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
3634607 4500 192073 Shewanella denitrificans
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Shewanella_denitrificans
-------------------------------------------------------------------
Shewanellaceae, family, g-proteobacteria
Shewanella denitrificans, species, g-proteobacteria
Alteromonadales, order, 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: 4471200
# phrap: 4532731
# db:
altered.
4500000
4501310 +/- 25137
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 0
Number of reads with percent X's >= 20%: 0 = 0.0%
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: 76435
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 0
Number of reads with percent X's >= 20%: 0 = 0.0%
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: 55
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 20190715
C = 16372146
G = 16553061
T = 19523333
N = 333850
X = 879384
GC fraction = 0.45
Total = 73852489
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634607_fasta.screen.contigs
-------------------------------------------------------------------
A 1237780
C 1041446
G 985529
T 1226269
N 450
fraction GC = 0.45
total bases = 4491474
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 AION reads.list > grep.reads.list.AION
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AION 4 500
-------------------------------------------------------------------
#Found 14642 total values totalling 55601928.0000. <3797.427127 +/- 9528.285333>
#Range: [ 525 - 262282 ]
#Most likely bin: [ 3000 - 3500 ] 4333 counts
#Median bin: [ 3000 - 3500 ] 4333 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 19 0.00 0.00 ]
|X 1000 - 1500 : [ 136 0.01 0.01 ]
|XX 1500 - 2000 : [ 165 0.01 0.02 ]
|XXXX 2000 - 2500 : [ 448 0.03 0.05 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 3224 0.22 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4333 0.30 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3735 0.26 0.82 ]
|XXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 2233 0.15 0.98 ]
|XXX 4500 - 5000 : [ 305 0.02 1.00 ]
| 5000 - 5500 : [ 2 0.00 1.00 ]
| 5500 - 6000 : [ 1 0.00 1.00 ]
#...
| 8000 - 8500 : [ 1 0.00 1.00 ]
#...
| 9000 - 9500 : [ 1 0.00 1.00 ]
| 9500 - 10000 : [ 1 0.00 1.00 ]
| 10000 - 10500 : [ 2 0.00 1.00 ]
#...
| 20000 - 20500 : [ 1 0.00 1.00 ]
#...
| 34000 - 34500 : [ 1 0.00 1.00 ]
#...
| 35000 - 35500 : [ 1 0.00 1.00 ]
#...
| 41500 - 42000 : [ 1 0.00 1.00 ]
#...
| 49500 - 50000 : [ 1 0.00 1.00 ]
#...
| 52500 - 53000 : [ 2 0.00 1.00 ]
| 53000 - 53500 : [ 1 0.00 1.00 ]
#...
| 84500 - 85000 : [ 1 0.00 1.00 ]
#...
| 86500 - 87000 : [ 1 0.00 1.00 ]
#...
| 113500 - 114000 : [ 1 0.00 1.00 ]
#...
| 114500 - 115000 : [ 1 0.00 1.00 ]
#...
| 132000 - 132500 : [ 2 0.00 1.00 ]
#...
| 133500 - 134000 : [ 1 0.00 1.00 ]
#...
| 135000 - 135500 : [ 1 0.00 1.00 ]
#...
| 142500 - 143000 : [ 1 0.00 1.00 ]
#...
| 164500 - 165000 : [ 1 0.00 1.00 ]
#...
| 206000 - 206500 : [ 1 0.00 1.00 ]
#...
| 238500 - 239000 : [ 1 0.00 1.00 ]
#...
| 260000 - 260500 : [ 1 0.00 1.00 ]
| 260500 - 261000 : [ 2 0.00 1.00 ]
| 261000 - 261500 : [ 8 0.00 1.00 ]
| 261500 - 262000 : [ 2 0.00 1.00 ]
| 262000 - 262500 : [ 3 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOO reads.list > grep.reads.list.AIOO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOO 4 500
-------------------------------------------------------------------
#Found 15758 total values totalling 111205422.0000. <7057.077167 +/- 10479.915020>
#Range: [ 256 - 570866 ]
#Most likely bin: [ 6500 - 7000 ] 2949 counts
#Median bin: [ 6500 - 7000 ] 2949 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
| 500 - 1000 : [ 8 0.00 0.00 ]
|XX 1000 - 1500 : [ 124 0.01 0.01 ]
|XX 1500 - 2000 : [ 132 0.01 0.02 ]
|XX 2000 - 2500 : [ 165 0.01 0.03 ]
|XXX 2500 - 3000 : [ 200 0.01 0.04 ]
|XXX 3000 - 3500 : [ 222 0.01 0.05 ]
|XXX 3500 - 4000 : [ 251 0.02 0.07 ]
|XXXX 4000 - 4500 : [ 263 0.02 0.09 ]
|XXX 4500 - 5000 : [ 244 0.02 0.10 ]
|XXXXX 5000 - 5500 : [ 393 0.02 0.13 ]
|XXXXXXXXXXXXXX 5500 - 6000 : [ 1056 0.07 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2478 0.16 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2949 0.19 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 2874 0.18 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 2307 0.15 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1593 0.10 0.97 ]
|XXXXXX 8500 - 9000 : [ 451 0.03 1.00 ]
| 9000 - 9500 : [ 4 0.00 1.00 ]
| 9500 - 10000 : [ 1 0.00 1.00 ]
| 10000 - 10500 : [ 2 0.00 1.00 ]
| 10500 - 11000 : [ 5 0.00 1.00 ]
| 11000 - 11500 : [ 1 0.00 1.00 ]
| 11500 - 12000 : [ 1 0.00 1.00 ]
| 12000 - 12500 : [ 1 0.00 1.00 ]
| 12500 - 13000 : [ 3 0.00 1.00 ]
| 13000 - 13500 : [ 1 0.00 1.00 ]
#...
