Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-12-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3635487 3000 1757 Thermoanaerobacter ethanolicus
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Thermoanaerobacter_ethanolicus
-------------------------------------------------------------------
Thermoanaerobacteriaceae, family, eubacteria
Clostridia, class, eubacteria
Thermoanaerobacteriales, order, eubacteria
Thermoanaerobacter ethanolicus, species, eubacteria
Thermoanaerobacter, genus, eubacteria
Firmicutes (Gram-positive bacteria), phylum, eubacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2309535
# phrap: 2116262
# db:
altered.
3000000
2475265 +/- 379339
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 8040
Number of reads with percent X's >= 20%: 145 = 0.5%
Number of reads with percent X's >= 50%: 85 = 0.3%
Number of reads with percent X's >= 80%: 11 = 0.0%
Total reads in project: 31870
Total bp X'd : 360513
reads >= 20% >= 50% >= 80% screened
Nr with L09136 5354 55 34 0
Nr with LRS 1 1 0 0
Nr with pCC1Fos 2592 3 2 0
Nr with pMCL200_JGI_XZX+XZK 93 86 49 11
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 9556216
C = 5284216
G = 5257572
T = 9498457
N = 119459
X = 360513
GC fraction = 0.35
Total = 30076433
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3635487_fasta.screen.contigs
-------------------------------------------------------------------
A 748486
C 413194
G 391149
T 771503
N 148
fraction GC = 0.35
total bases = 2324480
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 AOTU reads.list > grep.reads.list.AOTU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOTU 4 500
-------------------------------------------------------------------
#Found 5817 total values totalling 18750229.0000. <3223.350352 +/- 440.200767>
#Range: [ 652 - 8909 ]
#Most likely bin: [ 3000 - 3500 ] 3040 counts
#Median bin: [ 3000 - 3500 ] 3040 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 10 0.00 0.00 ]
| 1000 - 1500 : [ 18 0.00 0.00 ]
| 1500 - 2000 : [ 14 0.00 0.01 ]
| 2000 - 2500 : [ 37 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 1462 0.25 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3040 0.52 0.79 ]
|XXXXXXXXXXXXXXXX 3500 - 4000 : [ 1199 0.21 0.99 ]
| 4000 - 4500 : [ 17 0.00 1.00 ]
#...
| 6000 - 6500 : [ 4 0.00 1.00 ]
| 6500 - 7000 : [ 4 0.00 1.00 ]
#...
| 7500 - 8000 : [ 2 0.00 1.00 ]
| 8000 - 8500 : [ 5 0.00 1.00 ]
| 8500 - 9000 : [ 5 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTW reads.list > grep.reads.list.AOTW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOTW 4 500
-------------------------------------------------------------------
#Found 4638 total values totalling 31732494.0000. <6841.848642 +/- 4479.792106>
#Range: [ 1007 - 97648 ]
#Most likely bin: [ 6000 - 6500 ] 1418 counts
#Median bin: [ 6500 - 7000 ] 998 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1000 - 1500 : [ 22 0.00 0.00 ]
| 1500 - 2000 : [ 15 0.00 0.01 ]
| 2000 - 2500 : [ 10 0.00 0.01 ]
|X 2500 - 3000 : [ 23 0.00 0.02 ]
| 3000 - 3500 : [ 14 0.00 0.02 ]
|X 3500 - 4000 : [ 20 0.00 0.02 ]
| 4000 - 4500 : [ 15 0.00 0.03 ]
| 4500 - 5000 : [ 14 0.00 0.03 ]
| 5000 - 5500 : [ 15 0.00 0.03 ]
|XXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 629 0.14 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1418 0.31 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 998 0.22 0.69 ]
|XXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 744 0.16 0.85 ]
|XXXXXXXXXXXXXX 7500 - 8000 : [ 487 0.11 0.95 ]
|XXXXX 8000 - 8500 : [ 167 0.04 0.99 ]
| 8500 - 9000 : [ 5 0.00 0.99 ]
| 9000 - 9500 : [ 2 0.00 0.99 ]
| 9500 - 10000 : [ 3 0.00 0.99 ]
| 10000 - 10500 : [ 8 0.00 0.99 ]
| 10500 - 11000 : [ 3 0.00 0.99 ]
| 11000 - 11500 : [ 5 0.00 1.00 ]
| 11500 - 12000 : [ 3 0.00 1.00 ]
| 12000 - 12500 : [ 2 0.00 1.00 ]
| 12500 - 13000 : [ 1 0.00 1.00 ]
| 13000 - 13500 : [ 1 0.00 1.00 ]
#...
| 16500 - 17000 : [ 1 0.00 1.00 ]
#...
