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
3634478 4500 863 Syntrophomonas wolfei
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Syntrophomonas_wolfei
-------------------------------------------------------------------
Clostridiales, order, eubacteria
Clostridia, class, eubacteria
Syntrophomonadaceae, family, eubacteria
Firmicutes (Gram-positive bacteria), phylum, eubacteria
Syntrophomonas wolfei, species, eubacteria
Syntrophomonas, genus, eubacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2910698
# phrap: 2740391
# db:
altered.
4500000
3383696 +/- 792402
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 6753
Number of reads with percent X's >= 20%: 130 = 0.4%
Number of reads with percent X's >= 50%: 83 = 0.2%
Number of reads with percent X's >= 80%: 16 = 0.0%
Total reads in project: 33558
Total bp X'd : 306786
reads >= 20% >= 50% >= 80% screened
Nr with L09136 6009 55 33 8
Nr with pCC1Fos 645 1 0 0
Nr with pMCL200_JGI_XZX+XZK 99 74 50 8
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 19
Number of reads with percent X's >= 20%: 2 = 0.6%
Number of reads with percent X's >= 50%: 0 = 0.0%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 320
Total bp X'd : 1196
reads >= 20% >= 50% >= 80% screened
Nr with L09136 13 1 0 0
Nr with pCC1Fos 4 1 0 0
Nr with pMCL200_JGI_XZX+XZK 2 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 8960840
C = 7476833
G = 7280589
T = 9004955
N = 164527
X = 306786
GC fraction = 0.44
Total = 33194530
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634478_fasta.screen.contigs
-------------------------------------------------------------------
A 816127
C 667553
G 664870
T 821585
N 22425
fraction GC = 0.45
total bases = 2992560
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 AHYO reads.list > grep.reads.list.AHYO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYO 4 500
-------------------------------------------------------------------
#Found 6276 total values totalling 21328428.0000. <3398.411090 +/- 2690.009179>
#Range: [ 1043 - 153640 ]
#Most likely bin: [ 3000 - 3500 ] 3779 counts
#Median bin: [ 3000 - 3500 ] 3779 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 15 0.00 0.00 ]
| 1500 - 2000 : [ 15 0.00 0.00 ]
| 2000 - 2500 : [ 25 0.00 0.01 ]
|XXXXX 2500 - 3000 : [ 457 0.07 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3779 0.60 0.68 ]
|XXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1931 0.31 0.99 ]
|X 4000 - 4500 : [ 52 0.01 1.00 ]
#...
| 152000 - 152500 : [ 1 0.00 1.00 ]
#...
| 153500 - 154000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIGA reads.list > grep.reads.list.AIGA
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIGA 4 500
-------------------------------------------------------------------
#Found 5348 total values totalling 36139363.0000. <6757.547307 +/- 1985.145151>
#Range: [ 984 - 136623 ]
#Most likely bin: [ 6000 - 6500 ] 1273 counts
#Median bin: [ 6500 - 7000 ] 1187 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 3 0.00 0.00 ]
| 1000 - 1500 : [ 8 0.00 0.00 ]
| 1500 - 2000 : [ 7 0.00 0.00 ]
| 2000 - 2500 : [ 10 0.00 0.01 ]
| 2500 - 3000 : [ 6 0.00 0.01 ]
| 3000 - 3500 : [ 14 0.00 0.01 ]
| 3500 - 4000 : [ 11 0.00 0.01 ]
| 4000 - 4500 : [ 12 0.00 0.01 ]
| 4500 - 5000 : [ 14 0.00 0.02 ]
|X 5000 - 5500 : [ 23 0.00 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 814 0.15 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1273 0.24 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1187 0.22 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 899 0.17 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 775 0.14 0.95 ]
|XXXXXXXX 8000 - 8500 : [ 248 0.05 0.99 ]
|X 8500 - 9000 : [ 21 0.00 1.00 ]
| 9000 - 9500 : [ 5 0.00 1.00 ]
| 9500 - 10000 : [ 1 0.00 1.00 ]
| 10000 - 10500 : [ 10 0.00 1.00 ]
| 10500 - 11000 : [ 6 0.00 1.00 ]
#...
