Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-13-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634480 12000 4924 Pichia stipitis
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Pichia_stipitis
-------------------------------------------------------------------
Saccharomycotina, subphylum, ascomycetes
Pichia stipitis, species, ascomycetes
Pichia, genus, ascomycetes
Saccharomycetaceae, family, ascomycetes
Saccharomycetales (budding yeasts), order, ascomycetes
Saccharomycetes, class, ascomycetes
Ascomycota (ascomycetes), phylum, ascomycetes
Fungi (fungi), kingdom, fungi
Fungi/Metazoa group, eukaryotes
cellular organisms
Eukaryota (eucaryotes), superkingdom, eukaryotes
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 15289652
# phrap: 14684766
# db:
altered.
12000000
13991472 +/- 1429672
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 48200
Number of reads with percent X's >= 20%: 1400 = 0.6%
Number of reads with percent X's >= 50%: 843 = 0.4%
Number of reads with percent X's >= 80%: 92 = 0.0%
Total reads in project: 216268
Total bp X'd : 2433204
reads >= 20% >= 50% >= 80% screened
Nr with L09136 44392 331 193 32
Nr with pCC1Fos 2351 16 12 0
Nr with pMCL200_JGI_XZX+XZK 1457 1053 638 60
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 13
Number of reads with percent X's >= 20%: 4 = 4.3%
Number of reads with percent X's >= 50%: 4 = 4.3%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 92
Total bp X'd : 2742
reads >= 20% >= 50% >= 80% screened
Nr with L09136 9 1 1 0
Nr with pCC1Fos 1 0 0 0
Nr with pMCL200_JGI_XZX+XZK 3 3 3 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 60913131
C = 43347212
G = 43237862
T = 58682972
N = 1065993
X = 2433204
GC fraction = 0.41
Total = 209680374
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634480_fasta.screen.contigs
-------------------------------------------------------------------
A 4535231
C 3179422
G 3166402
T 4537290
N 5849
fraction GC = 0.41
total bases = 15424194
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 AHYX reads.list > grep.reads.list.AHYX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYX 4 500
-------------------------------------------------------------------
#Found 59176 total values totalling 195899661.0000. <3310.457973 +/- 3897.331016>
#Range: [ 583 - 488141 ]
#Most likely bin: [ 3000 - 3500 ] 31370 counts
#Median bin: [ 3000 - 3500 ] 31370 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 19 0.00 0.00 ]
| 1000 - 1500 : [ 189 0.00 0.00 ]
| 1500 - 2000 : [ 252 0.00 0.01 ]
|X 2000 - 2500 : [ 761 0.01 0.02 ]
|XXXXXXXXXXXXXXX 2500 - 3000 : [ 11566 0.20 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 31370 0.53 0.75 ]
|XXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 14431 0.24 0.99 ]
|X 4000 - 4500 : [ 557 0.01 1.00 ]
| 4500 - 5000 : [ 5 0.00 1.00 ]
| 5000 - 5500 : [ 3 0.00 1.00 ]
#...
| 7500 - 8000 : [ 1 0.00 1.00 ]
| 8000 - 8500 : [ 1 0.00 1.00 ]
| 8500 - 9000 : [ 1 0.00 1.00 ]
#...
| 10500 - 11000 : [ 6 0.00 1.00 ]
#...
| 12000 - 12500 : [ 1 0.00 1.00 ]
#...
| 40000 - 40500 : [ 1 0.00 1.00 ]
#...
| 100500 - 101000 : [ 1 0.00 1.00 ]
#...
| 149500 - 150000 : [ 1 0.00 1.00 ]
#...
| 163500 - 164000 : [ 1 0.00 1.00 ]
#...
| 196000 - 196500 : [ 1 0.00 1.00 ]
#...
| 206500 - 207000 : [ 1 0.00 1.00 ]
#...
| 271000 - 271500 : [ 1 0.00 1.00 ]
#...
| 281500 - 282000 : [ 1 0.00 1.00 ]
#...
| 284000 - 284500 : [ 1 0.00 1.00 ]
#...
| 299000 - 299500 : [ 1 0.00 1.00 ]
#...
| 317500 - 318000 : [ 1 0.00 1.00 ]
#...
| 325500 - 326000 : [ 1 0.00 1.00 ]
#...