| 51500 - 52000 : [ 1 0.00 1.00 ]
#...
| 61000 - 61500 : [ 1 0.00 1.00 ]
| 61500 - 62000 : [ 1 0.00 1.00 ]
#...
| 95500 - 96000 : [ 5 0.00 1.00 ]
| 96000 - 96500 : [ 1 0.00 1.00 ]
| 96500 - 97000 : [ 2 0.00 1.00 ]
#...
| 97500 - 98000 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTX reads.list > grep.reads.list.AOTX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOTX 4 500
-------------------------------------------------------------------
#Found 1128 total values totalling 43972534.0000. <38982.742908 +/- 11483.264707>
#Range: [ 1855 - 134656 ]
#Most likely bin: [ 35500 - 36000 ] 59 counts
#Median bin: [ 37500 - 38000 ] 52 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1500 - 2000 : [ 1 0.00 0.00 ]
|X 2000 - 2500 : [ 1 0.00 0.00 ]
|X 2500 - 3000 : [ 1 0.00 0.00 ]
|X 3000 - 3500 : [ 1 0.00 0.00 ]
#...
|X 5000 - 5500 : [ 1 0.00 0.00 ]
#...
|X 7000 - 7500 : [ 1 0.00 0.01 ]
#...
|X 16500 - 17000 : [ 1 0.00 0.01 ]
#...
|X 21500 - 22000 : [ 1 0.00 0.01 ]
|X 22000 - 22500 : [ 1 0.00 0.01 ]
#...
|X 23000 - 23500 : [ 1 0.00 0.01 ]
#...
|X 25000 - 25500 : [ 2 0.00 0.01 ]
#...
|X 26000 - 26500 : [ 2 0.00 0.01 ]
#...
|X 27000 - 27500 : [ 1 0.00 0.01 ]
|X 27500 - 28000 : [ 2 0.00 0.02 ]
|X 28000 - 28500 : [ 1 0.00 0.02 ]
|X 28500 - 29000 : [ 1 0.00 0.02 ]
|X 29000 - 29500 : [ 1 0.00 0.02 ]
|XXXXX 29500 - 30000 : [ 8 0.01 0.02 ]
|XXXX 30000 - 30500 : [ 6 0.01 0.03 ]
|XXX 30500 - 31000 : [ 4 0.00 0.03 ]
|XXXXXXXX 31000 - 31500 : [ 12 0.01 0.04 ]
|XXXXXX 31500 - 32000 : [ 9 0.01 0.05 ]
|XXXXXXXXXXXXXXXXX 32000 - 32500 : [ 25 0.02 0.07 ]
|XXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 27 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 32 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 45 0.04 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 34 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 56 0.05 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 47 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 59 0.05 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 49 0.04 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 57 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 55 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 52 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 43 0.04 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 48 0.04 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 36 0.03 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 44 0.04 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 46 0.04 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 48 0.04 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 42 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 32 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 29 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 31 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 34 0.03 0.91 ]
|XXXXXXXXXXXX 43500 - 44000 : [ 17 0.02 0.93 ]
|XXXXXXXXXXXXXX 44000 - 44500 : [ 20 0.02 0.95 ]
|XXXXXXXXXXXX 44500 - 45000 : [ 17 0.02 0.96 ]
|XXXXXXX 45000 - 45500 : [ 10 0.01 0.97 ]
|XXXXX 45500 - 46000 : [ 7 0.01 0.98 ]
|XX 46000 - 46500 : [ 3 0.00 0.98 ]
|XXX 46500 - 47000 : [ 4 0.00 0.98 ]
#...
|X 83500 - 84000 : [ 1 0.00 0.98 ]
#...
|X 88000 - 88500 : [ 1 0.00 0.98 ]
#...
|X 89000 - 89500 : [ 1 0.00 0.98 ]
|X 89500 - 90000 : [ 1 0.00 0.99 ]
#...
|X 91000 - 91500 : [ 1 0.00 0.99 ]
#...
|X 106000 - 106500 : [ 1 0.00 0.99 ]
#...
|X 109500 - 110000 : [ 1 0.00 0.99 ]
#...
|X 112500 - 113000 : [ 1 0.00 0.99 ]
#...
|X 122000 - 122500 : [ 1 0.00 0.99 ]
#...
|X 124000 - 124500 : [ 1 0.00 0.99 ]
|X 124500 - 125000 : [ 2 0.00 0.99 ]
#...
|X 127500 - 128000 : [ 2 0.00 0.99 ]
|X 128000 - 128500 : [ 1 0.00 1.00 ]
#...
|X 129000 - 129500 : [ 2 0.00 1.00 ]
#...
|X 131500 - 132000 : [ 1 0.00 1.00 ]
#...