| 22500 - 23000 : [ 1 0.00 1.00 ]
#...
| 39000 - 39500 : [ 1 0.00 1.00 ]
#...
| 51500 - 52000 : [ 1 0.00 1.00 ]
#...
| 53500 - 54000 : [ 1 0.00 1.00 ]
#...
| 79500 - 80000 : [ 1 0.00 1.00 ]
#...
| 115000 - 115500 : [ 1 0.00 1.00 ]
#...
| 159000 - 159500 : [ 1 0.00 1.00 ]
#...
| 262500 - 263000 : [ 1 0.00 1.00 ]
#...
| 263500 - 264000 : [ 1 0.00 1.00 ]
| 264000 - 264500 : [ 3 0.00 1.00 ]
| 264500 - 265000 : [ 3 0.00 1.00 ]
| 265000 - 265500 : [ 3 0.00 1.00 ]
| 265500 - 266000 : [ 5 0.00 1.00 ]
| 266000 - 266500 : [ 4 0.00 1.00 ]
#...
| 570500 - 571000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOP reads.list > grep.reads.list.AIOP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOP 4 500
-------------------------------------------------------------------
#Found 465 total values totalling 19005995.0000. <40873.107527 +/- 26942.477233>
#Range: [ 25433 - 302147 ]
#Most likely bin: [ 36500 - 37000 ] 35 counts
#Median bin: [ 37500 - 38000 ] 27 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 25000 - 25500 : [ 1 0.00 0.00 ]
#...
|X 29000 - 29500 : [ 1 0.00 0.00 ]
#...
|X 30000 - 30500 : [ 1 0.00 0.01 ]
|XX 30500 - 31000 : [ 2 0.00 0.01 ]
|XXXXXX 31000 - 31500 : [ 5 0.01 0.02 ]
|XXXXXXXXXXX 31500 - 32000 : [ 10 0.02 0.04 ]
|XXXXX 32000 - 32500 : [ 4 0.01 0.05 ]
|XXXXXX 32500 - 33000 : [ 5 0.01 0.06 ]
|XXXXXX 33000 - 33500 : [ 5 0.01 0.07 ]
|XXXXXXXXXXXXX 33500 - 34000 : [ 11 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 20 0.04 0.14 ]
|XXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 17 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 20 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 27 0.06 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 21 0.05 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 35 0.08 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 31 0.07 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 27 0.06 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 26 0.06 0.58 ]
|XXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 16 0.03 0.61 ]
|XXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 18 0.04 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 23 0.05 0.70 ]
|XXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 18 0.04 0.74 ]
|XXXXXXXXXXXXXXXXX 40500 - 41000 : [ 15 0.03 0.77 ]
|XXXXXXXXXXXXXXXX 41000 - 41500 : [ 14 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 17 0.04 0.84 ]
|XXXXXXXXXXXXX 42000 - 42500 : [ 11 0.02 0.86 ]
|XXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 17 0.04 0.90 ]
|XXXXXXXXXXXXXXXXX 43000 - 43500 : [ 15 0.03 0.93 ]
|XXXXXXXXX 43500 - 44000 : [ 8 0.02 0.95 ]
|XXXXXX 44000 - 44500 : [ 5 0.01 0.96 ]
|XXXXXX 44500 - 45000 : [ 5 0.01 0.97 ]
|XXXXXX 45000 - 45500 : [ 5 0.01 0.98 ]
|XXX 45500 - 46000 : [ 3 0.01 0.99 ]
|X 46000 - 46500 : [ 1 0.00 0.99 ]
#...
|X 289500 - 290000 : [ 1 0.00 0.99 ]
#...
