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
3634505 3900 158080 Chromohalobacter salexigens
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Chromohalobacter_salexigens
-------------------------------------------------------------------
Chromohalobacter salexigens, species, g-proteobacteria
Oceanospirillales, order, g-proteobacteria
Chromohalobacter, genus, g-proteobacteria
Halomonadaceae, family, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3685675
# phrap: 3790920
# db:
altered.
3900000
3792198 +/- 87502
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 20451
Number of reads with percent X's >= 20%: 3684 = 6.4%
Number of reads with percent X's >= 50%: 3504 = 6.1%
Number of reads with percent X's >= 80%: 2784 = 4.9%
Total reads in project: 57296
Total bp X'd : 3444496
reads >= 20% >= 50% >= 80% screened
Nr with L09136 16089 1087 965 859
Nr with pCC1Fos 1744 10 5 0
Nr with pMCL200_JGI_XZX+XZK 2618 2587 2534 1925
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 2260
Number of reads with percent X's >= 20%: 2207 = 29.7%
Number of reads with percent X's >= 50%: 2170 = 29.2%
Number of reads with percent X's >= 80%: 1878 = 25.3%
Total reads in project: 7435
Total bp X'd : 1816348
reads >= 20% >= 50% >= 80% screened
Nr with L09136 921 888 866 823
Nr with pCC1Fos 13 2 1 0
Nr with pMCL200_JGI_XZX+XZK 1326 1317 1303 1055
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 8103643
C = 13793823
G = 13808719
T = 8037365
N = 218161
X = 867532
GC fraction = 0.62
Total = 44829243
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634505_fasta.screen.contigs
-------------------------------------------------------------------
A 668736
C 1184099
G 1181374
T 666891
N 1602
fraction GC = 0.64
total bases = 3702702
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 QCMC reads.list > grep.reads.list.QCMC
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.QCMC 4 500
-------------------------------------------------------------------
#Found 923 total values totalling 7629809.0000. <8266.315276 +/- 3407.116261>
#Range: [ 914 - 68562 ]
#Most likely bin: [ 8500 - 9000 ] 162 counts
#Median bin: [ 8000 - 8500 ] 158 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
|XX 1000 - 1500 : [ 10 0.01 0.01 ]
|X 1500 - 2000 : [ 5 0.01 0.02 ]
|X 2000 - 2500 : [ 6 0.01 0.02 ]
| 2500 - 3000 : [ 2 0.00 0.03 ]
|XX 3000 - 3500 : [ 9 0.01 0.04 ]
|XX 3500 - 4000 : [ 9 0.01 0.05 ]
|X 4000 - 4500 : [ 5 0.01 0.05 ]
|XXXX 4500 - 5000 : [ 15 0.02 0.07 ]
|XX 5000 - 5500 : [ 8 0.01 0.08 ]
|XXX 5500 - 6000 : [ 13 0.01 0.09 ]
|XXXXX 6000 - 6500 : [ 19 0.02 0.11 ]
|XXXXXXXXXXXX 6500 - 7000 : [ 48 0.05 0.16 ]
|XXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 83 0.09 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 102 0.11 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 158 0.17 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 162 0.18 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 113 0.12 0.83 ]
|XXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 75 0.08 0.91 ]
|XXXXXXXXXX 10000 - 10500 : [ 40 0.04 0.96 ]
|XXXXX 10500 - 11000 : [ 22 0.02 0.98 ]
|XXX 11000 - 11500 : [ 11 0.01 0.99 ]
|X 11500 - 12000 : [ 3 0.00 1.00 ]
#...
| 41500 - 42000 : [ 1 0.00 1.00 ]
#...
| 63000 - 63500 : [ 1 0.00 1.00 ]
#...
| 68500 - 69000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFA reads.list > grep.reads.list.AIFA
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFA 4 500
-------------------------------------------------------------------
#Found 15742 total values totalling 63029423.0000. <4003.901855 +/- 2113.274709>
#Range: [ 635 - 202579 ]
#Most likely bin: [ 4000 - 4500 ] 5069 counts
#Median bin: [ 3500 - 4000 ] 4673 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 10 0.00 0.00 ]
| 1000 - 1500 : [ 38 0.00 0.00 ]
| 1500 - 2000 : [ 35 0.00 0.01 ]
| 2000 - 2500 : [ 41 0.00 0.01 ]
|XX 2500 - 3000 : [ 267 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2814 0.18 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 4673 0.30 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 5069 0.32 0.82 ]
|XXXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 2554 0.16 0.98 ]
|XX 5000 - 5500 : [ 223 0.01 1.00 ]
| 5500 - 6000 : [ 4 0.00 1.00 ]
| 6000 - 6500 : [ 2 0.00 1.00 ]
#...
