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
3635680 7000 NULL Burkholderia cenocepacia
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Burkholderia_cenocepacia
-------------------------------------------------------------------
Burkholderiaceae, family, b-proteobacteria
Burkholderia cenocepacia, species, b-proteobacteria
Burkholderia cepacia complex, species group, b-proteobacteria
Burkholderiales, order, b-proteobacteria
Burkholderia, genus, b-proteobacteria
Betaproteobacteria, class, b-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 7411268
# phrap: 7189858
# db:
altered.
7000000
7200375 +/- 168064
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 20242
Number of reads with percent X's >= 20%: 494 = 0.5%
Number of reads with percent X's >= 50%: 339 = 0.3%
Number of reads with percent X's >= 80%: 73 = 0.1%
Total reads in project: 98828
Total bp X'd : 1061894
reads >= 20% >= 50% >= 80% screened
Nr with L09136 18887 49 26 1
Nr with pCC1Fos 827 2 0 0
Nr with pMCL200_JGI_XZX+XZK 528 443 313 72
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 7
Number of reads with percent X's >= 20%: 4 = 0.8%
Number of reads with percent X's >= 50%: 1 = 0.2%
Number of reads with percent X's >= 80%: 1 = 0.2%
Total reads in project: 483
Total bp X'd : 1617
reads >= 20% >= 50% >= 80% screened
Nr with L09136 2 0 0 0
Nr with pMCL200_JGI_XZX+XZK 5 4 1 1
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 16249553
C = 29743662
G = 29697506
T = 15835972
N = 437294
X = 1061894
GC fraction = 0.64
Total = 93025881
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3635680_fasta.screen.contigs
-------------------------------------------------------------------
A 1254893
C 2520493
G 2482380
T 1257074
N 2181
fraction GC = 0.67
total bases = 7517021
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 APSG reads.list > grep.reads.list.APSG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APSG 4 500
-------------------------------------------------------------------
#Found 20267 total values totalling 75280112.0000. <3714.418118 +/- 5967.778168>
#Range: [ 634 - 413793 ]
#Most likely bin: [ 3000 - 3500 ] 8576 counts
#Median bin: [ 3500 - 4000 ] 7845 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 30 0.00 0.00 ]
| 1500 - 2000 : [ 17 0.00 0.00 ]
| 2000 - 2500 : [ 63 0.00 0.01 ]
|XXXXX 2500 - 3000 : [ 1006 0.05 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 8576 0.42 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 7845 0.39 0.87 ]
|XXXXXXXXXXXX 4000 - 4500 : [ 2639 0.13 1.00 ]
| 4500 - 5000 : [ 60 0.00 1.00 ]
#...
| 7000 - 7500 : [ 2 0.00 1.00 ]
| 7500 - 8000 : [ 2 0.00 1.00 ]
| 8000 - 8500 : [ 2 0.00 1.00 ]
#...
| 21500 - 22000 : [ 1 0.00 1.00 ]
#...
| 32000 - 32500 : [ 1 0.00 1.00 ]
#...
| 34000 - 34500 : [ 1 0.00 1.00 ]
| 34500 - 35000 : [ 1 0.00 1.00 ]
#...
| 52000 - 52500 : [ 1 0.00 1.00 ]
#...
| 54000 - 54500 : [ 1 0.00 1.00 ]
#...
| 65500 - 66000 : [ 1 0.00 1.00 ]
#...
| 74000 - 74500 : [ 1 0.00 1.00 ]
#...
| 85500 - 86000 : [ 1 0.00 1.00 ]
#...
| 103500 - 104000 : [ 1 0.00 1.00 ]
#...
| 113000 - 113500 : [ 1 0.00 1.00 ]
#...
| 129500 - 130000 : [ 1 0.00 1.00 ]
#...
| 137000 - 137500 : [ 1 0.00 1.00 ]
#...
| 140000 - 140500 : [ 1 0.00 1.00 ]
#...
| 148000 - 148500 : [ 1 0.00 1.00 ]
#...
| 160500 - 161000 : [ 1 0.00 1.00 ]
#...
| 188000 - 188500 : [ 1 0.00 1.00 ]
#...
| 204000 - 204500 : [ 1 0.00 1.00 ]
#...
| 211500 - 212000 : [ 1 0.00 1.00 ]
#...
| 227000 - 227500 : [ 1 0.00 1.00 ]
#...
| 259500 - 260000 : [ 1 0.00 1.00 ]
#...