|X 296500 - 297000 : [ 1 0.00 0.99 ]
#...
|X 298000 - 298500 : [ 1 0.00 1.00 ]
#...
|X 299000 - 299500 : [ 1 0.00 1.00 ]
#...
|X 302000 - 302500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIOO 6530 +- 1627 (n=7684)
# AION 3252 +- 731 (n=7284)
# AIOP 37850 +- 3192 (n=214)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634607_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
AION 40704 -1 -1 96 698 40500 89 651 92 659
AIOO 47232 -1 -1 93 674 46992 78 666 88 660
AIOP 5376 -1 -1 72 374 3840 49 456 61 427
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AION 20254 90 646 93 659 20246 89 656 92 659
AIOO 23274 73 663 84 649 23718 84 669 92 669
AIOP 1920 51 479 61 444 1920 48 432 61 409
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634607_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
204 36720 18846 92.38 96.23 AION @
244 37599 20315 83.26 86.73 AIOO @
20 2116 1265 63.25 65.89 AIOP @
] 76435 40426 86.38 cumulative total@@
LIBRARY PLATE ID COUNT [ AION 204 AIOO 244 AIOP 20 ] for 468 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 3634607_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 91332 total values totalling 49234076.0000. <539.067096 +/- 295.088454>
#Range: [ 0 - 931 ]
#Most likely bin: [ 0 - 50 ] 14468 counts
#Median bin: [ 650 - 700 ] 8090 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 14468 0.16 0.16 ]
|XXXXX 50 - 100 : [ 1893 0.02 0.18 ]
|XXXX 100 - 150 : [ 1364 0.01 0.19 ]
|XXX 150 - 200 : [ 1261 0.01 0.21 ]
|XXXX 200 - 250 : [ 1296 0.01 0.22 ]
|XXXX 250 - 300 : [ 1585 0.02 0.24 ]
|XXXX 300 - 350 : [ 1540 0.02 0.26 ]
|XXXXX 350 - 400 : [ 1764 0.02 0.28 ]
|XXXXXX 400 - 450 : [ 2143 0.02 0.30 ]
|XXXXXXX 450 - 500 : [ 2420 0.03 0.33 ]
|XXXXXXXXX 500 - 550 : [ 3167 0.03 0.36 ]
|XXXXXXXXXXXX 550 - 600 : [ 4208 0.05 0.41 ]
|XXXXXXXXXXXXXXXXX 600 - 650 : [ 6012 0.07 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 8090 0.09 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 11296 0.12 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 14199 0.16 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 11991 0.13 0.97 ]
|XXXXXXX 850 - 900 : [ 2561 0.03 1.00 ]
| 900 - 950 : [ 74 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AION
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AION 3634607_fasta.screen.trimQ15.SaF > reads.trim15.AION.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AION.rl 2 50
-------------------------------------------------------------------
#Found 40500 total values totalling 23652962.0000. <584.023753 +/- 251.698425>
#Range: [ 0 - 931 ]
#Most likely bin: [ 750 - 800 ] 7159 counts
#Median bin: [ 650 - 700 ] 4694 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 3612 0.09 0.09 ]
|XXXX 50 - 100 : [ 659 0.02 0.11 ]
|XXX 100 - 150 : [ 529 0.01 0.12 ]
|XXX 150 - 200 : [ 515 0.01 0.13 ]
|XXX 200 - 250 : [ 548 0.01 0.14 ]
|XXXX 250 - 300 : [ 673 0.02 0.16 ]
|XXXX 300 - 350 : [ 725 0.02 0.18 ]
|XXXXX 350 - 400 : [ 883 0.02 0.20 ]
|XXXXXX 400 - 450 : [ 1038 0.03 0.23 ]
|XXXXXX 450 - 500 : [ 1153 0.03 0.26 ]
|XXXXXXXXX 500 - 550 : [ 1526 0.04 0.29 ]
|XXXXXXXXXXXX 550 - 600 : [ 2078 0.05 0.34 ]
|XXXXXXXXXXXXXXXXXX 600 - 650 : [ 3147 0.08 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4694 0.12 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6775 0.17 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 7159 0.18 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4129 0.10 0.98 ]
|XXX 850 - 900 : [ 625 0.02 1.00 ]
