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 in progress (or initial analysis of completed)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3436494 1500 1525 Moorella thermoacetica
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Moorella_thermoacetica
-------------------------------------------------------------------
Thermoanaerobacteriaceae, family, eubacteria
Clostridia, class, eubacteria
Thermoanaerobacteriales, order, eubacteria
Moorella, genus, eubacteria
Moorella group, eubacteria
Moorella thermoacetica, species, eubacteria
Firmicutes (Gram-positive bacteria), phylum, eubacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2834810
# phrap: 2627223
# db:
altered.
1500000
2320677 +/- 586462
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 46968
Number of reads with percent X's >= 20%: 5224 = 8.4%
Number of reads with percent X's >= 50%: 4748 = 7.7%
Number of reads with percent X's >= 80%: 3310 = 5.3%
Total reads in project: 61901
Total bp X'd : 7122243
reads >= 20% >= 50% >= 80% screened
Nr with L09136 9405 254 155 111
Nr with LRS 76 76 74 73
Nr with pCC1Fos 1464 2 2 2
Nr with pMCL200_JGI_XZX+XZK 36023 4892 4517 3124
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 6077
Number of reads with percent X's >= 20%: 4647 = 57.4%
Number of reads with percent X's >= 50%: 4485 = 55.4%
Number of reads with percent X's >= 80%: 3263 = 40.3%
Total reads in project: 8093
Total bp X'd : 4224802
reads >= 20% >= 50% >= 80% screened
Nr with L09136 203 124 118 109
Nr with LRS 76 76 74 73
Nr with pCC1Fos 22 2 2 2
Nr with pMCL200_JGI_XZX+XZK 5776 4445 4291 3079
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 12275057
C = 14673498
G = 14780344
T = 11854012
N = 372005
X = 7122243
GC fraction = 0.48
Total = 61077159
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436494_fasta.screen.contigs
-------------------------------------------------------------------
A 661858
C 790264
G 778535
T 661839
N 735
fraction GC = 0.54
total bases = 2893231
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 AAOP reads.list > grep.reads.list.AAOP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAOP 4 500
-------------------------------------------------------------------
#Found 8732 total values totalling 29492327.0000. <3377.499656 +/- 725.766308>
#Range: [ 796 - 11270 ]
#Most likely bin: [ 3000 - 3500 ] 2539 counts
#Median bin: [ 3000 - 3500 ] 2539 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 31 0.00 0.00 ]
|XX 1000 - 1500 : [ 132 0.02 0.02 ]
|XX 1500 - 2000 : [ 116 0.01 0.03 ]
|XXXX 2000 - 2500 : [ 249 0.03 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2161 0.25 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2539 0.29 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1847 0.21 0.81 ]
|XXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1051 0.12 0.93 ]
|XXXXXXXX 4500 - 5000 : [ 502 0.06 0.99 ]
|XX 5000 - 5500 : [ 101 0.01 1.00 ]
| 5500 - 6000 : [ 1 0.00 1.00 ]
#...
| 10000 - 10500 : [ 1 0.00 1.00 ]
#...
| 11000 - 11500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAOR reads.list > grep.reads.list.AAOR
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAOR 4 500
-------------------------------------------------------------------
#Found 4490 total values totalling 28933038.0000. <6443.883742 +/- 2534.224570>
#Range: [ 884 - 32221 ]
#Most likely bin: [ 7500 - 8000 ] 472 counts
#Median bin: [ 6500 - 7000 ] 274 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 4 0.00 0.00 ]
|XXXXXXXX 1000 - 1500 : [ 94 0.02 0.02 ]
|XXXXXXXXXXXXX 1500 - 2000 : [ 151 0.03 0.06 ]
|XXXXXXXXXXXXX 2000 - 2500 : [ 158 0.04 0.09 ]
|XXXXXXXXXXXXXX 2500 - 3000 : [ 168 0.04 0.13 ]
|XXXXXXXXXXXX 3000 - 3500 : [ 142 0.03 0.16 ]
|XXXXXXXXXXXXXXX 3500 - 4000 : [ 175 0.04 0.20 ]
|XXXXXXXXXXXXXXX 4000 - 4500 : [ 172 0.04 0.24 ]
|XXXXXXXXXXXXXXXXX 4500 - 5000 : [ 206 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXX 5000 - 5500 : [ 216 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 238 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 259 0.06 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 274 0.06 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 392 0.09 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 472 0.11 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 433 0.10 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 354 0.08 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 273 0.06 0.93 ]
|XXXXXXXXXXXXX 9500 - 10000 : [ 152 0.03 0.97 ]
|XXXXXXX 10000 - 10500 : [ 86 0.02 0.98 ]
|XXX 10500 - 11000 : [ 39 0.01 0.99 ]
|X 11000 - 11500 : [ 16 0.00 1.00 ]
|X 11500 - 12000 : [ 10 0.00 1.00 ]
| 12000 - 12500 : [ 1 0.00 1.00 ]
#...
| 13000 - 13500 : [ 1 0.00 1.00 ]
#...
| 30000 - 30500 : [ 2 0.00 1.00 ]
| 30500 - 31000 : [ 1 0.00 1.00 ]
#...
