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
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Project Size(KB) TaxID GenusSpecies
3634497 3000 1757 Thermoanaerobacter ethanolicus
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Thermoanaerobacter_ethanolicus
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Thermoanaerobacteriaceae, family, eubacteria
Clostridia, class, eubacteria
Thermoanaerobacteriales, order, eubacteria
Thermoanaerobacter ethanolicus, species, eubacteria
Thermoanaerobacter, genus, eubacteria
Firmicutes (Gram-positive bacteria), phylum, eubacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2359496
# phrap: 2187652
# db:
altered.
3000000
2515716 +/- 349552
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 6799
Number of reads with percent X's >= 20%: 206 = 0.6%
Number of reads with percent X's >= 50%: 111 = 0.3%
Number of reads with percent X's >= 80%: 16 = 0.1%
Total reads in project: 31972
Total bp X'd : 351557
reads >= 20% >= 50% >= 80% screened
Nr with L09136 5439 126 60 0
Nr with pCC1Fos 1243 1 0 0
Nr with pMCL200_JGI_XZX+XZK 117 79 51 16
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 953
Number of reads with percent X's >= 20%: 1 = 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: 2450
Total bp X'd : 38687
reads >= 20% >= 50% >= 80% screened
Nr with L09136 4 0 0 0
Nr with pCC1Fos 949 1 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 9125613
C = 5547124
G = 5494235
T = 9206056
N = 138846
X = 351557
GC fraction = 0.37
Total = 29863431
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634497_fasta.screen.contigs
-------------------------------------------------------------------
A 746290
C 452007
G 371795
T 805722
N 131
fraction GC = 0.35
total bases = 2375945
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 AIBT reads.list > grep.reads.list.AIBT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBT 4 500
-------------------------------------------------------------------
#Found 5704 total values totalling 20172585.0000. <3536.568198 +/- 743.823226>
#Range: [ 818 - 22650 ]
#Most likely bin: [ 3500 - 4000 ] 1890 counts
#Median bin: [ 3500 - 4000 ] 1890 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 4 0.00 0.00 ]
|X 1000 - 1500 : [ 61 0.01 0.01 ]
|XX 1500 - 2000 : [ 117 0.02 0.03 ]
|XXXXX 2000 - 2500 : [ 214 0.04 0.07 ]
|XXXXXXXXXXXXXX 2500 - 3000 : [ 673 0.12 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1404 0.25 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1890 0.33 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1051 0.18 0.95 ]
|XXXXX 4500 - 5000 : [ 228 0.04 0.99 ]
|X 5000 - 5500 : [ 46 0.01 1.00 ]
| 5500 - 6000 : [ 12 0.00 1.00 ]
| 6000 - 6500 : [ 2 0.00 1.00 ]
#...
| 14000 - 14500 : [ 1 0.00 1.00 ]
#...
| 22500 - 23000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBU reads.list > grep.reads.list.AIBU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBU 4 500
-------------------------------------------------------------------
#Found 6345 total values totalling 43591806.0000. <6870.260993 +/- 1032.415430>
#Range: [ 939 - 26451 ]
#Most likely bin: [ 7000 - 7500 ] 1748 counts
#Median bin: [ 7000 - 7500 ] 1748 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
|X 1000 - 1500 : [ 24 0.00 0.00 ]
|X 1500 - 2000 : [ 37 0.01 0.01 ]
|X 2000 - 2500 : [ 29 0.00 0.01 ]
|X 2500 - 3000 : [ 33 0.01 0.02 ]
|X 3000 - 3500 : [ 22 0.00 0.02 ]
| 3500 - 4000 : [ 18 0.00 0.03 ]
|X 4000 - 4500 : [ 26 0.00 0.03 ]
|X 4500 - 5000 : [ 22 0.00 0.03 ]
|XX 5000 - 5500 : [ 72 0.01 0.04 ]
|XXXXXXXXX 5500 - 6000 : [ 391 0.06 0.11 ]
|XXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 894 0.14 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1544 0.24 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1748 0.28 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1133 0.18 0.94 ]
|XXXXXXXX 8000 - 8500 : [ 343 0.05 1.00 ]
| 8500 - 9000 : [ 6 0.00 1.00 ]
#...
| 10000 - 10500 : [ 1 0.00 1.00 ]
#...
| 26000 - 26500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBW reads.list > grep.reads.list.AIBW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBW 4 500
-------------------------------------------------------------------
#Found -1 total values totalling 0.0000. <-0.000000 +/- 0.000000>
#Range: [ - ]
#Most likely bin: [ 0 - 500 ] 1 counts
#Median bin: [ 0 - 500 ] counts
#Histogram Bins Count Fraction Cum_Fraction
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AYGG reads.list > grep.reads.list.AYGG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AYGG 4 500
-------------------------------------------------------------------
#Found 39 total values totalling 1262207.0000. <32364.282051 +/- 6113.821806>
#Range: [ 8138 - 41857 ]
#Most likely bin: [ 34000 - 34500 ] 6 counts
#Median bin: [ 34000 - 34500 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 8000 - 8500 : [ 1 0.03 0.03 ]
#...
|XXXXXXX 15500 - 16000 : [ 1 0.03 0.05 ]
#...
|XXXXXXX 20500 - 21000 : [ 1 0.03 0.08 ]
#...
|XXXXXXX 25000 - 25500 : [ 1 0.03 0.10 ]
#...