| 136500 - 137000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIGB reads.list > grep.reads.list.AIGB
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIGB 4 500
-------------------------------------------------------------------
#Found 953 total values totalling 37026245.0000. <38852.303253 +/- 3495.683167>
#Range: [ 21037 - 46824 ]
#Most likely bin: [ 37500 - 38000 ] 69 counts
#Median bin: [ 38500 - 39000 ] 46 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 21000 - 21500 : [ 1 0.00 0.00 ]
#...
|X 23500 - 24000 : [ 1 0.00 0.00 ]
#...
|X 27000 - 27500 : [ 1 0.00 0.00 ]
|X 27500 - 28000 : [ 1 0.00 0.00 ]
#...
|XX 29500 - 30000 : [ 3 0.00 0.01 ]
#...
|XX 30500 - 31000 : [ 3 0.00 0.01 ]
|XXXX 31000 - 31500 : [ 7 0.01 0.02 ]
|XXX 31500 - 32000 : [ 5 0.01 0.02 ]
|XXXXX 32000 - 32500 : [ 9 0.01 0.03 ]
|XXXXXX 32500 - 33000 : [ 10 0.01 0.04 ]
|XXXXXXXXX 33000 - 33500 : [ 15 0.02 0.06 ]
|XXXXXXXXXXXX 33500 - 34000 : [ 20 0.02 0.08 ]
|XXXXXXXXXXXXXX 34000 - 34500 : [ 24 0.03 0.10 ]
|XXXXXXXXXXXXXXXX 34500 - 35000 : [ 27 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 32 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 38 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 45 0.05 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 39 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 46 0.05 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 69 0.07 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 52 0.05 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 46 0.05 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 47 0.05 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 56 0.06 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 45 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 45 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 48 0.05 0.77 ]
|XXXXXXXXXXXXXXXXX 41500 - 42000 : [ 30 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 35 0.04 0.84 ]
|XXXXXXXXXXXXXXXX 42500 - 43000 : [ 27 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 34 0.04 0.90 ]
|XXXXXXXXXXXXX 43500 - 44000 : [ 23 0.02 0.93 ]
|XXXXXXXXXX 44000 - 44500 : [ 18 0.02 0.95 ]
|XXXXXXXXX 44500 - 45000 : [ 16 0.02 0.96 ]
|XXXXXXXXXXXXX 45000 - 45500 : [ 22 0.02 0.99 ]
|XX 45500 - 46000 : [ 4 0.00 0.99 ]
|XXX 46000 - 46500 : [ 6 0.01 1.00 ]
|XX 46500 - 47000 : [ 3 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIGA 6733 +- 872 (n=5254)
# AHYO 3338 +- 428 (n=6220)
# AIGB 38860 +- 3354 (n=756)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634478_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
AHYO 15360 94 762 97 759 14181 99 733 100 747
AIGA 16128 81 728 93 667 13070 100 729 100 725
AIGB 7680 79 548 87 488 6307 95 564 100 583
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHYO 7132 99 729 100 749 7049 99 737 100 745
AIGA 6527 100 734 100 731 6543 100 723 100 720
AIGB 3148 95 556 100 574 3159 95 571 100 592
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634478_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
84 13070 6620 78.81 82.09 AIGA @
80 14181 7241 90.51 94.28 AHYO @
40 6307 3410 85.25 88.80 AIGB @
] 33558 17271 84.66 cumulative total@@
LIBRARY PLATE ID COUNT [ AIGA 84 AHYO 80 AIGB 40 ] for 204 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 3634478_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 33558 total values totalling 23211035.0000. <691.669200 +/- 182.702007>
#Range: [ 15 - 977 ]
#Most likely bin: [ 750 - 800 ] 7885 counts
#Median bin: [ 750 - 800 ] 7885 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 151 0.00 0.00 ]
|XX 50 - 100 : [ 320 0.01 0.01 ]