| 900 - 950 : [ 32 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOO 3634607_fasta.screen.trimQ15.SaF > reads.trim15.AIOO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOO.rl 2 50
-------------------------------------------------------------------
#Found 46992 total values totalling 24685941.0000. <525.322204 +/- 315.553243>
#Range: [ 0 - 923 ]
#Most likely bin: [ 0 - 50 ] 9150 counts
#Median bin: [ 650 - 700 ] 3219 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 9150 0.19 0.19 ]
|XXXX 50 - 100 : [ 989 0.02 0.22 ]
|XXX 100 - 150 : [ 717 0.02 0.23 ]
|XXX 150 - 200 : [ 643 0.01 0.24 ]
|XXX 200 - 250 : [ 638 0.01 0.26 ]
|XXX 250 - 300 : [ 675 0.01 0.27 ]
|XXX 300 - 350 : [ 696 0.01 0.29 ]
|XXX 350 - 400 : [ 798 0.02 0.30 ]
|XXXX 400 - 450 : [ 1000 0.02 0.33 ]
|XXXXX 450 - 500 : [ 1143 0.02 0.35 ]
|XXXXXX 500 - 550 : [ 1471 0.03 0.38 ]
|XXXXXXXXX 550 - 600 : [ 1973 0.04 0.42 ]
|XXXXXXXXXXXX 600 - 650 : [ 2688 0.06 0.48 ]
|XXXXXXXXXXXXXX 650 - 700 : [ 3219 0.07 0.55 ]
|XXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4390 0.09 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6982 0.15 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7843 0.17 0.96 ]
|XXXXXXXX 850 - 900 : [ 1935 0.04 1.00 ]
| 900 - 950 : [ 42 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOP 3634607_fasta.screen.trimQ15.SaF > reads.trim15.AIOP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOP.rl 2 50
-------------------------------------------------------------------
#Found 3840 total values totalling 895173.0000. <233.117969 +/- 259.117633>
#Range: [ 0 - 869 ]
#Most likely bin: [ 0 - 50 ] 1706 counts
#Median bin: [ 50 - 100 ] 245 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1706 0.44 0.44 ]
|XXXXXX 50 - 100 : [ 245 0.06 0.51 ]
|XXX 100 - 150 : [ 118 0.03 0.54 ]
|XX 150 - 200 : [ 103 0.03 0.57 ]
|XXX 200 - 250 : [ 110 0.03 0.59 ]
|XXXXXX 250 - 300 : [ 237 0.06 0.66 ]
|XXX 300 - 350 : [ 119 0.03 0.69 ]
|XX 350 - 400 : [ 83 0.02 0.71 ]
|XX 400 - 450 : [ 105 0.03 0.74 ]
|XXX 450 - 500 : [ 124 0.03 0.77 ]
|XXXX 500 - 550 : [ 170 0.04 0.81 ]
|XXXX 550 - 600 : [ 157 0.04 0.85 ]
|XXXX 600 - 650 : [ 177 0.05 0.90 ]
|XXXX 650 - 700 : [ 177 0.05 0.95 ]
|XXX 700 - 750 : [ 131 0.03 0.98 ]
|X 750 - 800 : [ 58 0.02 0.99 ]
| 800 - 850 : [ 19 0.00 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AZPC
trimt JAZZ trim 15 readlength histogram for AZPF
trimt JAZZ trim 15 readlength histogram for AZPG
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634607
-------------------------------------------------------------------
AION.000001.000100 pUC18.fa LRS.fasta
AION.000101.000200 pUC18.fa LRS.fasta
AION.000201.000300 pUC18.fa LRS.fasta
AIOO.000001.000100 pMCL200.fa LRS.fasta
AIOO.000101.000200 pMCL200.fa LRS.fasta
AIOO.000201.000300 pMCL200.fa LRS.fasta
AIOP.000001.000100 pCC1Fos.fa LRS.fasta
AION.000001.000100 pUC18.fa LRS.fasta
AION.000101.000200 pUC18.fa LRS.fasta
AION.000201.000300 pUC18.fa LRS.fasta
AIOO.000001.000100 pMCL200.fa LRS.fasta
AIOO.000101.000200 pMCL200.fa LRS.fasta
AIOO.000201.000300 pMCL200.fa LRS.fasta
AIOP.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634607_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634607_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 76076 total values totalling 34155.1920. <0.448961 +/- 0.047014>
#Range: [ 0.0714 - 1 ]
#Most likely bin: [ 0.465 - 0.47 ] 3685 counts
#Median bin: [ 0.45 - 0.455 ] 3555 counts
#Entropy = 5.2361 bits
| 0.07 - 0.075 : [ 1 0.00 0.00 ]
#...
