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
3634605 4500 62322 Shewanella baltica
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Shewanella_baltica
-------------------------------------------------------------------
Shewanellaceae, family, g-proteobacteria
Alteromonadales, order, g-proteobacteria
Shewanella baltica, species, g-proteobacteria
Shewanella, genus, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 5044127
# phrap: 4721774
# db:
altered.
4500000
4755300 +/- 223400
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 12397
Number of reads with percent X's >= 20%: 662 = 1.0%
Number of reads with percent X's >= 50%: 453 = 0.7%
Number of reads with percent X's >= 80%: 21 = 0.0%
Total reads in project: 66447
Total bp X'd : 813831
reads >= 20% >= 50% >= 80% screened
Nr with L09136 11585 560 416 19
Nr with pCC1Fos 654 49 7 0
Nr with pMCL200_JGI_XZX+XZK 158 53 30 2
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 15
Number of reads with percent X's >= 20%: 3 = 6.2%
Number of reads with percent X's >= 50%: 2 = 4.2%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 48
Total bp X'd : 1889
reads >= 20% >= 50% >= 80% screened
Nr with L09136 8 2 1 0
Nr with pCC1Fos 6 0 0 0
Nr with pMCL200_JGI_XZX+XZK 1 1 1 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 16898981
C = 14365865
G = 14433648
T = 16339137
N = 342404
X = 813831
GC fraction = 0.46
Total = 63193866
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634605_fasta.screen.contigs
-------------------------------------------------------------------
A 1363969
C 1180954
G 1170519
T 1368506
N 370
fraction GC = 0.46
total bases = 5084318
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 AIOC reads.list > grep.reads.list.AIOC
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOC 4 500
-------------------------------------------------------------------
#Found 11594 total values totalling 38876437.0000. <3353.151371 +/- 876.737864>
#Range: [ 190 - 51509 ]
#Most likely bin: [ 3000 - 3500 ] 5471 counts
#Median bin: [ 3000 - 3500 ] 5471 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
| 500 - 1000 : [ 14 0.00 0.00 ]
| 1000 - 1500 : [ 54 0.00 0.01 ]
|X 1500 - 2000 : [ 77 0.01 0.01 ]
|XX 2000 - 2500 : [ 286 0.02 0.04 ]
|XXXXXXXXXXX 2500 - 3000 : [ 1555 0.13 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 5471 0.47 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3583 0.31 0.95 ]
|XXXX 4000 - 4500 : [ 536 0.05 1.00 ]
| 4500 - 5000 : [ 6 0.00 1.00 ]
#...
| 8000 - 8500 : [ 1 0.00 1.00 ]
#...
| 15500 - 16000 : [ 1 0.00 1.00 ]
#...
| 19000 - 19500 : [ 2 0.00 1.00 ]
#...
| 21500 - 22000 : [ 1 0.00 1.00 ]
| 22000 - 22500 : [ 2 0.00 1.00 ]
#...
| 24000 - 24500 : [ 1 0.00 1.00 ]
#...
| 33000 - 33500 : [ 1 0.00 1.00 ]
#...
| 38000 - 38500 : [ 1 0.00 1.00 ]
#...
| 51500 - 52000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOF reads.list > grep.reads.list.AIOF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOF 4 500
-------------------------------------------------------------------
#Found 11560 total values totalling 84016682.0000. <7267.879066 +/- 1806.674151>
#Range: [ 988 - 101692 ]
#Most likely bin: [ 7000 - 7500 ] 3098 counts
#Median bin: [ 7000 - 7500 ] 3098 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 14 0.00 0.00 ]
| 1500 - 2000 : [ 20 0.00 0.00 ]
| 2000 - 2500 : [ 20 0.00 0.00 ]
| 2500 - 3000 : [ 20 0.00 0.01 ]
| 3000 - 3500 : [ 23 0.00 0.01 ]
| 3500 - 4000 : [ 22 0.00 0.01 ]
| 4000 - 4500 : [ 12 0.00 0.01 ]
| 4500 - 5000 : [ 16 0.00 0.01 ]
|X 5000 - 5500 : [ 54 0.00 0.02 ]
|XXXX 5500 - 6000 : [ 297 0.03 0.04 ]
|XXXXXXXXXXX 6000 - 6500 : [ 852 0.07 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2766 0.24 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 3098 0.27 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 2535 0.22 0.84 ]
|XXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1523 0.13 0.98 ]
|XXXX 8500 - 9000 : [ 278 0.02 1.00 ]
#...