|XXXXXXX 27000 - 27500 : [ 1 0.03 0.13 ]
#...
|XXXXXXX 28000 - 28500 : [ 1 0.03 0.15 ]
#...
|XXXXXXX 29000 - 29500 : [ 1 0.03 0.18 ]
|XXXXXXX 29500 - 30000 : [ 1 0.03 0.21 ]
#...
|XXXXXXX 30500 - 31000 : [ 1 0.03 0.23 ]
#...
|XXXXXXXXXXXXXXXXXXXX 31500 - 32000 : [ 3 0.08 0.31 ]
|XXXXXXXXXXXXX 32000 - 32500 : [ 2 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 3 0.08 0.44 ]
|XXXXXXX 33000 - 33500 : [ 1 0.03 0.46 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 6 0.15 0.62 ]
|XXXXXXXXXXXXX 34500 - 35000 : [ 2 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 3 0.08 0.74 ]
|XXXXXXXXXXXXX 35500 - 36000 : [ 2 0.05 0.79 ]
|XXXXXXX 36000 - 36500 : [ 1 0.03 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 4 0.10 0.92 ]
#...
|XXXXXXXXXXXXX 38500 - 39000 : [ 2 0.05 0.97 ]
#...
|XXXXXXX 41500 - 42000 : [ 1 0.03 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIBT 3400 +- 1016 (n=2779)
# AIBU 6814 +- 1324 (n=3187)
# AYGG 33247 +- 4336 (n=22)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634497_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
AIBT 16896 84 580 91 575 14067 98 586 100 603
AIBU 16896 88 790 95 748 14752 100 793 100 792
AIBW 3072 14 371 28 116 576 73 570 100 510
AYGG 6144 80 512 89 469 2577 91 507 100 522
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIBT 6991 98 581 100 599 7076 98 590 100 607
AIBU 7353 100 797 100 795 7399 100 790 100 789
AIBW 92 10 364 100 187 484 85 575 100 571
AYGG 1289 90 504 100 505 1288 92 511 100 538
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634497_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
88 14752 7455 84.72 88.25 AIBU @
88 14067 7935 90.17 93.93 AIBT @
16 576 551 34.44 35.87 AIBW @
32 2577 1876 58.62 61.07 AYGG @
] 31972 17817 79.54 cumulative total@@
LIBRARY PLATE ID COUNT [ AIBT 88 AIBU 88 AIBW 16 AYGG 32 ] for 224 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 3634497_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 31972 total values totalling 21223195.0000. <663.805674 +/- 197.221472>
#Range: [ 12 - 939 ]
#Most likely bin: [ 800 - 850 ] 6366 counts
#Median bin: [ 700 - 750 ] 4100 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 50 : [ 270 0.01 0.01 ]
|XXX 50 - 100 : [ 417 0.01 0.02 ]
|XX 100 - 150 : [ 378 0.01 0.03 ]
|XXX 150 - 200 : [ 434 0.01 0.05 ]
|XXX 200 - 250 : [ 446 0.01 0.06 ]
|XXXX 250 - 300 : [ 586 0.02 0.08 ]
|XXXX 300 - 350 : [ 649 0.02 0.10 ]
|XXXXX 350 - 400 : [ 743 0.02 0.12 ]
|XXXXX 400 - 450 : [ 778 0.02 0.15 ]
|XXXXXX 450 - 500 : [ 972 0.03 0.18 ]
|XXXXXXXX 500 - 550 : [ 1196 0.04 0.21 ]
|XXXXXXXXXX 550 - 600 : [ 1526 0.05 0.26 ]
|XXXXXXXXXXXXX 600 - 650 : [ 2005 0.06 0.33 ]
|XXXXXXXXXXXXXXXXXX 650 - 700 : [ 2807 0.09 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4100 0.13 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6092 0.19 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6366 0.20 0.93 ]
|XXXXXXXXXXXXX 850 - 900 : [ 2128 0.07 1.00 ]
| 900 - 950 : [ 79 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBT 3634497_fasta.screen.trimQ15.SaF > reads.trim15.AIBT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBT.rl 2 50
-------------------------------------------------------------------
#Found 14067 total values totalling 8094801.0000. <575.446151 +/- 182.170566>
#Range: [ 25 - 861 ]
#Most likely bin: [ 700 - 750 ] 2467 counts
#Median bin: [ 600 - 650 ] 1600 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 51 0.00 0.00 ]
|XXXX 50 - 100 : [ 225 0.02 0.02 ]
|XXXX 100 - 150 : [ 264 0.02 0.04 ]
|XXXXX 150 - 200 : [ 280 0.02 0.06 ]
|XXXXX 200 - 250 : [ 312 0.02 0.08 ]
|XXXXXX 250 - 300 : [ 357 0.03 0.11 ]
|XXXXXXX 300 - 350 : [ 426 0.03 0.14 ]
|XXXXXXXXX 350 - 400 : [ 549 0.04 0.18 ]
|XXXXXXXXXX 400 - 450 : [ 616 0.04 0.22 ]
|XXXXXXXXXXXX 450 - 500 : [ 769 0.05 0.27 ]
|XXXXXXXXXXXXXXXX 500 - 550 : [ 969 0.07 0.34 ]
|XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1220 0.09 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1600 0.11 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2152 0.15 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2467 0.18 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1612 0.11 0.99 ]
|XXX 800 - 850 : [ 196 0.01 1.00 ]
| 850 - 900 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBU 3634497_fasta.screen.trimQ15.SaF > reads.trim15.AIBU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBU.rl 2 50
-------------------------------------------------------------------
#Found 14752 total values totalling 11677742.0000. <791.603986 +/- 88.554609>
#Range: [ 23 - 939 ]
#Most likely bin: [ 800 - 850 ] 6103 counts
#Median bin: [ 800 - 850 ] 6103 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 9 0.00 0.00 ]