| 32000 - 32500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAOS reads.list > grep.reads.list.AAOS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAOS 4 500
-------------------------------------------------------------------
#Found 641 total values totalling 23994027.0000. <37432.179407 +/- 4811.834677>
#Range: [ 15152 - 59975 ]
#Most likely bin: [ 35500 - 36000 ] 46 counts
#Median bin: [ 37000 - 37500 ] 32 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 15000 - 15500 : [ 1 0.00 0.00 ]
#...
|X 16500 - 17000 : [ 1 0.00 0.00 ]
#...
|X 18500 - 19000 : [ 1 0.00 0.00 ]
|X 19000 - 19500 : [ 1 0.00 0.01 ]
#...
|X 20000 - 20500 : [ 1 0.00 0.01 ]
#...
|X 25500 - 26000 : [ 1 0.00 0.01 ]
#...
|X 26500 - 27000 : [ 1 0.00 0.01 ]
|X 27000 - 27500 : [ 1 0.00 0.01 ]
#...
|XX 28500 - 29000 : [ 2 0.00 0.02 ]
|XXX 29000 - 29500 : [ 3 0.00 0.02 ]
|XX 29500 - 30000 : [ 2 0.00 0.02 ]
|XXX 30000 - 30500 : [ 4 0.01 0.03 ]
|XXX 30500 - 31000 : [ 4 0.01 0.04 ]
|XXXX 31000 - 31500 : [ 5 0.01 0.04 ]
|XXXX 31500 - 32000 : [ 5 0.01 0.05 ]
|XXXXXXXXX 32000 - 32500 : [ 10 0.02 0.07 ]
|XXXXXXXXXXX 32500 - 33000 : [ 13 0.02 0.09 ]
|XXXXXXXXXXXXXX 33000 - 33500 : [ 16 0.02 0.11 ]
|XXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 24 0.04 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 33 0.05 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 26 0.04 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 41 0.06 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 46 0.07 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 43 0.07 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 35 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 32 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 42 0.07 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 37 0.06 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 42 0.07 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 28 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 28 0.04 0.83 ]
|XXXXXXXXXXXXXX 40000 - 40500 : [ 16 0.02 0.85 ]
|XXXXXXXXXXXXXXXXX 40500 - 41000 : [ 20 0.03 0.88 ]
|XXXXXXXXXXXXX 41000 - 41500 : [ 15 0.02 0.90 ]
|XXXXXXXXX 41500 - 42000 : [ 10 0.02 0.92 ]
|XXXXXXX 42000 - 42500 : [ 8 0.01 0.93 ]
|XXXX 42500 - 43000 : [ 5 0.01 0.94 ]
|XXXX 43000 - 43500 : [ 5 0.01 0.95 ]
|XXX 43500 - 44000 : [ 4 0.01 0.95 ]
|XXX 44000 - 44500 : [ 3 0.00 0.96 ]
|X 44500 - 45000 : [ 1 0.00 0.96 ]
|XX 45000 - 45500 : [ 2 0.00 0.96 ]
#...
|X 51500 - 52000 : [ 1 0.00 0.97 ]
|XX 52000 - 52500 : [ 2 0.00 0.97 ]
|X 52500 - 53000 : [ 1 0.00 0.97 ]
|XXX 53000 - 53500 : [ 4 0.01 0.98 ]
|XX 53500 - 54000 : [ 2 0.00 0.98 ]
|XX 54000 - 54500 : [ 2 0.00 0.98 ]
|X 54500 - 55000 : [ 1 0.00 0.98 ]
|XX 55000 - 55500 : [ 2 0.00 0.99 ]
|X 55500 - 56000 : [ 1 0.00 0.99 ]
#...
|XX 56500 - 57000 : [ 2 0.00 0.99 ]
#...
|X 57500 - 58000 : [ 1 0.00 0.99 ]
|XX 58000 - 58500 : [ 2 0.00 1.00 ]
|X 58500 - 59000 : [ 1 0.00 1.00 ]
#...
|X 59500 - 60000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACOB reads.list > grep.reads.list.ACOB
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACOB 4 500
-------------------------------------------------------------------
#Found 8163 total values totalling 59166689.0000. <7248.154968 +/- 1818.132028>
#Range: [ 573 - 37624 ]
#Most likely bin: [ 6500 - 7000 ] 1506 counts
#Median bin: [ 7000 - 7500 ] 1409 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 5 0.00 0.00 ]
|X 1000 - 1500 : [ 36 0.00 0.01 ]
|X 1500 - 2000 : [ 33 0.00 0.01 ]
|X 2000 - 2500 : [ 36 0.00 0.01 ]
|X 2500 - 3000 : [ 35 0.00 0.02 ]
|X 3000 - 3500 : [ 49 0.01 0.02 ]
|X 3500 - 4000 : [ 29 0.00 0.03 ]
|X 4000 - 4500 : [ 42 0.01 0.03 ]
|XX 4500 - 5000 : [ 84 0.01 0.04 ]
|XXXXX 5000 - 5500 : [ 190 0.02 0.07 ]
|XXXXXXXXXXXXX 5500 - 6000 : [ 504 0.06 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 983 0.12 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1506 0.18 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1409 0.17 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1167 0.14 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 873 0.11 0.86 ]
|XXXXXXXXXXXXXXX 8500 - 9000 : [ 571 0.07 0.93 ]
|XXXXXXXXXX 9000 - 9500 : [ 359 0.04 0.97 ]
|XXXX 9500 - 10000 : [ 165 0.02 0.99 ]
|X 10000 - 10500 : [ 45 0.01 0.99 ]
| 10500 - 11000 : [ 5 0.00 1.00 ]
#...