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 14500 - 15000 : [ 1 0.00 1.00 ]
#...
| 23500 - 24000 : [ 1 0.00 1.00 ]
#...
| 32500 - 33000 : [ 1 0.00 1.00 ]
#...
| 41500 - 42000 : [ 1 0.00 1.00 ]
| 42000 - 42500 : [ 1 0.00 1.00 ]
#...
| 100500 - 101000 : [ 1 0.00 1.00 ]
#...
| 101500 - 102000 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOG reads.list > grep.reads.list.AIOG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOG 4 500
-------------------------------------------------------------------
#Found 352 total values totalling 13225959.0000. <37573.747159 +/- 6480.111024>
#Range: [ 19734 - 136032 ]
#Most likely bin: [ 36500 - 37000 ] 21 counts
#Median bin: [ 37000 - 37500 ] 17 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 19500 - 20000 : [ 1 0.00 0.00 ]
#...
|XX 26500 - 27000 : [ 1 0.00 0.01 ]
|XX 27000 - 27500 : [ 1 0.00 0.01 ]
#...
|XX 28500 - 29000 : [ 1 0.00 0.01 ]
|XX 29000 - 29500 : [ 1 0.00 0.01 ]
|XXXX 29500 - 30000 : [ 2 0.01 0.02 ]
|XXXX 30000 - 30500 : [ 2 0.01 0.03 ]
|XXXXXXXXXX 30500 - 31000 : [ 5 0.01 0.04 ]
|XXXX 31000 - 31500 : [ 2 0.01 0.05 ]
|XXXXXXXXXXXXX 31500 - 32000 : [ 7 0.02 0.07 ]
|XXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 11 0.03 0.10 ]
|XXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 10 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 12 0.03 0.16 ]
|XXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 10 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 19 0.05 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 16 0.05 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 14 0.04 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 17 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 17 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 21 0.06 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 17 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 19 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 12 0.03 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 17 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 15 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 12 0.03 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 19 0.05 0.80 ]
|XXXXXXXXXXX 40500 - 41000 : [ 6 0.02 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 14 0.04 0.86 ]
|XXXXXXXXXXXXXXXXX 41500 - 42000 : [ 9 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 12 0.03 0.91 ]
|XXXXXXXX 42500 - 43000 : [ 4 0.01 0.93 ]
|XXXXXXXXXXX 43000 - 43500 : [ 6 0.02 0.94 ]
|XXXXXXXXXXXXX 43500 - 44000 : [ 7 0.02 0.96 ]
|XXXXXXXX 44000 - 44500 : [ 4 0.01 0.97 ]
|XXXXXXXXXX 44500 - 45000 : [ 5 0.01 0.99 ]
|XX 45000 - 45500 : [ 1 0.00 0.99 ]
#...
|XX 46000 - 46500 : [ 1 0.00 0.99 ]
|XX 46500 - 47000 : [ 1 0.00 1.00 ]
#...