| 488000 - 488500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYY reads.list > grep.reads.list.AHYY
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYY 4 500
-------------------------------------------------------------------
#Found 35055 total values totalling 227242420.0000. <6482.453858 +/- 3483.076761>
#Range: [ 50 - 539484 ]
#Most likely bin: [ 6000 - 6500 ] 8958 counts
#Median bin: [ 6500 - 7000 ] 8172 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 500 : [ 211 0.01 0.01 ]
| 500 - 1000 : [ 71 0.00 0.01 ]
|X 1000 - 1500 : [ 152 0.00 0.01 ]
|X 1500 - 2000 : [ 187 0.01 0.02 ]
|X 2000 - 2500 : [ 151 0.00 0.02 ]
|X 2500 - 3000 : [ 162 0.00 0.03 ]
|X 3000 - 3500 : [ 243 0.01 0.03 ]
|X 3500 - 4000 : [ 277 0.01 0.04 ]
|XX 4000 - 4500 : [ 360 0.01 0.05 ]
|XXX 4500 - 5000 : [ 564 0.02 0.07 ]
|XXXX 5000 - 5500 : [ 878 0.03 0.09 ]
|XXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 4242 0.12 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 8958 0.26 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 8172 0.23 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 5760 0.16 0.87 ]
|XXXXXXXXXXXXXXXX 7500 - 8000 : [ 3673 0.10 0.97 ]
|XXXX 8000 - 8500 : [ 928 0.03 1.00 ]
| 8500 - 9000 : [ 29 0.00 1.00 ]
| 9000 - 9500 : [ 8 0.00 1.00 ]
| 9500 - 10000 : [ 5 0.00 1.00 ]
| 10000 - 10500 : [ 8 0.00 1.00 ]
| 10500 - 11000 : [ 2 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 ]
#...
| 13000 - 13500 : [ 1 0.00 1.00 ]
#...
| 26000 - 26500 : [ 3 0.00 1.00 ]
#...
| 27500 - 28000 : [ 1 0.00 1.00 ]
#...
| 41500 - 42000 : [ 1 0.00 1.00 ]
#...
| 48000 - 48500 : [ 1 0.00 1.00 ]
#...
| 101500 - 102000 : [ 1 0.00 1.00 ]
#...
| 174500 - 175000 : [ 1 0.00 1.00 ]
#...
| 232000 - 232500 : [ 1 0.00 1.00 ]
#...
| 539000 - 539500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYZ reads.list > grep.reads.list.AHYZ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYZ 4 500
-------------------------------------------------------------------
#Found 2778 total values totalling 100856626.0000. <36305.480922 +/- 8401.294939>
#Range: [ 997 - 326680 ]
#Most likely bin: [ 35500 - 36000 ] 194 counts
#Median bin: [ 36000 - 36500 ] 188 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 2 0.00 0.00 ]
| 1500 - 2000 : [ 2 0.00 0.00 ]
|X 2000 - 2500 : [ 3 0.00 0.00 ]
#...
| 3000 - 3500 : [ 2 0.00 0.00 ]
| 3500 - 4000 : [ 2 0.00 0.00 ]
|X 4000 - 4500 : [ 4 0.00 0.01 ]
| 4500 - 5000 : [ 2 0.00 0.01 ]
| 5000 - 5500 : [ 2 0.00 0.01 ]
|X 5500 - 6000 : [ 3 0.00 0.01 ]
| 6000 - 6500 : [ 2 0.00 0.01 ]
| 6500 - 7000 : [ 1 0.00 0.01 ]
#...
| 7500 - 8000 : [ 1 0.00 0.01 ]
#...
| 8500 - 9000 : [ 1 0.00 0.01 ]
#...
| 12000 - 12500 : [ 1 0.00 0.01 ]
#...
| 20000 - 20500 : [ 1 0.00 0.01 ]
#...
| 22000 - 22500 : [ 2 0.00 0.01 ]
| 22500 - 23000 : [ 1 0.00 0.01 ]
| 23000 - 23500 : [ 1 0.00 0.01 ]
#...
| 24000 - 24500 : [ 1 0.00 0.01 ]
| 24500 - 25000 : [ 1 0.00 0.01 ]
| 25000 - 25500 : [ 1 0.00 0.01 ]
|X 25500 - 26000 : [ 4 0.00 0.01 ]
|X 26000 - 26500 : [ 3 0.00 0.02 ]
| 26500 - 27000 : [ 2 0.00 0.02 ]
| 27000 - 27500 : [ 2 0.00 0.02 ]
|X 27500 - 28000 : [ 7 0.00 0.02 ]
|XX 28000 - 28500 : [ 10 0.00 0.02 ]
|XX 28500 - 29000 : [ 9 0.00 0.03 ]
|XXX 29000 - 29500 : [ 16 0.01 0.03 ]
|XXXX 29500 - 30000 : [ 18 0.01 0.04 ]
|XXXXX 30000 - 30500 : [ 22 0.01 0.05 ]
|XXXXX 30500 - 31000 : [ 26 0.01 0.06 ]
|XXXXXXX 31000 - 31500 : [ 32 0.01 0.07 ]
|XXXXXXXXXX 31500 - 32000 : [ 49 0.02 0.09 ]
|XXXXXXXXXXXXX 32000 - 32500 : [ 61 0.02 0.11 ]
|XXXXXXXXXXXXXXXXX 32500 - 33000 : [ 81 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 99 0.04 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 129 0.05 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 121 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 174 0.06 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 161 0.06 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 194 0.07 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 188 0.07 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 191 0.07 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 165 0.06 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 161 0.06 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 122 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 132 0.05 0.80 ]
|XXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 103 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 86 0.03 0.87 ]
|XXXXXXXXXXXXXXXXX 40000 - 40500 : [ 81 0.03 0.89 ]
|XXXXXXXXXXXXXX 40500 - 41000 : [ 69 0.02 0.92 ]
|XXXXXXXXXXX 41000 - 41500 : [ 55 0.02 0.94 ]
|XXXXXXXXX 41500 - 42000 : [ 46 0.02 0.96 ]
|XXXXXXX 42000 - 42500 : [ 36 0.01 0.97 ]
|XXXXX 42500 - 43000 : [ 22 0.01 0.98 ]
|XXXXX 43000 - 43500 : [ 22 0.01 0.98 ]
|XXX 43500 - 44000 : [ 16 0.01 0.99 ]
|XX 44000 - 44500 : [ 10 0.00 0.99 ]
|X 44500 - 45000 : [ 4 0.00 1.00 ]
|X 45000 - 45500 : [ 7 0.00 1.00 ]
| 45500 - 46000 : [ 1 0.00 1.00 ]
| 46000 - 46500 : [ 1 0.00 1.00 ]
#...