| 50 - 100 : [ 20 0.00 0.00 ]
| 100 - 150 : [ 19 0.00 0.00 ]
| 150 - 200 : [ 34 0.00 0.01 ]
| 200 - 250 : [ 25 0.00 0.01 ]
| 250 - 300 : [ 35 0.00 0.01 ]
| 300 - 350 : [ 30 0.00 0.01 ]
| 350 - 400 : [ 23 0.00 0.01 ]
| 400 - 450 : [ 36 0.00 0.02 ]
| 450 - 500 : [ 45 0.00 0.02 ]
| 500 - 550 : [ 44 0.00 0.02 ]
| 550 - 600 : [ 76 0.01 0.03 ]
|X 600 - 650 : [ 114 0.01 0.03 ]
|XX 650 - 700 : [ 347 0.02 0.06 ]
|XXXXXXXXX 700 - 750 : [ 1304 0.09 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4288 0.29 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6103 0.41 0.85 ]
|XXXXXXXXXXXXXX 850 - 900 : [ 2121 0.14 0.99 ]
|X 900 - 950 : [ 79 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBW 3634497_fasta.screen.trimQ15.SaF > reads.trim15.AIBW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBW.rl 2 50
-------------------------------------------------------------------
#Found 576 total values totalling 244029.0000. <423.661458 +/- 288.932707>
#Range: [ 12 - 864 ]
#Most likely bin: [ 0 - 50 ] 128 counts
#Median bin: [ 450 - 500 ] 45 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 128 0.22 0.22 ]
|XXXXXXXXX 50 - 100 : [ 30 0.05 0.27 ]
|XXXX 100 - 150 : [ 14 0.02 0.30 ]
|XXX 150 - 200 : [ 9 0.02 0.31 ]
|XXX 200 - 250 : [ 11 0.02 0.33 ]
|XXXX 250 - 300 : [ 12 0.02 0.35 ]
|XXXXX 300 - 350 : [ 17 0.03 0.38 ]
|XXXXXXX 350 - 400 : [ 21 0.04 0.42 ]
|XXXXXXX 400 - 450 : [ 22 0.04 0.46 ]
|XXXXXXXXXXXXXX 450 - 500 : [ 45 0.08 0.54 ]
|XXXXXXX 500 - 550 : [ 23 0.04 0.58 ]
|XXXXXXXX 550 - 600 : [ 26 0.05 0.62 ]
|XXXXXXXXXXXX 600 - 650 : [ 40 0.07 0.69 ]
|XXXXXXXXXXXX 650 - 700 : [ 39 0.07 0.76 ]
|XXXXXXXXXXXXXXXXX 700 - 750 : [ 53 0.09 0.85 ]
|XXXXXXXXXXXXXXXXXX 750 - 800 : [ 56 0.10 0.95 ]
|XXXXXXXXX 800 - 850 : [ 28 0.05 1.00 ]
|X 850 - 900 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AYGG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AYGG 3634497_fasta.screen.trimQ15.SaF > reads.trim15.AYGG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AYGG.rl 2 50
-------------------------------------------------------------------
#Found 2577 total values totalling 1206623.0000. <468.227784 +/- 224.983934>
#Range: [ 19 - 886 ]
#Most likely bin: [ 700 - 750 ] 276 counts
#Median bin: [ 500 - 550 ] 160 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXX 0 - 50 : [ 82 0.03 0.03 ]
|XXXXXXXXXXXXXXXXXXXXX 50 - 100 : [ 142 0.06 0.09 ]
|XXXXXXXXXXXX 100 - 150 : [ 81 0.03 0.12 ]
|XXXXXXXXXXXXXXXX 150 - 200 : [ 111 0.04 0.16 ]
|XXXXXXXXXXXXXX 200 - 250 : [ 98 0.04 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 182 0.07 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 300 - 350 : [ 176 0.07 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXX 350 - 400 : [ 150 0.06 0.40 ]
|XXXXXXXXXXXXXXX 400 - 450 : [ 104 0.04 0.44 ]
|XXXXXXXXXXXXXXXX 450 - 500 : [ 113 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 160 0.06 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 204 0.08 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 251 0.10 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 269 0.10 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 276 0.11 0.93 ]
|XXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 136 0.05 0.98 ]
|XXXXXX 800 - 850 : [ 39 0.02 1.00 ]
| 850 - 900 : [ 3 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AYGH
trimt JAZZ trim 15 readlength histogram for AYGI
trimt JAZZ trim 15 readlength histogram for SCNB
trimt JAZZ trim 15 readlength histogram for BPBX
trimt JAZZ trim 15 readlength histogram for BPBY
trimt JAZZ trim 15 readlength histogram for BPBZ
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634497
-------------------------------------------------------------------
AIBT.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIBT.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIBU.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIBW.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AYGG.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AIBT.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIBT.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIBU.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIBW.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AYGG.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634497_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634497_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 31770 total values totalling 11738.8877. <0.369496 +/- 0.096866>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.34 - 0.345 ] 1445 counts
#Median bin: [ 0.345 - 0.35 ] 1414 counts
#Entropy = 5.5832 bits
| 0 - 0.005 : [ 13 4.09e-04 4.09e-04 13 ]
#...