|XX 100 - 150 : [ 360 0.01 0.02 ]
|XX 150 - 200 : [ 366 0.01 0.04 ]
|XX 200 - 250 : [ 413 0.01 0.05 ]
|XX 250 - 300 : [ 492 0.01 0.06 ]
|XXX 300 - 350 : [ 586 0.02 0.08 ]
|XXX 350 - 400 : [ 629 0.02 0.10 ]
|XXX 400 - 450 : [ 592 0.02 0.12 ]
|XXXX 450 - 500 : [ 712 0.02 0.14 ]
|XXXX 500 - 550 : [ 868 0.03 0.16 ]
|XXXXXX 550 - 600 : [ 1177 0.04 0.20 ]
|XXXXXXXX 600 - 650 : [ 1665 0.05 0.25 ]
|XXXXXXXXXXXXXX 650 - 700 : [ 2803 0.08 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4747 0.14 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 7885 0.23 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7108 0.21 0.92 ]
|XXXXXXXXXXXX 850 - 900 : [ 2341 0.07 0.99 ]
|XX 900 - 950 : [ 328 0.01 1.00 ]
| 950 - 1000 : [ 15 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYO 3634478_fasta.screen.trimQ15.SaF > reads.trim15.AHYO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYO.rl 2 50
-------------------------------------------------------------------
#Found 14181 total values totalling 10305922.0000. <726.741556 +/- 164.665775>
#Range: [ 21 - 977 ]
#Most likely bin: [ 800 - 850 ] 3619 counts
#Median bin: [ 750 - 800 ] 3248 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 38 0.00 0.00 ]
|X 50 - 100 : [ 94 0.01 0.01 ]
|X 100 - 150 : [ 110 0.01 0.02 ]
|X 150 - 200 : [ 122 0.01 0.03 ]
|X 200 - 250 : [ 123 0.01 0.03 ]
|X 250 - 300 : [ 106 0.01 0.04 ]
|XX 300 - 350 : [ 150 0.01 0.05 ]
|XX 350 - 400 : [ 160 0.01 0.06 ]
|XX 400 - 450 : [ 191 0.01 0.08 ]
|XXX 450 - 500 : [ 246 0.02 0.09 ]
|XXX 500 - 550 : [ 297 0.02 0.12 ]
|XXXXX 550 - 600 : [ 436 0.03 0.15 ]
|XXXXXXX 600 - 650 : [ 591 0.04 0.19 ]
|XXXXXXXXXXX 650 - 700 : [ 1002 0.07 0.26 ]
|XXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1715 0.12 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3248 0.23 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3619 0.26 0.86 ]
|XXXXXXXXXXXXXXXXXX 850 - 900 : [ 1604 0.11 0.98 ]
|XXX 900 - 950 : [ 314 0.02 1.00 ]
| 950 - 1000 : [ 15 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIGA
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIGA 3634478_fasta.screen.trimQ15.SaF > reads.trim15.AIGA.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIGA.rl 2 50
-------------------------------------------------------------------
#Found 13070 total values totalling 9505868.0000. <727.304361 +/- 136.806035>
#Range: [ 31 - 928 ]
#Most likely bin: [ 750 - 800 ] 4005 counts
#Median bin: [ 750 - 800 ] 4005 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 7 0.00 0.00 ]
| 50 - 100 : [ 22 0.00 0.00 ]
| 100 - 150 : [ 50 0.00 0.01 ]
|X 150 - 200 : [ 71 0.01 0.01 ]
|X 200 - 250 : [ 99 0.01 0.02 ]
|X 250 - 300 : [ 108 0.01 0.03 ]
|X 300 - 350 : [ 142 0.01 0.04 ]
|XX 350 - 400 : [ 173 0.01 0.05 ]
|XX 400 - 450 : [ 159 0.01 0.06 ]
|XX 450 - 500 : [ 188 0.01 0.08 ]
|XX 500 - 550 : [ 220 0.02 0.09 ]
|XXX 550 - 600 : [ 262 0.02 0.11 ]
|XXXXX 600 - 650 : [ 458 0.04 0.15 ]
|XXXXXXXXXX 650 - 700 : [ 1028 0.08 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2256 0.17 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4005 0.31 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3141 0.24 0.95 ]
|XXXXXXX 850 - 900 : [ 670 0.05 1.00 ]
| 900 - 950 : [ 11 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIGB
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIGB 3634478_fasta.screen.trimQ15.SaF > reads.trim15.AIGB.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIGB.rl 2 50
-------------------------------------------------------------------
#Found 6307 total values totalling 3399245.0000. <538.963850 +/- 221.673905>
#Range: [ 15 - 921 ]