|XX 136000 - 136500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIOG 37463 +- 3750 (n=173)
# AIOF 7170 +- 888 (n=5818)
# AIOC 3157 +- 927 (n=5972)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634605_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
AIOC 35712 -1 -1 95 603 35555 90 564 93 582
AIOF 33792 -1 -1 97 707 33792 91 734 97 726
AIOG 5376 -1 -1 79 386 5376 59 569 79 487
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIOC 17584 89 553 93 573 17971 91 575 94 591
AIOF 16896 91 731 98 723 16896 91 737 97 728
AIOG 2688 59 583 76 497 2688 60 556 81 477
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634605_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
180 32338 16562 92.01 95.84 AIOC @
176 30691 15510 88.12 91.80 AIOF @
28 3418 1974 70.50 73.44 AIOG @
] 66447 34046 88.66 cumulative total@@
LIBRARY PLATE ID COUNT [ AIOC 180 AIOF 176 AIOG 28 ] for 384 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 3634605_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 74723 total values totalling 42468605.0000. <568.347162 +/- 259.716456>
#Range: [ 0 - 978 ]
#Most likely bin: [ 750 - 800 ] 12013 counts
#Median bin: [ 650 - 700 ] 9319 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 7500 0.10 0.10 ]
|XXXXX 50 - 100 : [ 1499 0.02 0.12 ]
|XXXX 100 - 150 : [ 1124 0.02 0.14 ]
|XXX 150 - 200 : [ 981 0.01 0.15 ]
|XXXX 200 - 250 : [ 1221 0.02 0.16 ]
|XXXX 250 - 300 : [ 1178 0.02 0.18 ]
|XXXXX 300 - 350 : [ 1368 0.02 0.20 ]
|XXXXX 350 - 400 : [ 1603 0.02 0.22 ]
|XXXXXX 400 - 450 : [ 1952 0.03 0.25 ]
|XXXXXXX 450 - 500 : [ 2155 0.03 0.28 ]
|XXXXXXXXX 500 - 550 : [ 2698 0.04 0.31 ]
|XXXXXXXXXXXXX 550 - 600 : [ 3961 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 6265 0.08 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 9319 0.12 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 11547 0.15 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 12013 0.16 0.89 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7173 0.10 0.98 ]
|XXXX 850 - 900 : [ 1065 0.01 1.00 ]
| 900 - 950 : [ 99 0.00 1.00 ]
| 950 - 1000 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOC
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOC 3634605_fasta.screen.trimQ15.SaF > reads.trim15.AIOC.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOC.rl 2 50
-------------------------------------------------------------------
#Found 35555 total values totalling 18076907.0000. <508.420953 +/- 231.817432>
#Range: [ 0 - 978 ]
#Most likely bin: [ 650 - 700 ] 5903 counts
#Median bin: [ 550 - 600 ] 3168 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2779 0.08 0.08 ]
|XXXXXX 50 - 100 : [ 903 0.03 0.10 ]
|XXXXXX 100 - 150 : [ 854 0.02 0.13 ]
|XXXXX 150 - 200 : [ 783 0.02 0.15 ]
|XXXXXX 200 - 250 : [ 905 0.03 0.18 ]
|XXXXXX 250 - 300 : [ 905 0.03 0.20 ]
|XXXXXXX 300 - 350 : [ 1069 0.03 0.23 ]
|XXXXXXXXX 350 - 400 : [ 1261 0.04 0.27 ]
|XXXXXXXXXXX 400 - 450 : [ 1570 0.04 0.31 ]
|XXXXXXXXXXXX 450 - 500 : [ 1793 0.05 0.36 ]
|XXXXXXXXXXXXXXX 500 - 550 : [ 2207 0.06 0.42 ]
|XXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 3168 0.09 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 4703 0.13 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5903 0.17 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4581 0.13 0.94 ]
|XXXXXXXXXX 750 - 800 : [ 1511 0.04 0.98 ]
|XX 800 - 850 : [ 293 0.01 0.99 ]
|XX 850 - 900 : [ 271 0.01 1.00 ]
|X 900 - 950 : [ 94 0.00 1.00 ]
| 950 - 1000 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOF 3634605_fasta.screen.trimQ15.SaF > reads.trim15.AIOF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOF.rl 2 50