| 265000 - 265500 : [ 1 0.00 1.00 ]
#...
| 327500 - 328000 : [ 1 0.00 1.00 ]
#...
| 413500 - 414000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APSH reads.list > grep.reads.list.APSH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APSH 4 500
-------------------------------------------------------------------
#Found 19055 total values totalling 124575774.0000. <6537.694778 +/- 1612.360104>
#Range: [ 801 - 130868 ]
#Most likely bin: [ 6500 - 7000 ] 3858 counts
#Median bin: [ 6500 - 7000 ] 3858 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 7 0.00 0.00 ]
|X 1000 - 1500 : [ 59 0.00 0.00 ]
|X 1500 - 2000 : [ 55 0.00 0.01 ]
| 2000 - 2500 : [ 48 0.00 0.01 ]
|X 2500 - 3000 : [ 100 0.01 0.01 ]
|XX 3000 - 3500 : [ 213 0.01 0.03 ]
|XXXX 3500 - 4000 : [ 411 0.02 0.05 ]
|XXXXXX 4000 - 4500 : [ 572 0.03 0.08 ]
|XXXXXXXX 4500 - 5000 : [ 726 0.04 0.11 ]
|XXXXXXXXXX 5000 - 5500 : [ 969 0.05 0.17 ]
|XXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1662 0.09 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2983 0.16 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 3858 0.20 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 3828 0.20 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 2183 0.11 0.93 ]
|XXXXXXXXXX 8000 - 8500 : [ 922 0.05 0.98 ]
|XXXX 8500 - 9000 : [ 340 0.02 0.99 ]
|X 9000 - 9500 : [ 93 0.00 1.00 ]
| 9500 - 10000 : [ 21 0.00 1.00 ]
#...
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 11500 - 12000 : [ 1 0.00 1.00 ]
#...
| 38000 - 38500 : [ 1 0.00 1.00 ]
#...
| 67000 - 67500 : [ 1 0.00 1.00 ]
#...
| 130500 - 131000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APSI reads.list > grep.reads.list.APSI
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APSI 4 500
-------------------------------------------------------------------
#Found 1072 total values totalling 41263151.0000. <38491.745336 +/- 3900.298772>
#Range: [ 25530 - 47071 ]
#Most likely bin: [ 39000 - 39500 ] 58 counts
#Median bin: [ 38000 - 38500 ] 54 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 25500 - 26000 : [ 1 0.00 0.00 ]
#...
|X 26500 - 27000 : [ 1 0.00 0.00 ]
#...
|X 28000 - 28500 : [ 1 0.00 0.00 ]
|X 28500 - 29000 : [ 1 0.00 0.00 ]
|X 29000 - 29500 : [ 2 0.00 0.01 ]
|XXX 29500 - 30000 : [ 4 0.00 0.01 ]
|XX 30000 - 30500 : [ 3 0.00 0.01 ]
|XXX 30500 - 31000 : [ 4 0.00 0.02 ]
|XXXX 31000 - 31500 : [ 6 0.01 0.02 ]
|XXXXXXXXX 31500 - 32000 : [ 13 0.01 0.03 ]
|XXXXXXXXXX 32000 - 32500 : [ 14 0.01 0.05 ]
|XXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 33 0.03 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 33 0.03 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 38 0.04 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 41 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 34 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 46 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 35 0.03 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 38 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 41 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 52 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 49 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 54 0.05 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 42 0.04 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 58 0.05 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 37 0.03 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 40 0.04 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 42 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 41 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 40 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 27 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 44 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 27 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 37 0.03 0.91 ]
|XXXXXXXXXXXXXXXXXXX 44000 - 44500 : [ 28 0.03 0.94 ]
|XXXXXXXXXXXX 44500 - 45000 : [ 18 0.02 0.96 ]
|XXXXXXXXXXXXXX 45000 - 45500 : [ 20 0.02 0.97 ]
|XXXXXXX 45500 - 46000 : [ 10 0.01 0.98 ]
|XXXXXX 46000 - 46500 : [ 9 0.01 0.99 ]
|XXXXX 46500 - 47000 : [ 7 0.01 1.00 ]
|X 47000 - 47500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# APSG 3408 +- 512 (n=10315)
# APSI 38375 +- 3833 (n=516)
# APSH 6418 +- 1442 (n=9687)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3635680_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
APSG 52992 -1 -1 96 629 49417 99 591 100 606
APSH 51072 -1 -1 95 650 44918 99 681 100 677
APSI 7680 83 584 72 354 4493 94 490 100 501
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
APSG 25244 99 597 100 616 24173 98 584 100 596
APSH 22697 99 689 100 686 22221 99 673 100 668
APSI 2093 94 483 100 502 2400 95 496 100 501
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3635680_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
268 49417 24982 93.22 97.10 APSG @
264 44918 23146 87.67 91.33 APSH @
36 4493 2629 73.03 76.07 APSI @
] 98828 50757 89.36 cumulative total@@
LIBRARY PLATE ID COUNT [ APSG 268 APSH 264 APSI 36 ] for 568 total 96 well plate ids.