| 23000 - 23500 : [ 1 0.00 1.00 ]
| 23500 - 24000 : [ 3 0.00 1.00 ]
| 24000 - 24500 : [ 6 0.00 1.00 ]
| 24500 - 25000 : [ 5 0.00 1.00 ]
| 25000 - 25500 : [ 12 0.00 1.00 ]
| 25500 - 26000 : [ 3 0.00 1.00 ]
| 26000 - 26500 : [ 6 0.00 1.00 ]
#...
| 37500 - 38000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AAOS 36639 +- 3349 (n=314)
# ACOB 6978 +- 2024 (n=4191)
# AAOP 3272 +- 775 (n=4465)
# AAOR 6056 +- 2676 (n=2324)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436494_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
AAOP 20640 -1 -1 99 669 20615 96 669 98 672
AAOR 13056 -1 -1 96 670 12988 78 564 95 626
AAOS 3072 -1 -1 99 749 3072 97 751 99 760
ACOB 25344 -1 -1 97 700 25226 80 571 94 622
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AAOP 10358 96 664 98 675 10257 96 675 97 668
AAOR 6498 78 553 95 624 6490 78 574 95 628
AAOS 1536 96 747 98 734 1536 99 755 99 787
ACOB 12602 78 562 93 612 12624 83 579 96 633
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436494_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 61901 30305 95.90 cumulative total @@
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 3436494_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 61901 total values totalling 32882802.0000. <531.216006 +/- 253.472047>
#Range: [ 0 - 901 ]
#Most likely bin: [ 700 - 750 ] 11645 counts
#Median bin: [ 600 - 650 ] 7913 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 7732 0.12 0.12 ]
|XXX 50 - 100 : [ 985 0.02 0.14 ]
|XXX 100 - 150 : [ 849 0.01 0.15 ]
|XXX 150 - 200 : [ 901 0.01 0.17 ]
|XXX 200 - 250 : [ 858 0.01 0.18 ]
|XXX 250 - 300 : [ 984 0.02 0.20 ]
|XXX 300 - 350 : [ 1010 0.02 0.22 ]
|XXXX 350 - 400 : [ 1188 0.02 0.23 ]
|XXXXX 400 - 450 : [ 1455 0.02 0.26 ]
|XXXXXX 450 - 500 : [ 1804 0.03 0.29 ]
|XXXXXXXXX 500 - 550 : [ 2621 0.04 0.33 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 4314 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 7913 0.13 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 11430 0.18 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 11645 0.19 0.90 ]
|XXXXXXXXXXXXXXXXXX 750 - 800 : [ 5226 0.08 0.98 ]
|XXX 800 - 850 : [ 918 0.01 1.00 ]
| 850 - 900 : [ 67 0.00 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAOP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAOP 3436494_fasta.screen.trimQ15.SaF > reads.trim15.AAOP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAOP.rl 2 50
-------------------------------------------------------------------
#Found 20615 total values totalling 13253696.0000. <642.915159 +/- 155.204728>
#Range: [ 0 - 834 ]
#Most likely bin: [ 650 - 700 ] 6341 counts
#Median bin: [ 650 - 700 ] 6341 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 0 - 50 : [ 743 0.04 0.04 ]
|X 50 - 100 : [ 85 0.00 0.04 ]
| 100 - 150 : [ 59 0.00 0.04 ]
| 150 - 200 : [ 67 0.00 0.05 ]
| 200 - 250 : [ 62 0.00 0.05 ]
| 250 - 300 : [ 77 0.00 0.05 ]
|X 300 - 350 : [ 95 0.00 0.06 ]
|X 350 - 400 : [ 135 0.01 0.06 ]
|X 400 - 450 : [ 154 0.01 0.07 ]
|X 450 - 500 : [ 160 0.01 0.08 ]
|XX 500 - 550 : [ 324 0.02 0.10 ]
|XXXXXXX 550 - 600 : [ 1057 0.05 0.15 ]
|XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3307 0.16 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 6341 0.31 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6238 0.30 0.92 ]
|XXXXXXXXXX 750 - 800 : [ 1657 0.08 1.00 ]
| 800 - 850 : [ 54 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAOR
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAOR 3436494_fasta.screen.trimQ15.SaF > reads.trim15.AAOR.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAOR.rl 2 50
-------------------------------------------------------------------
#Found 12988 total values totalling 5720170.0000. <440.419618 +/- 261.411393>
#Range: [ 0 - 818 ]
#Most likely bin: [ 0 - 50 ] 2745 counts
#Median bin: [ 550 - 600 ] 1555 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2745 0.21 0.21 ]
|XX 50 - 100 : [ 120 0.01 0.22 ]
|XX 100 - 150 : [ 112 0.01 0.23 ]
|XX 150 - 200 : [ 159 0.01 0.24 ]
|XXX 200 - 250 : [ 185 0.01 0.26 ]
|XXXX 250 - 300 : [ 254 0.02 0.28 ]
