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
3634469 2400 1092 Chlorobium limicola
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Chlorobium_limicola
-------------------------------------------------------------------
Chlorobium/Pelodictyon group, green sulfur bacteria
Chlorobiaceae, family, green sulfur bacteria
Chlorobiales, order, green sulfur bacteria
Chlorobia, class, green sulfur bacteria
Bacteroidetes/Chlorobi group, superphylum, eubacteria
Chlorobium limicola, species, green sulfur bacteria
Chlorobium, genus, green sulfur bacteria
Chlorobi, phylum, green sulfur bacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2736515
# phrap: 2802634
# db:
altered.
2400000
2646383 +/- 176297
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 8497
Number of reads with percent X's >= 20%: 82 = 0.2%
Number of reads with percent X's >= 50%: 39 = 0.1%
Number of reads with percent X's >= 80%: 10 = 0.0%
Total reads in project: 41986
Total bp X'd : 354211
reads >= 20% >= 50% >= 80% screened
Nr with L09136 7597 60 27 2
Nr with pCC1Fos 867 0 0 0
Nr with pMCL200_JGI_XZX+XZK 33 22 12 8
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 21
Number of reads with percent X's >= 20%: 1 = 0.7%
Number of reads with percent X's >= 50%: 1 = 0.7%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 140
Total bp X'd : 1037
reads >= 20% >= 50% >= 80% screened
Nr with L09136 7 1 1 0
Nr with pCC1Fos 14 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
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A = 9635456
C = 9948858
G = 9957999
T = 9373520
N = 184499
X = 354211
GC fraction = 0.50
Total = 39454543
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634469_fasta.screen.contigs
-------------------------------------------------------------------
A 681050
C 720285
G 697078
T 663001
N 501
fraction GC = 0.51
total bases = 2761915
Libraries and Reads
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Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
-------------------------------------------------------------------
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXA reads.list > grep.reads.list.AHXA
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXA 4 500
-------------------------------------------------------------------
#Found 8185 total values totalling 39791309.0000. <4861.491631 +/- 7272.812369>
#Range: [ 522 - 371031 ]
#Most likely bin: [ 4000 - 4500 ] 1599 counts
#Median bin: [ 4500 - 5000 ] 1488 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 15 0.00 0.00 ]
|X 1000 - 1500 : [ 22 0.00 0.00 ]
|X 1500 - 2000 : [ 37 0.00 0.01 ]
|X 2000 - 2500 : [ 38 0.00 0.01 ]
|XX 2500 - 3000 : [ 67 0.01 0.02 ]
|XXXXXXXXXXXXXXXXX 3000 - 3500 : [ 682 0.08 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1405 0.17 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1599 0.20 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 1488 0.18 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5000 - 5500 : [ 1231 0.15 0.80 ]
|XXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 829 0.10 0.91 ]
|XXXXXXXXXXXX 6000 - 6500 : [ 472 0.06 0.96 ]
|XXXXX 6500 - 7000 : [ 212 0.03 0.99 ]
|X 7000 - 7500 : [ 58 0.01 1.00 ]
| 7500 - 8000 : [ 7 0.00 1.00 ]
| 8000 - 8500 : [ 2 0.00 1.00 ]
| 8500 - 9000 : [ 1 0.00 1.00 ]
#...
| 9500 - 10000 : [ 1 0.00 1.00 ]
| 10000 - 10500 : [ 4 0.00 1.00 ]
| 10500 - 11000 : [ 2 0.00 1.00 ]
#...
| 12500 - 13000 : [ 1 0.00 1.00 ]
#...
| 13500 - 14000 : [ 1 0.00 1.00 ]
#...
| 14500 - 15000 : [ 1 0.00 1.00 ]
#...
| 43500 - 44000 : [ 1 0.00 1.00 ]
#...
| 104000 - 104500 : [ 1 0.00 1.00 ]
#...
| 110000 - 110500 : [ 1 0.00 1.00 ]
#...
| 167500 - 168000 : [ 1 0.00 1.00 ]
| 168000 - 168500 : [ 2 0.00 1.00 ]
| 168500 - 169000 : [ 1 0.00 1.00 ]
| 169000 - 169500 : [ 1 0.00 1.00 ]
#...
| 370000 - 370500 : [ 1 0.00 1.00 ]
#...