|X 133500 - 134000 : [ 1 0.00 1.00 ]
#...
|X 134500 - 135000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AOTX 37613 +- 4582 (n=533)
# AOTU 3093 +- 516 (n=2943)
# AOTW 6509 +- 1100 (n=2307)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3635487_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
AOTU 15360 87 626 93 640 15267 88 627 93 640
AOTW 13056 90 779 96 736 13056 89 779 96 769
AOTX 8160 78 601 87 534 8160 78 621 87 612
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AOTU 7645 87 628 94 641 7622 88 625 92 639
AOTW 6528 89 778 96 768 6528 89 780 95 770
AOTX 4224 75 624 85 608 3936 81 617 89 616
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3635487_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
68 11689 5888 86.59 90.20 AOTW @
40 6705 3573 89.33 93.05 AOTX @
80 13476 6996 87.45 91.09 AOTU @
] 31870 16457 87.54 cumulative total@@
LIBRARY PLATE ID COUNT [ AOTW 68 AOTX 40 AOTU 80 ] for 188 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 3635487_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 36483 total values totalling 21493992.0000. <589.150892 +/- 277.825545>
#Range: [ 0 - 990 ]
#Most likely bin: [ 750 - 800 ] 6342 counts
#Median bin: [ 700 - 750 ] 4924 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 4592 0.13 0.13 ]
|XXX 50 - 100 : [ 472 0.01 0.14 ]
|XX 100 - 150 : [ 344 0.01 0.15 ]
|XX 150 - 200 : [ 364 0.01 0.16 ]
|XX 200 - 250 : [ 388 0.01 0.17 ]
|XXX 250 - 300 : [ 460 0.01 0.18 ]
|XXXX 300 - 350 : [ 558 0.02 0.20 ]
|XXXX 350 - 400 : [ 628 0.02 0.21 ]
|XXXX 400 - 450 : [ 608 0.02 0.23 ]
|XXXXX 450 - 500 : [ 786 0.02 0.25 ]
|XXXXXXX 500 - 550 : [ 1057 0.03 0.28 ]
|XXXXXXXXXX 550 - 600 : [ 1611 0.04 0.33 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 2387 0.07 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3513 0.10 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4924 0.13 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6342 0.17 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5509 0.15 0.95 ]
|XXXXXXXXXXX 850 - 900 : [ 1817 0.05 1.00 ]
|X 900 - 950 : [ 119 0.00 1.00 ]
| 950 - 1000 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOTU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTU 3635487_fasta.screen.trimQ15.SaF > reads.trim15.AOTU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOTU.rl 2 50
-------------------------------------------------------------------
#Found 15267 total values totalling 8390558.0000. <549.587869 +/- 253.337359>
#Range: [ 0 - 990 ]
#Most likely bin: [ 700 - 750 ] 2548 counts
#Median bin: [ 600 - 650 ] 1675 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1735 0.11 0.11 ]
|XXX 50 - 100 : [ 172 0.01 0.12 ]
|XX 100 - 150 : [ 158 0.01 0.14 ]
|XXX 150 - 200 : [ 176 0.01 0.15 ]
|XXX 200 - 250 : [ 217 0.01 0.16 ]
|XXXX 250 - 300 : [ 247 0.02 0.18 ]
|XXXXX 300 - 350 : [ 288 0.02 0.20 ]
|XXXXXX 350 - 400 : [ 372 0.02 0.22 ]
|XXXXXXX 400 - 450 : [ 417 0.03 0.25 ]
|XXXXXXXX 450 - 500 : [ 514 0.03 0.28 ]
|XXXXXXXXXXXX 500 - 550 : [ 755 0.05 0.33 ]
|XXXXXXXXXXXXXXXXX 550 - 600 : [ 1111 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1675 0.11 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2382 0.16 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2548 0.17 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1419 0.09 0.93 ]
|XXXXXXXXXX 800 - 850 : [ 618 0.04 0.97 ]
|XXXXXX 850 - 900 : [ 400 0.03 1.00 ]
|X 900 - 950 : [ 59 0.00 1.00 ]
| 950 - 1000 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOTW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTW 3635487_fasta.screen.trimQ15.SaF > reads.trim15.AOTW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOTW.rl 2 50