| 0.025 - 0.03 : [ 1 3.15e-05 4.41e-04 14 ]
#...
| 0.04 - 0.045 : [ 1 3.15e-05 4.72e-04 15 ]
#...
| 0.07 - 0.075 : [ 1 3.15e-05 5.04e-04 16 ]
#...
| 0.085 - 0.09 : [ 1 3.15e-05 5.35e-04 17 ]
#...
| 0.095 - 0.1 : [ 1 3.15e-05 5.67e-04 18 ]
#...
| 0.105 - 0.11 : [ 1 3.15e-05 5.98e-04 19 ]
#...
| 0.115 - 0.12 : [ 1 3.15e-05 6.30e-04 20 ]
#...
| 0.125 - 0.13 : [ 1 3.15e-05 6.61e-04 21 ]
#...
| 0.135 - 0.14 : [ 2 6.30e-05 7.24e-04 23 ]
#...
| 0.145 - 0.15 : [ 1 3.15e-05 7.55e-04 24 ]
| 0.15 - 0.155 : [ 1 3.15e-05 7.87e-04 25 ]
| 0.155 - 0.16 : [ 2 6.30e-05 8.50e-04 27 ]
| 0.16 - 0.165 : [ 3 9.44e-05 9.44e-04 30 ]
| 0.165 - 0.17 : [ 1 3.15e-05 9.76e-04 31 ]
| 0.17 - 0.175 : [ 3 9.44e-05 1.07e-03 34 ]
#...
| 0.18 - 0.185 : [ 2 6.30e-05 1.13e-03 36 ]
| 0.185 - 0.19 : [ 1 3.15e-05 1.16e-03 37 ]
| 0.19 - 0.195 : [ 4 1.26e-04 1.29e-03 41 ]
| 0.195 - 0.2 : [ 1 3.15e-05 1.32e-03 42 ]
| 0.2 - 0.205 : [ 11 3.46e-04 1.67e-03 53 ]
| 0.205 - 0.21 : [ 6 1.89e-04 1.86e-03 59 ]
| 0.21 - 0.215 : [ 4 1.26e-04 1.98e-03 63 ]
| 0.215 - 0.22 : [ 12 3.78e-04 2.36e-03 75 ]
| 0.22 - 0.225 : [ 4 1.26e-04 2.49e-03 79 ]
| 0.225 - 0.23 : [ 15 4.72e-04 2.96e-03 94 ]
|X 0.23 - 0.235 : [ 22 6.92e-04 3.65e-03 116 ]
|X 0.235 - 0.24 : [ 38 1.20e-03 4.85e-03 154 ]
|X 0.24 - 0.245 : [ 27 8.50e-04 5.70e-03 181 ]
|X 0.245 - 0.25 : [ 46 1.45e-03 7.15e-03 227 ]
|XXX 0.25 - 0.255 : [ 126 3.97e-03 1.11e-02 353 ]
|XXXX 0.255 - 0.26 : [ 128 4.03e-03 1.51e-02 481 ]
|XXXX 0.26 - 0.265 : [ 158 4.97e-03 2.01e-02 639 ]
|XXXXXX 0.265 - 0.27 : [ 208 6.55e-03 2.67e-02 847 ]
|XXXXXXXXX 0.27 - 0.275 : [ 323 1.02e-02 3.68e-02 1170 ]
|XXXXXXXXXXXX 0.275 - 0.28 : [ 421 1.33e-02 5.01e-02 1591 ]
|XXXXXXXXXXXXXX 0.28 - 0.285 : [ 511 1.61e-02 6.62e-02 2102 ]
|XXXXXXXXXXXXXXXXX 0.285 - 0.29 : [ 624 1.96e-02 8.58e-02 2726 ]
|XXXXXXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 731 2.30e-02 1.09e-01 3457 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.295 - 0.3 : [ 799 2.51e-02 1.34e-01 4256 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 897 2.82e-02 1.62e-01 5153 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 1008 3.17e-02 1.94e-01 6161 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 1104 3.47e-02 2.29e-01 7265 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 1193 3.76e-02 2.66e-01 8458 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 1333 4.20e-02 3.08e-01 9791 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 1400 4.41e-02 3.52e-01 11191 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 1423 4.48e-02 3.97e-01 12614 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 1385 4.36e-02 4.41e-01 13999 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 1445 4.55e-02 4.86e-01 15444 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 1414 4.45e-02 5.31e-01 16858 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 1385 4.36e-02 5.74e-01 18243 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 1352 4.26e-02 6.17e-01 19595 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 1245 3.92e-02 6.56e-01 20840 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 1114 3.51e-02 6.91e-01 21954 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 1030 3.24e-02 7.23e-01 22984 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 964 3.03e-02 7.54e-01 23948 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 814 2.56e-02 7.79e-01 24762 ]
|XXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 753 2.37e-02 8.03e-01 25515 ]
|XXXXXXXXXXXXXXX 0.39 - 0.395 : [ 531 1.67e-02 8.20e-01 26046 ]
|XXXXXXXXXXXX 0.395 - 0.4 : [ 440 1.38e-02 8.34e-01 26486 ]
|XXXXXXXXXXXX 0.4 - 0.405 : [ 443 1.39e-02 8.48e-01 26929 ]
|XXXXXXXXX 0.405 - 0.41 : [ 328 1.03e-02 8.58e-01 27257 ]
|XXXXXXX 0.41 - 0.415 : [ 249 7.84e-03 8.66e-01 27506 ]
|XXXXXX 0.415 - 0.42 : [ 228 7.18e-03 8.73e-01 27734 ]
|XXXXX 0.42 - 0.425 : [ 182 5.73e-03 8.79e-01 27916 ]
|XXXXX 0.425 - 0.43 : [ 167 5.26e-03 8.84e-01 28083 ]
|XXXX 0.43 - 0.435 : [ 144 4.53e-03 8.88e-01 28227 ]
|XXX 0.435 - 0.44 : [ 122 3.84e-03 8.92e-01 28349 ]
|XX 0.44 - 0.445 : [ 89 2.80e-03 8.95e-01 28438 ]
|XX 0.445 - 0.45 : [ 71 2.23e-03 8.97e-01 28509 ]
|X 0.45 - 0.455 : [ 46 1.45e-03 8.99e-01 28555 ]
|XX 0.455 - 0.46 : [ 58 1.83e-03 9.01e-01 28613 ]
|X 0.46 - 0.465 : [ 54 1.70e-03 9.02e-01 28667 ]
|X 0.465 - 0.47 : [ 50 1.57e-03 9.04e-01 28717 ]
|X 0.47 - 0.475 : [ 47 1.48e-03 9.05e-01 28764 ]
|X 0.475 - 0.48 : [ 43 1.35e-03 9.07e-01 28807 ]
|X 0.48 - 0.485 : [ 44 1.38e-03 9.08e-01 28851 ]
|X 0.485 - 0.49 : [ 46 1.45e-03 9.10e-01 28897 ]
|X 0.49 - 0.495 : [ 29 9.13e-04 9.10e-01 28926 ]
|X 0.495 - 0.5 : [ 27 8.50e-04 9.11e-01 28953 ]
|X 0.5 - 0.505 : [ 48 1.51e-03 9.13e-01 29001 ]
|X 0.505 - 0.51 : [ 39 1.23e-03 9.14e-01 29040 ]
|X 0.51 - 0.515 : [ 32 1.01e-03 9.15e-01 29072 ]
|X 0.515 - 0.52 : [ 36 1.13e-03 9.16e-01 29108 ]
|X 0.52 - 0.525 : [ 19 5.98e-04 9.17e-01 29127 ]
|X 0.525 - 0.53 : [ 26 8.18e-04 9.18e-01 29153 ]
|X 0.53 - 0.535 : [ 35 1.10e-03 9.19e-01 29188 ]
|X 0.535 - 0.54 : [ 43 1.35e-03 9.20e-01 29231 ]
|X 0.54 - 0.545 : [ 38 1.20e-03 9.21e-01 29269 ]
|X 0.545 - 0.55 : [ 50 1.57e-03 9.23e-01 29319 ]
|XX 0.55 - 0.555 : [ 75 2.36e-03 9.25e-01 29394 ]
|XX 0.555 - 0.56 : [ 58 1.83e-03 9.27e-01 29452 ]
|XX 0.56 - 0.565 : [ 61 1.92e-03 9.29e-01 29513 ]
|XX 0.565 - 0.57 : [ 62 1.95e-03 9.31e-01 29575 ]
|X 0.57 - 0.575 : [ 54 1.70e-03 9.33e-01 29629 ]
|X 0.575 - 0.58 : [ 41 1.29e-03 9.34e-01 29670 ]
|X 0.58 - 0.585 : [ 39 1.23e-03 9.35e-01 29709 ]
|X 0.585 - 0.59 : [ 22 6.92e-04 9.36e-01 29731 ]
|X 0.59 - 0.595 : [ 33 1.04e-03 9.37e-01 29764 ]
| 0.595 - 0.6 : [ 18 5.67e-04 9.37e-01 29782 ]
|X 0.6 - 0.605 : [ 35 1.10e-03 9.39e-01 29817 ]
|X 0.605 - 0.61 : [ 43 1.35e-03 9.40e-01 29860 ]
|X 0.61 - 0.615 : [ 29 9.13e-04 9.41e-01 29889 ]
|X 0.615 - 0.62 : [ 32 1.01e-03 9.42e-01 29921 ]
|X 0.62 - 0.625 : [ 23 7.24e-04 9.43e-01 29944 ]
|XX 0.625 - 0.63 : [ 58 1.83e-03 9.44e-01 30002 ]
|XX 0.63 - 0.635 : [ 60 1.89e-03 9.46e-01 30062 ]
|XX 0.635 - 0.64 : [ 62 1.95e-03 9.48e-01 30124 ]
|XX 0.64 - 0.645 : [ 65 2.05e-03 9.50e-01 30189 ]