| 180000 - 180500 : [ 1 0.00 1.00 ]
#...
| 216500 - 217000 : [ 1 0.00 1.00 ]
#...
| 326500 - 327000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTG reads.list > grep.reads.list.AOTG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOTG 4 500
-------------------------------------------------------------------
#Found 3012 total values totalling 19872800.0000. <6597.875166 +/- 969.117900>
#Range: [ 929 - 8838 ]
#Most likely bin: [ 6000 - 6500 ] 731 counts
#Median bin: [ 6500 - 7000 ] 675 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
| 1000 - 1500 : [ 5 0.00 0.00 ]
| 1500 - 2000 : [ 9 0.00 0.01 ]
| 2000 - 2500 : [ 7 0.00 0.01 ]
|X 2500 - 3000 : [ 12 0.00 0.01 ]
|X 3000 - 3500 : [ 12 0.00 0.02 ]
|X 3500 - 4000 : [ 15 0.00 0.02 ]
|X 4000 - 4500 : [ 21 0.01 0.03 ]
|XX 4500 - 5000 : [ 35 0.01 0.04 ]
|XXXXXX 5000 - 5500 : [ 106 0.04 0.07 ]
|XXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 388 0.13 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 731 0.24 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 675 0.22 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 507 0.17 0.84 ]
|XXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 330 0.11 0.95 ]
|XXXXXXXX 8000 - 8500 : [ 141 0.05 0.99 ]
|X 8500 - 9000 : [ 16 0.01 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
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# AHYY 6296 +- 1291 (n=16179)
# AHYX 3122 +- 403 (n=26528)
# AOTG 6506 +- 1093 (n=1461)
# AHYZ 36343 +- 3609 (n=1131)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634480_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
AHYX 152832 -1 -1 96 708 152034 88 662 91 666
AHYY 109824 -1 -1 92 636 109049 77 589 87 612
AHYZ 20832 -1 -1 91 585 7776 91 651 96 660
AOTG 7680 -1 -1 97 736 7680 92 764 97 759
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHYX 76379 88 654 91 663 75655 87 671 91 669
AHYY 54100 73 575 84 597 54949 81 602 90 626
AHYZ 3936 92 650 96 657 3840 91 651 96 663
AOTG 3840 92 760 97 754 3840 92 769 97 765
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634480_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
564 79687 43530 77.18 80.40 AHYY @
40 6837 3465 86.62 90.23 AOTG @
40 7073 3642 91.05 94.84 AHYZ @
777 122671 64492 83.00 86.46 AHYX @
] 216268 115129 81.02 cumulative total@@
LIBRARY PLATE ID COUNT [ AHYY 564 AHYZ 40 AOTG 40 AHYX 777 ] for 1421 total 96 well plate ids.
Only indicates plates present in input file.
Make no assumption regarding plates (not) present in project that do not appear above.