Only indicates plates present in input file.
Make no assumption regarding plates (not) present in project that do not appear above.
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trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3635680_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 98828 total values totalling 61330081.0000. <620.573937 +/- 182.102058>
#Range: [ 11 - 1010 ]
#Most likely bin: [ 700 - 750 ] 16917 counts
#Median bin: [ 650 - 700 ] 14796 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 199 0.00 0.00 ]
|XX 50 - 100 : [ 1041 0.01 0.01 ]
|XXX 100 - 150 : [ 1426 0.01 0.03 ]
|XXXX 150 - 200 : [ 1667 0.02 0.04 ]
|XXXXX 200 - 250 : [ 1918 0.02 0.06 ]
|XXXXX 250 - 300 : [ 2286 0.02 0.09 ]
|XXXXX 300 - 350 : [ 2308 0.02 0.11 ]
|XXXXXX 350 - 400 : [ 2669 0.03 0.14 ]
|XXXXXXX 400 - 450 : [ 3140 0.03 0.17 ]
|XXXXXXXXX 450 - 500 : [ 3741 0.04 0.21 ]
|XXXXXXXXXXX 500 - 550 : [ 4856 0.05 0.26 ]
|XXXXXXXXXXXXXXXXX 550 - 600 : [ 7025 0.07 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 10441 0.11 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 14796 0.15 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 16917 0.17 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 14445 0.15 0.90 ]
|XXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7834 0.08 0.98 ]
|XXXX 850 - 900 : [ 1831 0.02 1.00 ]
|X 900 - 950 : [ 266 0.00 1.00 ]
| 950 - 1000 : [ 20 0.00 1.00 ]
| 1000 - 1050 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APSG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APSG 3635680_fasta.screen.trimQ15.SaF > reads.trim15.APSG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APSG.rl 2 50
-------------------------------------------------------------------
#Found 49417 total values totalling 28847152.0000. <583.749560 +/- 176.879226>
#Range: [ 11 - 1010 ]
#Most likely bin: [ 650 - 700 ] 9084 counts
#Median bin: [ 600 - 650 ] 6830 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 110 0.00 0.00 ]
|XXX 50 - 100 : [ 571 0.01 0.01 ]
|XXXX 100 - 150 : [ 885 0.02 0.03 ]
|XXXXX 150 - 200 : [ 1032 0.02 0.05 ]
|XXXXX 200 - 250 : [ 1123 0.02 0.08 ]
|XXXXX 250 - 300 : [ 1209 0.02 0.10 ]
|XXXXXX 300 - 350 : [ 1355 0.03 0.13 ]
|XXXXXXX 350 - 400 : [ 1646 0.03 0.16 ]
|XXXXXXXX 400 - 450 : [ 1924 0.04 0.20 ]
|XXXXXXXXXX 450 - 500 : [ 2346 0.05 0.25 ]
|XXXXXXXXXXXXX 500 - 550 : [ 2927 0.06 0.31 ]
|XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 4547 0.09 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 6830 0.14 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 9084 0.18 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8449 0.17 0.89 ]
|XXXXXXXXXXXXXXXXX 750 - 800 : [ 3970 0.08 0.97 ]
|XXX 800 - 850 : [ 772 0.02 0.99 ]
|XX 850 - 900 : [ 402 0.01 1.00 ]
|X 900 - 950 : [ 213 0.00 1.00 ]
| 950 - 1000 : [ 20 0.00 1.00 ]
| 1000 - 1050 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APSH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APSH 3635680_fasta.screen.trimQ15.SaF > reads.trim15.APSH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APSH.rl 2 50
-------------------------------------------------------------------
#Found 44918 total values totalling 30386473.0000. <676.487666 +/- 164.187597>
#Range: [ 16 - 930 ]
#Most likely bin: [ 750 - 800 ] 10253 counts
#Median bin: [ 700 - 750 ] 8118 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 53 0.00 0.00 ]
|X 50 - 100 : [ 256 0.01 0.01 ]
|X 100 - 150 : [ 362 0.01 0.01 ]
|XX 150 - 200 : [ 456 0.01 0.03 ]
|XX 200 - 250 : [ 582 0.01 0.04 ]
|XX 250 - 300 : [ 624 0.01 0.05 ]
|XXX 300 - 350 : [ 672 0.01 0.07 ]
|XXX 350 - 400 : [ 806 0.02 0.08 ]
|XXXX 400 - 450 : [ 974 0.02 0.11 ]