#Most likely bin: [ 700 - 750 ] 776 counts
#Median bin: [ 600 - 650 ] 616 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 0 - 50 : [ 106 0.02 0.02 ]
|XXXXXXXXXXX 50 - 100 : [ 204 0.03 0.05 ]
|XXXXXXXXXX 100 - 150 : [ 200 0.03 0.08 ]
|XXXXXXXXX 150 - 200 : [ 173 0.03 0.11 ]
|XXXXXXXXXX 200 - 250 : [ 191 0.03 0.14 ]
|XXXXXXXXXXXXXX 250 - 300 : [ 278 0.04 0.18 ]
|XXXXXXXXXXXXXXX 300 - 350 : [ 294 0.05 0.23 ]
|XXXXXXXXXXXXXXX 350 - 400 : [ 296 0.05 0.28 ]
|XXXXXXXXXXXX 400 - 450 : [ 242 0.04 0.31 ]
|XXXXXXXXXXXXXX 450 - 500 : [ 278 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXX 500 - 550 : [ 351 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 479 0.08 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 616 0.10 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 773 0.12 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 776 0.12 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 632 0.10 0.93 ]
|XXXXXXXXXXXXXXXXXX 800 - 850 : [ 348 0.06 0.99 ]
|XXX 850 - 900 : [ 67 0.01 1.00 ]
| 900 - 950 : [ 3 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AWZG
trimt JAZZ trim 15 readlength histogram for AWZH
trimt JAZZ trim 15 readlength histogram for AWZI
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634478
-------------------------------------------------------------------
AHYO.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHYO.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AHYP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIGA.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIGB.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AHYO.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHYO.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AHYP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIGA.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIGB.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634478_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634478_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 33427 total values totalling 14925.5915. <0.446513 +/- 0.051352>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.44 - 0.445 ] 1442 counts
#Median bin: [ 0.445 - 0.45 ] 1363 counts
#Entropy = 5.3807 bits
| 0 - 0.005 : [ 1 2.99e-05 2.99e-05 ]
#...
| 0.165 - 0.17 : [ 1 2.99e-05 5.98e-05 ]
| 0.17 - 0.175 : [ 1 2.99e-05 8.97e-05 ]
#...
| 0.2 - 0.205 : [ 2 5.98e-05 1.50e-04 ]
#...
| 0.215 - 0.22 : [ 1 2.99e-05 1.79e-04 ]
| 0.22 - 0.225 : [ 1 2.99e-05 2.09e-04 ]
| 0.225 - 0.23 : [ 6 1.79e-04 3.89e-04 ]
| 0.23 - 0.235 : [ 2 5.98e-05 4.49e-04 ]
| 0.235 - 0.24 : [ 2 5.98e-05 5.09e-04 ]
| 0.24 - 0.245 : [ 7 2.09e-04 7.18e-04 ]
| 0.245 - 0.25 : [ 8 2.39e-04 9.57e-04 ]
| 0.25 - 0.255 : [ 12 3.59e-04 1.32e-03 ]
| 0.255 - 0.26 : [ 8 2.39e-04 1.56e-03 ]
| 0.26 - 0.265 : [ 8 2.39e-04 1.79e-03 ]
| 0.265 - 0.27 : [ 15 4.49e-04 2.24e-03 ]
|X 0.27 - 0.275 : [ 22 6.58e-04 2.90e-03 ]
| 0.275 - 0.28 : [ 18 5.38e-04 3.44e-03 ]
|X 0.28 - 0.285 : [ 19 5.68e-04 4.01e-03 ]
|X 0.285 - 0.29 : [ 27 8.08e-04 4.82e-03 ]
|X 0.29 - 0.295 : [ 29 8.68e-04 5.68e-03 ]
|X 0.295 - 0.3 : [ 41 1.23e-03 6.91e-03 ]
|X 0.3 - 0.305 : [ 54 1.62e-03 8.53e-03 ]
|XX 0.305 - 0.31 : [ 60 1.79e-03 1.03e-02 ]
|XX 0.31 - 0.315 : [ 56 1.68e-03 1.20e-02 ]
|XX 0.315 - 0.32 : [ 65 1.94e-03 1.39e-02 ]
|XX 0.32 - 0.325 : [ 74 2.21e-03 1.62e-02 ]
|XX 0.325 - 0.33 : [ 76 2.27e-03 1.84e-02 ]
|XXX 0.33 - 0.335 : [ 111 3.32e-03 2.17e-02 ]
|XXXX 0.335 - 0.34 : [ 136 4.07e-03 2.58e-02 ]
|XXXX 0.34 - 0.345 : [ 139 4.16e-03 3.00e-02 ]
|XXXXX 0.345 - 0.35 : [ 175 5.24e-03 3.52e-02 ]
|XXXXXX 0.35 - 0.355 : [ 214 6.40e-03 4.16e-02 ]