| 371000 - 371500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXB reads.list > grep.reads.list.AHXB
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXB 4 500
-------------------------------------------------------------------
#Found 7438 total values totalling 58268777.0000. <7833.930761 +/- 13095.329648>
#Range: [ 944 - 399840 ]
#Most likely bin: [ 7500 - 8000 ] 1831 counts
#Median bin: [ 7000 - 7500 ] 1629 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 8 0.00 0.00 ]
| 1500 - 2000 : [ 15 0.00 0.00 ]
| 2000 - 2500 : [ 10 0.00 0.00 ]
| 2500 - 3000 : [ 15 0.00 0.01 ]
| 3000 - 3500 : [ 15 0.00 0.01 ]
| 3500 - 4000 : [ 14 0.00 0.01 ]
| 4000 - 4500 : [ 8 0.00 0.01 ]
| 4500 - 5000 : [ 12 0.00 0.01 ]
| 5000 - 5500 : [ 10 0.00 0.01 ]
|XX 5500 - 6000 : [ 95 0.01 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1124 0.15 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1507 0.20 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1629 0.22 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1831 0.25 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1087 0.15 0.99 ]
| 8500 - 9000 : [ 12 0.00 0.99 ]
| 9000 - 9500 : [ 1 0.00 0.99 ]
| 9500 - 10000 : [ 3 0.00 0.99 ]
| 10000 - 10500 : [ 3 0.00 0.99 ]
| 10500 - 11000 : [ 5 0.00 1.00 ]
| 11000 - 11500 : [ 4 0.00 1.00 ]
| 11500 - 12000 : [ 2 0.00 1.00 ]
| 12000 - 12500 : [ 2 0.00 1.00 ]
| 12500 - 13000 : [ 1 0.00 1.00 ]
#...
| 22000 - 22500 : [ 1 0.00 1.00 ]
#...
| 62500 - 63000 : [ 1 0.00 1.00 ]
#...
| 81000 - 81500 : [ 1 0.00 1.00 ]
#...
| 82000 - 82500 : [ 1 0.00 1.00 ]
#...
| 84000 - 84500 : [ 1 0.00 1.00 ]
| 84500 - 85000 : [ 1 0.00 1.00 ]
#...
| 105500 - 106000 : [ 1 0.00 1.00 ]
#...
| 146000 - 146500 : [ 1 0.00 1.00 ]
#...
| 170000 - 170500 : [ 4 0.00 1.00 ]
| 170500 - 171000 : [ 1 0.00 1.00 ]
#...
| 171500 - 172000 : [ 1 0.00 1.00 ]
| 172000 - 172500 : [ 1 0.00 1.00 ]
#...
| 177500 - 178000 : [ 1 0.00 1.00 ]
#...
| 281500 - 282000 : [ 1 0.00 1.00 ]
#...
| 315500 - 316000 : [ 1 0.00 1.00 ]
#...
| 371500 - 372000 : [ 3 0.00 1.00 ]
| 372000 - 372500 : [ 1 0.00 1.00 ]
#...
| 387000 - 387500 : [ 1 0.00 1.00 ]
#...
| 399500 - 400000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXC reads.list > grep.reads.list.AHXC
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXC 4 500
-------------------------------------------------------------------
#Found 651 total values totalling 24005842.0000. <36875.333333 +/- 4234.577668>
#Range: [ 20612 - 46751 ]
#Most likely bin: [ 36000 - 36500 ] 51 counts
#Median bin: [ 36500 - 37000 ] 30 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 20500 - 21000 : [ 2 0.00 0.00 ]
#...
|X 23500 - 24000 : [ 1 0.00 0.00 ]
#...
|XX 24500 - 25000 : [ 2 0.00 0.01 ]
#...