|XXXX 450 - 500 : [ 1131 0.03 0.13 ]
|XXXXXX 500 - 550 : [ 1607 0.04 0.17 ]
|XXXXXXXX 550 - 600 : [ 2110 0.05 0.21 ]
|XXXXXXXXXXXXX 600 - 650 : [ 3224 0.07 0.29 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5272 0.12 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8118 0.18 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 10253 0.23 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6959 0.15 0.97 ]
|XXXXX 850 - 900 : [ 1406 0.03 1.00 ]
| 900 - 950 : [ 53 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APSI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APSI 3635680_fasta.screen.trimQ15.SaF > reads.trim15.APSI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APSI.rl 2 50
-------------------------------------------------------------------
#Found 4493 total values totalling 2096456.0000. <466.604941 +/- 214.302990>
#Range: [ 23 - 887 ]
#Most likely bin: [ 250 - 300 ] 453 counts
#Median bin: [ 450 - 500 ] 264 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 0 - 50 : [ 36 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXX 50 - 100 : [ 214 0.05 0.06 ]
|XXXXXXXXXXXXXXXX 100 - 150 : [ 179 0.04 0.10 ]
|XXXXXXXXXXXXXXXX 150 - 200 : [ 179 0.04 0.14 ]
|XXXXXXXXXXXXXXXXXXX 200 - 250 : [ 213 0.05 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 453 0.10 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 300 - 350 : [ 281 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXXX 350 - 400 : [ 217 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXX 400 - 450 : [ 242 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXX 450 - 500 : [ 264 0.06 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 322 0.07 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 368 0.08 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 387 0.09 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 440 0.10 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 350 0.08 0.92 ]
|XXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 222 0.05 0.97 ]
|XXXXXXXXX 800 - 850 : [ 103 0.02 0.99 ]
|XX 850 - 900 : [ 23 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATTF
trimt JAZZ trim 15 readlength histogram for ATTG
trimt JAZZ trim 15 readlength histogram for ATTH
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3635680
-------------------------------------------------------------------
APSG.000001.000100 pUC18.fa pUC18.fa LRS.fasta
APSG.000101.000200 pUC18.fa pUC18.fa LRS.fasta
APSG.000201.000300 pUC18.fa pUC18.fa LRS.fasta
APSH.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
APSH.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
APSH.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
APSI.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
APSG.000001.000100 pUC18.fa pUC18.fa LRS.fasta
APSG.000101.000200 pUC18.fa pUC18.fa LRS.fasta
APSG.000201.000300 pUC18.fa pUC18.fa LRS.fasta
APSH.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
APSH.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
APSH.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
APSI.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3635680_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3635680_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 98591 total values totalling 65526.5639. <0.664630 +/- 0.049835>
#Range: [ 0 - 0.9583 ]
#Most likely bin: [ 0.675 - 0.68 ] 5109 counts
#Median bin: [ 0.67 - 0.675 ] 4960 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.31 - 0.315 : [ 2 0.00 0.00 ]
| 0.315 - 0.32 : [ 1 0.00 0.00 ]
| 0.32 - 0.325 : [ 1 0.00 0.00 ]
| 0.325 - 0.33 : [ 1 0.00 0.00 ]
| 0.33 - 0.335 : [ 2 0.00 0.00 ]
| 0.335 - 0.34 : [ 1 0.00 0.00 ]
#...