|XX 0.645 - 0.65 : [ 73 2.30e-03 9.53e-01 30262 ]
|XX 0.65 - 0.655 : [ 78 2.46e-03 9.55e-01 30340 ]
|XX 0.655 - 0.66 : [ 89 2.80e-03 9.58e-01 30429 ]
|XX 0.66 - 0.665 : [ 83 2.61e-03 9.60e-01 30512 ]
|XX 0.665 - 0.67 : [ 87 2.74e-03 9.63e-01 30599 ]
|XXX 0.67 - 0.675 : [ 105 3.31e-03 9.66e-01 30704 ]
|XXX 0.675 - 0.68 : [ 109 3.43e-03 9.70e-01 30813 ]
|XXX 0.68 - 0.685 : [ 93 2.93e-03 9.73e-01 30906 ]
|XX 0.685 - 0.69 : [ 90 2.83e-03 9.76e-01 30996 ]
|XXX 0.69 - 0.695 : [ 118 3.71e-03 9.79e-01 31114 ]
|XXX 0.695 - 0.7 : [ 94 2.96e-03 9.82e-01 31208 ]
|XX 0.7 - 0.705 : [ 88 2.77e-03 9.85e-01 31296 ]
|XX 0.705 - 0.71 : [ 71 2.23e-03 9.87e-01 31367 ]
|XX 0.71 - 0.715 : [ 58 1.83e-03 9.89e-01 31425 ]
|X 0.715 - 0.72 : [ 45 1.42e-03 9.91e-01 31470 ]
|X 0.72 - 0.725 : [ 45 1.42e-03 9.92e-01 31515 ]
|X 0.725 - 0.73 : [ 51 1.61e-03 9.94e-01 31566 ]
|X 0.73 - 0.735 : [ 44 1.38e-03 9.95e-01 31610 ]
|X 0.735 - 0.74 : [ 33 1.04e-03 9.96e-01 31643 ]
| 0.74 - 0.745 : [ 13 4.09e-04 9.96e-01 31656 ]
| 0.745 - 0.75 : [ 12 3.78e-04 9.97e-01 31668 ]
| 0.75 - 0.755 : [ 16 5.04e-04 9.97e-01 31684 ]
| 0.755 - 0.76 : [ 16 5.04e-04 9.98e-01 31700 ]
| 0.76 - 0.765 : [ 7 2.20e-04 9.98e-01 31707 ]
| 0.765 - 0.77 : [ 5 1.57e-04 9.98e-01 31712 ]
| 0.77 - 0.775 : [ 6 1.89e-04 9.98e-01 31718 ]
| 0.775 - 0.78 : [ 1 3.15e-05 9.98e-01 31719 ]
| 0.78 - 0.785 : [ 5 1.57e-04 9.99e-01 31724 ]
| 0.785 - 0.79 : [ 4 1.26e-04 9.99e-01 31728 ]
| 0.79 - 0.795 : [ 3 9.44e-05 9.99e-01 31731 ]
| 0.795 - 0.8 : [ 1 3.15e-05 9.99e-01 31732 ]
| 0.8 - 0.805 : [ 4 1.26e-04 9.99e-01 31736 ]
| 0.805 - 0.81 : [ 2 6.30e-05 9.99e-01 31738 ]
| 0.81 - 0.815 : [ 6 1.89e-04 9.99e-01 31744 ]
| 0.815 - 0.82 : [ 1 3.15e-05 9.99e-01 31745 ]
| 0.82 - 0.825 : [ 4 1.26e-04 9.99e-01 31749 ]
| 0.825 - 0.83 : [ 4 1.26e-04 9.99e-01 31753 ]
| 0.83 - 0.835 : [ 1 3.15e-05 9.99e-01 31754 ]
| 0.835 - 0.84 : [ 1 3.15e-05 1.00e+00 31755 ]
| 0.84 - 0.845 : [ 1 3.15e-05 1.00e+00 31756 ]
| 0.845 - 0.85 : [ 2 6.30e-05 1.00e+00 31758 ]
#...
| 0.855 - 0.86 : [ 1 3.15e-05 1.00e+00 31759 ]
#...
| 0.865 - 0.87 : [ 1 3.15e-05 1.00e+00 31760 ]
| 0.87 - 0.875 : [ 1 3.15e-05 1.00e+00 31761 ]
#...
| 0.89 - 0.895 : [ 2 6.30e-05 1.00e+00 31763 ]
| 0.895 - 0.9 : [ 1 3.15e-05 1.00e+00 31764 ]
#...
| 0.915 - 0.92 : [ 3 9.44e-05 1.00e+00 31767 ]
#...
| 0.965 - 0.97 : [ 1 3.15e-05 1.00e+00 31768 ]
#...
| 1 - 1.005 : [ 2 6.30e-05 1.00e+00 31770 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 130. 397 reads; 24800 bp (untrimmed), 24780 (trimmed).
Contig 131. 406 reads; 30286 bp (untrimmed), 30213 (trimmed).
Contig 132. 408 reads; 44642 bp (untrimmed), 44585 (trimmed).
Contig 133. 416 reads; 33245 bp (untrimmed), 33202 (trimmed).
Contig 134. 449 reads; 32209 bp (untrimmed), 32156 (trimmed).
Contig 135. 452 reads; 32791 bp (untrimmed), 32660 (trimmed).
Contig 136. 453 reads; 32393 bp (untrimmed), 32343 (trimmed).
Contig 137. 456 reads; 31818 bp (untrimmed), 31717 (trimmed).
Contig 138. 485 reads; 34373 bp (untrimmed), 34322 (trimmed).
Contig 139. 489 reads; 31379 bp (untrimmed), 31352 (trimmed).