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trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3634480_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 276539 total values totalling 148312703.0000. <536.317492 +/- 285.831890>
#Range: [ 0 - 967 ]
#Most likely bin: [ 750 - 800 ] 43443 counts
#Median bin: [ 650 - 700 ] 26573 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 39471 0.14 0.14 ]
|XXXXX 50 - 100 : [ 5852 0.02 0.16 ]
|XXXXX 100 - 150 : [ 4948 0.02 0.18 ]
|XXXX 150 - 200 : [ 4735 0.02 0.20 ]
|XXXX 200 - 250 : [ 4382 0.02 0.21 ]
|XXXX 250 - 300 : [ 4867 0.02 0.23 ]
|XXXXX 300 - 350 : [ 5233 0.02 0.25 ]
|XXXXXX 350 - 400 : [ 6177 0.02 0.27 ]
|XXXXXX 400 - 450 : [ 6784 0.02 0.30 ]
|XXXXXXX 450 - 500 : [ 8101 0.03 0.33 ]
|XXXXXXXXXX 500 - 550 : [ 10715 0.04 0.37 ]
|XXXXXXXXXXXXX 550 - 600 : [ 14551 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXX 600 - 650 : [ 20132 0.07 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 26573 0.10 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 34343 0.12 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 43443 0.16 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 30860 0.11 0.98 ]
|XXXXX 850 - 900 : [ 5272 0.02 1.00 ]
| 900 - 950 : [ 99 0.00 1.00 ]
| 950 - 1000 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYX 3634480_fasta.screen.trimQ15.SaF > reads.trim15.AHYX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYX.rl 2 50
-------------------------------------------------------------------
#Found 152034 total values totalling 88512919.0000. <582.191608 +/- 269.675308>
#Range: [ 0 - 967 ]
#Most likely bin: [ 750 - 800 ] 29093 counts
#Median bin: [ 650 - 700 ] 13653 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 16203 0.11 0.11 ]
|XXXX 50 - 100 : [ 2648 0.02 0.12 ]
|XXX 100 - 150 : [ 2208 0.01 0.14 ]
|XXX 150 - 200 : [ 2123 0.01 0.15 ]
|XXX 200 - 250 : [ 2188 0.01 0.17 ]
|XXX 250 - 300 : [ 2321 0.02 0.18 ]
|XXX 300 - 350 : [ 2537 0.02 0.20 ]
|XXXX 350 - 400 : [ 2956 0.02 0.22 ]
|XXXXX 400 - 450 : [ 3510 0.02 0.24 ]
|XXXXXX 450 - 500 : [ 4088 0.03 0.27 ]
|XXXXXXX 500 - 550 : [ 5380 0.04 0.30 ]
|XXXXXXXXXX 550 - 600 : [ 7115 0.05 0.35 ]
|XXXXXXXXXXXXX 600 - 650 : [ 9763 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXX 650 - 700 : [ 13653 0.09 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 20093 0.13 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 29093 0.19 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 22110 0.15 0.97 ]
|XXXXX 850 - 900 : [ 3965 0.03 1.00 ]
| 900 - 950 : [ 79 0.00 1.00 ]
| 950 - 1000 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYY 3634480_fasta.screen.trimQ15.SaF > reads.trim15.AHYY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYY.rl 2 50
-------------------------------------------------------------------
#Found 109049 total values totalling 49770076.0000. <456.401031 +/- 294.984280>
#Range: [ 0 - 928 ]
#Most likely bin: [ 0 - 50 ] 22146 counts
#Median bin: [ 550 - 600 ] 7071 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 22146 0.20 0.20 ]
|XXXXX 50 - 100 : [ 3020 0.03 0.23 ]
|XXXXX 100 - 150 : [ 2645 0.02 0.26 ]
|XXXXX 150 - 200 : [ 2554 0.02 0.28 ]
|XXXX 200 - 250 : [ 2112 0.02 0.30 ]
|XXXX 250 - 300 : [ 2380 0.02 0.32 ]
|XXXXX 300 - 350 : [ 2499 0.02 0.34 ]
|XXXXX 350 - 400 : [ 2932 0.03 0.37 ]
|XXXXXX 400 - 450 : [ 3098 0.03 0.40 ]
|XXXXXXX 450 - 500 : [ 3865 0.04 0.43 ]
|XXXXXXXXX 500 - 550 : [ 5120 0.05 0.48 ]
|XXXXXXXXXXXXX 550 - 600 : [ 7071 0.06 0.55 ]
|XXXXXXXXXXXXXXXXX 600 - 650 : [ 9514 0.09 0.63 ]
|XXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 11121 0.10 0.73 ]
|XXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 11267 0.10 0.84 ]
|XXXXXXXXXXXXXXXXXXX 750 - 800 : [ 10603 0.10 0.93 ]
|XXXXXXXXXXX 800 - 850 : [ 6156 0.06 0.99 ]
|XX 850 - 900 : [ 928 0.01 1.00 ]
| 900 - 950 : [ 18 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYZ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYZ 3634480_fasta.screen.trimQ15.SaF > reads.trim15.AHYZ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYZ.rl 2 50
-------------------------------------------------------------------
#Found 7776 total values totalling 4636984.0000. <596.319959 +/- 227.837594>
#Range: [ 0 - 871 ]
#Most likely bin: [ 700 - 750 ] 1859 counts