| 0.345 - 0.35 : [ 3 0.00 0.00 ]
| 0.35 - 0.355 : [ 3 0.00 0.00 ]
| 0.355 - 0.36 : [ 4 0.00 0.00 ]
| 0.36 - 0.365 : [ 2 0.00 0.00 ]
| 0.365 - 0.37 : [ 7 0.00 0.00 ]
| 0.37 - 0.375 : [ 4 0.00 0.00 ]
| 0.375 - 0.38 : [ 5 0.00 0.00 ]
| 0.38 - 0.385 : [ 6 0.00 0.00 ]
| 0.385 - 0.39 : [ 7 0.00 0.00 ]
| 0.39 - 0.395 : [ 5 0.00 0.00 ]
| 0.395 - 0.4 : [ 5 0.00 0.00 ]
| 0.4 - 0.405 : [ 10 0.00 0.00 ]
| 0.405 - 0.41 : [ 9 0.00 0.00 ]
| 0.41 - 0.415 : [ 9 0.00 0.00 ]
| 0.415 - 0.42 : [ 17 0.00 0.00 ]
| 0.42 - 0.425 : [ 8 0.00 0.00 ]
| 0.425 - 0.43 : [ 12 0.00 0.00 ]
| 0.43 - 0.435 : [ 21 0.00 0.00 ]
| 0.435 - 0.44 : [ 30 0.00 0.00 ]
| 0.44 - 0.445 : [ 35 0.00 0.00 ]
| 0.445 - 0.45 : [ 31 0.00 0.00 ]
| 0.45 - 0.455 : [ 39 0.00 0.00 ]
| 0.455 - 0.46 : [ 46 0.00 0.00 ]
| 0.46 - 0.465 : [ 43 0.00 0.00 ]
| 0.465 - 0.47 : [ 62 0.00 0.00 ]
|X 0.47 - 0.475 : [ 73 0.00 0.01 ]
|X 0.475 - 0.48 : [ 74 0.00 0.01 ]
|X 0.48 - 0.485 : [ 69 0.00 0.01 ]
|X 0.485 - 0.49 : [ 75 0.00 0.01 ]
|X 0.49 - 0.495 : [ 101 0.00 0.01 ]
|X 0.495 - 0.5 : [ 67 0.00 0.01 ]
|X 0.5 - 0.505 : [ 171 0.00 0.01 ]
|X 0.505 - 0.51 : [ 110 0.00 0.01 ]
|X 0.51 - 0.515 : [ 130 0.00 0.01 ]
|X 0.515 - 0.52 : [ 163 0.00 0.01 ]
|X 0.52 - 0.525 : [ 182 0.00 0.02 ]
|XX 0.525 - 0.53 : [ 217 0.00 0.02 ]
|XX 0.53 - 0.535 : [ 251 0.00 0.02 ]
|XX 0.535 - 0.54 : [ 256 0.00 0.02 ]
|XX 0.54 - 0.545 : [ 308 0.00 0.03 ]
|XX 0.545 - 0.55 : [ 295 0.00 0.03 ]
|XXX 0.55 - 0.555 : [ 418 0.00 0.03 ]
|XXX 0.555 - 0.56 : [ 411 0.00 0.04 ]
|XXXX 0.56 - 0.565 : [ 450 0.00 0.04 ]
|XXXXX 0.565 - 0.57 : [ 580 0.01 0.05 ]
|XXXXX 0.57 - 0.575 : [ 606 0.01 0.06 ]
|XXXXX 0.575 - 0.58 : [ 641 0.01 0.06 ]
|XXXXXX 0.58 - 0.585 : [ 741 0.01 0.07 ]
|XXXXXX 0.585 - 0.59 : [ 760 0.01 0.08 ]
|XXXXXXX 0.59 - 0.595 : [ 880 0.01 0.09 ]
|XXXXXXX 0.595 - 0.6 : [ 892 0.01 0.09 ]
|XXXXXXXXX 0.6 - 0.605 : [ 1108 0.01 0.11 ]
|XXXXXXXXX 0.605 - 0.61 : [ 1200 0.01 0.12 ]
|XXXXXXXXXXX 0.61 - 0.615 : [ 1382 0.01 0.13 ]
|XXXXXXXXXXXX 0.615 - 0.62 : [ 1548 0.02 0.15 ]
|XXXXXXXXXXXXX 0.62 - 0.625 : [ 1684 0.02 0.17 ]
|XXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 2086 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 2351 0.02 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 2841 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 3111 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 3477 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 3886 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 4286 0.04 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 4694 0.05 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 4804 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 4960 0.05 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 5109 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 5102 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 5069 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 4602 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 4253 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 3839 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 3422 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 3043 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 2525 0.03 0.91 ]
|XXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 2042 0.02 0.93 ]
|XXXXXXXXXXXXX 0.725 - 0.73 : [ 1679 0.02 0.95 ]
|XXXXXXXXXX 0.73 - 0.735 : [ 1322 0.01 0.96 ]
|XXXXXXX 0.735 - 0.74 : [ 891 0.01 0.97 ]
|XXXXXX 0.74 - 0.745 : [ 735 0.01 0.98 ]
|XXXX 0.745 - 0.75 : [ 526 0.01 0.98 ]
|XXX 0.75 - 0.755 : [ 439 0.00 0.99 ]
|XX 0.755 - 0.76 : [ 293 0.00 0.99 ]
|XX 0.76 - 0.765 : [ 233 0.00 0.99 ]
|X 0.765 - 0.77 : [ 160 0.00 0.99 ]
|X 0.77 - 0.775 : [ 125 0.00 1.00 ]
|X 0.775 - 0.78 : [ 90 0.00 1.00 ]
|X 0.78 - 0.785 : [ 89 0.00 1.00 ]
| 0.785 - 0.79 : [ 43 0.00 1.00 ]
| 0.79 - 0.795 : [ 36 0.00 1.00 ]
| 0.795 - 0.8 : [ 16 0.00 1.00 ]
| 0.8 - 0.805 : [ 37 0.00 1.00 ]
| 0.805 - 0.81 : [ 15 0.00 1.00 ]
| 0.81 - 0.815 : [ 22 0.00 1.00 ]
| 0.815 - 0.82 : [ 10 0.00 1.00 ]
| 0.82 - 0.825 : [ 4 0.00 1.00 ]
| 0.825 - 0.83 : [ 10 0.00 1.00 ]
| 0.83 - 0.835 : [ 4 0.00 1.00 ]
| 0.835 - 0.84 : [ 1 0.00 1.00 ]
| 0.84 - 0.845 : [ 8 0.00 1.00 ]
| 0.845 - 0.85 : [ 5 0.00 1.00 ]
| 0.85 - 0.855 : [ 3 0.00 1.00 ]
| 0.855 - 0.86 : [ 2 0.00 1.00 ]
| 0.86 - 0.865 : [ 3 0.00 1.00 ]
#...
| 0.88 - 0.885 : [ 3 0.00 1.00 ]
| 0.885 - 0.89 : [ 1 0.00 1.00 ]
#...
| 0.895 - 0.9 : [ 1 0.00 1.00 ]
| 0.9 - 0.905 : [ 2 0.00 1.00 ]
| 0.905 - 0.91 : [ 2 0.00 1.00 ]
| 0.91 - 0.915 : [ 1 0.00 1.00 ]
#...
| 0.925 - 0.93 : [ 1 0.00 1.00 ]
#...
| 0.945 - 0.95 : [ 1 0.00 1.00 ]
#...
| 0.955 - 0.96 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 258. 1157 reads; 85202 bp (untrimmed), 85117 (trimmed).
Contig 259. 1157 reads; 82547 bp (untrimmed), 82221 (trimmed).
Contig 260. 1231 reads; 90934 bp (untrimmed), 90786 (trimmed).
Contig 261. 1414 reads; 106576 bp (untrimmed), 106466 (trimmed).
Contig 262. 1421 reads; 111634 bp (untrimmed), 111558 (trimmed).
Contig 263. 1444 reads; 90333 bp (untrimmed), 90228 (trimmed).
Contig 264. 1519 reads; 92058 bp (untrimmed), 91971 (trimmed).
Contig 265. 1558 reads; 125222 bp (untrimmed), 125164 (trimmed).
Contig 266. 1660 reads; 125973 bp (untrimmed), 125506 (trimmed).
Contig 267. 1669 reads; 127882 bp (untrimmed), 127863 (trimmed).
Contig 268. 1810 reads; 135973 bp (untrimmed), 135559 (trimmed).
Contig 269. 1820 reads; 136140 bp (untrimmed), 136140 (trimmed).
Contig 270. 2137 reads; 164971 bp (untrimmed), 164750 (trimmed).
Contig 271. 2196 reads; 156431 bp (untrimmed), 156212 (trimmed).
Contig 272. 2213 reads; 158357 bp (untrimmed), 158095 (trimmed).
Contig 273. 2436 reads; 182843 bp (untrimmed), 182494 (trimmed).
Contig 274. 2501 reads; 182481 bp (untrimmed), 181829 (trimmed).
Contig 275. 3097 reads; 226149 bp (untrimmed), 225929 (trimmed).
Contig 276. 3279 reads; 251172 bp (untrimmed), 250876 (trimmed).