-------------------------------------------------------------------
#Found 33792 total values totalling 22521337.0000. <666.469490 +/- 236.737228>
#Range: [ 0 - 915 ]
#Most likely bin: [ 750 - 800 ] 10100 counts
#Median bin: [ 750 - 800 ] 10100 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXX 0 - 50 : [ 3029 0.09 0.09 ]
| 50 - 100 : [ 94 0.00 0.09 ]
| 100 - 150 : [ 94 0.00 0.10 ]
| 150 - 200 : [ 97 0.00 0.10 ]
|X 200 - 250 : [ 161 0.00 0.10 ]
|X 250 - 300 : [ 155 0.00 0.11 ]
|X 300 - 350 : [ 204 0.01 0.11 ]
|X 350 - 400 : [ 253 0.01 0.12 ]
|X 400 - 450 : [ 270 0.01 0.13 ]
|X 450 - 500 : [ 256 0.01 0.14 ]
|XX 500 - 550 : [ 379 0.01 0.15 ]
|XX 550 - 600 : [ 599 0.02 0.17 ]
|XXXXX 600 - 650 : [ 1224 0.04 0.20 ]
|XXXXXXXXXXXX 650 - 700 : [ 2941 0.09 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6410 0.19 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 10100 0.30 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6739 0.20 0.98 ]
|XXX 850 - 900 : [ 782 0.02 1.00 ]
| 900 - 950 : [ 5 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOG 3634605_fasta.screen.trimQ15.SaF > reads.trim15.AIOG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOG.rl 2 50
-------------------------------------------------------------------
#Found 5376 total values totalling 1870361.0000. <347.909412 +/- 311.438150>
#Range: [ 0 - 887 ]
#Most likely bin: [ 0 - 50 ] 1692 counts
#Median bin: [ 250 - 300 ] 118 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1692 0.31 0.31 ]
|XXXXXXXXXXXX 50 - 100 : [ 502 0.09 0.41 ]
|XXXX 100 - 150 : [ 176 0.03 0.44 ]
|XX 150 - 200 : [ 101 0.02 0.46 ]
|XXXX 200 - 250 : [ 155 0.03 0.49 ]
|XXX 250 - 300 : [ 118 0.02 0.51 ]
|XX 300 - 350 : [ 95 0.02 0.53 ]
|XX 350 - 400 : [ 89 0.02 0.54 ]
|XXX 400 - 450 : [ 112 0.02 0.57 ]
|XXX 450 - 500 : [ 106 0.02 0.59 ]
|XXX 500 - 550 : [ 112 0.02 0.61 ]
|XXXXX 550 - 600 : [ 194 0.04 0.64 ]
|XXXXXXXX 600 - 650 : [ 338 0.06 0.70 ]
|XXXXXXXXXXX 650 - 700 : [ 475 0.09 0.79 ]
|XXXXXXXXXXXXX 700 - 750 : [ 556 0.10 0.90 ]
|XXXXXXXXXX 750 - 800 : [ 402 0.07 0.97 ]
|XXX 800 - 850 : [ 141 0.03 1.00 ]
| 850 - 900 : [ 12 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATHA
trimt JAZZ trim 15 readlength histogram for AZPH
trimt JAZZ trim 15 readlength histogram for AZPI
trimt JAZZ trim 15 readlength histogram for AZPN
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634605
-------------------------------------------------------------------
AIOC.000001.000100 pUC18.fa LRS.fasta
AIOC.000101.000200 pUC18.fa LRS.fasta
AIOF.000001.000100 pMCL200.fa LRS.fasta
AIOF.000101.000200 pMCL200.fa LRS.fasta
AIOG.000001.000100 pCC1Fos.fa pMCL200.fa pCC1Fos.fa pMCL200.fa LRS.fasta
AIOC.000001.000100 pUC18.fa LRS.fasta
AIOC.000101.000200 pUC18.fa LRS.fasta
AIOF.000001.000100 pMCL200.fa LRS.fasta
AIOF.000101.000200 pMCL200.fa LRS.fasta
AIOG.000001.000100 pCC1Fos.fa pMCL200.fa pCC1Fos.fa pMCL200.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634605_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634605_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 66191 total values totalling 30466.7958. <0.460286 +/- 0.045733>
#Range: [ 0 - 0.84 ]
#Most likely bin: [ 0.48 - 0.485 ] 3227 counts
#Median bin: [ 0.465 - 0.47 ] 3134 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.12 - 0.125 : [ 1 0.00 0.00 ]
#...
| 0.165 - 0.17 : [ 2 0.00 0.00 ]
| 0.17 - 0.175 : [ 1 0.00 0.00 ]
#...
| 0.18 - 0.185 : [ 1 0.00 0.00 ]
#...
| 0.19 - 0.195 : [ 1 0.00 0.00 ]
#...
| 0.2 - 0.205 : [ 5 0.00 0.00 ]
| 0.205 - 0.21 : [ 2 0.00 0.00 ]
| 0.21 - 0.215 : [ 1 0.00 0.00 ]
#...