-------------------------------------------------------------------
#Found 13056 total values totalling 9101230.0000. <697.091759 +/- 255.350653>
#Range: [ 0 - 943 ]
#Most likely bin: [ 800 - 850 ] 4298 counts
#Median bin: [ 750 - 800 ] 3885 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXX 0 - 50 : [ 1346 0.10 0.10 ]
| 50 - 100 : [ 39 0.00 0.11 ]
| 100 - 150 : [ 36 0.00 0.11 ]
| 150 - 200 : [ 30 0.00 0.11 ]
| 200 - 250 : [ 33 0.00 0.11 ]
| 250 - 300 : [ 38 0.00 0.12 ]
| 300 - 350 : [ 35 0.00 0.12 ]
| 350 - 400 : [ 45 0.00 0.12 ]
| 400 - 450 : [ 49 0.00 0.13 ]
|X 450 - 500 : [ 72 0.01 0.13 ]
|X 500 - 550 : [ 69 0.01 0.14 ]
|X 550 - 600 : [ 74 0.01 0.14 ]
|X 600 - 650 : [ 110 0.01 0.15 ]
|XX 650 - 700 : [ 263 0.02 0.17 ]
|XXXXXXXXXXXX 700 - 750 : [ 1323 0.10 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3885 0.30 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4298 0.33 0.90 ]
|XXXXXXXXXXXX 850 - 900 : [ 1266 0.10 1.00 ]
| 900 - 950 : [ 45 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOTX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTX 3635487_fasta.screen.trimQ15.SaF > reads.trim15.AOTX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOTX.rl 2 50
-------------------------------------------------------------------
#Found 8160 total values totalling 4002204.0000. <490.466176 +/- 298.976188>
#Range: [ 0 - 938 ]
#Most likely bin: [ 0 - 50 ] 1511 counts
#Median bin: [ 600 - 650 ] 602 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1511 0.19 0.19 ]
|XXXXXXX 50 - 100 : [ 261 0.03 0.22 ]
|XXXX 100 - 150 : [ 150 0.02 0.24 ]
|XXXX 150 - 200 : [ 158 0.02 0.25 ]
|XXXX 200 - 250 : [ 138 0.02 0.27 ]
|XXXXX 250 - 300 : [ 175 0.02 0.29 ]
|XXXXXX 300 - 350 : [ 235 0.03 0.32 ]
|XXXXXX 350 - 400 : [ 211 0.03 0.35 ]
|XXXX 400 - 450 : [ 142 0.02 0.37 ]
|XXXXX 450 - 500 : [ 200 0.02 0.39 ]
|XXXXXX 500 - 550 : [ 233 0.03 0.42 ]
|XXXXXXXXXXX 550 - 600 : [ 426 0.05 0.47 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 602 0.07 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 868 0.11 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1053 0.13 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1038 0.13 0.91 ]
|XXXXXXXXXXXXXXXX 800 - 850 : [ 593 0.07 0.98 ]
|XXXX 850 - 900 : [ 151 0.02 1.00 ]
| 900 - 950 : [ 15 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AUFP
trimt JAZZ trim 15 readlength histogram for AUFS
trimt JAZZ trim 15 readlength histogram for AUFT
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3635487
-------------------------------------------------------------------
AOTU.000001.000100 pUC18.fa LRS.fasta
AOTW.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AOTX.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AUFP.000001.000100
AOTU.000001.000100 pUC18.fa LRS.fasta
AOTW.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AOTX.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AUFP.000001.000100
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3635487_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3635487_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 31683 total values totalling 10960.5685. <0.345945 +/- 0.049055>
#Range: [ 0.0263 - 0.75 ]
#Most likely bin: [ 0.335 - 0.34 ] 1643 counts
#Median bin: [ 0.34 - 0.345 ] 1559 counts
#Entropy = 5.1922 bits
| 0.025 - 0.03 : [ 1 0.00 0.00 ]
#...
| 0.075 - 0.08 : [ 1 0.00 0.00 ]
#...
| 0.105 - 0.11 : [ 2 0.00 0.00 ]
#...
| 0.125 - 0.13 : [ 1 0.00 0.00 ]
#...