|XX 25500 - 26000 : [ 3 0.00 0.01 ]
|X 26000 - 26500 : [ 1 0.00 0.01 ]
|XX 26500 - 27000 : [ 2 0.00 0.02 ]
|X 27000 - 27500 : [ 1 0.00 0.02 ]
|X 27500 - 28000 : [ 1 0.00 0.02 ]
|XX 28000 - 28500 : [ 2 0.00 0.02 ]
|XX 28500 - 29000 : [ 2 0.00 0.03 ]
|XXXX 29000 - 29500 : [ 5 0.01 0.03 ]
|XXXX 29500 - 30000 : [ 5 0.01 0.04 ]
|XXXXX 30000 - 30500 : [ 6 0.01 0.05 ]
|XXXXXX 30500 - 31000 : [ 8 0.01 0.06 ]
|XXXXXXXXXXXXXXX 31000 - 31500 : [ 19 0.03 0.09 ]
|XXXXXXXXX 31500 - 32000 : [ 11 0.02 0.11 ]
|XXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 27 0.04 0.15 ]
|XXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 27 0.04 0.19 ]
|XXXXXXXXXXXXX 33000 - 33500 : [ 17 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 24 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 23 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 26 0.04 0.33 ]
|XXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 25 0.04 0.37 ]
|XXXXXXXXXXXXXXXXX 35500 - 36000 : [ 22 0.03 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 51 0.08 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 30 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 24 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 38 0.06 0.62 ]
|XXXXXXXXXXXXXXXXX 38000 - 38500 : [ 22 0.03 0.66 ]
|XXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 24 0.04 0.69 ]
|XXXXXXXXXXXXXXX 39000 - 39500 : [ 19 0.03 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 29 0.04 0.77 ]
|XXXXXXXXX 40000 - 40500 : [ 12 0.02 0.78 ]
|XXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 23 0.04 0.82 ]
|XXXXXXXXXXXXXXXX 41000 - 41500 : [ 21 0.03 0.85 ]
|XXXXXXXXXXXXX 41500 - 42000 : [ 17 0.03 0.88 ]
|XXXXXXXXX 42000 - 42500 : [ 12 0.02 0.90 ]
|XXXXXXXXXXX 42500 - 43000 : [ 14 0.02 0.92 ]
|XXXXXXXXX 43000 - 43500 : [ 12 0.02 0.94 ]
|XXXXXXX 43500 - 44000 : [ 9 0.01 0.95 ]
|XXXXXXXXX 44000 - 44500 : [ 11 0.02 0.97 ]
|XXXXX 44500 - 45000 : [ 7 0.01 0.98 ]
|XXXX 45000 - 45500 : [ 5 0.01 0.99 ]
|XXX 45500 - 46000 : [ 4 0.01 0.99 ]
|XX 46000 - 46500 : [ 3 0.00 1.00 ]
|XX 46500 - 47000 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHXC 37424 +- 3978 (n=270)
# AHXB 7125 +- 906 (n=3673)
# AHXA 4473 +- 1164 (n=4258)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634469_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
AHXA 24576 90 629 94 620 24408 88 597 93 607
AHXB 18528 95 748 96 703 18432 94 742 97 731
AHXC 3072 80 553 90 539 3072 81 566 90 598
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHXA 12217 89 591 93 603 12191 88 604 93 612
AHXB 9216 93 731 97 719 9216 95 753 97 742
AHXC 1536 80 563 90 580 1536 81 568 90 616
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634469_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
16 2629 1401 87.56 91.21 AHXC @
112 21968 10156 90.68 94.46 AHXA @
96 17389 8838 92.06 95.90 AHXB @
] 41986 20395 91.05 cumulative total@@
LIBRARY PLATE ID COUNT [ AHXC 16 AHXA 112 AHXB 96 ] for 224 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.
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trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3634469_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 45912 total values totalling 27247541.0000. <593.473188 +/- 251.798445>
#Range: [ 0 - 984 ]
#Most likely bin: [ 750 - 800 ] 8287 counts
#Median bin: [ 650 - 700 ] 5111 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXX 0 - 50 : [ 3786 0.08 0.08 ]
|XXXX 50 - 100 : [ 728 0.02 0.10 ]
|XXX 100 - 150 : [ 643 0.01 0.11 ]
|XXX 150 - 200 : [ 616 0.01 0.13 ]
|XXX 200 - 250 : [ 655 0.01 0.14 ]
|XXXX 250 - 300 : [ 803 0.02 0.16 ]
|XXXX 300 - 350 : [ 891 0.02 0.18 ]
|XXXXX 350 - 400 : [ 973 0.02 0.20 ]
|XXXXX 400 - 450 : [ 1098 0.02 0.22 ]
|XXXXXX 450 - 500 : [ 1276 0.03 0.25 ]
|XXXXXXXX 500 - 550 : [ 1579 0.03 0.28 ]
|XXXXXXXXXXX 550 - 600 : [ 2251 0.05 0.33 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 3396 0.07 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5111 0.11 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7127 0.16 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8287 0.18 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5149 0.11 0.97 ]
|XXXXXX 850 - 900 : [ 1287 0.03 0.99 ]
|X 900 - 950 : [ 238 0.01 1.00 ]
| 950 - 1000 : [ 18 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXA
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXA 3634469_fasta.screen.trimQ15.SaF > reads.trim15.AHXA.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXA.rl 2 50