| 0.22 - 0.225 : [ 1 0.00 0.00 ]
| 0.225 - 0.23 : [ 6 0.00 0.00 ]
| 0.23 - 0.235 : [ 4 0.00 0.00 ]
| 0.235 - 0.24 : [ 1 0.00 0.00 ]
| 0.24 - 0.245 : [ 7 0.00 0.00 ]
| 0.245 - 0.25 : [ 4 0.00 0.00 ]
| 0.25 - 0.255 : [ 8 0.00 0.00 ]
| 0.255 - 0.26 : [ 15 0.00 0.00 ]
| 0.26 - 0.265 : [ 14 0.00 0.00 ]
| 0.265 - 0.27 : [ 18 0.00 0.00 ]
| 0.27 - 0.275 : [ 16 0.00 0.00 ]
| 0.275 - 0.28 : [ 11 0.00 0.00 ]
| 0.28 - 0.285 : [ 14 0.00 0.00 ]
| 0.285 - 0.29 : [ 22 0.00 0.00 ]
|X 0.29 - 0.295 : [ 44 0.00 0.00 ]
| 0.295 - 0.3 : [ 34 0.00 0.00 ]
|X 0.3 - 0.305 : [ 54 0.00 0.00 ]
|X 0.305 - 0.31 : [ 50 0.00 0.01 ]
|X 0.31 - 0.315 : [ 60 0.00 0.01 ]
|X 0.315 - 0.32 : [ 88 0.00 0.01 ]
|X 0.32 - 0.325 : [ 91 0.00 0.01 ]
|X 0.325 - 0.33 : [ 112 0.00 0.01 ]
|XX 0.33 - 0.335 : [ 150 0.00 0.01 ]
|XX 0.335 - 0.34 : [ 150 0.00 0.01 ]
|XX 0.34 - 0.345 : [ 174 0.00 0.02 ]
|XX 0.345 - 0.35 : [ 193 0.00 0.02 ]
|XXX 0.35 - 0.355 : [ 230 0.00 0.02 ]
|XXXX 0.355 - 0.36 : [ 287 0.00 0.03 ]
|XXXX 0.36 - 0.365 : [ 302 0.00 0.03 ]
|XXXX 0.365 - 0.37 : [ 338 0.01 0.04 ]
|XXXXX 0.37 - 0.375 : [ 375 0.01 0.04 ]
|XXXXXXX 0.375 - 0.38 : [ 530 0.01 0.05 ]
|XXXXXXXX 0.38 - 0.385 : [ 618 0.01 0.06 ]
|XXXXXXXX 0.385 - 0.39 : [ 646 0.01 0.07 ]
|XXXXXXXXX 0.39 - 0.395 : [ 744 0.01 0.08 ]
|XXXXXXXXXX 0.395 - 0.4 : [ 802 0.01 0.09 ]
|XXXXXXXXXXXXX 0.4 - 0.405 : [ 1043 0.02 0.11 ]
|XXXXXXXXXXXXXXX 0.405 - 0.41 : [ 1177 0.02 0.13 ]
|XXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 1323 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 1523 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 1686 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 2005 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 2060 0.03 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 2075 0.03 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 2383 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 2531 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 2951 0.04 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 2993 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 3069 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 3134 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 3146 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 3146 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 3227 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 2984 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 2905 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 2402 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 2533 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 2040 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1846 0.03 0.91 ]
|XXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1462 0.02 0.93 ]
|XXXXXXXXXXXXXX 0.52 - 0.525 : [ 1125 0.02 0.95 ]
|XXXXXXXXXXX 0.525 - 0.53 : [ 890 0.01 0.97 ]
|XXXXXXXX 0.53 - 0.535 : [ 624 0.01 0.97 ]
|XXXXXX 0.535 - 0.54 : [ 459 0.01 0.98 ]
|XXXX 0.54 - 0.545 : [ 305 0.00 0.99 ]
|XXX 0.545 - 0.55 : [ 230 0.00 0.99 ]
|XX 0.55 - 0.555 : [ 182 0.00 0.99 ]
|XX 0.555 - 0.56 : [ 131 0.00 0.99 ]
|X 0.56 - 0.565 : [ 85 0.00 1.00 ]
|X 0.565 - 0.57 : [ 63 0.00 1.00 ]
|X 0.57 - 0.575 : [ 49 0.00 1.00 ]
| 0.575 - 0.58 : [ 35 0.00 1.00 ]
| 0.58 - 0.585 : [ 21 0.00 1.00 ]
| 0.585 - 0.59 : [ 17 0.00 1.00 ]
| 0.59 - 0.595 : [ 16 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 : [ 9 0.00 1.00 ]
| 0.61 - 0.615 : [ 3 0.00 1.00 ]
| 0.615 - 0.62 : [ 9 0.00 1.00 ]
| 0.62 - 0.625 : [ 4 0.00 1.00 ]
| 0.625 - 0.63 : [ 9 0.00 1.00 ]
| 0.63 - 0.635 : [ 3 0.00 1.00 ]
| 0.635 - 0.64 : [ 4 0.00 1.00 ]
| 0.64 - 0.645 : [ 5 0.00 1.00 ]
| 0.645 - 0.65 : [ 4 0.00 1.00 ]
| 0.65 - 0.655 : [ 1 0.00 1.00 ]
| 0.655 - 0.66 : [ 2 0.00 1.00 ]
#...