| 7000 - 7500 : [ 2 0.00 1.00 ]
| 7500 - 8000 : [ 1 0.00 1.00 ]
#...
| 8500 - 9000 : [ 1 0.00 1.00 ]
#...
| 12000 - 12500 : [ 1 0.00 1.00 ]
#...
| 18000 - 18500 : [ 1 0.00 1.00 ]
#...
| 33000 - 33500 : [ 1 0.00 1.00 ]
#...
| 51500 - 52000 : [ 1 0.00 1.00 ]
| 52000 - 52500 : [ 1 0.00 1.00 ]
#...
| 71000 - 71500 : [ 1 0.00 1.00 ]
#...
| 129000 - 129500 : [ 1 0.00 1.00 ]
#...
| 202500 - 203000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFB reads.list > grep.reads.list.AIFB
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFB 4 500
-------------------------------------------------------------------
#Found 1394 total values totalling 11127490.0000. <7982.417504 +/- 2091.421015>
#Range: [ 713 - 41492 ]
#Most likely bin: [ 8000 - 8500 ] 245 counts
#Median bin: [ 8000 - 8500 ] 245 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 4 0.00 0.00 ]
|XX 1000 - 1500 : [ 15 0.01 0.01 ]
|XX 1500 - 2000 : [ 10 0.01 0.02 ]
|XX 2000 - 2500 : [ 13 0.01 0.03 ]
|XX 2500 - 3000 : [ 10 0.01 0.04 ]
|XXX 3000 - 3500 : [ 17 0.01 0.05 ]
|XX 3500 - 4000 : [ 13 0.01 0.06 ]
|XXX 4000 - 4500 : [ 16 0.01 0.07 ]
|XXXX 4500 - 5000 : [ 22 0.02 0.09 ]
|XXX 5000 - 5500 : [ 19 0.01 0.10 ]
|XXX 5500 - 6000 : [ 21 0.02 0.11 ]
|XXXXXX 6000 - 6500 : [ 35 0.03 0.14 ]
|XXXXXXXXXX 6500 - 7000 : [ 62 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 118 0.08 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 165 0.12 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 245 0.18 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 238 0.17 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 159 0.11 0.85 ]
|XXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 110 0.08 0.93 ]
|XXXXXXXXX 10000 - 10500 : [ 56 0.04 0.97 ]
|XXXXX 10500 - 11000 : [ 28 0.02 0.99 ]
|XX 11000 - 11500 : [ 12 0.01 1.00 ]
|X 11500 - 12000 : [ 5 0.00 1.00 ]
#...
| 41000 - 41500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFC reads.list > grep.reads.list.AIFC
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFC 4 500
-------------------------------------------------------------------
#Found 1301 total values totalling 51087089.0000. <39267.554958 +/- 3152.877491>
#Range: [ 29100 - 53546 ]
#Most likely bin: [ 39500 - 40000 ] 85 counts
#Median bin: [ 39000 - 39500 ] 82 counts
#Histogram Bins Count Fraction Cum_Fraction
| 29000 - 29500 : [ 1 0.00 0.00 ]
|X 29500 - 30000 : [ 2 0.00 0.00 ]
#...
|X 30500 - 31000 : [ 3 0.00 0.00 ]
|XX 31000 - 31500 : [ 5 0.00 0.01 ]
|X 31500 - 32000 : [ 3 0.00 0.01 ]
|XXXX 32000 - 32500 : [ 8 0.01 0.02 ]
|XXXX 32500 - 33000 : [ 8 0.01 0.02 ]
|XXXXXX 33000 - 33500 : [ 12 0.01 0.03 ]
|XXXXXXXX 33500 - 34000 : [ 16 0.01 0.04 ]
|XXXXXXXXXXX 34000 - 34500 : [ 24 0.02 0.06 ]
|XXXXXXXXXXXXXXXX 34500 - 35000 : [ 34 0.03 0.09 ]
|XXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 40 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 46 0.04 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 58 0.04 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 51 0.04 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 83 0.06 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 58 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 83 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 65 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 82 0.06 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 85 0.07 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 75 0.06 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 54 0.04 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 64 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 75 0.06 0.80 ]
|XXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 40 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 59 0.05 0.87 ]
|XXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 43 0.03 0.90 ]
|XXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 42 0.03 0.94 ]
|XXXXXXXXXXXXXXX 44000 - 44500 : [ 32 0.02 0.96 ]
|XXXXXXXX 44500 - 45000 : [ 17 0.01 0.97 ]
|XXXXXXXX 45000 - 45500 : [ 17 0.01 0.99 ]
|XXXX 45500 - 46000 : [ 9 0.01 0.99 ]
|X 46000 - 46500 : [ 3 0.00 1.00 ]
| 46500 - 47000 : [ 1 0.00 1.00 ]
| 47000 - 47500 : [ 1 0.00 1.00 ]
#...