| 0.135 - 0.14 : [ 1 0.00 0.00 ]
| 0.14 - 0.145 : [ 2 0.00 0.00 ]
| 0.145 - 0.15 : [ 1 0.00 0.00 ]
| 0.15 - 0.155 : [ 5 0.00 0.00 ]
| 0.155 - 0.16 : [ 3 0.00 0.00 ]
| 0.16 - 0.165 : [ 4 0.00 0.00 ]
| 0.165 - 0.17 : [ 2 0.00 0.00 ]
| 0.17 - 0.175 : [ 6 0.00 0.00 ]
| 0.175 - 0.18 : [ 3 0.00 0.00 ]
| 0.18 - 0.185 : [ 5 0.00 0.00 ]
| 0.185 - 0.19 : [ 3 0.00 0.00 ]
| 0.19 - 0.195 : [ 2 0.00 0.00 ]
| 0.195 - 0.2 : [ 6 0.00 0.00 ]
| 0.2 - 0.205 : [ 4 0.00 0.00 ]
| 0.205 - 0.21 : [ 6 0.00 0.00 ]
| 0.21 - 0.215 : [ 16 0.00 0.00 ]
| 0.215 - 0.22 : [ 11 0.00 0.00 ]
| 0.22 - 0.225 : [ 9 0.00 0.00 ]
| 0.225 - 0.23 : [ 16 0.00 0.00 ]
|X 0.23 - 0.235 : [ 29 0.00 0.00 ]
|X 0.235 - 0.24 : [ 37 0.00 0.01 ]
|X 0.24 - 0.245 : [ 50 0.00 0.01 ]
|X 0.245 - 0.25 : [ 55 0.00 0.01 ]
|XXX 0.25 - 0.255 : [ 109 0.00 0.01 ]
|XXXX 0.255 - 0.26 : [ 160 0.01 0.02 ]
|XXXXX 0.26 - 0.265 : [ 198 0.01 0.02 ]
|XXXXXXX 0.265 - 0.27 : [ 285 0.01 0.03 ]
|XXXXXXXX 0.27 - 0.275 : [ 320 0.01 0.04 ]
|XXXXXXXXX 0.275 - 0.28 : [ 387 0.01 0.05 ]
|XXXXXXXXXXXX 0.28 - 0.285 : [ 478 0.02 0.07 ]
|XXXXXXXXXXXXXX 0.285 - 0.29 : [ 594 0.02 0.09 ]
|XXXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 709 0.02 0.11 ]
|XXXXXXXXXXXXXXXXXXX 0.295 - 0.3 : [ 798 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 1003 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 1147 0.04 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 1196 0.04 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 1369 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 1451 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 1479 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 1575 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 1643 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 1559 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 1467 0.05 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 1541 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 1528 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 1399 0.04 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 1198 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 1075 0.03 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 1058 0.03 0.82 ]
|XXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 883 0.03 0.85 ]
|XXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 702 0.02 0.87 ]
|XXXXXXXXXXXXXX 0.39 - 0.395 : [ 574 0.02 0.89 ]
|XXXXXXXXXXXX 0.395 - 0.4 : [ 491 0.02 0.90 ]
|XXXXXXXXXXX 0.4 - 0.405 : [ 449 0.01 0.92 ]
|XXXXXXXXX 0.405 - 0.41 : [ 361 0.01 0.93 ]
|XXXXXXX 0.41 - 0.415 : [ 281 0.01 0.94 ]
|XXXXXXX 0.415 - 0.42 : [ 275 0.01 0.95 ]
|XXXXX 0.42 - 0.425 : [ 197 0.01 0.95 ]
|XXX 0.425 - 0.43 : [ 141 0.00 0.96 ]
|XXX 0.43 - 0.435 : [ 111 0.00 0.96 ]
|XX 0.435 - 0.44 : [ 102 0.00 0.96 ]
|XX 0.44 - 0.445 : [ 77 0.00 0.97 ]
|XX 0.445 - 0.45 : [ 86 0.00 0.97 ]
|X 0.45 - 0.455 : [ 60 0.00 0.97 ]
|XX 0.455 - 0.46 : [ 64 0.00 0.97 ]
|X 0.46 - 0.465 : [ 50 0.00 0.98 ]
|X 0.465 - 0.47 : [ 54 0.00 0.98 ]
|X 0.47 - 0.475 : [ 47 0.00 0.98 ]
|X 0.475 - 0.48 : [ 41 0.00 0.98 ]
|X 0.48 - 0.485 : [ 42 0.00 0.98 ]
|X 0.485 - 0.49 : [ 37 0.00 0.98 ]
|X 0.49 - 0.495 : [ 41 0.00 0.98 ]
|X 0.495 - 0.5 : [ 27 0.00 0.98 ]
|X 0.5 - 0.505 : [ 39 0.00 0.99 ]
|X 0.505 - 0.51 : [ 33 0.00 0.99 ]
|X 0.51 - 0.515 : [ 33 0.00 0.99 ]
|X 0.515 - 0.52 : [ 29 0.00 0.99 ]
|X 0.52 - 0.525 : [ 25 0.00 0.99 ]
|X 0.525 - 0.53 : [ 24 0.00 0.99 ]
|X 0.53 - 0.535 : [ 23 0.00 0.99 ]
| 0.535 - 0.54 : [ 17 0.00 0.99 ]
|X 0.54 - 0.545 : [ 26 0.00 0.99 ]
|X 0.545 - 0.55 : [ 30 0.00 0.99 ]
|X 0.55 - 0.555 : [ 38 0.00 0.99 ]
|X 0.555 - 0.56 : [ 23 0.00 1.00 ]
| 0.56 - 0.565 : [ 16 0.00 1.00 ]
| 0.565 - 0.57 : [ 12 0.00 1.00 ]
| 0.57 - 0.575 : [ 10 0.00 1.00 ]
| 0.575 - 0.58 : [ 15 0.00 1.00 ]
| 0.58 - 0.585 : [ 11 0.00 1.00 ]
| 0.585 - 0.59 : [ 7 0.00 1.00 ]
| 0.59 - 0.595 : [ 8 0.00 1.00 ]
| 0.595 - 0.6 : [ 4 0.00 1.00 ]
| 0.6 - 0.605 : [ 12 0.00 1.00 ]
| 0.605 - 0.61 : [ 10 0.00 1.00 ]
| 0.61 - 0.615 : [ 4 0.00 1.00 ]
| 0.615 - 0.62 : [ 3 0.00 1.00 ]
| 0.62 - 0.625 : [ 3 0.00 1.00 ]
#...