| 0.155 - 0.16 : [ 1 0.00 0.00 ]
| 0.16 - 0.165 : [ 4 0.00 0.00 ]
| 0.165 - 0.17 : [ 4 0.00 0.00 ]
| 0.17 - 0.175 : [ 1 0.00 0.00 ]
| 0.175 - 0.18 : [ 1 0.00 0.00 ]
| 0.18 - 0.185 : [ 1 0.00 0.00 ]
| 0.185 - 0.19 : [ 2 0.00 0.00 ]
| 0.19 - 0.195 : [ 2 0.00 0.00 ]
| 0.195 - 0.2 : [ 1 0.00 0.00 ]
| 0.2 - 0.205 : [ 2 0.00 0.00 ]
| 0.205 - 0.21 : [ 5 0.00 0.00 ]
| 0.21 - 0.215 : [ 1 0.00 0.00 ]
| 0.215 - 0.22 : [ 2 0.00 0.00 ]
| 0.22 - 0.225 : [ 4 0.00 0.00 ]
| 0.225 - 0.23 : [ 4 0.00 0.00 ]
| 0.23 - 0.235 : [ 3 0.00 0.00 ]
| 0.235 - 0.24 : [ 2 0.00 0.00 ]
| 0.24 - 0.245 : [ 10 0.00 0.00 ]
| 0.245 - 0.25 : [ 1 0.00 0.00 ]
| 0.25 - 0.255 : [ 6 0.00 0.00 ]
| 0.255 - 0.26 : [ 12 0.00 0.00 ]
| 0.26 - 0.265 : [ 9 0.00 0.00 ]
| 0.265 - 0.27 : [ 11 0.00 0.00 ]
| 0.27 - 0.275 : [ 18 0.00 0.00 ]
| 0.275 - 0.28 : [ 15 0.00 0.00 ]
| 0.28 - 0.285 : [ 30 0.00 0.00 ]
| 0.285 - 0.29 : [ 32 0.00 0.00 ]
|X 0.29 - 0.295 : [ 52 0.00 0.00 ]
|X 0.295 - 0.3 : [ 51 0.00 0.00 ]
|X 0.3 - 0.305 : [ 105 0.00 0.01 ]
|X 0.305 - 0.31 : [ 113 0.00 0.01 ]
|X 0.31 - 0.315 : [ 136 0.00 0.01 ]
|XX 0.315 - 0.32 : [ 160 0.00 0.01 ]
|XX 0.32 - 0.325 : [ 176 0.00 0.01 ]
|XX 0.325 - 0.33 : [ 170 0.00 0.02 ]
|XXX 0.33 - 0.335 : [ 231 0.00 0.02 ]
|XXX 0.335 - 0.34 : [ 258 0.00 0.02 ]
|XXX 0.34 - 0.345 : [ 317 0.00 0.03 ]
|XXX 0.345 - 0.35 : [ 321 0.00 0.03 ]
|XXXX 0.35 - 0.355 : [ 379 0.00 0.03 ]
|XXXXX 0.355 - 0.36 : [ 427 0.01 0.04 ]
|XXXXXX 0.36 - 0.365 : [ 540 0.01 0.05 ]
|XXXXXX 0.365 - 0.37 : [ 598 0.01 0.06 ]
|XXXXXXX 0.37 - 0.375 : [ 677 0.01 0.06 ]
|XXXXXXXXXXX 0.375 - 0.38 : [ 968 0.01 0.08 ]
|XXXXXXXXXXX 0.38 - 0.385 : [ 1009 0.01 0.09 ]
|XXXXXXXXXXXX 0.385 - 0.39 : [ 1145 0.02 0.11 ]
|XXXXXXXXXXXXXX 0.39 - 0.395 : [ 1287 0.02 0.12 ]
|XXXXXXXXXXXXXXX 0.395 - 0.4 : [ 1393 0.02 0.14 ]
|XXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 1627 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 1760 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 1940 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 2183 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 2454 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 2663 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 2837 0.04 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 3071 0.04 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 3239 0.04 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 3368 0.04 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 3555 0.05 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 3493 0.05 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 3617 0.05 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 3685 0.05 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 3365 0.04 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 3234 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 3080 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 2873 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 2440 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1939 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 2159 0.03 0.91 ]
|XXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1506 0.02 0.93 ]
|XXXXXXXXXXXXX 0.51 - 0.515 : [ 1225 0.02 0.95 ]
|XXXXXXXXXX 0.515 - 0.52 : [ 954 0.01 0.96 ]
|XXXXXXXX 0.52 - 0.525 : [ 722 0.01 0.97 ]
|XXXXXX 0.525 - 0.53 : [ 517 0.01 0.98 ]
|XXXX 0.53 - 0.535 : [ 391 0.01 0.98 ]
|XXXX 0.535 - 0.54 : [ 323 0.00 0.98 ]
|XXX 0.54 - 0.545 : [ 248 0.00 0.99 ]
|XX 0.545 - 0.55 : [ 179 0.00 0.99 ]
|X 0.55 - 0.555 : [ 130 0.00 0.99 ]
|X 0.555 - 0.56 : [ 96 0.00 0.99 ]
|X 0.56 - 0.565 : [ 64 0.00 0.99 ]
|X 0.565 - 0.57 : [ 57 0.00 0.99 ]
|X 0.57 - 0.575 : [ 86 0.00 1.00 ]
|X 0.575 - 0.58 : [ 57 0.00 1.00 ]
| 0.58 - 0.585 : [ 30 0.00 1.00 ]
| 0.585 - 0.59 : [ 25 0.00 1.00 ]
| 0.59 - 0.595 : [ 22 0.00 1.00 ]
| 0.595 - 0.6 : [ 10 0.00 1.00 ]
| 0.6 - 0.605 : [ 28 0.00 1.00 ]
| 0.605 - 0.61 : [ 13 0.00 1.00 ]
| 0.61 - 0.615 : [ 13 0.00 1.00 ]
| 0.615 - 0.62 : [ 12 0.00 1.00 ]
| 0.62 - 0.625 : [ 10 0.00 1.00 ]
| 0.625 - 0.63 : [ 19 0.00 1.00 ]
| 0.63 - 0.635 : [ 8 0.00 1.00 ]
| 0.635 - 0.64 : [ 8 0.00 1.00 ]
| 0.64 - 0.645 : [ 9 0.00 1.00 ]
| 0.645 - 0.65 : [ 3 0.00 1.00 ]
| 0.65 - 0.655 : [ 9 0.00 1.00 ]
| 0.655 - 0.66 : [ 3 0.00 1.00 ]
#...