-------------------------------------------------------------------
#Found 24408 total values totalling 12960293.0000. <530.985456 +/- 252.745375>
#Range: [ 0 - 984 ]
#Most likely bin: [ 700 - 750 ] 3410 counts
#Median bin: [ 600 - 650 ] 2540 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2280 0.09 0.09 ]
|XXXXXX 50 - 100 : [ 530 0.02 0.12 ]
|XXXXXX 100 - 150 : [ 513 0.02 0.14 ]
|XXXXXX 150 - 200 : [ 477 0.02 0.16 ]
|XXXXXX 200 - 250 : [ 507 0.02 0.18 ]
|XXXXXXX 250 - 300 : [ 562 0.02 0.20 ]
|XXXXXXXX 300 - 350 : [ 660 0.03 0.23 ]
|XXXXXXXXX 350 - 400 : [ 750 0.03 0.26 ]
|XXXXXXXXXX 400 - 450 : [ 887 0.04 0.29 ]
|XXXXXXXXXXXX 450 - 500 : [ 1064 0.04 0.34 ]
|XXXXXXXXXXXXXXXX 500 - 550 : [ 1332 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1793 0.07 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2540 0.10 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3286 0.13 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3410 0.14 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1942 0.08 0.92 ]
|XXXXXXXXXXX 800 - 850 : [ 927 0.04 0.96 ]
|XXXXXXXX 850 - 900 : [ 705 0.03 0.99 ]
|XXX 900 - 950 : [ 225 0.01 1.00 ]
| 950 - 1000 : [ 18 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXB
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXB 3634469_fasta.screen.trimQ15.SaF > reads.trim15.AHXB.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXB.rl 2 50
-------------------------------------------------------------------
#Found 18432 total values totalling 12873405.0000. <698.426921 +/- 203.635906>
#Range: [ 0 - 927 ]
#Most likely bin: [ 750 - 800 ] 6089 counts
#Median bin: [ 750 - 800 ] 6089 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 0 - 50 : [ 1011 0.05 0.05 ]
|X 50 - 100 : [ 95 0.01 0.06 ]
| 100 - 150 : [ 76 0.00 0.06 ]
| 150 - 200 : [ 72 0.00 0.07 ]
|X 200 - 250 : [ 78 0.00 0.07 ]
|X 250 - 300 : [ 83 0.00 0.08 ]
|X 300 - 350 : [ 91 0.00 0.08 ]
|X 350 - 400 : [ 81 0.00 0.09 ]
|X 400 - 450 : [ 115 0.01 0.09 ]
|X 450 - 500 : [ 129 0.01 0.10 ]
|X 500 - 550 : [ 154 0.01 0.11 ]
|XX 550 - 600 : [ 288 0.02 0.12 ]
|XXXX 600 - 650 : [ 586 0.03 0.16 ]
|XXXXXXXXXX 650 - 700 : [ 1466 0.08 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3327 0.18 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6089 0.33 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4108 0.22 0.97 ]
|XXXX 850 - 900 : [ 570 0.03 1.00 ]
| 900 - 950 : [ 13 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXC
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXC 3634469_fasta.screen.trimQ15.SaF > reads.trim15.AHXC.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXC.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 1413843.0000. <460.235352 +/- 276.310440>
#Range: [ 0 - 892 ]
#Most likely bin: [ 0 - 50 ] 495 counts
#Median bin: [ 550 - 600 ] 170 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 495 0.16 0.16 ]
|XXXXXXXX 50 - 100 : [ 103 0.03 0.19 ]
|XXXX 100 - 150 : [ 54 0.02 0.21 ]
|XXXXX 150 - 200 : [ 67 0.02 0.23 ]
|XXXXXX 200 - 250 : [ 70 0.02 0.26 ]
|XXXXXXXXXXXXX 250 - 300 : [ 158 0.05 0.31 ]
|XXXXXXXXXXX 300 - 350 : [ 140 0.05 0.35 ]
|XXXXXXXXXXX 350 - 400 : [ 142 0.05 0.40 ]
|XXXXXXXX 400 - 450 : [ 96 0.03 0.43 ]
|XXXXXXX 450 - 500 : [ 83 0.03 0.46 ]
|XXXXXXXX 500 - 550 : [ 93 0.03 0.49 ]
|XXXXXXXXXXXXXX 550 - 600 : [ 170 0.06 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 270 0.09 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 359 0.12 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 390 0.13 0.88 ]
|XXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 256 0.08 0.96 ]
|XXXXXXXXX 800 - 850 : [ 114 0.04 1.00 ]
|X 850 - 900 : [ 12 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634469
-------------------------------------------------------------------
AHXA.000001.000100 pUC18.fa LRS.fasta
AHXA.000101.000200 pUC18.fa LRS.fasta
AHXB.000001.000100 pMCL200.fa LRS.fasta
AHXB.000101.000200 pMCL200.fa LRS.fasta
AHXC.000001.000100 pCC1Fos.fa LRS.fasta
AHXA.000001.000100 pUC18.fa LRS.fasta
AHXA.000101.000200 pUC18.fa LRS.fasta
AHXB.000001.000100 pMCL200.fa LRS.fasta
AHXB.000101.000200 pMCL200.fa LRS.fasta
AHXC.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634469_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634469_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 41829 total values totalling 21342.4681. <0.510231 +/- 0.056095>
#Range: [ 0 - 0.7916 ]
#Most likely bin: [ 0.5 - 0.505 ] 1886 counts
#Median bin: [ 0.51 - 0.515 ] 1755 counts
| 0 - 0.005 : [ 2 0.00 0.00 ]
#...