|XXXX 300 - 350 : [ 282 0.02 0.30 ]
|XXXXX 350 - 400 : [ 351 0.03 0.32 ]
|XXXXXX 400 - 450 : [ 444 0.03 0.36 ]
|XXXXXXXXX 450 - 500 : [ 632 0.05 0.41 ]
|XXXXXXXXXXXXXX 500 - 550 : [ 957 0.07 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1555 0.12 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2260 0.17 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1975 0.15 0.93 ]
|XXXXXXXXXXXX 700 - 750 : [ 798 0.06 0.99 ]
|XX 750 - 800 : [ 153 0.01 1.00 ]
| 800 - 850 : [ 6 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAOS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAOS 3436494_fasta.screen.trimQ15.SaF > reads.trim15.AAOS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAOS.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 2245708.0000. <731.024740 +/- 150.840708>
#Range: [ 0 - 901 ]
#Most likely bin: [ 750 - 800 ] 1251 counts
#Median bin: [ 750 - 800 ] 1251 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 0 - 50 : [ 79 0.03 0.03 ]
| 50 - 100 : [ 6 0.00 0.03 ]
| 100 - 150 : [ 2 0.00 0.03 ]
| 150 - 200 : [ 4 0.00 0.03 ]
| 200 - 250 : [ 12 0.00 0.03 ]
| 250 - 300 : [ 15 0.00 0.04 ]
| 300 - 350 : [ 15 0.00 0.04 ]
| 350 - 400 : [ 11 0.00 0.05 ]
|X 400 - 450 : [ 20 0.01 0.05 ]
| 450 - 500 : [ 12 0.00 0.06 ]
| 500 - 550 : [ 13 0.00 0.06 ]
|X 550 - 600 : [ 31 0.01 0.07 ]
|XX 600 - 650 : [ 67 0.02 0.09 ]
|XXXXX 650 - 700 : [ 168 0.05 0.15 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 643 0.21 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1251 0.41 0.76 ]
|XXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 665 0.22 0.98 ]
|XX 850 - 900 : [ 57 0.02 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AGXN
trimt JAZZ trim 15 readlength histogram for ACOB
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACOB 3436494_fasta.screen.trimQ15.SaF > reads.trim15.ACOB.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACOB.rl 2 50
-------------------------------------------------------------------
#Found 25226 total values totalling 11663228.0000. <462.349481 +/- 275.627332>
#Range: [ 0 - 885 ]
#Most likely bin: [ 0 - 50 ] 4165 counts
#Median bin: [ 550 - 600 ] 1671 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 4165 0.17 0.17 ]
|XXXXXXX 50 - 100 : [ 774 0.03 0.20 ]
|XXXXXX 100 - 150 : [ 676 0.03 0.22 ]
|XXXXXX 150 - 200 : [ 671 0.03 0.25 ]
|XXXXXX 200 - 250 : [ 599 0.02 0.27 ]
|XXXXXX 250 - 300 : [ 638 0.03 0.30 ]
|XXXXXX 300 - 350 : [ 618 0.02 0.32 ]
|XXXXXXX 350 - 400 : [ 691 0.03 0.35 ]
|XXXXXXXX 400 - 450 : [ 837 0.03 0.38 ]
|XXXXXXXXXX 450 - 500 : [ 1000 0.04 0.42 ]
|XXXXXXXXXXXXX 500 - 550 : [ 1327 0.05 0.48 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 1671 0.07 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2279 0.09 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2946 0.12 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3966 0.16 0.91 ]
|XXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2165 0.09 0.99 ]
|XX 800 - 850 : [ 193 0.01 1.00 ]
| 850 - 900 : [ 10 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436494
-------------------------------------------------------------------
AAOP.000001.000100 pUC18.fa.4 LRS.fasta
AAOP.000101.000200 pUC18.fa.4 LRS.fasta
AAOR.000001.000100 pMCL200.fa.4 LRS.fasta
AAOS.000001.000100 pCC1Fos.fa.4 LRS.fasta
ACOB.000001.000100 pMCL200.fa.4 LRS.fasta
ACOB.000101.000200 pMCL200.fa.4 LRS.fasta
AAOP.000001.000100 pUC18.fa.4 LRS.fasta
AAOP.000101.000200 pUC18.fa.4 LRS.fasta
AAOR.000001.000100 pMCL200.fa.4 LRS.fasta
AAOS.000001.000100 pCC1Fos.fa.4 LRS.fasta
ACOB.000001.000100 pMCL200.fa.4 LRS.fasta
ACOB.000101.000200 pMCL200.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436494_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436494_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 54290 total values totalling 30014.7304. <0.552859 +/- 0.073435>
#Range: [ 0 - 0.9656 ]
#Most likely bin: [ 0.58 - 0.585 ] 1897 counts
#Median bin: [ 0.56 - 0.565 ] 1706 counts
| 0 - 0.005 : [ 6 0.00 0.00 ]
#...
| 0.08 - 0.085 : [ 1 0.00 0.00 ]
#...
| 0.14 - 0.145 : [ 1 0.00 0.00 ]
#...
| 0.155 - 0.16 : [ 1 0.00 0.00 ]
#...