| 0.63 - 0.635 : [ 2 0.00 1.00 ]
| 0.635 - 0.64 : [ 2 0.00 1.00 ]
| 0.64 - 0.645 : [ 1 0.00 1.00 ]
| 0.645 - 0.65 : [ 4 0.00 1.00 ]
| 0.65 - 0.655 : [ 2 0.00 1.00 ]
| 0.655 - 0.66 : [ 2 0.00 1.00 ]
| 0.66 - 0.665 : [ 1 0.00 1.00 ]
| 0.665 - 0.67 : [ 1 0.00 1.00 ]
| 0.67 - 0.675 : [ 2 0.00 1.00 ]
| 0.675 - 0.68 : [ 1 0.00 1.00 ]
| 0.68 - 0.685 : [ 2 0.00 1.00 ]
| 0.685 - 0.69 : [ 1 0.00 1.00 ]
| 0.69 - 0.695 : [ 2 0.00 1.00 ]
| 0.695 - 0.7 : [ 2 0.00 1.00 ]
#...
| 0.705 - 0.71 : [ 1 0.00 1.00 ]
#...
| 0.72 - 0.725 : [ 1 0.00 1.00 ]
#...
| 0.75 - 0.755 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 83. 306 reads; 22887 bp (untrimmed), 22845 (trimmed).
Contig 84. 325 reads; 38186 bp (untrimmed), 38084 (trimmed).
Contig 85. 327 reads; 17600 bp (untrimmed), 17583 (trimmed).
Contig 86. 359 reads; 38738 bp (untrimmed), 38599 (trimmed).
Contig 87. 383 reads; 30036 bp (untrimmed), 29949 (trimmed).
Contig 88. 387 reads; 23437 bp (untrimmed), 23411 (trimmed).
Contig 89. 403 reads; 29540 bp (untrimmed), 29512 (trimmed).
Contig 90. 420 reads; 34353 bp (untrimmed), 34220 (trimmed).
Contig 91. 428 reads; 32445 bp (untrimmed), 32348 (trimmed).
Contig 92. 441 reads; 33182 bp (untrimmed), 33030 (trimmed).
Contig 93. 482 reads; 41543 bp (untrimmed), 41482 (trimmed).
Contig 94. 510 reads; 37221 bp (untrimmed), 37138 (trimmed).
Contig 95. 545 reads; 32353 bp (untrimmed), 31941 (trimmed).
Contig 96. 554 reads; 39936 bp (untrimmed), 39604 (trimmed).
Contig 97. 580 reads; 44621 bp (untrimmed), 44527 (trimmed).
Contig 98. 696 reads; 49775 bp (untrimmed), 49567 (trimmed).
Contig 99. 725 reads; 36502 bp (untrimmed), 36335 (trimmed).
Contig 100. 737 reads; 41216 bp (untrimmed), 41137 (trimmed).
Contig 101. 819 reads; 45580 bp (untrimmed), 45541 (trimmed).
Contig 102. 828 reads; 57756 bp (untrimmed), 57718 (trimmed).
Contig 103. 980 reads; 70413 bp (untrimmed), 70182 (trimmed).
Contig 104. 1164 reads; 81222 bp (untrimmed), 81107 (trimmed).
Contig 105. 1313 reads; 93850 bp (untrimmed), 93735 (trimmed).
Contig 106. 1427 reads; 114134 bp (untrimmed), 114092 (trimmed).
Contig 107. 1481 reads; 90422 bp (untrimmed), 90098 (trimmed).
Contig 108. 3992 reads; 233462 bp (untrimmed), 233192 (trimmed).
Contig 109. 5399 reads; 309330 bp (untrimmed), 309218 (trimmed).