Contig 140. 494 reads; 33970 bp (untrimmed), 33668 (trimmed).
Contig 141. 564 reads; 37807 bp (untrimmed), 37786 (trimmed).
Contig 142. 701 reads; 41769 bp (untrimmed), 41648 (trimmed).
Contig 143. 762 reads; 64576 bp (untrimmed), 64532 (trimmed).
Contig 144. 793 reads; 47760 bp (untrimmed), 47719 (trimmed).
Contig 145. 867 reads; 58277 bp (untrimmed), 58239 (trimmed).
Contig 146. 868 reads; 56412 bp (untrimmed), 56344 (trimmed).
Contig 147. 882 reads; 61925 bp (untrimmed), 61771 (trimmed).
Contig 148. 883 reads; 85793 bp (untrimmed), 85469 (trimmed).
Contig 149. 930 reads; 63651 bp (untrimmed), 63595 (trimmed).
Contig 150. 970 reads; 60576 bp (untrimmed), 60486 (trimmed).
Contig 151. 1011 reads; 67113 bp (untrimmed), 67006 (trimmed).
Contig 152. 1128 reads; 54143 bp (untrimmed), 53994 (trimmed).
Contig 153. 1275 reads; 73039 bp (untrimmed), 72971 (trimmed).
Contig 154. 1339 reads; 103073 bp (untrimmed), 102953 (trimmed).
Contig 155. 1516 reads; 104697 bp (untrimmed), 104604 (trimmed).
Contig 156. 1901 reads; 131554 bp (untrimmed), 131422 (trimmed).
--------------------------------------------------------------
Totals 29522 reads; 2375945 bp (untrimmed), 2359496 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2373393 bases = 10.72 +- 6.43 = 0.71 +- 5.84
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 153 total values totalling 987.9300. <6.457059 +/- 4.569328>
#Range: [ 1.13 - 24.15 ]
#Most likely bin: [ 2 - 2.5 ] 15 counts
#Median bin: [ 5 - 5.5 ] 5 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXX 1 - 1.5 : [ 6 0.04 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 12 0.08 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 15 0.10 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 15 0.10 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 13 0.08 0.40 ]
|XXXXXXXXXXXXXXXX 3.5 - 4 : [ 6 0.04 0.44 ]
|XXXXXXXXXXXXX 4 - 4.5 : [ 5 0.03 0.47 ]
|XXXXX 4.5 - 5 : [ 2 0.01 0.48 ]
|XXXXXXXXXXXXX 5 - 5.5 : [ 5 0.03 0.52 ]
|XXXXXXXXXXXXXXXX 5.5 - 6 : [ 6 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 7 0.05 0.60 ]
|XXXXX 6.5 - 7 : [ 2 0.01 0.61 ]
|XXXXX 7 - 7.5 : [ 2 0.01 0.63 ]
|XXXXXXXXXXXXXXXX 7.5 - 8 : [ 6 0.04 0.67 ]
|XXXXXXXXXXX 8 - 8.5 : [ 4 0.03 0.69 ]
|XXXXXXXXXXXXXXXX 8.5 - 9 : [ 6 0.04 0.73 ]
|XXXXX 9 - 9.5 : [ 2 0.01 0.75 ]
|XXXXX 9.5 - 10 : [ 2 0.01 0.76 ]
|XXXXXXXXXXXXX 10 - 10.5 : [ 5 0.03 0.79 ]
|XXXXXXXX 10.5 - 11 : [ 3 0.02 0.81 ]
|XXX 11 - 11.5 : [ 1 0.01 0.82 ]
|XXXXXXXXXXX 11.5 - 12 : [ 4 0.03 0.84 ]
|XXXXXXXXXXX 12 - 12.5 : [ 4 0.03 0.87 ]
|XXXXXXXXXXXXXXXX 12.5 - 13 : [ 6 0.04 0.91 ]
|XXXXXXXX 13 - 13.5 : [ 3 0.02 0.93 ]
|XXXXXXXXXXX 13.5 - 14 : [ 4 0.03 0.95 ]
|XXX 14 - 14.5 : [ 1 0.01 0.96 ]
|XXXXX 14.5 - 15 : [ 2 0.01 0.97 ]
|XXX 15 - 15.5 : [ 1 0.01 0.98 ]
#...
|XXX 17.5 - 18 : [ 1 0.01 0.99 ]
#...
|XXXXX 24 - 24.5 : [ 2 0.01 1.00 ]
-------------------------------------------------------------------
Histogram of Major Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000
-------------------------------------------------------------------
#Found 94 total values totalling 816.4100. <8.685213 +/- 3.954588>
#Range: [ 2.40 - 24.04 ]
#Most likely bin: [ 6 - 6.5 ] 7 counts
#Median bin: [ 8 - 8.5 ] 4 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 2 - 2.5 : [ 1 0.01 0.01 ]
|XXXXXXXXXXX 2.5 - 3 : [ 2 0.02 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 6 0.06 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 4 0.04 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 4 0.04 0.18 ]
|XXXXXX 4.5 - 5 : [ 1 0.01 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 5 0.05 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 4 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 7 0.07 0.36 ]
|XXXXXXXXXXX 6.5 - 7 : [ 2 0.02 0.38 ]
|XXXXXXXXXXX 7 - 7.5 : [ 2 0.02 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 6 0.06 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 4 0.04 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 6 0.06 0.57 ]
|XXXXXXXXXXX 9 - 9.5 : [ 2 0.02 0.60 ]
|XXXXXXXXXXX 9.5 - 10 : [ 2 0.02 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 5 0.05 0.67 ]
|XXXXXXXXXXXXXXXXX 10.5 - 11 : [ 3 0.03 0.70 ]
|XXXXXX 11 - 11.5 : [ 1 0.01 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 4 0.04 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 4 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 6 0.06 0.86 ]
|XXXXXXXXXXXXXXXXX 13 - 13.5 : [ 3 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 4 0.04 0.94 ]
|XXXXXX 14 - 14.5 : [ 1 0.01 0.95 ]
|XXXXXXXXXXX 14.5 - 15 : [ 2 0.02 0.97 ]
|XXXXXX 15 - 15.5 : [ 1 0.01 0.98 ]
#...