| 0.16 - 0.165 : [ 2 0.00 0.00 ]
| 0.165 - 0.17 : [ 1 0.00 0.00 ]
| 0.17 - 0.175 : [ 1 0.00 0.00 ]
| 0.175 - 0.18 : [ 1 0.00 0.00 ]
#...
| 0.19 - 0.195 : [ 1 0.00 0.00 ]
#...
| 0.205 - 0.21 : [ 2 0.00 0.00 ]
| 0.21 - 0.215 : [ 2 0.00 0.00 ]
| 0.215 - 0.22 : [ 1 0.00 0.00 ]
| 0.22 - 0.225 : [ 1 0.00 0.00 ]
| 0.225 - 0.23 : [ 2 0.00 0.00 ]
| 0.23 - 0.235 : [ 3 0.00 0.00 ]
| 0.235 - 0.24 : [ 2 0.00 0.00 ]
| 0.24 - 0.245 : [ 1 0.00 0.00 ]
#...
| 0.25 - 0.255 : [ 7 0.00 0.00 ]
| 0.255 - 0.26 : [ 7 0.00 0.00 ]
| 0.26 - 0.265 : [ 10 0.00 0.00 ]
| 0.265 - 0.27 : [ 17 0.00 0.00 ]
| 0.27 - 0.275 : [ 14 0.00 0.00 ]
| 0.275 - 0.28 : [ 10 0.00 0.00 ]
| 0.28 - 0.285 : [ 16 0.00 0.00 ]
| 0.285 - 0.29 : [ 17 0.00 0.00 ]
|X 0.29 - 0.295 : [ 24 0.00 0.00 ]
| 0.295 - 0.3 : [ 18 0.00 0.00 ]
|X 0.3 - 0.305 : [ 29 0.00 0.00 ]
|X 0.305 - 0.31 : [ 37 0.00 0.01 ]
|X 0.31 - 0.315 : [ 35 0.00 0.01 ]
|X 0.315 - 0.32 : [ 42 0.00 0.01 ]
|X 0.32 - 0.325 : [ 41 0.00 0.01 ]
|X 0.325 - 0.33 : [ 57 0.00 0.01 ]
|X 0.33 - 0.335 : [ 65 0.00 0.01 ]
|XX 0.335 - 0.34 : [ 73 0.00 0.01 ]
|XX 0.34 - 0.345 : [ 85 0.00 0.01 ]
|XX 0.345 - 0.35 : [ 78 0.00 0.02 ]
|XX 0.35 - 0.355 : [ 71 0.00 0.02 ]
|XX 0.355 - 0.36 : [ 89 0.00 0.02 ]
|XX 0.36 - 0.365 : [ 92 0.00 0.02 ]
|XX 0.365 - 0.37 : [ 97 0.00 0.03 ]
|XX 0.37 - 0.375 : [ 87 0.00 0.03 ]
|XX 0.375 - 0.38 : [ 104 0.00 0.03 ]
|XXX 0.38 - 0.385 : [ 122 0.00 0.03 ]
|XXX 0.385 - 0.39 : [ 120 0.00 0.04 ]
|XXX 0.39 - 0.395 : [ 125 0.00 0.04 ]
|XXX 0.395 - 0.4 : [ 140 0.00 0.04 ]
|XXX 0.4 - 0.405 : [ 165 0.00 0.05 ]
|XXX 0.405 - 0.41 : [ 165 0.00 0.05 ]
|XXXX 0.41 - 0.415 : [ 194 0.00 0.05 ]
|XXXX 0.415 - 0.42 : [ 187 0.00 0.06 ]
|XXXXX 0.42 - 0.425 : [ 245 0.01 0.06 ]
|XXXXXX 0.425 - 0.43 : [ 267 0.01 0.07 ]
|XXXXXXX 0.43 - 0.435 : [ 317 0.01 0.08 ]
|XXXXXXXX 0.435 - 0.44 : [ 389 0.01 0.09 ]
|XXXXXXXXX 0.44 - 0.445 : [ 443 0.01 0.10 ]
|XXXXXXXXXXX 0.445 - 0.45 : [ 498 0.01 0.11 ]
|XXXXXXXXXXXXX 0.45 - 0.455 : [ 629 0.02 0.13 ]
|XXXXXXXXXXXXXXX 0.455 - 0.46 : [ 691 0.02 0.14 ]
|XXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 775 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 941 0.02 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 1046 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 1156 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 1305 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1488 0.04 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1537 0.04 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1490 0.04 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1886 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1741 0.04 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1755 0.04 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1849 0.04 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1782 0.04 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1782 