| 48000 - 48500 : [ 1 0.00 1.00 ]
#...
| 53500 - 54000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIFB 7594 +- 2687 (n=730)
# QCMC 7580 +- 2427 (n=483)
# AIFC 39365 +- 3066 (n=642)
# AIFA 3861 +- 712 (n=7996)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634505_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
AIFA 37632 -1 -1 97 728 35182 100 718 100 728
AIFB 7680 -1 -1 88 479 3770 90 374 100 411
AIFC 4608 -1 -1 95 647 4289 99 666 100 691
QCMC 7680 -1 -1 94 635 4660 100 669 100 686
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIFA 17296 100 715 100 732 17886 100 721 100 724
AIFB 1709 85 337 100 374 2061 94 401 100 442
AIFC 2155 99 680 100 693 2134 98 652 100 690
QCMC 2326 100 675 100 692 2334 100 663 100 679
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634505_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
20 4660 1202 60.10 62.60 QCMC @
192 35182 17555 91.43 95.24 AIFA @
40 3770 2155 53.88 56.12 AIFB @
24 4289 2203 91.79 95.62 AIFC @
] 47901 23115 83.75 cumulative total@@
LIBRARY PLATE ID COUNT [ QCMC 20 AIFA 192 AIFB 40 AIFC 24 ] for 276 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 3634505_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 47901 total values totalling 32414099.0000. <676.689401 +/- 173.512621>
#Range: [ 17 - 932 ]
#Most likely bin: [ 750 - 800 ] 11398 counts
#Median bin: [ 700 - 750 ] 8694 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 109 0.00 0.00 ]
|XX 50 - 100 : [ 450 0.01 0.01 ]
|XX 100 - 150 : [ 518 0.01 0.02 ]
|XX 150 - 200 : [ 569 0.01 0.03 ]
|XX 200 - 250 : [ 594 0.01 0.05 ]
|XXX 250 - 300 : [ 735 0.02 0.06 ]
|XXX 300 - 350 : [ 776 0.02 0.08 ]
|XXX 350 - 400 : [ 899 0.02 0.10 ]
|XXX 400 - 450 : [ 947 0.02 0.12 ]
|XXX 450 - 500 : [ 963 0.02 0.14 ]
|XXXXX 500 - 550 : [ 1301 0.03 0.16 ]
|XXXXXXX 550 - 600 : [ 1952 0.04 0.20 ]
|XXXXXXXXXXX 600 - 650 : [ 3129 0.07 0.27 ]
|XXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5320 0.11 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8694 0.18 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 11398 0.24 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7950 0.17 0.97 ]
|XXXXXX 850 - 900 : [ 1570 0.03 1.00 ]
| 900 - 950 : [ 27 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for QCMC
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep QCMC 3634505_fasta.screen.trimQ15.SaF > reads.trim15.QCMC.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.QCMC.rl 2 50
-------------------------------------------------------------------
#Found 4660 total values totalling 3108216.0000. <666.999142 +/- 144.559537>
#Range: [ 27 - 876 ]
#Most likely bin: [ 700 - 750 ] 1391 counts
#Median bin: [ 700 - 750 ] 1391 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 5 0.00 0.00 ]
| 50 - 100 : [ 9 0.00 0.00 ]
|X 100 - 150 : [ 39 0.01 0.01 ]
|X 150 - 200 : [ 51 0.01 0.02 ]
|XX 200 - 250 : [ 56 0.01 0.03 ]
|XX 250 - 300 : [ 61 0.01 0.05 ]
|XX 300 - 350 : [ 64 0.01 0.06 ]
|XX 350 - 400 : [ 78 0.02 0.08 ]
|XXX 400 - 450 : [ 92 0.02 0.10 ]
|XX 450 - 500 : [ 75 0.02 0.11 ]
|XXX 500 - 550 : [ 118 0.03 0.14 ]
|XXXXX 550 - 600 : [ 168 0.04 0.18 ]
|XXXXXXXXXX 600 - 650 : [ 346 0.07 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 842 0.18 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1391 0.30 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1073 0.23 0.96 ]
|XXXXX 800 - 850 : [ 191 0.04 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIFA
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFA 3634505_fasta.screen.trimQ15.SaF > reads.trim15.AIFA.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFA.rl 2 50
-------------------------------------------------------------------
#Found 35182 total values totalling 25189530.0000. <715.977773 +/- 131.770340>
#Range: [ 17 - 932 ]
#Most likely bin: [ 750 - 800 ] 9248 counts
#Median bin: [ 750 - 800 ] 9248 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 24 0.00 0.00 ]
| 50 - 100 : [ 85 0.00 0.00 ]
| 100 - 150 : [ 112 0.00 0.01 ]
|X 150 - 200 : [ 139 0.00 0.01 ]
|X 200 - 250 : [ 183 0.01 0.02 ]
|X 250 - 300 : [ 247 0.01 0.02 ]
|X 300 - 350 : [ 303 0.01 0.03 ]
|XX 350 - 400 : [ 374 0.01 0.04 ]