Contig 277. 3302 reads; 233246 bp (untrimmed), 233024 (trimmed).
Contig 278. 3491 reads; 272509 bp (untrimmed), 271873 (trimmed).
Contig 279. 3639 reads; 261963 bp (untrimmed), 261513 (trimmed).
Contig 280. 3684 reads; 265853 bp (untrimmed), 265783 (trimmed).
Contig 281. 3924 reads; 289687 bp (untrimmed), 289093 (trimmed).
Contig 282. 4188 reads; 314447 bp (untrimmed), 314127 (trimmed).
Contig 283. 4772 reads; 338740 bp (untrimmed), 338615 (trimmed).
Contig 284. 9409 reads; 647021 bp (untrimmed), 646956 (trimmed).
--------------------------------------------------------------
Totals 98345 reads; 7517021 bp (untrimmed), 7411268 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 7431287 bases = 11.01 +- 4.39 = 0.18 +- 3.78
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 183 total values totalling 1140.0800. <6.229945 +/- 4.529255>
#Range: [ 1.04 - 21.43 ]
#Most likely bin: [ 1.5 - 2 ] 48 counts
#Median bin: [ 6 - 6.5 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 1 - 1.5 : [ 18 0.10 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 48 0.26 0.36 ]
|XXXXXXXXXXXX 2 - 2.5 : [ 14 0.08 0.44 ]
|XXXXXX 2.5 - 3 : [ 7 0.04 0.48 ]
#...
|X 3.5 - 4 : [ 1 0.01 0.48 ]
#...
|X 5 - 5.5 : [ 1 0.01 0.49 ]
|XX 5.5 - 6 : [ 2 0.01 0.50 ]
|XX 6 - 6.5 : [ 2 0.01 0.51 ]
|XX 6.5 - 7 : [ 2 0.01 0.52 ]
|XX 7 - 7.5 : [ 3 0.02 0.54 ]
|XX 7.5 - 8 : [ 3 0.02 0.55 ]
|XX 8 - 8.5 : [ 3 0.02 0.57 ]
|XX 8.5 - 9 : [ 2 0.01 0.58 ]
|XXXX 9 - 9.5 : [ 5 0.03 0.61 ]
|XXX 9.5 - 10 : [ 4 0.02 0.63 ]
|XXXXXXXX 10 - 10.5 : [ 10 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 21 0.11 0.80 ]
|XXXXXXXXXXXXXXXX 11 - 11.5 : [ 19 0.10 0.90 ]
|XXXXXXXXX 11.5 - 12 : [ 11 0.06 0.96 ]
|XX 12 - 12.5 : [ 3 0.02 0.98 ]
|X 12.5 - 13 : [ 1 0.01 0.98 ]
|X 13 - 13.5 : [ 1 0.01 0.99 ]
|X 13.5 - 14 : [ 1 0.01 0.99 ]
#...
|X 21 - 21.5 : [ 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 94 total values totalling 974.1300. <10.363085 +/- 2.079584>
#Range: [ 3.61 - 21.43 ]
#Most likely bin: [ 10.5 - 11 ] 21 counts
#Median bin: [ 10.5 - 11 ] 21 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 3.5 - 4 : [ 1 0.01 0.01 ]
#...
|XXXX 5.5 - 6 : [ 2 0.02 0.03 ]
|XX 6 - 6.5 : [ 1 0.01 0.04 ]
|XXXX 6.5 - 7 : [ 2 0.02 0.06 ]
|XXXXXX 7 - 7.5 : [ 3 0.03 0.10 ]
|XXXXXX 7.5 - 8 : [ 3 0.03 0.13 ]
|XXXXXX 8 - 8.5 : [ 3 0.03 0.16 ]
|XXXX 8.5 - 9 : [ 2 0.02 0.18 ]
|XXXXXXXXXX 9 - 9.5 : [ 5 0.05 0.23 ]
|XXXXXXXX 9.5 - 10 : [ 4 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 10 0.11 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 21 0.22 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 19 0.20 0.81 ]
|XXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 11 0.12 0.93 ]
|XXXXXX 12 - 12.5 : [ 3 0.03 0.96 ]
|XX 12.5 - 13 : [ 1 0.01 0.97 ]
|XX 13 - 13.5 : [ 1 0.01 0.98 ]
|XX 13.5 - 14 : [ 1 0.01 0.99 ]
#...