| 0.2 - 0.205 : [ 1 0.00 0.00 ]
| 0.205 - 0.21 : [ 2 0.00 0.00 ]
| 0.21 - 0.215 : [ 2 0.00 0.00 ]
| 0.215 - 0.22 : [ 5 0.00 0.00 ]
| 0.22 - 0.225 : [ 3 0.00 0.00 ]
| 0.225 - 0.23 : [ 4 0.00 0.00 ]
| 0.23 - 0.235 : [ 2 0.00 0.00 ]
| 0.235 - 0.24 : [ 3 0.00 0.00 ]
| 0.24 - 0.245 : [ 6 0.00 0.00 ]
| 0.245 - 0.25 : [ 3 0.00 0.00 ]
| 0.25 - 0.255 : [ 16 0.00 0.00 ]
| 0.255 - 0.26 : [ 6 0.00 0.00 ]
| 0.26 - 0.265 : [ 5 0.00 0.00 ]
| 0.265 - 0.27 : [ 17 0.00 0.00 ]
| 0.27 - 0.275 : [ 16 0.00 0.00 ]
| 0.275 - 0.28 : [ 16 0.00 0.00 ]
| 0.28 - 0.285 : [ 15 0.00 0.00 ]
| 0.285 - 0.29 : [ 16 0.00 0.00 ]
|X 0.29 - 0.295 : [ 30 0.00 0.00 ]
|X 0.295 - 0.3 : [ 29 0.00 0.00 ]
|X 0.3 - 0.305 : [ 30 0.00 0.00 ]
|X 0.305 - 0.31 : [ 52 0.00 0.01 ]
|X 0.31 - 0.315 : [ 54 0.00 0.01 ]
|X 0.315 - 0.32 : [ 51 0.00 0.01 ]
|XX 0.32 - 0.325 : [ 73 0.00 0.01 ]
|XX 0.325 - 0.33 : [ 78 0.00 0.01 ]
|X 0.33 - 0.335 : [ 68 0.00 0.01 ]
|XX 0.335 - 0.34 : [ 95 0.00 0.01 ]
|XX 0.34 - 0.345 : [ 116 0.00 0.02 ]
|XXX 0.345 - 0.35 : [ 123 0.00 0.02 ]
|XX 0.35 - 0.355 : [ 105 0.00 0.02 ]
|XX 0.355 - 0.36 : [ 111 0.00 0.02 ]
|XX 0.36 - 0.365 : [ 112 0.00 0.02 ]
|XXX 0.365 - 0.37 : [ 125 0.00 0.03 ]
|XX 0.37 - 0.375 : [ 108 0.00 0.03 ]
|XXX 0.375 - 0.38 : [ 122 0.00 0.03 ]
|XXX 0.38 - 0.385 : [ 127 0.00 0.03 ]
|XXX 0.385 - 0.39 : [ 140 0.00 0.03 ]
|XXX 0.39 - 0.395 : [ 142 0.00 0.04 ]
|XXX 0.395 - 0.4 : [ 157 0.00 0.04 ]
|XXXX 0.4 - 0.405 : [ 188 0.00 0.04 ]
|XXXX 0.405 - 0.41 : [ 206 0.00 0.05 ]
|XXXXX 0.41 - 0.415 : [ 216 0.00 0.05 ]
|XXXXX 0.415 - 0.42 : [ 239 0.00 0.06 ]
|XXXXXX 0.42 - 0.425 : [ 266 0.00 0.06 ]
|XXXXXX 0.425 - 0.43 : [ 271 0.00 0.07 ]
|XXXXXX 0.43 - 0.435 : [ 302 0.01 0.07 ]
|XXXXXX 0.435 - 0.44 : [ 288 0.01 0.08 ]
|XXXXXXX 0.44 - 0.445 : [ 338 0.01 0.08 ]
|XXXXXXXX 0.445 - 0.45 : [ 388 0.01 0.09 ]
|XXXXXXX 0.45 - 0.455 : [ 349 0.01 0.10 ]
|XXXXXXXXX 0.455 - 0.46 : [ 417 0.01 0.10 ]
|XXXXXXXXXXX 0.46 - 0.465 : [ 519 0.01 0.11 ]
|XXXXXXXXXXX 0.465 - 0.47 : [ 523 0.01 0.12 ]
|XXXXXXXXXXXX 0.47 - 0.475 : [ 568 0.01 0.13 ]
|XXXXXXXXXXXXX 0.475 - 0.48 : [ 632 0.01 0.15 ]
|XXXXXXXXXXXXXX 0.48 - 0.485 : [ 685 0.01 0.16 ]
|XXXXXXXXXXXXXXX 0.485 - 0.49 : [ 690 0.01 0.17 ]
|XXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 799 0.01 0.19 ]
|XXXXXXXXXXXXXXX 0.495 - 0.5 : [ 691 0.01 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1053 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 863 0.02 0.23 ]
|XXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 947 0.02 0.25 ]
|XXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1008 0.02 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1155 0.02 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1184 0.02 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1314 0.02 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1356 0.02 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1366 0.03 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1394 0.03 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1506 0.03 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1668 0.03 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1706 0.03 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1798 0.03 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1844 0.03 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1817 0.03 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1897 0.03 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1832 