| 0.665 - 0.67 : [ 4 0.00 1.00 ]
#...
| 0.675 - 0.68 : [ 3 0.00 1.00 ]
| 0.68 - 0.685 : [ 1 0.00 1.00 ]
#...
| 0.695 - 0.7 : [ 3 0.00 1.00 ]
| 0.7 - 0.705 : [ 2 0.00 1.00 ]
| 0.705 - 0.71 : [ 2 0.00 1.00 ]
#...
| 0.72 - 0.725 : [ 1 0.00 1.00 ]
#...
| 0.8 - 0.805 : [ 1 0.00 1.00 ]
#...
| 0.82 - 0.825 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 92. 831 reads; 53748 bp (untrimmed), 53729 (trimmed).
Contig 93. 868 reads; 49531 bp (untrimmed), 49448 (trimmed).
Contig 94. 898 reads; 53398 bp (untrimmed), 53168 (trimmed).
Contig 95. 928 reads; 48734 bp (untrimmed), 48658 (trimmed).
Contig 96. 928 reads; 52546 bp (untrimmed), 52509 (trimmed).
Contig 97. 1002 reads; 67925 bp (untrimmed), 67801 (trimmed).
Contig 98. 1024 reads; 61072 bp (untrimmed), 60990 (trimmed).
Contig 99. 1177 reads; 73106 bp (untrimmed), 73088 (trimmed).
Contig 100. 1224 reads; 61665 bp (untrimmed), 61639 (trimmed).
Contig 101. 1381 reads; 91705 bp (untrimmed), 91524 (trimmed).
Contig 102. 1432 reads; 82207 bp (untrimmed), 82164 (trimmed).
Contig 103. 1445 reads; 97901 bp (untrimmed), 97560 (trimmed).
Contig 104. 1540 reads; 84460 bp (untrimmed), 84411 (trimmed).
Contig 105. 1614 reads; 74542 bp (untrimmed), 74523 (trimmed).
Contig 106. 1634 reads; 105243 bp (untrimmed), 105191 (trimmed).
Contig 107. 1692 reads; 82987 bp (untrimmed), 82943 (trimmed).
Contig 108. 1828 reads; 89139 bp (untrimmed), 88546 (trimmed).
Contig 109. 1964 reads; 112415 bp (untrimmed), 112341 (trimmed).
Contig 110. 1966 reads; 124624 bp (untrimmed), 124530 (trimmed).
Contig 111. 2099 reads; 103638 bp (untrimmed), 103547 (trimmed).
Contig 112. 2172 reads; 142608 bp (untrimmed), 142394 (trimmed).
Contig 113. 2415 reads; 129856 bp (untrimmed), 129735 (trimmed).
Contig 114. 3272 reads; 166401 bp (untrimmed), 166032 (trimmed).
Contig 115. 3883 reads; 188262 bp (untrimmed), 188143 (trimmed).
Contig 116. 3895 reads; 224815 bp (untrimmed), 224709 (trimmed).
Contig 117. 8276 reads; 439976 bp (untrimmed), 439855 (trimmed).
Contig 118. 8600 reads; 453215 bp (untrimmed), 452941 (trimmed).