|XX 21 - 21.5 : [ 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 102 2 reads 1859 bases = 1.04 +- 0.21 = 0.05 +- 0.98
Contig 106 2 reads 1784 bases = 1.07 +- 0.25 = 1.07 +- 0.25
Contig 138 3 reads 2669 bases = 1.11 +- 0.31 = 0.36 +- 0.99
Contig 105 2 reads 1014 bases = 1.19 +- 0.39 = -0.81 +- 0.39
Contig 133 3 reads 2396 bases = 1.20 +- 0.40 = 0.44 +- 1.09
Contig 104 2 reads 1480 bases = 1.22 +- 0.42 = 1.22 +- 0.42
Contig 160 3 reads 2295 bases = 1.22 +- 0.41 = 0.38 +- 0.96
Contig 107 2 reads 1627 bases = 1.24 +- 0.43 = 1.24 +- 0.43
Contig 150 3 reads 2281 bases = 1.27 +- 0.44 = 1.27 +- 0.44
Contig 144 3 reads 2036 bases = 1.30 +- 0.46 = 1.30 +- 0.46
Contig 101 2 reads 1696 bases = 1.32 +- 0.47 = 0.13 +- 0.81
Contig 119 3 reads 2031 bases = 1.32 +- 0.46 = 0.50 +- 0.66
Contig 124 3 reads 2284 bases = 1.33 +- 0.47 = 1.33 +- 0.47
Contig 175 4 reads 2917 bases = 1.35 +- 0.48 = 0.74 +- 1.09
Contig 159 3 reads 2205 bases = 1.37 +- 0.48 = 1.37 +- 0.48
Contig 120 3 reads 2008 bases = 1.39 +- 0.49 = 0.64 +- 0.80
Contig 158 3 reads 2027 bases = 1.47 +- 0.50 = 0.53 +- 0.50
Contig 122 3 reads 2015 bases = 1.48 +- 0.50 = 1.48 +- 0.50
Contig 139 3 reads 1856 bases = 1.50 +- 0.50 = 0.51 +- 0.50
Contig 146 3 reads 1895 bases = 1.52 +- 0.52 = 1.52 +- 0.52
Contig 244 636 reads 46251 bases = 11.43 +- 4.65 = 0.36 +- 4.54
Contig 275 3097 reads 226149 bases = 11.45 +- 5.30 = -0.03 +- 3.85
Contig 201 70 reads 5213 bases = 11.50 +- 5.40 = 1.16 +- 3.22
Contig 274 2501 reads 182481 bases = 11.58 +- 3.95 = 0.01 +- 3.84
Contig 280 3684 reads 265853 bases = 11.59 +- 3.77 = 0.06 +- 3.55
Contig 279 3639 reads 261963 bases = 11.61 +- 3.82 = 0.18 +- 3.97
Contig 271 2196 reads 156431 bases = 11.64 +- 4.14 = 0.08 +- 3.91
Contig 272 2213 reads 158357 bases = 11.68 +- 3.95 = 0.33 +- 3.63
Contig 259 1157 reads 82547 bases = 11.69 +- 3.68 = 0.28 +- 3.45
Contig 232 426 reads 30665 bases = 11.76 +- 4.21 = 0.13 +- 3.34
Contig 283 4772 reads 338740 bases = 11.80 +- 4.38 = -0.05 +- 3.99
Contig 277 3302 reads 233246 bases = 11.92 +- 4.23 = 0.13 +- 4.02
Contig 234 520 reads 35572 bases = 11.97 +- 3.51 = 0.16 +- 3.45
Contig 248 805 reads 56477 bases = 12.09 +- 4.48 = 0.31 +- 4.30
Contig 284 9409 reads 647021 bases = 12.14 +- 5.15 = 0.01 +- 3.80
Contig 242 613 reads 41698 bases = 12.23 +- 5.04 = 0.13 +- 4.25
Contig 238 576 reads 38067 bases = 12.66 +- 4.61 = 0.92 +- 4.25
Contig 263 1444 reads 90333 bases = 13.21 +- 4.91 = 0.04 +- 4.24
Contig 264 1519 reads 92058 bases = 13.82 +- 3.88 = 0.16 +- 3.88
Contig 206 75 reads 2773 bases = 21.43 +- 12.96 = 16.52 +- 9.29
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1365
HQ Discrepant reads = 102
Chimeric reads = 277
Suspect alignments = 506
-------------------------------------------------------------------
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: 48
node_space: 24
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/microbe2/3635680/edit_dir.27Aug04.QD