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1682 0.04 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1723 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1471 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1416 0.03 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1270 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1151 0.03 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1054 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 868 0.02 0.89 ]
|XXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 763 0.02 0.91 ]
|XXXXXXXXXXXXXX 0.575 - 0.58 : [ 651 0.02 0.92 ]
|XXXXXXXXXXXX 0.58 - 0.585 : [ 566 0.01 0.93 ]
|XXXXXXXXX 0.585 - 0.59 : [ 406 0.01 0.94 ]
|XXXXXXXX 0.59 - 0.595 : [ 371 0.01 0.95 ]
|XXXXXX 0.595 - 0.6 : [ 260 0.01 0.96 ]
|XXXXXX 0.6 - 0.605 : [ 295 0.01 0.97 ]
|XXXXXX 0.605 - 0.61 : [ 303 0.01 0.97 ]
|XXXXXX 0.61 - 0.615 : [ 287 0.01 0.98 ]
|XXXXX 0.615 - 0.62 : [ 215 0.01 0.99 ]
|XXX 0.62 - 0.625 : [ 154 0.00 0.99 ]
|XX 0.625 - 0.63 : [ 116 0.00 0.99 ]
|XX 0.63 - 0.635 : [ 86 0.00 0.99 ]
|X 0.635 - 0.64 : [ 60 0.00 1.00 ]
|X 0.64 - 0.645 : [ 39 0.00 1.00 ]
|X 0.645 - 0.65 : [ 29 0.00 1.00 ]
|X 0.65 - 0.655 : [ 25 0.00 1.00 ]
|X 0.655 - 0.66 : [ 25 0.00 1.00 ]
| 0.66 - 0.665 : [ 12 0.00 1.00 ]
| 0.665 - 0.67 : [ 11 0.00 1.00 ]
| 0.67 - 0.675 : [ 11 0.00 1.00 ]
| 0.675 - 0.68 : [ 8 0.00 1.00 ]
| 0.68 - 0.685 : [ 6 0.00 1.00 ]
| 0.685 - 0.69 : [ 6 0.00 1.00 ]
| 0.69 - 0.695 : [ 4 0.00 1.00 ]
| 0.695 - 0.7 : [ 4 0.00 1.00 ]
| 0.7 - 0.705 : [ 1 0.00 1.00 ]
| 0.705 - 0.71 : [ 1 0.00 1.00 ]
| 0.71 - 0.715 : [ 1 0.00 1.00 ]
#...
| 0.72 - 0.725 : [ 1 0.00 1.00 ]
#...
| 0.73 - 0.735 : [ 1 0.00 1.00 ]
#...
| 0.775 - 0.78 : [ 1 0.00 1.00 ]
#...
| 0.79 - 0.795 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 77. 530 reads; 33888 bp (untrimmed), 33653 (trimmed).
Contig 78. 554 reads; 36762 bp (untrimmed), 36545 (trimmed).
Contig 79. 654 reads; 38404 bp (untrimmed), 38313 (trimmed).
Contig 80. 672 reads; 48484 bp (untrimmed), 48061 (trimmed).
Contig 81. 744 reads; 58658 bp (untrimmed), 58602 (trimmed).
Contig 82. 747 reads; 50755 bp (untrimmed), 50368 (trimmed).
Contig 83. 752 reads; 49151 bp (untrimmed), 48838 (trimmed).
Contig 84. 760 reads; 47642 bp (untrimmed), 47549 (trimmed).
Contig 85. 785 reads; 48753 bp (untrimmed), 48619 (trimmed).
Contig 86. 842 reads; 55975 bp (untrimmed), 55875 (trimmed).
Contig 87. 863 reads; 53217 bp (untrimmed), 53102 (trimmed).
Contig 88. 891 reads; 50584 bp (untrimmed), 50258 (trimmed).
Contig 89. 916 reads; 67661 bp (untrimmed), 67228 (trimmed).
Contig 90. 922 reads; 67185 bp (untrimmed), 67066 (trimmed).
Contig 91. 941 reads; 55100 bp (untrimmed), 54977 (trimmed).
Contig 92. 1114 reads; 77836 bp (untrimmed), 77652 (trimmed).
Contig 93. 1199 reads; 69684 bp (untrimmed), 69590 (trimmed).