#Median bin: [ 650 - 700 ] 1360 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 0 - 50 : [ 511 0.07 0.07 ]
|XXXX 50 - 100 : [ 168 0.02 0.09 ]
|XX 100 - 150 : [ 84 0.01 0.10 ]
|X 150 - 200 : [ 49 0.01 0.10 ]
|X 200 - 250 : [ 62 0.01 0.11 ]
|XXX 250 - 300 : [ 154 0.02 0.13 ]
|XXXX 300 - 350 : [ 181 0.02 0.16 ]
|XXXXXX 350 - 400 : [ 264 0.03 0.19 ]
|XXX 400 - 450 : [ 144 0.02 0.21 ]
|XXX 450 - 500 : [ 118 0.02 0.22 ]
|XXXX 500 - 550 : [ 165 0.02 0.24 ]
|XXXXXX 550 - 600 : [ 281 0.04 0.28 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 692 0.09 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1360 0.17 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1859 0.24 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1298 0.17 0.95 ]
|XXXXXXXX 800 - 850 : [ 374 0.05 1.00 ]
| 850 - 900 : [ 12 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOTG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTG 3634480_fasta.screen.trimQ15.SaF > reads.trim15.AOTG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOTG.rl 2 50
-------------------------------------------------------------------
#Found 7680 total values totalling 5392724.0000. <702.177604 +/- 224.843843>
#Range: [ 0 - 905 ]
#Most likely bin: [ 750 - 800 ] 2449 counts
#Median bin: [ 750 - 800 ] 2449 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 0 - 50 : [ 611 0.08 0.08 ]
| 50 - 100 : [ 16 0.00 0.08 ]
| 100 - 150 : [ 11 0.00 0.08 ]
| 150 - 200 : [ 9 0.00 0.08 ]
| 200 - 250 : [ 20 0.00 0.09 ]
| 250 - 300 : [ 12 0.00 0.09 ]
| 300 - 350 : [ 16 0.00 0.09 ]
| 350 - 400 : [ 25 0.00 0.09 ]
|X 400 - 450 : [ 32 0.00 0.10 ]
| 450 - 500 : [ 30 0.00 0.10 ]
|X 500 - 550 : [ 50 0.01 0.11 ]
|X 550 - 600 : [ 84 0.01 0.12 ]
|XXX 600 - 650 : [ 163 0.02 0.14 ]
|XXXXXXX 650 - 700 : [ 439 0.06 0.20 ]
|XXXXXXXXXXXXXXXXXX 700 - 750 : [ 1124 0.15 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2449 0.32 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2220 0.29 0.95 ]
|XXXXXX 850 - 900 : [ 367 0.05 1.00 ]
| 900 - 950 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634480
-------------------------------------------------------------------
AHYX.000001.000100 pUC18.fa LRS.fasta
AHYX.000101.000200 pUC18.fa LRS.fasta
AHYX.000201.000300 pUC18.fa LRS.fasta
AHYX.000301.000400 pUC18.fa LRS.fasta
AHYX.000401.000500 pUC18.fa LRS.fasta
AHYX.000501.000600 pUC18.fa LRS.fasta
AHYX.000601.000700 pUC18.fa LRS.fasta
AHYX.000701.000800 pUC18.fa LRS.fasta
AHYX.000801.000900 pUC18.fa LRS.fasta
AHYY.000001.000100 pMCL200.fa LRS.fasta
AHYY.000101.000200 pMCL200.fa LRS.fasta
AHYY.000201.000300 pMCL200.fa LRS.fasta
AHYY.000301.000400 pMCL200.fa LRS.fasta
AHYY.000401.000500 pMCL200.fa LRS.fasta
AHYY.000501.000600 pMCL200.fa LRS.fasta
AHYZ.000001.000100 pCC1Fos.fa LRS.fasta
AHYZ.000101.000200 pCC1Fos.fa LRS.fasta
AOTG.000001.000100 pMCL200.fa LRS.fasta
AHYX.000001.000100 pUC18.fa LRS.fasta
AHYX.000101.000200 pUC18.fa LRS.fasta
AHYX.000201.000300 pUC18.fa LRS.fasta
AHYX.000301.000400 pUC18.fa LRS.fasta
AHYX.000401.000500 pUC18.fa LRS.fasta
AHYX.000501.000600 pUC18.fa LRS.fasta
AHYX.000601.000700 pUC18.fa LRS.fasta
AHYX.000701.000800 pUC18.fa LRS.fasta
AHYX.000801.000900 pUC18.fa LRS.fasta
AHYY.000001.000100 pMCL200.fa LRS.fasta
AHYY.000101.000200 pMCL200.fa LRS.fasta
AHYY.000201.000300 pMCL200.fa LRS.fasta
AHYY.000301.000400 pMCL200.fa LRS.fasta
AHYY.000401.000500 pMCL200.fa LRS.fasta
AHYY.000501.000600 pMCL200.fa LRS.fasta
AHYZ.000001.000100 pCC1Fos.fa LRS.fasta
AHYZ.000101.000200 pCC1Fos.fa LRS.fasta
AOTG.000001.000100 pMCL200.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634480_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634480_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 215419 total values totalling 88513.6603. <0.410891 +/- 0.042206>
#Range: [ 0 - 0.8379 ]
#Most likely bin: [ 0.4 - 0.405 ] 11223 counts
#Median bin: [ 0.405 - 0.41 ] 11097 counts
| 0 - 0.005 : [ 2 0.00 0.00 ]
#...
| 0.055 - 0.06 : [ 1 0.00 0.00 ]
#...
| 0.085 - 0.09 : [ 1 0.00 0.00 ]
| 0.09 - 0.095 : [ 1 0.00 0.00 ]
#...
| 0.105 - 0.11 : [ 1 0.00 0.00 ]
#...
| 0.125 - 0.13 : [ 3 0.00 0.00 ]
| 0.13 - 0.135 : [ 1 0.00 0.00 ]
| 0.135 - 0.14 : [ 1 0.00 0.00 ]
| 0.14 - 0.145 : [ 1 0.00 0.00 ]
| 0.145 - 0.15 : [ 1 0.00 0.00 ]
| 0.15 - 0.155 : [ 4 0.00 0.00 ]
#...