|XXXXXXX 0.355 - 0.36 : [ 245 7.33e-03 4.89e-02 ]
|XXXXXXXXX 0.36 - 0.365 : [ 309 9.24e-03 5.82e-02 ]
|XXXXXXXXX 0.365 - 0.37 : [ 321 9.60e-03 6.78e-02 ]
|XXXXXXXXXX 0.37 - 0.375 : [ 371 1.11e-02 7.89e-02 ]
|XXXXXXXXXXXX 0.375 - 0.38 : [ 417 1.25e-02 9.14e-02 ]
|XXXXXXXXXXXXX 0.38 - 0.385 : [ 464 1.39e-02 1.05e-01 ]
|XXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 578 1.73e-02 1.23e-01 ]
|XXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 625 1.87e-02 1.41e-01 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 784 2.35e-02 1.65e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 836 2.50e-02 1.90e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 946 2.83e-02 2.18e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 1056 3.16e-02 2.50e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 1134 3.39e-02 2.84e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 1179 3.53e-02 3.19e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 1226 3.67e-02 3.55e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 1316 3.94e-02 3.95e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 1308 3.91e-02 4.34e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 1442 4.31e-02 4.77e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 1363 4.08e-02 5.18e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 1319 3.95e-02 5.57e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 1331 3.98e-02 5.97e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 1312 3.92e-02 6.36e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 1338 4.00e-02 6.76e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 1178 3.52e-02 7.12e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 1178 3.52e-02 7.47e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 1109 3.32e-02 7.80e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 953 2.85e-02 8.09e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 953 2.85e-02 8.37e-01 ]
|XXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 723 2.16e-02 8.59e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 812 2.43e-02 8.83e-01 ]
|XXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 699 2.09e-02 9.04e-01 ]
|XXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 561 1.68e-02 9.21e-01 ]
|XXXXXXXXXXXXXX 0.515 - 0.52 : [ 492 1.47e-02 9.35e-01 ]
|XXXXXXXXXXXX 0.52 - 0.525 : [ 416 1.24e-02 9.48e-01 ]
|XXXXXXXXXX 0.525 - 0.53 : [ 356 1.07e-02 9.59e-01 ]
|XXXXXXXX 0.53 - 0.535 : [ 273 8.17e-03 9.67e-01 ]
|XXXXXXX 0.535 - 0.54 : [ 238 7.12e-03 9.74e-01 ]
|XXXXX 0.54 - 0.545 : [ 193 5.77e-03 9.80e-01 ]
|XXXX 0.545 - 0.55 : [ 154 4.61e-03 9.84e-01 ]
|XXXX 0.55 - 0.555 : [ 140 4.19e-03 9.88e-01 ]
|XX 0.555 - 0.56 : [ 89 2.66e-03 9.91e-01 ]
|XX 0.56 - 0.565 : [ 69 2.06e-03 9.93e-01 ]
|XX 0.565 - 0.57 : [ 55 1.65e-03 9.95e-01 ]
|X 0.57 - 0.575 : [ 25 7.48e-04 9.96e-01 ]
|X 0.575 - 0.58 : [ 32 9.57e-04 9.96e-01 ]
|X 0.58 - 0.585 : [ 22 6.58e-04 9.97e-01 ]
| 0.585 - 0.59 : [ 13 3.89e-04 9.98e-01 ]
| 0.59 - 0.595 : [ 9 2.69e-04 9.98e-01 ]
| 0.595 - 0.6 : [ 3 8.97e-05 9.98e-01 ]
| 0.6 - 0.605 : [ 11 3.29e-04 9.98e-01 ]
| 0.605 - 0.61 : [ 9 2.69e-04 9.98e-01 ]
| 0.61 - 0.615 : [ 5 1.50e-04 9.99e-01 ]
| 0.615 - 0.62 : [ 4 1.20e-04 9.99e-01 ]
| 0.62 - 0.625 : [ 2 5.98e-05 9.99e-01 ]
| 0.625 - 0.63 : [ 6 1.79e-04 9.99e-01 ]
| 0.63 - 0.635 : [ 3 8.97e-05 9.99e-01 ]
| 0.635 - 0.64 : [ 1 2.99e-05 9.99e-01 ]
| 0.64 - 0.645 : [ 3 8.97e-05 9.99e-01 ]
| 0.645 - 0.65 : [ 2 5.98e-05 9.99e-01 ]
| 0.65 - 0.655 : [ 4 1.20e-04 9.99e-01 ]
| 0.655 - 0.66 : [ 3 8.97e-05 9.99e-01 ]
| 0.66 - 0.665 : [ 1 2.99e-05 9.99e-01 ]
| 0.665 - 0.67 : [ 1 2.99e-05 1.00e+00 ]
#...