Contig 94. 1246 reads; 80994 bp (untrimmed), 80278 (trimmed).
Contig 95. 1344 reads; 88843 bp (untrimmed), 88569 (trimmed).
Contig 96. 1366 reads; 95831 bp (untrimmed), 95724 (trimmed).
Contig 97. 1623 reads; 94768 bp (untrimmed), 94443 (trimmed).
Contig 98. 2028 reads; 121276 bp (untrimmed), 120874 (trimmed).
Contig 99. 2054 reads; 144307 bp (untrimmed), 144101 (trimmed).
Contig 100. 2385 reads; 152535 bp (untrimmed), 152313 (trimmed).
Contig 101. 2396 reads; 134530 bp (untrimmed), 134430 (trimmed).
Contig 102. 2401 reads; 150944 bp (untrimmed), 150845 (trimmed).
Contig 103. 2437 reads; 136359 bp (untrimmed), 136303 (trimmed).
--------------------------------------------------------------
Totals 41846 reads; 2761915 bp (untrimmed), 2736515 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2747135 bases = 12.31 +- 5.46 = 0.53 +- 4.83
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 86 total values totalling 783.1100. <9.105930 +/- 4.854747>
#Range: [ 1.70 - 20.70 ]
#Most likely bin: [ 2 - 2.5 ] 10 counts
#Median bin: [ 11 - 11.5 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXX 1.5 - 2 : [ 3 0.03 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 10 0.12 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 6 0.07 0.22 ]
|XXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 5 0.06 0.28 ]
|XXXXXXXX 3.5 - 4 : [ 2 0.02 0.30 ]
#...
|XXXXXXXX 4.5 - 5 : [ 2 0.02 0.33 ]
#...
|XXXX 6.5 - 7 : [ 1 0.01 0.34 ]
|XXXXXXXX 7 - 7.5 : [ 2 0.02 0.36 ]
#...
|XXXX 8 - 8.5 : [ 1 0.01 0.37 ]
|XXXX 8.5 - 9 : [ 1 0.01 0.38 ]
|XXXXXXXX 9 - 9.5 : [ 2 0.02 0.41 ]
|XXXX 9.5 - 10 : [ 1 0.01 0.42 ]
|XXXXXXXX 10 - 10.5 : [ 2 0.02 0.44 ]
|XXXXXXXX 10.5 - 11 : [ 2 0.02 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 6 0.07 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.08 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 8 0.09 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 9 0.10 0.81 ]
|XXXXXXXXXXXX 13 - 13.5 : [ 3 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 6 0.07 0.92 ]
|XXXXXXXX 14 - 14.5 : [ 2 0.02 0.94 ]
|XXXXXXXX 14.5 - 15 : [ 2 0.02 0.97 ]
|XXXX 15 - 15.5 : [ 1 0.01 0.98 ]
#...
|XXXX 20 - 20.5 : [ 1 0.01 0.99 ]
|XXXX 20.5 - 21 : [ 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 65 total values totalling 721.3000. <11.096923 +/- 3.724143>
#Range: [ 2.25 - 20.70 ]
#Most likely bin: [ 12.5 - 13 ] 9 counts
#Median bin: [ 12 - 12.5 ] 8 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 2 - 2.5 : [ 1 0.02 0.02 ]
|XXXX 2.5 - 3 : [ 1 0.02 0.03 ]
|XXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 4 0.06 0.09 ]
|XXXX 3.5 - 4 : [ 1 0.02 0.11 ]
#...
|XXXX 4.5 - 5 : [ 1 0.02 0.12 ]
#...
|XXXX 6.5 - 7 : [ 1 0.02 0.14 ]
|XXXXXXXXX 7 - 7.5 : [ 2 0.03 0.17 ]
#...
|XXXX 8 - 8.5 : [ 1 0.02 0.18 ]
|XXXX 8.5 - 9 : [ 1 0.02 0.20 ]
|XXXXXXXXX 9 - 9.5 : [ 2 0.03 0.23 ]
|XXXX 9.5 - 10 : [ 1 0.02 0.25 ]
|XXXXXXXXX 10 - 10.5 : [ 2 0.03 0.28 ]
|XXXX 10.5 - 11 : [ 1 0.02 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 6 0.09 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.11 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 8 0.12 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 9 0.14 0.75 ]
|XXXXXXXXXXXXX 13 - 13.5 : [ 3 0.05 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 6 0.09 0.89 ]
|XXXXXXXXX 14 - 14.5 : [ 2 0.03 0.92 ]
|XXXXXXXXX 14.5 - 15 : [ 2 0.03 0.95 ]
|XXXX 15 - 15.5 : [ 1 0.02 0.97 ]
#...