|XX 400 - 450 : [ 446 0.01 0.05 ]
|XX 450 - 500 : [ 553 0.02 0.07 ]
|XXX 500 - 550 : [ 805 0.02 0.09 ]
|XXXXXX 550 - 600 : [ 1367 0.04 0.13 ]
|XXXXXXXXXX 600 - 650 : [ 2326 0.07 0.20 ]
|XXXXXXXXXXXXXXXX 650 - 700 : [ 3802 0.11 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6303 0.18 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 9248 0.26 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7317 0.21 0.96 ]
|XXXXXXX 850 - 900 : [ 1521 0.04 1.00 ]
| 900 - 950 : [ 27 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIFB
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFB 3634505_fasta.screen.trimQ15.SaF > reads.trim15.AIFB.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFB.rl 2 50
-------------------------------------------------------------------
#Found 3770 total values totalling 1292575.0000. <342.858090 +/- 183.128659>
#Range: [ 25 - 797 ]
#Most likely bin: [ 150 - 200 ] 339 counts
#Median bin: [ 300 - 350 ] 280 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 0 - 50 : [ 60 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 50 - 100 : [ 322 0.09 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 100 - 150 : [ 336 0.09 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 150 - 200 : [ 339 0.09 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 200 - 250 : [ 315 0.08 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 300 0.08 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 300 - 350 : [ 280 0.07 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 350 - 400 : [ 311 0.08 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 400 - 450 : [ 313 0.08 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 450 - 500 : [ 272 0.07 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 290 0.08 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 279 0.07 0.91 ]
|XXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 194 0.05 0.96 ]
|XXXXXXXXXXXXXX 650 - 700 : [ 119 0.03 0.99 ]
|XXXX 700 - 750 : [ 34 0.01 1.00 ]
|X 750 - 800 : [ 6 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIFC
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFC 3634505_fasta.screen.trimQ15.SaF > reads.trim15.AIFC.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFC.rl 2 50
-------------------------------------------------------------------
#Found 4289 total values totalling 2823778.0000. <658.376778 +/- 174.847005>
#Range: [ 18 - 881 ]
#Most likely bin: [ 750 - 800 ] 1071 counts
#Median bin: [ 700 - 750 ] 966 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 20 0.00 0.00 ]
|X 50 - 100 : [ 34 0.01 0.01 ]
|X 100 - 150 : [ 31 0.01 0.02 ]
|X 150 - 200 : [ 40 0.01 0.03 ]
|X 200 - 250 : [ 40 0.01 0.04 ]
|XXXXX 250 - 300 : [ 127 0.03 0.07 ]
|XXXXX 300 - 350 : [ 129 0.03 0.10 ]
|XXXXX 350 - 400 : [ 136 0.03 0.13 ]
|XXXX 400 - 450 : [ 96 0.02 0.15 ]
|XX 450 - 500 : [ 63 0.01 0.17 ]
|XXX 500 - 550 : [ 88 0.02 0.19 ]
|XXXXX 550 - 600 : [ 138 0.03 0.22 ]
|XXXXXXXXXX 600 - 650 : [ 263 0.06 0.28 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 557 0.13 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 966 0.23 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1071 0.25 0.89 ]
|XXXXXXXXXXXXXXXXX 800 - 850 : [ 442 0.10 0.99 ]
|XX 850 - 900 : [ 48 0.01 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634505
-------------------------------------------------------------------
AIFA.000001.000100 pUC18.fa LRS.fasta
AIFA.000101.000200 pUC18.fa LRS.fasta
AIFB.000001.000100 pMCL200.fa LRS.fasta
AIFC.000001.000100 pCC1Fos.fa LRS.fasta
QCMC.000001.000100 pMCL200.fa LRS.fasta
AIFA.000001.000100 pUC18.fa LRS.fasta
AIFA.000101.000200 pUC18.fa LRS.fasta
AIFB.000001.000100 pMCL200.fa LRS.fasta
AIFC.000001.000100 pCC1Fos.fa LRS.fasta
QCMC.000001.000100 pMCL200.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634505_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634505_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 47788 total values totalling 30303.0730. <0.634115 +/- 0.053579>
#Range: [ 0.2877 - 0.8644 ]
#Most likely bin: [ 0.64 - 0.645 ] 2691 counts
#Median bin: [ 0.64 - 0.645 ] 2691 counts
| 0.285 - 0.29 : [ 1 0.00 0.00 ]
| 0.29 - 0.295 : [ 1 0.00 0.00 ]
#...