0.03 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 1762 0.03 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 1673 0.03 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1734 0.03 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1525 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1423 0.03 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1302 0.02 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1189 0.02 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 1147 0.02 0.89 ]
|XXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 957 0.02 0.91 ]
|XXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 871 0.02 0.92 ]
|XXXXXXXXXXXXXXX 0.64 - 0.645 : [ 735 0.01 0.94 ]
|XXXXXXXXXXXXX 0.645 - 0.65 : [ 618 0.01 0.95 ]
|XXXXXXXXXXX 0.65 - 0.655 : [ 529 0.01 0.96 ]
|XXXXXXXXX 0.655 - 0.66 : [ 426 0.01 0.96 ]
|XXXXXXXX 0.66 - 0.665 : [ 363 0.01 0.97 ]
|XXXXXXX 0.665 - 0.67 : [ 333 0.01 0.98 ]
|XXXXX 0.67 - 0.675 : [ 232 0.00 0.98 ]
|XXXXX 0.675 - 0.68 : [ 216 0.00 0.99 ]
|XXX 0.68 - 0.685 : [ 142 0.00 0.99 ]
|XXX 0.685 - 0.69 : [ 119 0.00 0.99 ]
|XX 0.69 - 0.695 : [ 97 0.00 0.99 ]
|XX 0.695 - 0.7 : [ 78 0.00 0.99 ]
|XX 0.7 - 0.705 : [ 78 0.00 1.00 ]
|X 0.705 - 0.71 : [ 52 0.00 1.00 ]
|X 0.71 - 0.715 : [ 38 0.00 1.00 ]
| 0.715 - 0.72 : [ 20 0.00 1.00 ]
|X 0.72 - 0.725 : [ 25 0.00 1.00 ]
| 0.725 - 0.73 : [ 16 0.00 1.00 ]
| 0.73 - 0.735 : [ 16 0.00 1.00 ]
| 0.735 - 0.74 : [ 6 0.00 1.00 ]
| 0.74 - 0.745 : [ 10 0.00 1.00 ]
| 0.745 - 0.75 : [ 6 0.00 1.00 ]
| 0.75 - 0.755 : [ 15 0.00 1.00 ]
| 0.755 - 0.76 : [ 4 0.00 1.00 ]
| 0.76 - 0.765 : [ 3 0.00 1.00 ]
| 0.765 - 0.77 : [ 6 0.00 1.00 ]
| 0.77 - 0.775 : [ 7 0.00 1.00 ]
| 0.775 - 0.78 : [ 4 0.00 1.00 ]
| 0.78 - 0.785 : [ 7 0.00 1.00 ]
| 0.785 - 0.79 : [ 7 0.00 1.00 ]
| 0.79 - 0.795 : [ 3 0.00 1.00 ]
| 0.795 - 0.8 : [ 1 0.00 1.00 ]
| 0.8 - 0.805 : [ 4 0.00 1.00 ]
#...
| 0.81 - 0.815 : [ 1 0.00 1.00 ]
| 0.815 - 0.82 : [ 2 0.00 1.00 ]
| 0.82 - 0.825 : [ 1 0.00 1.00 ]
#...
| 0.83 - 0.835 : [ 2 0.00 1.00 ]
#...
| 0.84 - 0.845 : [ 2 0.00 1.00 ]
| 0.845 - 0.85 : [ 1 0.00 1.00 ]
| 0.85 - 0.855 : [ 2 0.00 1.00 ]
#...
| 0.89 - 0.895 : [ 1 0.00 1.00 ]
#...
| 0.965 - 0.97 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 283. 900 reads; 43122 bp (untrimmed), 43122 (trimmed).
Contig 284. 920 reads; 36536 bp (untrimmed), 36229 (trimmed).
Contig 285. 939 reads; 40344 bp (untrimmed), 39975 (trimmed).
Contig 286. 946 reads; 41956 bp (untrimmed), 41956 (trimmed).
Contig 287. 951 reads; 41635 bp (untrimmed), 41635 (trimmed).
Contig 288. 1003 reads; 42933 bp (untrimmed), 42933 (trimmed).
Contig 289. 1014 reads; 52154 bp (untrimmed), 52154 (trimmed).
Contig 290. 1052 reads; 55150 bp (untrimmed), 55108 (trimmed).
Contig 291. 1053 reads; 42239 bp (untrimmed), 42158 (trimmed).
Contig 292. 1094 reads; 49676 bp (untrimmed), 49626 (trimmed).
Contig 293. 1102 reads; 70940 bp (untrimmed), 70940 (trimmed).
Contig 294. 1188 reads; 46722 bp (untrimmed), 46684 (trimmed).
Contig 295. 1345 reads; 87846 bp (untrimmed), 87750 (trimmed).
Contig 296. 1461 reads; 63080 bp (untrimmed), 63074 (trimmed).
Contig 297. 1494 reads; 76873 bp (untrimmed), 76663 (trimmed).
Contig 298. 1531 reads; 86216 bp (untrimmed), 86164 (trimmed).
Contig 299. 1708 reads; 80685 bp (untrimmed), 80241 (trimmed).
Contig 300. 1739 reads; 73816 bp (untrimmed), 73809 (trimmed).
Contig 301. 1942 reads; 89030 bp (untrimmed), 88944 (trimmed).