|XXXX 20 - 20.5 : [ 1 0.02 0.98 ]
|XXXX 20.5 - 21 : [ 1 0.02 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 21 3 reads 1593 bases = 1.70 +- 0.87 = 1.70 +- 0.87
Contig 30 6 reads 1704 bases = 1.87 +- 0.62 = 1.40 +- 0.66
Contig 18 2 reads 961 bases = 1.89 +- 0.32 = 1.89 +- 0.32
Contig 19 3 reads 855 bases = 2.01 +- 0.72 = 0.63 +- 0.58
Contig 23 4 reads 1596 bases = 2.09 +- 0.68 = 1.18 +- 1.26
Contig 32 6 reads 2048 bases = 2.21 +- 0.52 = 0.30 +- 0.63
Contig 38 12 reads 3745 bases = 2.25 +- 1.18 = 0.96 +- 2.25
Contig 20 3 reads 858 bases = 2.31 +- 0.58 = 0.43 +- 0.50
Contig 28 6 reads 2032 bases = 2.32 +- 0.88 = -0.22 +- 1.08
Contig 31 6 reads 1847 bases = 2.43 +- 1.04 = 2.43 +- 1.04
Contig 25 5 reads 1353 bases = 2.44 +- 1.43 = 0.08 +- 1.20
Contig 35 8 reads 2647 bases = 2.44 +- 1.02 = 2.44 +- 1.02
Contig 22 4 reads 1288 bases = 2.45 +- 1.03 = -0.13 +- 0.90
Contig 36 8 reads 2377 bases = 2.60 +- 0.83 = 0.57 +- 1.54
Contig 41 13 reads 3509 bases = 2.60 +- 1.70 = 0.58 +- 1.65
Contig 33 6 reads 1975 bases = 2.62 +- 1.53 = -0.15 +- 0.88
Contig 24 4 reads 1205 bases = 2.66 +- 1.32 = 1.40 +- 0.55
Contig 29 6 reads 1688 bases = 2.69 +- 0.79 = 0.95 +- 1.46
Contig 34 7 reads 2065 bases = 2.87 +- 1.24 = 2.87 +- 1.24
Contig 43 18 reads 4599 bases = 3.07 +- 1.64 = 2.04 +- 1.38
Contig 69 375 reads 23525 bases = 12.67 +- 5.87 = 0.29 +- 6.05
Contig 76 521 reads 33674 bases = 12.75 +- 5.18 = 0.47 +- 5.12
Contig 85 785 reads 48753 bases = 12.81 +- 5.23 = 0.04 +- 4.77
Contig 84 760 reads 47642 bases = 12.86 +- 4.80 = 0.53 +- 4.32
Contig 64 313 reads 19153 bases = 13.01 +- 6.37 = 2.31 +- 5.14
Contig 102 2401 reads 150944 bases = 13.04 +- 4.46 = 0.21 +- 4.17
Contig 87 863 reads 53217 bases = 13.15 +- 4.35 = 0.82 +- 3.94
Contig 98 2028 reads 121276 bases = 13.63 +- 4.39 = 0.22 +- 4.61
Contig 74 474 reads 27929 bases = 13.65 +- 4.68 = 1.93 +- 5.15
Contig 79 654 reads 38404 bases = 13.69 +- 4.55 = 1.10 +- 5.26
Contig 65 322 reads 19286 bases = 13.71 +- 5.10 = 0.35 +- 4.36
Contig 97 1623 reads 94768 bases = 13.87 +- 5.44 = 0.30 +- 5.10
Contig 91 941 reads 55100 bases = 13.93 +- 10.70 = 0.15 +- 4.49
Contig 93 1199 reads 69684 bases = 14.16 +- 5.15 = 0.65 +- 4.80
Contig 103 2437 reads 136359 bases = 14.32 +- 4.79 = 0.20 +- 4.65
Contig 101 2396 reads 134530 bases = 14.53 +- 4.43 = 0.08 +- 4.67
Contig 88 891 reads 50584 bases = 14.53 +- 4.58 = 0.17 +- 4.36
Contig 56 205 reads 10713 bases = 15.43 +- 5.94 = 2.04 +- 3.35
Contig 55 197 reads 7753 bases = 20.35 +- 13.47 = 0.42 +- 3.94
Contig 58 233 reads 8815 bases = 20.70 +- 11.75 = 3.36 +- 5.82
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 396
HQ Discrepant reads = 14
Chimeric reads = 50
Suspect alignments = 586
-------------------------------------------------------------------
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/microbe3/3634469/edit_dir.28Sep04.QD