| 0.3 - 0.305 : [ 3 0.00 0.00 ]
#...
| 0.32 - 0.325 : [ 2 0.00 0.00 ]
#...
| 0.335 - 0.34 : [ 1 0.00 0.00 ]
| 0.34 - 0.345 : [ 3 0.00 0.00 ]
| 0.345 - 0.35 : [ 4 0.00 0.00 ]
| 0.35 - 0.355 : [ 2 0.00 0.00 ]
| 0.355 - 0.36 : [ 12 0.00 0.00 ]
| 0.36 - 0.365 : [ 13 0.00 0.00 ]
| 0.365 - 0.37 : [ 20 0.00 0.00 ]
| 0.37 - 0.375 : [ 23 0.00 0.00 ]
| 0.375 - 0.38 : [ 27 0.00 0.00 ]
| 0.38 - 0.385 : [ 26 0.00 0.00 ]
|X 0.385 - 0.39 : [ 44 0.00 0.00 ]
|X 0.39 - 0.395 : [ 51 0.00 0.00 ]
|X 0.395 - 0.4 : [ 43 0.00 0.01 ]
|X 0.4 - 0.405 : [ 60 0.00 0.01 ]
|X 0.405 - 0.41 : [ 52 0.00 0.01 ]
|X 0.41 - 0.415 : [ 44 0.00 0.01 ]
|X 0.415 - 0.42 : [ 57 0.00 0.01 ]
|X 0.42 - 0.425 : [ 51 0.00 0.01 ]
|X 0.425 - 0.43 : [ 61 0.00 0.01 ]
|X 0.43 - 0.435 : [ 64 0.00 0.01 ]
|X 0.435 - 0.44 : [ 43 0.00 0.01 ]
|X 0.44 - 0.445 : [ 63 0.00 0.02 ]
|X 0.445 - 0.45 : [ 65 0.00 0.02 ]
|X 0.45 - 0.455 : [ 57 0.00 0.02 ]
|X 0.455 - 0.46 : [ 53 0.00 0.02 ]
|X 0.46 - 0.465 : [ 57 0.00 0.02 ]
|X 0.465 - 0.47 : [ 64 0.00 0.02 ]
|X 0.47 - 0.475 : [ 78 0.00 0.02 ]
|X 0.475 - 0.48 : [ 45 0.00 0.02 ]
|X 0.48 - 0.485 : [ 50 0.00 0.03 ]
|X 0.485 - 0.49 : [ 68 0.00 0.03 ]
|X 0.49 - 0.495 : [ 99 0.00 0.03 ]
|X 0.495 - 0.5 : [ 64 0.00 0.03 ]
|X 0.5 - 0.505 : [ 100 0.00 0.03 ]
|X 0.505 - 0.51 : [ 92 0.00 0.03 ]
|X 0.51 - 0.515 : [ 99 0.00 0.04 ]
|XX 0.515 - 0.52 : [ 127 0.00 0.04 ]
|XX 0.52 - 0.525 : [ 124 0.00 0.04 ]
|XX 0.525 - 0.53 : [ 158 0.00 0.05 ]
|XXX 0.53 - 0.535 : [ 173 0.00 0.05 ]
|XXX 0.535 - 0.54 : [ 204 0.00 0.05 ]
|XXX 0.54 - 0.545 : [ 224 0.00 0.06 ]
|XXXX 0.545 - 0.55 : [ 256 0.01 0.06 ]
|XXXXX 0.55 - 0.555 : [ 305 0.01 0.07 ]
|XXXX 0.555 - 0.56 : [ 283 0.01 0.08 ]
|XXXXX 0.56 - 0.565 : [ 348 0.01 0.08 ]
|XXXXXX 0.565 - 0.57 : [ 376 0.01 0.09 ]
|XXXXXX 0.57 - 0.575 : [ 430 0.01 0.10 ]
|XXXXXXX 0.575 - 0.58 : [ 486 0.01 0.11 ]
|XXXXXXXXX 0.58 - 0.585 : [ 576 0.01 0.12 ]
|XXXXXXXXXX 0.585 - 0.59 : [ 669 0.01 0.14 ]
|XXXXXXXXXXXX 0.59 - 0.595 : [ 836 0.02 0.15 ]
|XXXXXXXXXXXXXX 0.595 - 0.6 : [ 923 0.02 0.17 ]
|XXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1159 0.02 0.20 ]
|XXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1232 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1366 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1645 0.03 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1628 0.03 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 2125 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 2281 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 2445 