Contig 302. 2004 reads; 86486 bp (untrimmed), 86358 (trimmed).
Contig 303. 2054 reads; 96149 bp (untrimmed), 95874 (trimmed).
Contig 304. 2124 reads; 92657 bp (untrimmed), 92608 (trimmed).
Contig 305. 2131 reads; 95782 bp (untrimmed), 95781 (trimmed).
Contig 306. 2330 reads; 96228 bp (untrimmed), 95959 (trimmed).
Contig 307. 3120 reads; 147447 bp (untrimmed), 147158 (trimmed).
Contig 308. 3310 reads; 132295 bp (untrimmed), 132255 (trimmed).
Contig 309. 4528 reads; 227241 bp (untrimmed), 227182 (trimmed).
--------------------------------------------------------------
Totals 53808 reads; 2893231 bp (untrimmed), 2834810 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2616848 bases = 15.31 +- 7.61 = 0.47 +- 6.71
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 70 total values totalling 846.4900. <12.092714 +/- 5.055125>
#Range: [ 2.79 - 19.15 ]
#Most likely bin: [ 16.5 - 17 ] 5 counts
#Median bin: [ 12.5 - 13 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXX 2.5 - 3 : [ 2 0.03 0.03 ]
#...
|XXXXXXXXXXXXXXXX 3.5 - 4 : [ 2 0.03 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 3 0.04 0.10 ]
|XXXXXXXXXXXXXXXX 4.5 - 5 : [ 2 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 4 0.06 0.19 ]
#...
|XXXXXXXXXXXXXXXX 6 - 6.5 : [ 2 0.03 0.21 ]
|XXXXXXXX 6.5 - 7 : [ 1 0.01 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 3 0.04 0.27 ]
|XXXXXXXX 7.5 - 8 : [ 1 0.01 0.29 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 5 0.07 0.36 ]
|XXXXXXXX 10 - 10.5 : [ 1 0.01 0.37 ]
|XXXXXXXXXXXXXXXX 10.5 - 11 : [ 2 0.03 0.40 ]
|XXXXXXXX 11 - 11.5 : [ 1 0.01 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.04 0.46 ]
|XXXXXXXX 12 - 12.5 : [ 1 0.01 0.47 ]
|XXXXXXXXXXXXXXXX 12.5 - 13 : [ 2 0.03 0.50 ]
|XXXXXXXXXXXXXXXX 13 - 13.5 : [ 2 0.03 0.53 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 3 0.04 0.57 ]
|XXXXXXXXXXXXXXXX 14.5 - 15 : [ 2 0.03 0.60 ]
|XXXXXXXXXXXXXXXX 15 - 15.5 : [ 2 0.03 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15.5 - 16 : [ 5 0.07 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 16 - 16.5 : [ 3 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 16.5 - 17 : [ 5 0.07 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 17 - 17.5 : [ 3 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 17.5 - 18 : [ 3 0.04 0.90 ]
|XXXXXXXXXXXXXXXX 18 - 18.5 : [ 2 0.03 0.93 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 18.5 - 19 : [ 3 0.04 0.97 ]
|XXXXXXXXXXXXXXXX 19 - 19.5 : [ 2 0.03 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 70 total values totalling 846.4900. <12.092714 +/- 5.055125>
#Range: [ 2.79 - 19.15 ]
#Most likely bin: [ 16.5 - 17 ] 5 counts
#Median bin: [ 12.5 - 13 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXX 2.5 - 3 : [ 2 0.03 0.03 ]
#...
|XXXXXXXXXXXXXXXX 3.5 - 4 : [ 2 0.03 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 3 0.04 0.10 ]
|XXXXXXXXXXXXXXXX 4.5 - 5 : [ 2 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 4 0.06 0.19 ]
#...