| 0.665 - 0.67 : [ 5 0.00 1.00 ]
| 0.67 - 0.675 : [ 1 0.00 1.00 ]
| 0.675 - 0.68 : [ 1 0.00 1.00 ]
| 0.68 - 0.685 : [ 2 0.00 1.00 ]
#...
| 0.69 - 0.695 : [ 3 0.00 1.00 ]
| 0.695 - 0.7 : [ 1 0.00 1.00 ]
#...
| 0.715 - 0.72 : [ 2 0.00 1.00 ]
#...
| 0.77 - 0.775 : [ 1 0.00 1.00 ]
#...
| 0.79 - 0.795 : [ 1 0.00 1.00 ]
#...
| 0.84 - 0.845 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 224. 684 reads; 62123 bp (untrimmed), 62116 (trimmed).
Contig 225. 704 reads; 52714 bp (untrimmed), 52698 (trimmed).
Contig 226. 704 reads; 61077 bp (untrimmed), 60999 (trimmed).
Contig 227. 717 reads; 48132 bp (untrimmed), 48132 (trimmed).
Contig 228. 828 reads; 68290 bp (untrimmed), 68226 (trimmed).
Contig 229. 876 reads; 58771 bp (untrimmed), 58682 (trimmed).
Contig 230. 894 reads; 64277 bp (untrimmed), 64200 (trimmed).
Contig 231. 899 reads; 55607 bp (untrimmed), 55414 (trimmed).
Contig 232. 903 reads; 82051 bp (untrimmed), 81983 (trimmed).
Contig 233. 1144 reads; 87893 bp (untrimmed), 87587 (trimmed).
Contig 234. 1203 reads; 91434 bp (untrimmed), 91388 (trimmed).
Contig 235. 1267 reads; 102240 bp (untrimmed), 102158 (trimmed).
Contig 236. 1417 reads; 81600 bp (untrimmed), 81053 (trimmed).
Contig 237. 1431 reads; 28535 bp (untrimmed), 28482 (trimmed).
Contig 238. 1433 reads; 68427 bp (untrimmed), 68400 (trimmed).
Contig 239. 1453 reads; 118284 bp (untrimmed), 117863 (trimmed).
Contig 240. 1491 reads; 107961 bp (untrimmed), 107929 (trimmed).
Contig 241. 1510 reads; 104915 bp (untrimmed), 104846 (trimmed).
Contig 242. 1532 reads; 103928 bp (untrimmed), 103870 (trimmed).
Contig 243. 1625 reads; 87530 bp (untrimmed), 87373 (trimmed).
Contig 244. 1664 reads; 147907 bp (untrimmed), 147877 (trimmed).
Contig 245. 1701 reads; 133530 bp (untrimmed), 133299 (trimmed).
Contig 246. 2054 reads; 138772 bp (untrimmed), 138730 (trimmed).
Contig 247. 2095 reads; 129274 bp (untrimmed), 128859 (trimmed).
Contig 248. 2309 reads; 145004 bp (untrimmed), 144910 (trimmed).
Contig 249. 3547 reads; 234066 bp (untrimmed), 233973 (trimmed).
Contig 250. 3649 reads; 151914 bp (untrimmed), 151798 (trimmed).