--------------------------------------------------------------
Totals 31697 reads; 2324480 bp (untrimmed), 2309535 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2323538 bases = 11.94 +- 6.96 = 0.98 +- 5.33
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 108 total values totalling 941.2500. <8.715278 +/- 6.223494>
#Range: [ 1.23 - 50.92 ]
#Most likely bin: [ 4.5 - 5 ] 8 counts
#Median bin: [ 7.5 - 8 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 1 - 1.5 : [ 2 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 5 0.05 0.06 ]
|XXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 4 0.04 0.10 ]
|XXXXXXXXXX 2.5 - 3 : [ 2 0.02 0.12 ]
|XXXXXXXXXXXXXXX 3 - 3.5 : [ 3 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 5 0.05 0.19 ]
|XXXXXXXXXXXXXXX 4 - 4.5 : [ 3 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 8 0.07 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 7 0.06 0.36 ]
|XXXXX 5.5 - 6 : [ 1 0.01 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 5 0.05 0.42 ]
|XXXXXXXXXXXXXXX 6.5 - 7 : [ 3 0.03 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 5 0.05 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 6 0.06 0.55 ]
|XXXXXXXXXXXXXXX 8 - 8.5 : [ 3 0.03 0.57 ]
|XXXXX 8.5 - 9 : [ 1 0.01 0.58 ]
|XXXXXXXXXXXXXXX 9 - 9.5 : [ 3 0.03 0.61 ]
|XXXXXXXXXX 9.5 - 10 : [ 2 0.02 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 5 0.05 0.68 ]
|XXXXXXXXXXXXXXX 10.5 - 11 : [ 3 0.03 0.70 ]
|XXXXXXXXXXXXXXX 11 - 11.5 : [ 3 0.03 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 5 0.05 0.78 ]
|XXXXXXXXXXXXXXX 12 - 12.5 : [ 3 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.04 0.84 ]
#...
|XXXXX 14 - 14.5 : [ 1 0.01 0.85 ]
|XXXXXXXXXXXXXXXXXXXX 14.5 - 15 : [ 4 0.04 0.89 ]
|XXXXXXXXXX 15 - 15.5 : [ 2 0.02 0.91 ]
|XXXXXXXXXX 15.5 - 16 : [ 2 0.02 0.93 ]
|XXXXXXXXXX 16 - 16.5 : [ 2 0.02 0.94 ]
#...
|XXXXX 17 - 17.5 : [ 1 0.01 0.95 ]
|XXXXXXXXXX 17.5 - 18 : [ 2 0.02 0.97 ]
#...
|XXXXX 21.5 - 22 : [ 1 0.01 0.98 ]
|XXXXX 22 - 22.5 : [ 1 0.01 0.99 ]
#...
|XXXXX 50.5 - 51 : [ 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 88 total values totalling 813.0400. <9.239091 +/- 4.210717>
#Range: [ 2.03 - 21.79 ]
#Most likely bin: [ 4.5 - 5 ] 7 counts
#Median bin: [ 8 - 8.5 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 2 - 2.5 : [ 1 0.01 0.01 ]
|XXXXXX 2.5 - 3 : [ 1 0.01 0.02 ]
|XXXXXX 3 - 3.5 : [ 1 0.01 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 4 0.05 0.08 ]
|XXXXXXXXXXX 4 - 4.5 : [ 2 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 7 0.08 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 6 0.07 0.25 ]
|XXXXXX 5.5 - 6 : [ 1 0.01 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 5 0.06 0.32 ]
|XXXXXXXXXXXXXXXXX 6.5 - 7 : [ 3 0.03 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 5 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 6 0.07 0.48 ]
|XXXXXXXXXXXXXXXXX 8 - 8.5 : [ 3 0.03 0.51 ]
|XXXXXX 8.5 - 9 : [ 1 0.01 0.52 ]
|XXXXXXXXXXX 9 - 9.5 : [ 2 0.02 0.55 ]
|XXXXXXXXXXX 9.5 - 10 : [ 2 0.02 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 5 0.06 0.62 ]
|XXXXXXXXXXXXXXXXX 10.5 - 11 : [ 3 0.03 0.66 ]
|XXXXXXXXXXXXXXXXX 11 - 11.5 : [ 3 0.03 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 5 0.06 0.75 ]
|XXXXXXXXXXXXXXXXX 12 - 12.5 : [ 3 0.03 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.05 0.83 ]
#...
|XXXXXX 14 - 14.5 : [ 1 0.01 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXX 14.5 - 15 : [ 4 0.05 0.89 ]
|XXXXXXXXXXX 15 - 15.5 : [ 2 0.02 0.91 ]
|XXXXXXXXXXX 15.5 - 16 : [ 2 0.02 0.93 ]
|XXXXXXXXXXX 16 - 16.5 : [ 2 0.02 0.95 ]
#...