| 0.16 - 0.165 : [ 1 0.00 0.00 ]
| 0.165 - 0.17 : [ 5 0.00 0.00 ]
| 0.17 - 0.175 : [ 5 0.00 0.00 ]
| 0.175 - 0.18 : [ 4 0.00 0.00 ]
| 0.18 - 0.185 : [ 5 0.00 0.00 ]
| 0.185 - 0.19 : [ 4 0.00 0.00 ]
| 0.19 - 0.195 : [ 7 0.00 0.00 ]
| 0.195 - 0.2 : [ 2 0.00 0.00 ]
| 0.2 - 0.205 : [ 8 0.00 0.00 ]
| 0.205 - 0.21 : [ 7 0.00 0.00 ]
| 0.21 - 0.215 : [ 11 0.00 0.00 ]
| 0.215 - 0.22 : [ 15 0.00 0.00 ]
| 0.22 - 0.225 : [ 14 0.00 0.00 ]
| 0.225 - 0.23 : [ 20 0.00 0.00 ]
| 0.23 - 0.235 : [ 21 0.00 0.00 ]
| 0.235 - 0.24 : [ 34 0.00 0.00 ]
| 0.24 - 0.245 : [ 29 0.00 0.00 ]
| 0.245 - 0.25 : [ 13 0.00 0.00 ]
| 0.25 - 0.255 : [ 58 0.00 0.00 ]
| 0.255 - 0.26 : [ 52 0.00 0.00 ]
| 0.26 - 0.265 : [ 53 0.00 0.00 ]
| 0.265 - 0.27 : [ 63 0.00 0.00 ]
| 0.27 - 0.275 : [ 88 0.00 0.00 ]
| 0.275 - 0.28 : [ 88 0.00 0.00 ]
| 0.28 - 0.285 : [ 122 0.00 0.00 ]
|X 0.285 - 0.29 : [ 159 0.00 0.00 ]
|X 0.29 - 0.295 : [ 199 0.00 0.01 ]
|X 0.295 - 0.3 : [ 236 0.00 0.01 ]
|X 0.3 - 0.305 : [ 299 0.00 0.01 ]
|X 0.305 - 0.31 : [ 377 0.00 0.01 ]
|XX 0.31 - 0.315 : [ 503 0.00 0.01 ]
|XX 0.315 - 0.32 : [ 597 0.00 0.01 ]
|XXX 0.32 - 0.325 : [ 777 0.00 0.02 ]
|XXXX 0.325 - 0.33 : [ 1040 0.00 0.02 ]
|XXXXX 0.33 - 0.335 : [ 1321 0.01 0.03 ]
|XXXXXX 0.335 - 0.34 : [ 1630 0.01 0.04 ]
|XXXXXXXX 0.34 - 0.345 : [ 2193 0.01 0.05 ]
|XXXXXXXXXX 0.345 - 0.35 : [ 2763 0.01 0.06 ]
|XXXXXXXXXXXXX 0.35 - 0.355 : [ 3578 0.02 0.08 ]
|XXXXXXXXXXXXXXX 0.355 - 0.36 : [ 4224 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 5357 0.02 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 6146 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 6944 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 8246 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 8934 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 9608 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 10144 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 10114 0.05 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 11223 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 11097 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 10805 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 10471 0.05 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 9962 0.05 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 9286 0.04 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 8656 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 8090 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 7490 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 6715 0.03 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 6074 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 5184 0.02 0.89 ]
|XXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 4365 0.02 0.91 ]
|XXXXXXXXXXXXX 0.465 - 0.47 : [ 3758 0.02 0.93 ]
|XXXXXXXXXXX 0.47 - 0.475 : [ 3000 0.01 0.94 ]
|XXXXXXXXX 0.475 - 0.48 : [ 2664 0.01 0.95 ]
|XXXXXXXX 0.48 - 0.485 : [ 2174 0.01 0.96 ]
|XXXXXX 0.485 - 0.49 : [ 1615 0.01 0.97 ]
|XXXXX 0.49 - 0.495 : [ 1305 0.01 0.98 ]
|XXX 0.495 - 0.5 : [ 808 0.00 0.98 ]
|XXXX 0.5 - 0.505 : [ 1087 0.01 0.98 ]
|XX 0.505 - 0.51 : [ 622 0.00 0.99 ]
|XX 0.51 - 0.515 : [ 575 0.00 0.99 ]
|XX 0.515 - 0.52 : [ 447 0.00 0.99 ]
|X 0.52 - 0.525 : [ 334 0.00 0.99 ]
|X 0.525 - 0.53 : [ 241 0.00 0.99 ]