| 0.675 - 0.68 : [ 2 5.98e-05 1.00e+00 ]
#...
| 0.685 - 0.69 : [ 1 2.99e-05 1.00e+00 ]
#...
| 0.695 - 0.7 : [ 1 2.99e-05 1.00e+00 ]
| 0.7 - 0.705 : [ 2 5.98e-05 1.00e+00 ]
| 0.705 - 0.71 : [ 1 2.99e-05 1.00e+00 ]
#...
| 0.715 - 0.72 : [ 2 5.98e-05 1.00e+00 ]
#...
| 0.735 - 0.74 : [ 2 5.98e-05 1.00e+00 ]
#...
| 0.75 - 0.755 : [ 1 2.99e-05 1.00e+00 ]
#...
| 0.76 - 0.765 : [ 1 2.99e-05 1.00e+00 ]
#...
| 0.84 - 0.845 : [ 1 2.99e-05 1.00e+00 ]
#...
| 1 - 1.005 : [ 2 5.98e-05 1.00e+00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 219. 409 reads; 32998 bp (untrimmed), 32693 (trimmed).
Contig 220. 432 reads; 40081 bp (untrimmed), 39950 (trimmed).
Contig 221. 432 reads; 40687 bp (untrimmed), 40318 (trimmed).
Contig 222. 439 reads; 26618 bp (untrimmed), 26458 (trimmed).
Contig 223. 452 reads; 34490 bp (untrimmed), 34455 (trimmed).
Contig 224. 455 reads; 43472 bp (untrimmed), 43324 (trimmed).
Contig 225. 479 reads; 32862 bp (untrimmed), 32747 (trimmed).
Contig 226. 507 reads; 30692 bp (untrimmed), 30597 (trimmed).
Contig 227. 549 reads; 55726 bp (untrimmed), 55601 (trimmed).
Contig 228. 552 reads; 46170 bp (untrimmed), 46109 (trimmed).
Contig 229. 574 reads; 37540 bp (untrimmed), 37076 (trimmed).
Contig 230. 589 reads; 54708 bp (untrimmed), 54183 (trimmed).
Contig 231. 621 reads; 55625 bp (untrimmed), 55529 (trimmed).
Contig 232. 639 reads; 54994 bp (untrimmed), 54624 (trimmed).
Contig 233. 678 reads; 68854 bp (untrimmed), 68349 (trimmed).
Contig 234. 725 reads; 60437 bp (untrimmed), 60241 (trimmed).
Contig 235. 733 reads; 60914 bp (untrimmed), 60754 (trimmed).
Contig 236. 757 reads; 60988 bp (untrimmed), 60748 (trimmed).
Contig 237. 775 reads; 52650 bp (untrimmed), 52154 (trimmed).
Contig 238. 782 reads; 65448 bp (untrimmed), 65066 (trimmed).
Contig 239. 941 reads; 76845 bp (untrimmed), 76757 (trimmed).
Contig 240. 1104 reads; 79107 bp (untrimmed), 78999 (trimmed).
Contig 241. 1164 reads; 87756 bp (untrimmed), 87582 (trimmed).