|XXXXXX 17 - 17.5 : [ 1 0.01 0.97 ]
|XXXXXXXXXXX 17.5 - 18 : [ 2 0.02 0.99 ]
#...
|XXXXXX 21.5 - 22 : [ 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 3 3 reads 506 bases = 1.23 +- 0.63 = 1.23 +- 0.63
Contig 9 4 reads 2188 bases = 1.49 +- 0.50 = 0.74 +- 1.13
Contig 12 4 reads 1985 bases = 1.59 +- 0.71 = 1.07 +- 1.30
Contig 11 4 reads 1625 bases = 1.68 +- 0.69 = 0.53 +- 0.55
Contig 2 2 reads 951 bases = 1.70 +- 0.46 = 1.70 +- 0.46
Contig 13 4 reads 1534 bases = 1.75 +- 0.60 = 1.75 +- 0.60
Contig 4 3 reads 1532 bases = 1.79 +- 0.70 = 1.79 +- 0.70
Contig 19 10 reads 3996 bases = 2.03 +- 0.89 = 0.90 +- 1.66
Contig 5 3 reads 1100 bases = 2.40 +- 0.68 = 2.40 +- 0.68
Contig 6 3 reads 1020 bases = 2.40 +- 0.73 = 2.40 +- 0.73
Contig 8 4 reads 1569 bases = 2.44 +- 1.19 = 1.15 +- 1.48
Contig 23 15 reads 5106 bases = 2.59 +- 1.35 = 2.16 +- 1.65
Contig 16 8 reads 2457 bases = 2.84 +- 1.13 = 2.52 +- 1.13
Contig 10 4 reads 1182 bases = 3.05 +- 1.20 = 1.54 +- 0.54
Contig 33 20 reads 4853 bases = 3.08 +- 1.09 = 0.77 +- 2.27
Contig 7 4 reads 1049 bases = 3.27 +- 1.03 = 3.27 +- 1.03
Contig 30 19 reads 4913 bases = 3.50 +- 1.85 = 1.72 +- 2.00
Contig 35 20 reads 4659 bases = 3.58 +- 1.76 = 0.35 +- 1.57
Contig 22 15 reads 3555 bases = 3.88 +- 1.58 = 2.95 +- 2.12
Contig 44 43 reads 9521 bases = 3.93 +- 1.70 = 1.05 +- 2.08
Contig 104 1164 reads 81222 bases = 12.60 +- 5.84 = -0.14 +- 5.04
Contig 102 828 reads 57756 bases = 12.61 +- 5.42 = 0.10 +- 5.59
Contig 68 144 reads 9811 bases = 12.78 +- 4.92 = 0.81 +- 3.74
Contig 67 143 reads 8872 bases = 14.13 +- 4.60 = 2.20 +- 4.32
Contig 107 1481 reads 90422 bases = 14.54 +- 5.55 = 1.03 +- 5.92
Contig 88 387 reads 23437 bases = 14.77 +- 6.18 = 3.05 +- 5.65
Contig 95 545 reads 32353 bases = 14.91 +- 7.18 = 2.72 +- 4.73
Contig 108 3992 reads 233462 bases = 14.98 +- 6.88 = 0.60 +- 6.47
Contig 43 43 reads 2569 bases = 15.27 +- 10.28 = 3.78 +- 4.64
Contig 109 5399 reads 309330 bases = 15.37 +- 8.88 = 0.54 +- 5.73
Contig 101 819 reads 45580 bases = 15.78 +- 6.27 = 1.09 +- 5.12
Contig 100 737 reads 41216 bases = 15.81 +- 6.34 = 1.94 +- 6.69
Contig 85 327 reads 17600 bases = 16.06 +- 6.16 = 2.95 +- 5.55
Contig 46 48 reads 2488 bases = 16.49 +- 8.24 = 2.36 +- 2.89
Contig 76 211 reads 11158 bases = 17.24 +- 7.78 = 3.95 +- 3.61
Contig 99 725 reads 36502 bases = 17.70 +- 6.55 = 1.03 +- 4.43
Contig 56 79 reads 3993 bases = 17.80 +- 11.77 = 1.82 +- 3.68
Contig 72 165 reads 6616 bases = 21.79 +- 6.82 = 4.65 +- 5.53
Contig 38 24 reads 1047 bases = 22.08 +- 4.46 = 22.08 +- 4.46
Contig 59 89 reads 1539 bases = 50.92 +- 29.95 = 10.83 +- 6.18
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 846
HQ Discrepant reads = 61
Chimeric reads = 59
Suspect alignments = 281
-------------------------------------------------------------------
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/microbe2/3635487/edit_dir.18Jan05.QD