|X 0.53 - 0.535 : [ 172 0.00 1.00 ]
|X 0.535 - 0.54 : [ 154 0.00 1.00 ]
|X 0.54 - 0.545 : [ 149 0.00 1.00 ]
| 0.545 - 0.55 : [ 105 0.00 1.00 ]
| 0.55 - 0.555 : [ 72 0.00 1.00 ]
| 0.555 - 0.56 : [ 74 0.00 1.00 ]
| 0.56 - 0.565 : [ 71 0.00 1.00 ]
| 0.565 - 0.57 : [ 60 0.00 1.00 ]
| 0.57 - 0.575 : [ 43 0.00 1.00 ]
| 0.575 - 0.58 : [ 35 0.00 1.00 ]
| 0.58 - 0.585 : [ 41 0.00 1.00 ]
| 0.585 - 0.59 : [ 28 0.00 1.00 ]
| 0.59 - 0.595 : [ 25 0.00 1.00 ]
| 0.595 - 0.6 : [ 14 0.00 1.00 ]
| 0.6 - 0.605 : [ 18 0.00 1.00 ]
| 0.605 - 0.61 : [ 19 0.00 1.00 ]
| 0.61 - 0.615 : [ 6 0.00 1.00 ]
| 0.615 - 0.62 : [ 11 0.00 1.00 ]
| 0.62 - 0.625 : [ 13 0.00 1.00 ]
| 0.625 - 0.63 : [ 11 0.00 1.00 ]
| 0.63 - 0.635 : [ 3 0.00 1.00 ]
| 0.635 - 0.64 : [ 4 0.00 1.00 ]
| 0.64 - 0.645 : [ 8 0.00 1.00 ]
| 0.645 - 0.65 : [ 2 0.00 1.00 ]
| 0.65 - 0.655 : [ 8 0.00 1.00 ]
| 0.655 - 0.66 : [ 12 0.00 1.00 ]
| 0.66 - 0.665 : [ 3 0.00 1.00 ]
| 0.665 - 0.67 : [ 3 0.00 1.00 ]
| 0.67 - 0.675 : [ 1 0.00 1.00 ]
| 0.675 - 0.68 : [ 6 0.00 1.00 ]
| 0.68 - 0.685 : [ 10 0.00 1.00 ]
| 0.685 - 0.69 : [ 9 0.00 1.00 ]
| 0.69 - 0.695 : [ 12 0.00 1.00 ]
| 0.695 - 0.7 : [ 6 0.00 1.00 ]
| 0.7 - 0.705 : [ 3 0.00 1.00 ]
| 0.705 - 0.71 : [ 2 0.00 1.00 ]
| 0.71 - 0.715 : [ 11 0.00 1.00 ]
| 0.715 - 0.72 : [ 2 0.00 1.00 ]
| 0.72 - 0.725 : [ 1 0.00 1.00 ]
| 0.725 - 0.73 : [ 2 0.00 1.00 ]
#...
| 0.75 - 0.755 : [ 1 0.00 1.00 ]
#...
| 0.76 - 0.765 : [ 3 0.00 1.00 ]
| 0.765 - 0.77 : [ 2 0.00 1.00 ]
#...
| 0.835 - 0.84 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 324. 2433 reads; 170943 bp (untrimmed), 170784 (trimmed).
Contig 325. 2582 reads; 181491 bp (untrimmed), 181491 (trimmed).
Contig 326. 2587 reads; 184191 bp (untrimmed), 183840 (trimmed).
Contig 327. 2611 reads; 147189 bp (untrimmed), 147155 (trimmed).
Contig 328. 2923 reads; 203380 bp (untrimmed), 203127 (trimmed).
Contig 329. 3051 reads; 230651 bp (untrimmed), 230502 (trimmed).
Contig 330. 3148 reads; 246368 bp (untrimmed), 246311 (trimmed).
Contig 331. 3337 reads; 260206 bp (untrimmed), 260103 (trimmed).
Contig 332. 3398 reads; 204545 bp (untrimmed), 204240 (trimmed).
Contig 333. 3426 reads; 260229 bp (untrimmed), 260182 (trimmed).
Contig 334. 3448 reads; 245156 bp (untrimmed), 245115 (trimmed).
Contig 335. 3465 reads; 236663 bp (untrimmed), 236556 (trimmed).
Contig 336. 3582 reads; 225426 bp (untrimmed), 225394 (trimmed).
Contig 337. 3812 reads; 291441 bp (untrimmed), 291433 (trimmed).
Contig 338. 3895 reads; 284571 bp (untrimmed), 284409 (trimmed).
Contig 339. 4118 reads; 297019 bp (untrimmed), 296699 (trimmed).
Contig 340. 4151 reads; 280359 bp (untrimmed), 280339 (trimmed).
Contig 341. 4326 reads; 323571 bp (untrimmed), 323452 (trimmed).
Contig 342. 4383 reads; 325149 bp (untrimmed), 325133 (trimmed).
Contig 343. 4484 reads; 302434 bp (untrimmed), 302267 (trimmed).
Contig 344. 4564 reads; 321302 bp (untrimmed), 321263 (trimmed).
Contig 345. 4789 reads; 356844 bp (untrimmed), 356814 (trimmed).
Contig 346. 5424 reads; 402795 bp (untrimmed), 402232 (trimmed).
Contig 347. 5866 reads; 416475 bp (untrimmed), 416404 (trimmed).
Contig 348. 7026 reads; 494080 bp (untrimmed), 493817 (trimmed).
Contig 349. 7903 reads; 544647 bp (untrimmed), 544496 (trimmed).
Contig 350. 9431 reads; 639225 bp (untrimmed), 639225 (trimmed).