--------------------------------------------------------------
Totals 76380 reads; 4491474 bp (untrimmed), 4471200 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4488117 bases = 14.94 +- 7.14 = 0.41 +- 5.69
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 113 total values totalling 1101.4300. <9.747168 +/- 5.811518>
#Range: [ 1.47 - 19.49 ]
#Most likely bin: [ 3 - 3.5 ] 9 counts
#Median bin: [ 10.5 - 11 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 1 - 1.5 : [ 1 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 9 0.08 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 9 0.08 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 5 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 9 0.08 0.29 ]
|XXXXXXXXX 3.5 - 4 : [ 2 0.02 0.31 ]
|XXXXXXXXX 4 - 4.5 : [ 2 0.02 0.33 ]
|XXXX 4.5 - 5 : [ 1 0.01 0.34 ]
|XXXX 5 - 5.5 : [ 1 0.01 0.35 ]
|XXXX 5.5 - 6 : [ 1 0.01 0.35 ]
#...
|XXXXXXXXXXXXX 6.5 - 7 : [ 3 0.03 0.38 ]
|XXXX 7 - 7.5 : [ 1 0.01 0.39 ]
|XXXXXXXXX 7.5 - 8 : [ 2 0.02 0.41 ]
#...
|XXXXXXXXX 8.5 - 9 : [ 2 0.02 0.42 ]
|XXXXXXXXX 9 - 9.5 : [ 2 0.02 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 5 0.04 0.49 ]
|XXXX 10 - 10.5 : [ 1 0.01 0.50 ]
|XXXXXXXXX 10.5 - 11 : [ 2 0.02 0.51 ]
|XXXX 11 - 11.5 : [ 1 0.01 0.52 ]
|XXXX 11.5 - 12 : [ 1 0.01 0.53 ]
|XXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 4 0.04 0.57 ]
|XXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.04 0.60 ]
|XXXXXXXXXXXXX 13 - 13.5 : [ 3 0.03 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 6 0.05 0.68 ]
|XXXX 14 - 14.5 : [ 1 0.01 0.69 ]
|XXXXXXXXXXXXXXXXXX 14.5 - 15 : [ 4 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15 - 15.5 : [ 8 0.07 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXX 15.5 - 16 : [ 5 0.04 0.84 ]
|XXXXXXXXXXXXX 16 - 16.5 : [ 3 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXX 16.5 - 17 : [ 5 0.04 0.91 ]
|XXXXXXXXXXXXX 17 - 17.5 : [ 3 0.03 0.94 ]
|XXXXXXXXXXXXXXXXXX 17.5 - 18 : [ 4 0.04 0.97 ]
|XXXX 18 - 18.5 : [ 1 0.01 0.98 ]
|XXXX 18.5 - 19 : [ 1 0.01 0.99 ]
|XXXX 19 - 19.5 : [ 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 81 total values totalling 1001.3400. <12.362222 +/- 4.481297>
#Range: [ 2.79 - 19.49 ]
#Most likely bin: [ 15 - 15.5 ] 7 counts
#Median bin: [ 13.5 - 14 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 2.5 - 3 : [ 1 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 5 0.06 0.07 ]
|XXXXXX 3.5 - 4 : [ 1 0.01 0.09 ]
|XXXXXXXXXXX 4 - 4.5 : [ 2 0.02 0.11 ]
#...
|XXXXXX 5 - 5.5 : [ 1 0.01 0.12 ]
#...
|XXXXXXXXXXXXXXXXX 6.5 - 7 : [ 3 0.04 0.16 ]
|XXXXXX 7 - 7.5 : [ 1 0.01 0.17 ]
|XXXXXXXXXXX 7.5 - 8 : [ 2 0.02 0.20 ]
#...