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 2691 0.06 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 2655 0.06 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 2608 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 2595 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 2411 0.05 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 2138 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 1988 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 1736 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 1603 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 1277 0.03 0.92 ]
|XXXXXXXXXXXXXX 0.69 - 0.695 : [ 955 0.02 0.94 ]
|XXXXXXXXXXXX 0.695 - 0.7 : [ 782 0.02 0.95 ]
|XXXXXXXXXX 0.7 - 0.705 : [ 659 0.01 0.97 ]
|XXXXXX 0.705 - 0.71 : [ 430 0.01 0.98 ]
|XXXXX 0.71 - 0.715 : [ 349 0.01 0.98 ]
|XXX 0.715 - 0.72 : [ 229 0.00 0.99 ]
|XXX 0.72 - 0.725 : [ 170 0.00 0.99 ]
|X 0.725 - 0.73 : [ 100 0.00 0.99 ]
|X 0.73 - 0.735 : [ 62 0.00 1.00 ]
|X 0.735 - 0.74 : [ 63 0.00 1.00 ]
|X 0.74 - 0.745 : [ 48 0.00 1.00 ]
| 0.745 - 0.75 : [ 21 0.00 1.00 ]
| 0.75 - 0.755 : [ 17 0.00 1.00 ]
| 0.755 - 0.76 : [ 17 0.00 1.00 ]
| 0.76 - 0.765 : [ 9 0.00 1.00 ]
| 0.765 - 0.77 : [ 11 0.00 1.00 ]
| 0.77 - 0.775 : [ 3 0.00 1.00 ]
| 0.775 - 0.78 : [ 3 0.00 1.00 ]
| 0.78 - 0.785 : [ 3 0.00 1.00 ]
| 0.785 - 0.79 : [ 1 0.00 1.00 ]
| 0.79 - 0.795 : [ 3 0.00 1.00 ]
#...
| 0.8 - 0.805 : [ 1 0.00 1.00 ]
| 0.805 - 0.81 : [ 1 0.00 1.00 ]
| 0.81 - 0.815 : [ 1 0.00 1.00 ]
| 0.815 - 0.82 : [ 3 0.00 1.00 ]
| 0.82 - 0.825 : [ 1 0.00 1.00 ]
| 0.825 - 0.83 : [ 1 0.00 1.00 ]
#...
| 0.855 - 0.86 : [ 1 0.00 1.00 ]
| 0.86 - 0.865 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 46. 437 reads; 32212 bp (untrimmed), 32082 (trimmed).
Contig 47. 489 reads; 38805 bp (untrimmed), 38699 (trimmed).
Contig 48. 627 reads; 51600 bp (untrimmed), 51597 (trimmed).
Contig 49. 661 reads; 50118 bp (untrimmed), 49929 (trimmed).
Contig 50. 680 reads; 54726 bp (untrimmed), 54676 (trimmed).
Contig 51. 838 reads; 64536 bp (untrimmed), 64460 (trimmed).
Contig 52. 873 reads; 63039 bp (untrimmed), 62546 (trimmed).
Contig 53. 947 reads; 72275 bp (untrimmed), 72184 (trimmed).
Contig 54. 972 reads; 77220 bp (untrimmed), 77002 (trimmed).
Contig 55. 983 reads; 73240 bp (untrimmed), 73174 (trimmed).
Contig 56. 1080 reads; 85493 bp (untrimmed), 85393 (trimmed).
Contig 57. 1139 reads; 96718 bp (untrimmed), 96599 (trimmed).
Contig 58. 1361 reads; 104325 bp (untrimmed), 104303 (trimmed).
Contig 59. 1384 reads; 96056 bp (untrimmed), 95906 (trimmed).