|XXXXXXXXXXXXXXXX 6 - 6.5 : [ 2 0.03 0.21 ]
|XXXXXXXX 6.5 - 7 : [ 1 0.01 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 3 0.04 0.27 ]
|XXXXXXXX 7.5 - 8 : [ 1 0.01 0.29 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 5 0.07 0.36 ]
|XXXXXXXX 10 - 10.5 : [ 1 0.01 0.37 ]
|XXXXXXXXXXXXXXXX 10.5 - 11 : [ 2 0.03 0.40 ]
|XXXXXXXX 11 - 11.5 : [ 1 0.01 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.04 0.46 ]
|XXXXXXXX 12 - 12.5 : [ 1 0.01 0.47 ]
|XXXXXXXXXXXXXXXX 12.5 - 13 : [ 2 0.03 0.50 ]
|XXXXXXXXXXXXXXXX 13 - 13.5 : [ 2 0.03 0.53 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 3 0.04 0.57 ]
|XXXXXXXXXXXXXXXX 14.5 - 15 : [ 2 0.03 0.60 ]
|XXXXXXXXXXXXXXXX 15 - 15.5 : [ 2 0.03 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15.5 - 16 : [ 5 0.07 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 16 - 16.5 : [ 3 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 16.5 - 17 : [ 5 0.07 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 17 - 17.5 : [ 3 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 17.5 - 18 : [ 3 0.04 0.90 ]
|XXXXXXXXXXXXXXXX 18 - 18.5 : [ 2 0.03 0.93 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 18.5 - 19 : [ 3 0.04 0.97 ]
|XXXXXXXXXXXXXXXX 19 - 19.5 : [ 2 0.03 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 233 10 reads 2745 bases = 2.79 +- 0.92 = 0.62 +- 1.62
Contig 236 12 reads 2881 bases = 2.80 +- 1.04 = 1.94 +- 1.21
Contig 248 24 reads 5350 bases = 3.65 +- 1.79 = 0.71 +- 2.90
Contig 235 11 reads 2340 bases = 3.81 +- 2.17 = 1.71 +- 2.59
Contig 252 34 reads 6206 bases = 4.02 +- 1.90 = 0.74 +- 2.51
Contig 255 53 reads 9834 bases = 4.14 +- 1.67 = 0.15 +- 3.68
Contig 247 23 reads 4398 bases = 4.28 +- 2.36 = 0.12 +- 2.69
Contig 251 30 reads 4868 bases = 4.93 +- 2.40 = 2.73 +- 2.99
Contig 253 40 reads 5885 bases = 4.94 +- 3.20 = 2.18 +- 2.36
Contig 241 14 reads 2219 bases = 5.00 +- 2.57 = 4.39 +- 2.18
Contig 242 16 reads 2358 bases = 5.00 +- 2.64 = 5.00 +- 2.64
Contig 256 66 reads 10228 bases = 5.24 +- 3.47 = 1.20 +- 2.87
Contig 246 21 reads 3248 bases = 5.27 +- 2.97 = 5.27 +- 2.97
Contig 250 29 reads 3486 bases = 6.09 +- 3.00 = 4.05 +- 1.76
Contig 244 16 reads 2011 bases = 6.17 +- 2.72 = 6.17 +- 2.72
Contig 260 85 reads 9793 bases = 6.72 +- 3.13 = 1.24 +- 3.59
Contig 262 110 reads 11346 bases = 7.34 +- 3.30 = -0.09 +- 4.22
Contig 257 70 reads 7111 bases = 7.42 +- 3.37 = 1.27 +- 3.89
Contig 249 26 reads 2529 bases = 7.47 +- 3.75 = 5.86 +- 3.59
Contig 254 49 reads 5147 bases = 7.57 +- 3.54 = 0.84 +- 2.09
Contig 281 747 reads 34286 bases = 16.41 +- 6.42 = 1.00 +- 6.25
Contig 280 683 reads 31455 bases = 16.43 +- 8.87 = 1.90 +- 6.71
Contig 301 1942 reads 89030 bases = 16.60 +- 8.10 = 0.09 +- 6.62
Contig 292 1094 reads 49676 bases = 16.68 +- 7.74 = 0.08 +- 6.85
Contig 305 2131 reads 95782 bases = 16.86 +- 8.61 = 0.04 +- 6.18
Contig 286 946 reads 41956 bases = 16.90 +- 7.78 = 1.11 +- 5.93
Contig 287 951 reads 41635 bases = 16.92 +- 7.33 = 0.06 +- 6.11
Contig 304 2124 reads 92657 bases = 17.29 +- 7.03 = 0.09 +- 6.69
Contig 302 2004 reads 86486 bases = 17.33 +- 8.44 = -0.08 +- 7.54
Contig 296 1461 reads 63080 bases = 17.40 +- 6.58 = 0.25 +- 6.22
Contig 288 1003 reads 42933 bases = 17.58 +- 7.86 = 0.50 +- 8.27
Contig 285 939 reads 40344 bases = 17.63 +- 8.43 = 0.16 +- 7.52
Contig 300 1739 reads 73816 bases = 17.74 +- 5.92 = 0.42 +- 6.34
Contig 278 451 reads 18868 bases = 18.06 +- 8.97 = 2.06 +- 6.07
Contig 306 2330 reads 96228 bases = 18.20 +- 10.60 = 0.50 +- 6.41
Contig 284 920 reads 36536 bases = 18.71 +- 7.13 = 1.38 +- 5.77
Contig 291 1053 reads 42239 bases = 18.75 +- 8.16 = 1.34 +- 7.69
Contig 270 241 reads 9851 bases = 18.80 +- 15.48 = 2.39 +- 4.31
Contig 308 3310 reads 132295 bases = 19.04 +- 7.22 = 0.14 +- 7.50
Contig 294 1188 reads 46722 bases = 19.15 +- 7.55 = 0.26 +- 6.13
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1354
HQ Discrepant reads = 21
Chimeric reads = 72
Suspect alignments = 591
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 3.01 SUN/Ultra-2
Equivalent to Phil Green's version 0.990329
Score matrix (set by value of penalty: -8)
A C G T N X
A 1 -8 -8 -8 0 -9
C -8 1 -8 -8 0 -9
G -8 -8 1 -8 0 -9
T -8 -8 -8 1 0 -9
N 0 0 0 0 0 0
X -9 -9 -9 -9 0 -9
gap_init: -10
gap_ext: -9
ins_gap_ext: -9
del_gap_ext: -9
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 55
maxmatch: 80
max_group_size: 20
minscore: 75
bandwidth: 14
indexwordsize: 10
vector_bound: 50
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 13
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -8
confirm_score: 30
node_seg: 32
node_space: 16
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/finished1/microbe/3436494/edit_dir.25Sep03.QC