|XXXXXXXXXXX 8.5 - 9 : [ 2 0.02 0.22 ]
|XXXXXXXXXXX 9 - 9.5 : [ 2 0.02 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 4 0.05 0.30 ]
|XXXXXX 10 - 10.5 : [ 1 0.01 0.31 ]
|XXXXXXXXXXX 10.5 - 11 : [ 2 0.02 0.33 ]
|XXXXXX 11 - 11.5 : [ 1 0.01 0.35 ]
|XXXXXX 11.5 - 12 : [ 1 0.01 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 4 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.05 0.46 ]
|XXXXXXXXXXXXXXXXX 13 - 13.5 : [ 3 0.04 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 6 0.07 0.57 ]
|XXXXXX 14 - 14.5 : [ 1 0.01 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXX 14.5 - 15 : [ 4 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15 - 15.5 : [ 7 0.09 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15.5 - 16 : [ 5 0.06 0.78 ]
|XXXXXXXXXXXXXXXXX 16 - 16.5 : [ 3 0.04 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 16.5 - 17 : [ 5 0.06 0.88 ]
|XXXXXXXXXXXXXXXXX 17 - 17.5 : [ 3 0.04 0.91 ]
|XXXXXXXXXXXXXXXXXXXXXXX 17.5 - 18 : [ 4 0.05 0.96 ]
|XXXXXX 18 - 18.5 : [ 1 0.01 0.98 ]
|XXXXXX 18.5 - 19 : [ 1 0.01 0.99 ]
|XXXXXX 19 - 19.5 : [ 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 24 5 reads 2884 bases = 1.47 +- 0.55 = 0.25 +- 1.45
Contig 7 2 reads 1187 bases = 1.51 +- 0.50 = 0.11 +- 0.69
Contig 12 3 reads 1648 bases = 1.61 +- 0.66 = 0.59 +- 0.50
Contig 6 2 reads 946 bases = 1.61 +- 0.49 = 1.61 +- 0.49
Contig 10 3 reads 1628 bases = 1.65 +- 0.48 = 1.65 +- 0.48
Contig 13 3 reads 1601 bases = 1.71 +- 0.66 = 1.71 +- 0.66
Contig 15 3 reads 1482 bases = 1.72 +- 0.74 = 0.43 +- 1.12
Contig 14 3 reads 1417 bases = 1.78 +- 0.71 = 1.78 +- 0.71
Contig 4 2 reads 979 bases = 1.87 +- 0.34 = 1.87 +- 0.34
Contig 19 4 reads 1637 bases = 1.92 +- 1.08 = -0.49 +- 0.50
Contig 29 6 reads 2707 bases = 2.01 +- 1.01 = 0.70 +- 0.57
Contig 11 3 reads 1365 bases = 2.02 +- 0.83 = 2.02 +- 0.83
Contig 23 5 reads 1727 bases = 2.03 +- 0.97 = 2.03 +- 0.97
Contig 16 4 reads 1536 bases = 2.14 +- 0.82 = 2.14 +- 0.82
Contig 21 4 reads 1522 bases = 2.20 +- 0.93 = 1.18 +- 1.27
Contig 22 4 reads 1528 bases = 2.22 +- 0.81 = 0.91 +- 0.54
Contig 26 6 reads 2460 bases = 2.28 +- 1.15 = 0.79 +- 1.76
Contig 20 4 reads 1497 bases = 2.35 +- 1.25 = 1.04 +- 1.56
Contig 9 3 reads 646 bases = 2.47 +- 0.81 = 2.47 +- 0.81
Contig 27 6 reads 1627 bases = 2.70 +- 1.26 = 1.51 +- 1.25
Contig 81 566 reads 31190 bases = 15.88 +- 6.81 = 0.45 +- 5.05
Contig 78 534 reads 29648 bases = 15.96 +- 5.73 = 1.90 +- 6.28
Contig 104 1540 reads 84460 bases = 16.07 +- 6.51 = -0.09 +- 5.17
Contig 74 499 reads 27009 bases = 16.18 +- 9.14 = 1.56 +- 6.76
Contig 113 2415 reads 129856 bases = 16.37 +- 6.45 = 0.61 +- 5.72
Contig 52 63 reads 3402 bases = 16.51 +- 11.33 = -0.15 +- 6.11
Contig 117 8276 reads 439976 bases = 16.58 +- 6.12 = 0.11 +- 5.56
Contig 118 8600 reads 453215 bases = 16.68 +- 6.52 = 0.17 +- 5.37
Contig 95 928 reads 48734 bases = 16.75 +- 7.19 = 0.59 +- 6.44
Contig 90 722 reads 37609 bases = 16.86 +- 6.71 = 1.35 +- 7.51
Contig 114 3272 reads 166401 bases = 17.16 +- 6.64 = 0.22 +- 5.22
Contig 91 816 reads 41483 bases = 17.36 +- 6.71 = 0.11 +- 4.85
Contig 100 1224 reads 61665 bases = 17.48 +- 6.82 = 0.09 +- 6.06
Contig 111 2099 reads 103638 bases = 17.76 +- 8.67 = 0.48 +- 7.45
Contig 76 514 reads 25257 bases = 17.79 +- 10.27 = 1.95 +- 4.53
Contig 107 1692 reads 82987 bases = 17.87 +- 6.54 = 0.77 +- 5.17
Contig 108 1828 reads 89139 bases = 17.96 +- 6.61 = 0.69 +- 4.85
Contig 115 3883 reads 188262 bases = 18.09 +- 10.98 = 0.27 +- 6.23
Contig 105 1614 reads 74542 bases = 18.91 +- 6.77 = 0.32 +- 5.18
Contig 87 627 reads 28398 bases = 19.49 +- 6.27 = 0.06 +- 3.97
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 31
Chimeric reads = 226
Suspect alignments = 584
-------------------------------------------------------------------
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/microbe3/3634607/edit_dir.12Jul04.QD