Contig 242. 1269 reads; 83992 bp (untrimmed), 83803 (trimmed).
Contig 243. 1299 reads; 101882 bp (untrimmed), 101646 (trimmed).
Contig 244. 1301 reads; 87660 bp (untrimmed), 87433 (trimmed).
Contig 245. 1365 reads; 88146 bp (untrimmed), 87858 (trimmed).
--------------------------------------------------------------
Totals 33238 reads; 2992560 bp (untrimmed), 2910698 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2920906 bases = 9.68 +- 4.97 = 0.17 +- 4.01
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 170 total values totalling 1151.8300. <6.775471 +/- 3.580697>
#Range: [ 1.14 - 14.19 ]
#Most likely bin: [ 2 - 2.5 ] 13 counts
#Median bin: [ 6.5 - 7 ] 8 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 8 0.05 0.05 ]
|XXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 6 0.04 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 13 0.08 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 10 0.06 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 10 0.06 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 8 0.05 0.32 ]
|XXXXXXXXXXXX 4 - 4.5 : [ 4 0.02 0.35 ]
|XXXXXXXXXXXX 4.5 - 5 : [ 4 0.02 0.37 ]
|XXXXXXXXX 5 - 5.5 : [ 3 0.02 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 9 0.05 0.44 ]
|XXXXXX 6 - 6.5 : [ 2 0.01 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 8 0.05 0.50 ]
|XXXXXX 7 - 7.5 : [ 2 0.01 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 10 0.06 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 8 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 10 0.06 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 9 0.05 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 7 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 11 0.06 0.84 ]
|XXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 6 0.04 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 7 0.04 0.91 ]
|XXXXXXXXXXXXXXX 11.5 - 12 : [ 5 0.03 0.94 ]
|XXXXXX 12 - 12.5 : [ 2 0.01 0.95 ]
|XXXXXXXXX 12.5 - 13 : [ 3 0.02 0.97 ]
|XXXXXX 13 - 13.5 : [ 2 0.01 0.98 ]
|XXX 13.5 - 14 : [ 1 0.01 0.99 ]
|XXXXXX 14 - 14.5 : [ 2 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 122 total values totalling 1021.0100. <8.368934 +/- 2.810738>
#Range: [ 3.07 - 14.19 ]
#Most likely bin: [ 10 - 10.5 ] 11 counts
#Median bin: [ 8.5 - 9 ] 10 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 6 0.05 0.05 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 7 0.06 0.11 ]
|XXXXXXXXXXX 4 - 4.5 : [ 3 0.02 0.13 ]
|XXXXXXXXXXX 4.5 - 5 : [ 3 0.02 0.16 ]
|XXXXXXXXXXX 5 - 5.5 : [ 3 0.02 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 8 0.07 0.25 ]
|XXXXXXX 6 - 6.5 : [ 2 0.02 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 6 0.05 0.31 ]
|XXXXXXX 7 - 7.5 : [ 2 0.02 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 10 0.08 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 8 0.07 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 10 0.08 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 8 0.07 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 7 0.06 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 11 0.09 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 6 0.05 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 7 0.06 0.88 ]
|XXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 5 0.04 0.92 ]