--------------------------------------------------------------
Totals 66399 reads; 5084318 bp (untrimmed), 5044127 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 5082740 bases = 11.18 +- 9.29 = 0.60 +- 4.47
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 246 total values totalling 1887.9200. <7.674472 +/- 5.124777>
#Range: [ 1.16 - 43.21 ]
#Most likely bin: [ 3 - 3.5 ] 17 counts
#Median bin: [ 7 - 7.5 ] 7 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 1 - 1.5 : [ 2 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 17 0.07 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 10 0.04 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 10 0.04 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 17 0.07 0.23 ]
|XXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 9 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 10 0.04 0.30 ]
|XXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 9 0.04 0.34 ]
|XXXXXXXXXXXXXXXX 5 - 5.5 : [ 7 0.03 0.37 ]
|XXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 9 0.04 0.41 ]
|XXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 9 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 8 0.03 0.48 ]
|XXXXXXXXXXXXXXXX 7 - 7.5 : [ 7 0.03 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 10 0.04 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 13 0.05 0.60 ]
|XXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 8 0.03 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 12 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 10 0.04 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 12 0.05 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 15 0.06 0.83 ]
|XXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 9 0.04 0.87 ]
|XXXXXXXXX 11.5 - 12 : [ 4 0.02 0.88 ]
|XXXXXXXXX 12 - 12.5 : [ 4 0.02 0.90 ]
|XXXXXXXXXXXXXXXX 12.5 - 13 : [ 7 0.03 0.93 ]
|XXXXXXX 13 - 13.5 : [ 3 0.01 0.94 ]
|XXXXXXXXX 13.5 - 14 : [ 4 0.02 0.96 ]
#...
|XX 14.5 - 15 : [ 1 0.00 0.96 ]
#...
|XX 15.5 - 16 : [ 1 0.00 0.96 ]
|XX 16 - 16.5 : [ 1 0.00 0.97 ]
#...
|XX 17.5 - 18 : [ 1 0.00 0.97 ]
#...
|XX 19 - 19.5 : [ 1 0.00 0.98 ]
#...
|XX 20.5 - 21 : [ 1 0.00 0.98 ]
#...
|XX 21.5 - 22 : [ 1 0.00 0.98 ]
|XXXXX 22 - 22.5 : [ 2 0.01 0.99 ]
#...
|XX 39 - 39.5 : [ 1 0.00 1.00 ]
#...
|XX 43 - 43.5 : [ 1 0.00 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 190 total values totalling 1698.2600. <8.938211 +/- 4.885462>
#Range: [ 2.85 - 43.21 ]
#Most likely bin: [ 10.5 - 11 ] 15 counts
#Median bin: [ 8.5 - 9 ] 8 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXX 2.5 - 3 : [ 3 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 8 0.04 0.06 ]
|XXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 7 0.04 0.09 ]
|XXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 8 0.04 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 9 0.05 0.18 ]
|XXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 7 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 9 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 8 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 7 0.04 0.35 ]
|XXXXXXXXXXXXXXXX 7 - 7.5 : [ 6 0.03 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 9 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 12 0.06 0.49 ]
|XXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 8 0.04 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 12 0.06 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 10 0.05 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 12 0.06 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 15 0.08 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 9 0.05 0.84 ]
|XXXXXXXXXXX 11.5 - 12 : [ 4 0.02 0.86 ]
|XXXXXXXX 12 - 12.5 : [ 3 0.02 0.87 ]
|XXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 7 0.04 0.91 ]
|XXXXXXXX 13 - 13.5 : [ 3 0.02 0.93 ]
|XXXXXXXXXXX 13.5 - 14 : [ 4 0.02 0.95 ]
#...
|XXX 14.5 - 15 : [ 1 0.01 0.95 ]
#...
|XXX 15.5 - 16 : [ 1 0.01 0.96 ]
|XXX 16 - 16.5 : [ 1 0.01 0.96 ]
#...
|XXX 17.5 - 18 : [ 1 0.01 0.97 ]
#...
|XXX 19 - 19.5 : [ 1 0.01 0.97 ]
#...
|XXX 20.5 - 21 : [ 1 0.01 0.98 ]
#...
|XXX 21.5 - 22 : [ 1 0.01 0.98 ]
|XXX 22 - 22.5 : [ 1 0.01 0.99 ]
#...
|XXX 39 - 39.5 : [ 1 0.01 0.99 ]
#...