Contig 60. 1390 reads; 101870 bp (untrimmed), 101776 (trimmed).
Contig 61. 1393 reads; 120851 bp (untrimmed), 120422 (trimmed).
Contig 62. 1412 reads; 110401 bp (untrimmed), 110276 (trimmed).
Contig 63. 1450 reads; 123726 bp (untrimmed), 123672 (trimmed).
Contig 64. 1519 reads; 112802 bp (untrimmed), 112665 (trimmed).
Contig 65. 1714 reads; 134868 bp (untrimmed), 134735 (trimmed).
Contig 66. 1790 reads; 146680 bp (untrimmed), 146678 (trimmed).
Contig 67. 1939 reads; 155290 bp (untrimmed), 154963 (trimmed).
Contig 68. 2184 reads; 159302 bp (untrimmed), 159246 (trimmed).
Contig 69. 2363 reads; 162379 bp (untrimmed), 161548 (trimmed).
Contig 70. 2464 reads; 181190 bp (untrimmed), 180853 (trimmed).
Contig 71. 4706 reads; 349896 bp (untrimmed), 349669 (trimmed).
Contig 72. 6964 reads; 507709 bp (untrimmed), 507577 (trimmed).
--------------------------------------------------------------
Totals 47831 reads; 3702702 bp (untrimmed), 3685675 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3698509 bases = 11.30 +- 4.47 = 0.16 +- 4.35
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 53 total values totalling 491.2100. <9.268113 +/- 7.323758>
#Range: [ 1.40 - 54.24 ]
#Most likely bin: [ 11.5 - 12 ] 8 counts
#Median bin: [ 10 - 10.5 ] 4 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 1 - 1.5 : [ 1 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 6 0.11 0.13 ]
|XXXXX 2 - 2.5 : [ 1 0.02 0.15 ]
|XXXXXXXXXX 2.5 - 3 : [ 2 0.04 0.19 ]
|XXXXXXXXXX 3 - 3.5 : [ 2 0.04 0.23 ]
#...
|XXXXXXXXXX 5 - 5.5 : [ 2 0.04 0.26 ]
#...
|XXXXXXXXXX 6 - 6.5 : [ 2 0.04 0.30 ]
#...
|XXXXXXXXXX 7.5 - 8 : [ 2 0.04 0.34 ]
#...
|XXXXXXXXXX 8.5 - 9 : [ 2 0.04 0.38 ]
|XXXXXXXXXXXXXXX 9 - 9.5 : [ 3 0.06 0.43 ]
|XXXXXXXXXX 9.5 - 10 : [ 2 0.04 0.47 ]
|XXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 4 0.08 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 6 0.11 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 5 0.09 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 8 0.15 0.91 ]
|XXXXX 12 - 12.5 : [ 1 0.02 0.92 ]
|XXXXXXXXXX 12.5 - 13 : [ 2 0.04 0.96 ]
#...
|XXXXX 14 - 14.5 : [ 1 0.02 0.98 ]
#...
|XXXXX 54 - 54.5 : [ 1 0.02 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 40 total values totalling 411.4700. <10.286750 +/- 2.015214>
#Range: [ 5.23 - 14.18 ]
#Most likely bin: [ 11.5 - 12 ] 8 counts
#Median bin: [ 10.5 - 11 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 5 - 5.5 : [ 2 0.05 0.05 ]
#...
|XXXXXXXXXX 6 - 6.5 : [ 2 0.05 0.10 ]
#...
|XXXXXXXXXX 7.5 - 8 : [ 2 0.05 0.15 ]
#...
|XXXXXXXXXX 8.5 - 9 : [ 2 0.05 0.20 ]
|XXXXXXXXXXXXXXX 9 - 9.5 : [ 3 0.07 0.28 ]
|XXXXXXXXXX 9.5 - 10 : [ 2 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 4 0.10 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 6 0.15 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 5 0.12 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 8 0.20 0.90 ]
|XXXXX 12 - 12.5 : [ 1 0.03 0.93 ]
|XXXXXXXXXX 12.5 - 13 : [ 2 0.05 0.97 ]
#...