|XXXXXXX 12 - 12.5 : [ 2 0.02 0.93 ]
|XXXXXXXXXXX 12.5 - 13 : [ 3 0.02 0.96 ]
|XXXXXXX 13 - 13.5 : [ 2 0.02 0.98 ]
|XXXX 13.5 - 14 : [ 1 0.01 0.98 ]
|XXXXXXX 14 - 14.5 : [ 2 0.02 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 83 2 reads 1363 bases = 1.14 +- 0.35 = 0.29 +- 0.88
Contig 78 2 reads 1221 bases = 1.18 +- 0.39 = 1.18 +- 0.39
Contig 76 2 reads 954 bases = 1.21 +- 0.41 = 1.21 +- 0.41
Contig 82 2 reads 950 bases = 1.23 +- 0.42 = 1.23 +- 0.42
Contig 80 2 reads 1042 bases = 1.27 +- 0.44 = 1.27 +- 0.44
Contig 88 3 reads 2169 bases = 1.30 +- 0.46 = 1.30 +- 0.46
Contig 87 3 reads 1053 bases = 1.32 +- 0.49 = 0.70 +- 0.46
Contig 79 2 reads 1428 bases = 1.41 +- 0.49 = 0.00 +- 0.77
Contig 85 3 reads 1434 bases = 1.61 +- 0.64 = 0.33 +- 0.68
Contig 89 3 reads 1741 bases = 1.61 +- 0.64 = 0.57 +- 1.32
Contig 81 2 reads 725 bases = 1.82 +- 0.38 = 0.18 +- 0.38
Contig 95 4 reads 1476 bases = 1.82 +- 0.68 = 0.63 +- 0.98
Contig 90 3 reads 1537 bases = 1.89 +- 0.78 = 1.89 +- 0.78
Contig 77 2 reads 958 bases = 1.90 +- 0.30 = 1.90 +- 0.30
Contig 84 3 reads 1261 bases = 2.08 +- 0.91 = 1.07 +- 0.40
Contig 101 5 reads 2130 bases = 2.10 +- 0.87 = 1.30 +- 1.55
Contig 116 8 reads 3047 bases = 2.16 +- 0.81 = -0.25 +- 1.32
Contig 96 4 reads 1451 bases = 2.16 +- 1.02 = 0.38 +- 1.14
Contig 115 8 reads 2385 bases = 2.18 +- 0.75 = 1.63 +- 0.95
Contig 92 4 reads 1523 bases = 2.23 +- 1.22 = 1.05 +- 0.65
Contig 193 210 reads 15990 bases = 11.20 +- 4.37 = 0.13 +- 3.58
Contig 144 27 reads 2033 bases = 11.21 +- 8.07 = 1.99 +- 2.71
Contig 208 320 reads 24708 bases = 11.37 +- 4.65 = -0.51 +- 3.68
Contig 188 188 reads 14111 bases = 11.39 +- 4.97 = 0.60 +- 3.65
Contig 241 1164 reads 87756 bases = 11.44 +- 4.40 = 0.15 +- 4.32
Contig 218 405 reads 29220 bases = 11.71 +- 4.46 = 1.63 +- 4.86
Contig 186 183 reads 13374 bases = 11.73 +- 4.18 = 1.14 +- 4.12
Contig 240 1104 reads 79107 bases = 11.75 +- 4.47 = 0.32 +- 4.31
Contig 212 336 reads 24546 bases = 11.85 +- 3.88 = 0.81 +- 3.10
Contig 175 111 reads 8195 bases = 11.99 +- 16.36 = 3.06 +- 4.01
Contig 214 347 reads 24703 bases = 12.03 +- 4.42 = -1.30 +- 3.81
Contig 237 775 reads 52650 bases = 12.33 +- 4.57 = -0.07 +- 4.40
Contig 225 479 reads 32862 bases = 12.64 +- 4.19 = -0.88 +- 3.59
Contig 244 1301 reads 87660 bases = 12.78 +- 4.12 = 0.43 +- 4.30
Contig 245 1365 reads 88146 bases = 12.92 +- 4.71 = -0.44 +- 4.25
Contig 242 1269 reads 83992 bases = 13.00 +- 4.44 = 0.12 +- 4.87
Contig 229 574 reads 37540 bases = 13.02 +- 4.72 = -0.36 +- 4.63
Contig 174 105 reads 6612 bases = 13.57 +- 8.37 = -5.52 +- 3.46
Contig 222 439 reads 26618 bases = 14.11 +- 4.23 = -0.36 +- 3.35
Contig 226 507 reads 30692 bases = 14.19 +- 7.42 = -0.58 +- 3.90
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1280
HQ Discrepant reads = 28
Chimeric reads = 13
Suspect alignments = 468
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 4.18 SUN Solaris 7,8
Score matrix /psf/QC/Applications/pphrap/matrix/score_matrix.8
A C G T N X
A 1 -8 -8 -8 0 0
C -8 1 -8 -8 0 0
G -8 -8 1 -8 0 0
T -8 -8 -8 1 0 0
N 0 0 0 0 0 0
X 0 0 0 0 0 0
gap_init: -10
gap_ext: -9
ins_gap_ext: -9
del_gap_ext: -9
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 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
File generated in /psf/project/microbe4/3634478/edit_dir.14Jul05.QD