|XXX 43 - 43.5 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 3 2 reads 1670 bases = 1.16 +- 0.36 = -0.03 +- 0.92
Contig 2 2 reads 1423 bases = 1.27 +- 0.45 = 1.27 +- 0.45
Contig 31 5 reads 2533 bases = 1.55 +- 0.55 = 0.68 +- 1.43
Contig 20 4 reads 2097 bases = 1.61 +- 0.75 = 0.97 +- 1.44
Contig 22 4 reads 2265 bases = 1.64 +- 0.78 = 0.02 +- 0.86
Contig 38 6 reads 2110 bases = 1.64 +- 0.66 = 0.61 +- 0.56
Contig 6 3 reads 1305 bases = 1.64 +- 0.84 = 0.84 +- 0.42
Contig 10 3 reads 1452 bases = 1.67 +- 0.86 = 1.67 +- 0.86
Contig 15 3 reads 1314 bases = 1.68 +- 0.60 = 1.68 +- 0.60
Contig 29 5 reads 2369 bases = 1.73 +- 0.75 = 0.45 +- 1.75
Contig 13 3 reads 1538 bases = 1.76 +- 0.77 = 0.51 +- 1.16
Contig 19 4 reads 2046 bases = 1.76 +- 0.76 = 0.89 +- 0.59
Contig 24 4 reads 1742 bases = 1.78 +- 0.41 = 0.87 +- 1.04
Contig 18 4 reads 2113 bases = 1.83 +- 0.87 = 1.83 +- 0.87
Contig 17 3 reads 1124 bases = 1.90 +- 0.63 = 1.90 +- 0.63
Contig 16 3 reads 1127 bases = 1.92 +- 0.87 = 0.28 +- 1.04
Contig 26 4 reads 1696 bases = 1.97 +- 0.89 = 0.93 +- 0.45
Contig 27 4 reads 1611 bases = 1.97 +- 0.97 = 0.78 +- 0.79
Contig 11 3 reads 1096 bases = 1.98 +- 0.67 = 1.09 +- 0.73
Contig 8 3 reads 1188 bases = 2.12 +- 0.87 = 2.12 +- 0.87
Contig 229 876 reads 58771 bases = 12.95 +- 3.93 = 1.01 +- 4.35
Contig 249 3547 reads 234066 bases = 12.99 +- 14.88 = 0.31 +- 4.23
Contig 206 443 reads 29140 bases = 13.01 +- 3.81 = 0.22 +- 3.97
Contig 216 584 reads 38672 bases = 13.09 +- 4.90 = -0.00 +- 4.78
Contig 220 600 reads 38880 bases = 13.32 +- 3.91 = -0.02 +- 3.68
Contig 189 266 reads 16942 bases = 13.52 +- 4.24 = 0.66 +- 3.92
Contig 248 2309 reads 145004 bases = 13.65 +- 8.18 = 0.55 +- 6.23
Contig 231 899 reads 55607 bases = 13.93 +- 4.24 = 0.28 +- 4.31
Contig 247 2095 reads 129274 bases = 13.97 +- 5.06 = 0.24 +- 4.53
Contig 236 1417 reads 81600 bases = 14.74 +- 20.87 = 0.55 +- 4.50
Contig 243 1625 reads 87530 bases = 15.90 +- 13.77 = 0.42 +- 4.29
Contig 217 588 reads 30710 bases = 16.38 +- 7.48 = 0.14 +- 6.34
Contig 238 1433 reads 68427 bases = 17.99 +- 9.95 = 0.51 +- 5.50
Contig 181 199 reads 8779 bases = 19.00 +- 28.16 = 0.15 +- 3.50
Contig 250 3649 reads 151914 bases = 20.70 +- 25.94 = 0.13 +- 5.16
Contig 135 77 reads 3125 bases = 21.78 +- 18.27 = 20.69 +- 17.99
Contig 146 103 reads 3812 bases = 22.35 +- 17.75 = 5.94 +- 5.94
Contig 120 47 reads 1212 bases = 22.36 +- 20.64 = 22.36 +- 20.64
Contig 200 371 reads 8187 bases = 39.23 +- 15.54 = 3.30 +- 7.03
Contig 237 1431 reads 28535 bases = 43.21 +- 22.95 = 3.83 +- 6.19
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1319
HQ Discrepant reads = 109
Chimeric reads = 241
Suspect alignments = 577
-------------------------------------------------------------------
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/microbe3/3634605/edit_dir.31Aug04.QD