reads 1038 bases = 2.51 +- 0.83 = 0.94 +- 0.53
Contig 9 3 reads 1170 bases = 2.57 +- 0.81 = 2.57 +- 0.81
Contig 8 3 reads 947 bases = 2.63 +- 0.56 = 0.71 +- 0.46
Contig 12 6 reads 1768 bases = 2.82 +- 1.24 = 2.82 +- 1.24
Contig 14 7 reads 1862 bases = 3.43 +- 2.35 = 3.43 +- 2.35
Contig 16 9 reads 1914 bases = 3.52 +- 1.67 = 1.14 +- 0.91
Contig 13 6 reads 1328 bases = 3.55 +- 1.66 = 3.55 +- 1.66
Contig 11 5 reads 903 bases = 3.89 +- 1.31 = 2.99 +- 0.84
Contig 22 40 reads 6888 bases = 4.59 +- 2.00 = 1.67 +- 1.34
Contig 15 8 reads 1439 bases = 4.60 +- 2.51 = 4.60 +- 2.51
Contig 28 62 reads 10254 bases = 4.97 +- 2.40 = 1.18 +- 2.08
Contig 29 79 reads 11998 bases = 5.32 +- 2.52 = 1.06 +- 2.92
Contig 18 11 reads 1532 bases = 5.42 +- 2.07 = 1.54 +- 0.82
Contig 23 42 reads 6182 bases = 5.62 +- 2.25 = 2.49 +- 3.24
Contig 17 9 reads 1217 bases = 5.71 +- 2.32 = 2.47 +- 1.45
Contig 26 47 reads 5788 bases = 6.27 +- 3.44 = 4.05 +- 3.00
Contig 24 45 reads 5623 bases = 6.65 +- 2.30 = 2.63 +- 2.56
Contig 51 844 reads 51280 bases = 13.14 +- 4.34 = 0.13 +- 3.98
Contig 40 450 reads 27595 bases = 13.15 +- 4.47 = 1.16 +- 4.03
Contig 48 732 reads 44125 bases = 13.20 +- 4.03 = 0.52 +- 3.28
Contig 63 1487 reads 90124 bases = 13.20 +- 4.45 = 0.27 +- 3.73
Contig 39 425 reads 26111 bases = 13.29 +- 4.29 = 1.59 +- 3.85
Contig 66 1703 reads 101596 bases = 13.32 +- 4.39 = 0.54 +- 4.21
Contig 71 2116 reads 126658 bases = 13.36 +- 5.10 = 0.47 +- 4.89
Contig 52 911 reads 54108 bases = 13.41 +- 4.62 = 0.59 +- 3.94
Contig 81 4282 reads 252923 bases = 13.55 +- 4.62 = 0.01 +- 4.55
Contig 80 3965 reads 231083 bases = 13.73 +- 4.34 = 0.01 +- 3.98
Contig 88 9028 reads 526235 bases = 13.74 +- 4.51 = 0.00 +- 4.36
Contig 86 6098 reads 349882 bases = 13.96 +- 4.38 = 0.07 +- 4.20
Contig 75 3078 reads 174647 bases = 13.99 +- 4.46 = 0.11 +- 4.23
Contig 87 8223 reads 464887 bases = 14.14 +- 6.62 = 0.05 +- 4.43
Contig 73 2380 reads 134866 bases = 14.19 +- 4.79 = 0.08 +- 4.16
Contig 62 1460 reads 82065 bases = 14.22 +- 4.56 = 0.55 +- 3.78
Contig 85 6032 reads 336516 bases = 14.33 +- 10.78 = 0.15 +- 4.21
Contig 84 5225 reads 285750 bases = 14.60 +- 8.38 = 0.25 +- 4.32
Contig 53 921 reads 50290 bases = 14.71 +- 4.77 = 0.79 +- 4.30
Contig 56 975 reads 36735 bases = 21.34 +- 5.28 = 0.24 +- 4.41
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1029
HQ Discrepant reads = 31
Chimeric reads = 92
Suspect alignments = 712
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 3.57 SUN/Ultra-2/3
Equivalent to Phil Green's version 0.990329
Score matrix (set by value of penalty: -2)
A C G T N X
A 1 -2 -2 -2 0 -3
C -2 1 -2 -2 0 -3
G -2 -2 1 -2 0 -3
T -2 -2 -2 1 0 -3
N 0 0 0 0 0 0
X -3 -3 -3 -3 0 -3
gap_init: -4
gap_ext: -3
ins_gap_ext: -3
del_gap_ext: -3
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 30
maxmatch: 55
max_group_size: 20
minscore: 55
bandwidth: 14
indexwordsize: 10
vector_bound: 20
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 13
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -5
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/microbe4/3436094/edit_dir.13Apr04.QD