|XXXXXX 17.5 - 18 : [ 1 0.01 0.99 ]
#...
|XXXXXX 24 - 24.5 : [ 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 3 reads 959 bases = 1.13 +- 0.48 = 1.13 +- 0.48
Contig 21 3 reads 1614 bases = 1.30 +- 0.46 = 0.53 +- 1.20
Contig 7 2 reads 1223 bases = 1.33 +- 0.47 = 0.31 +- 0.75
Contig 5 2 reads 964 bases = 1.37 +- 0.48 = 1.37 +- 0.48
Contig 4 2 reads 1084 bases = 1.45 +- 0.50 = -0.08 +- 0.74
Contig 6 2 reads 825 bases = 1.47 +- 0.50 = 1.47 +- 0.50
Contig 28 4 reads 2449 bases = 1.51 +- 0.72 = 0.73 +- 1.44
Contig 23 3 reads 1968 bases = 1.53 +- 0.53 = 1.53 +- 0.53
Contig 13 3 reads 1887 bases = 1.58 +- 0.59 = 1.58 +- 0.59
Contig 18 3 reads 1515 bases = 1.74 +- 0.69 = 1.74 +- 0.69
Contig 33 4 reads 1599 bases = 1.76 +- 0.68 = 1.76 +- 0.68
Contig 20 3 reads 1631 bases = 1.78 +- 0.74 = 1.78 +- 0.74
Contig 27 4 reads 1649 bases = 1.80 +- 0.65 = 1.36 +- 1.15
Contig 37 5 reads 2047 bases = 1.81 +- 0.66 = 1.81 +- 0.66
Contig 50 7 reads 2857 bases = 1.83 +- 0.98 = 0.19 +- 1.90
Contig 8 3 reads 1056 bases = 1.90 +- 0.32 = 1.90 +- 0.32
Contig 55 8 reads 2506 bases = 1.97 +- 0.59 = -0.03 +- 1.81
Contig 9 3 reads 1111 bases = 1.99 +- 0.87 = 1.99 +- 0.87
Contig 29 4 reads 1361 bases = 2.00 +- 0.59 = 2.00 +- 0.59
Contig 14 3 reads 1307 bases = 2.03 +- 0.87 = 2.03 +- 0.87
Contig 137 456 reads 31818 bases = 12.54 +- 6.86 = 1.42 +- 7.14
Contig 155 1516 reads 104697 bases = 12.57 +- 5.07 = 0.22 +- 5.32
Contig 149 930 reads 63651 bases = 12.62 +- 5.08 = 0.40 +- 4.70
Contig 156 1901 reads 131554 bases = 12.62 +- 5.45 = 0.08 +- 4.60
Contig 140 494 reads 33970 bases = 12.63 +- 5.59 = 0.87 +- 4.41
Contig 123 302 reads 20771 bases = 12.93 +- 6.56 = 0.36 +- 7.44
Contig 151 1011 reads 67113 bases = 13.01 +- 6.41 = 0.86 +- 4.45
Contig 145 867 reads 58277 bases = 13.17 +- 5.18 = 0.42 +- 4.51
Contig 141 564 reads 37807 bases = 13.22 +- 4.78 = 0.14 +- 5.60
Contig 139 489 reads 31379 bases = 13.50 +- 6.68 = 0.35 +- 7.85
Contig 146 868 reads 56412 bases = 13.59 +- 5.56 = 0.13 +- 5.34
Contig 150 970 reads 60576 bases = 13.86 +- 4.47 = 0.18 +- 4.99
Contig 130 397 reads 24800 bases = 13.91 +- 8.10 = 1.48 +- 4.73
Contig 105 128 reads 8154 bases = 14.35 +- 9.55 = 6.92 +- 9.22
Contig 142 701 reads 41769 bases = 14.54 +- 7.05 = 0.76 +- 6.69
Contig 144 793 reads 47760 bases = 14.55 +- 5.73 = 0.05 +- 5.27
Contig 153 1275 reads 73039 bases = 15.07 +- 5.43 = 0.38 +- 5.49
Contig 152 1128 reads 54143 bases = 17.92 +- 8.53 = 0.09 +- 6.67
Contig 127 365 reads 12978 bases = 24.04 +- 28.30 = 24.04 +- 28.30
Contig 84 45 reads 1730 bases = 24.15 +- 15.85 = 24.15 +- 15.85
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 993
HQ Discrepant reads = 128
Chimeric reads = 40
Suspect alignments = 364
-------------------------------------------------------------------
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/microbe2/3634497/edit_dir.03Nov05.QD