|XXXXX 14 - 14.5 : [ 1 0.03 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 3 2 reads 1156 bases = 1.40 +- 0.49 = 1.40 +- 0.49
Contig 10 2 reads 1037 bases = 1.56 +- 0.50 = 1.56 +- 0.50
Contig 11 2 reads 942 bases = 1.59 +- 0.49 = 1.59 +- 0.49
Contig 13 2 reads 1034 bases = 1.72 +- 0.45 = 1.72 +- 0.45
Contig 14 2 reads 995 bases = 1.80 +- 0.40 = 1.80 +- 0.40
Contig 9 2 reads 976 bases = 1.80 +- 0.40 = 1.80 +- 0.40
Contig 8 2 reads 528 bases = 1.95 +- 0.21 = 0.05 +- 0.21
Contig 17 3 reads 1277 bases = 2.10 +- 0.85 = 2.10 +- 0.85
Contig 20 5 reads 1706 bases = 2.58 +- 1.44 = 1.67 +- 0.70
Contig 18 3 reads 970 bases = 2.85 +- 0.40 = 2.85 +- 0.40
Contig 24 7 reads 2086 bases = 3.05 +- 1.31 = 1.38 +- 1.78
Contig 19 4 reads 1165 bases = 3.10 +- 1.10 = 3.10 +- 1.10
Contig 29 45 reads 7257 bases = 5.23 +- 2.76 = 1.08 +- 3.28
Contig 25 17 reads 2810 bases = 5.24 +- 2.25 = 0.27 +- 2.41
Contig 27 27 reads 3892 bases = 6.14 +- 2.58 = 1.58 +- 1.86
Contig 31 59 reads 7698 bases = 6.26 +- 3.38 = 0.77 +- 5.21
Contig 32 64 reads 7195 bases = 7.59 +- 3.40 = 1.78 +- 3.64
Contig 34 118 reads 12770 bases = 7.85 +- 3.91 = 0.41 +- 3.75
Contig 39 378 reads 38029 bases = 8.55 +- 3.05 = 0.41 +- 4.17
Contig 35 212 reads 20940 bases = 8.71 +- 3.47 = 0.89 +- 4.78
Contig 45 685 reads 54724 bases = 10.89 +- 4.13 = 0.45 +- 4.14
Contig 59 1979 reads 155293 bases = 10.89 +- 4.16 = 0.13 +- 4.27
Contig 49 1124 reads 85931 bases = 11.05 +- 4.48 = 0.36 +- 4.53
Contig 47 960 reads 72316 bases = 11.34 +- 4.41 = 0.23 +- 4.53
Contig 53 1386 reads 104335 bases = 11.35 +- 4.09 = 0.18 +- 4.34
Contig 46 857 reads 64536 bases = 11.38 +- 4.43 = -0.03 +- 3.83
Contig 64 5261 reads 392882 bases = 11.49 +- 4.08 = -0.00 +- 4.02
Contig 50 1148 reads 50119 bases = 11.68 +- 6.14 = -0.48 +- 6.30
Contig 58 1572 reads 115038 bases = 11.69 +- 3.93 = 0.23 +- 4.28
Contig 62 4615 reads 338744 bases = 11.73 +- 4.53 = 0.22 +- 4.28
Contig 63 4707 reads 342862 bases = 11.80 +- 4.50 = 0.06 +- 4.47
Contig 43 443 reads 32212 bases = 11.92 +- 4.72 = 0.62 +- 4.99
Contig 65 7397 reads 534933 bases = 11.95 +- 4.19 = 0.04 +- 4.39
Contig 52 1342 reads 96591 bases = 11.97 +- 4.56 = 0.01 +- 4.33
Contig 54 1405 reads 101870 bases = 11.98 +- 4.52 = 0.19 +- 4.81
Contig 40 384 reads 27620 bases = 12.20 +- 4.96 = 0.44 +- 4.43
Contig 56 1468 reads 99622 bases = 12.55 +- 4.46 = 0.18 +- 4.84
Contig 61 2405 reads 162379 bases = 12.72 +- 4.72 = 0.05 +- 4.56
Contig 28 33 reads 2059 bases = 14.18 +- 8.37 = 2.76 +- 5.14
Contig 30 55 reads 635 bases = 54.24 +- 3.79 = 0.24 +- 3.79
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1037
HQ Discrepant reads = 16
Chimeric reads = 37
Suspect alignments = 450
-------------------------------------------------------------------
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: -8)
A C G T N X
A 1 -8 -8 -8 0 -9
C -8 1 -8 -8 0 -9
G -8 -8 1 -8 0 -9
T -8 -8 -8 1 0 -9
N 0 0 0 0 0 0
X -9 -9 -9 -9 0 -9
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: 55
maxmatch: 80
max_group_size: 20
minscore: 75
bandwidth: 14
indexwordsize: 10
vector_bound: 50
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 20
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
max_subclone_size: 50000
File generated in /psf/project/microbe3/3634505/edit_dir.02Jun04.QD