--------------------------------------------------------------
Totals 216176 reads; 15424194 bp (untrimmed), 15289652 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 15290239 bases = 12.26 +- 6.36 = 0.16 +- 4.05
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 188 total values totalling 2375.8600. <12.637553 +/- 9.178947>
#Range: [ 1.22 - 110.76 ]
#Most likely bin: [ 11.5 - 12 ] 25 counts
#Median bin: [ 11.5 - 12 ] 25 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 1 - 1.5 : [ 2 0.01 0.01 ]
|XX 1.5 - 2 : [ 1 0.01 0.02 ]
|XX 2 - 2.5 : [ 1 0.01 0.02 ]
|XX 2.5 - 3 : [ 1 0.01 0.03 ]
|XX 3 - 3.5 : [ 1 0.01 0.03 ]
|XXX 3.5 - 4 : [ 2 0.01 0.04 ]
|XXXXXX 4 - 4.5 : [ 4 0.02 0.06 ]
|XXX 4.5 - 5 : [ 2 0.01 0.07 ]
|XXXXXX 5 - 5.5 : [ 4 0.02 0.10 ]
|XXX 5.5 - 6 : [ 2 0.01 0.11 ]
|XXXXXXXX 6 - 6.5 : [ 5 0.03 0.13 ]
|XX 6.5 - 7 : [ 1 0.01 0.14 ]
|XXX 7 - 7.5 : [ 2 0.01 0.15 ]
|XXXXXX 7.5 - 8 : [ 4 0.02 0.17 ]
|XXXXX 8 - 8.5 : [ 3 0.02 0.19 ]
|XXX 8.5 - 9 : [ 2 0.01 0.20 ]
|XXXXXX 9 - 9.5 : [ 4 0.02 0.22 ]
|XXXXXXXXXX 9.5 - 10 : [ 6 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 11 0.06 0.31 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 8 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 15 0.08 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 25 0.13 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 22 0.12 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 16 0.09 0.77 ]
|XX 13 - 13.5 : [ 1 0.01 0.77 ]
|XXXXXX 13.5 - 14 : [ 4 0.02 0.79 ]
|XXXXXX 14 - 14.5 : [ 4 0.02 0.81 ]
|XXXXXX 14.5 - 15 : [ 4 0.02 0.84 ]
|XXXXXXXX 15 - 15.5 : [ 5 0.03 0.86 ]
|XXXXX 15.5 - 16 : [ 3 0.02 0.88 ]
#...
|XXXXXX 16.5 - 17 : [ 4 0.02 0.90 ]
#...
|XXXXXX 18 - 18.5 : [ 4 0.02 0.92 ]
|XX 18.5 - 19 : [ 1 0.01 0.93 ]
|XXXXX 19 - 19.5 : [ 3 0.02 0.94 ]
#...
|XX 20 - 20.5 : [ 1 0.01 0.95 ]
#...
|XX 27 - 27.5 : [ 1 0.01 0.95 ]
#...
|XX 28 - 28.5 : [ 1 0.01 0.96 ]
|XX 28.5 - 29 : [ 1 0.01 0.96 ]
|XX 29 - 29.5 : [ 1 0.01 0.97 ]
#...
|XXX 31 - 31.5 : [ 2 0.01 0.98 ]
|XX 31.5 - 32 : [ 1 0.01 0.98 ]
#...
|XX 36.5 - 37 : [ 1 0.01 0.99 ]
#...
|XX 41 - 41.5 : [ 1 0.01 0.99 ]
#...
|XX 110.5 - 111 : [ 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 154 total values totalling 1949.4000. <12.658442 +/- 8.540076>
#Range: [ 4.44 - 110.76 ]
#Most likely bin: [ 11.5 - 12 ] 25 counts
#Median bin: [ 11.5 - 12 ] 25 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 4 - 4.5 : [ 2 0.01 0.01 ]
#...
|XXXXX 5 - 5.5 : [ 3 0.02 0.03 ]
|XX 5.5 - 6 : [ 1 0.01 0.04 ]
|XX 6 - 6.5 : [ 1 0.01 0.05 ]
|XX 6.5 - 7 : [ 1 0.01 0.05 ]
|XXX 7 - 7.5 : [ 2 0.01 0.06 ]
|XX 7.5 - 8 : [ 1 0.01 0.07 ]
|XXX 8 - 8.5 : [ 2 0.01 0.08 ]
|XXX 8.5 - 9 : [ 2 0.01 0.10 ]
|XXXXXX 9 - 9.5 : [ 4 0.03 0.12 ]
|XXXXXXXXXX 9.5 - 10 : [ 6 0.04 0.16 ]
|XXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 11 0.07 0.23 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 8 0.05 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 15 0.10 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 25 0.16 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 22 0.14 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 16 0.10 0.79 ]
|XX 13 - 13.5 : [ 1 0.01 0.80 ]
|XXXXX 13.5 - 14 : [ 3 0.02 0.82 ]
|XXXXXX 14 - 14.5 : [ 4 0.03 0.84 ]
|XXXXXX 14.5 - 15 : [ 4 0.03 0.87 ]
|XXXXXXXX 15 - 15.5 : [ 5 0.03 0.90 ]
|XXX 15.5 - 16 : [ 2 0.01 0.92 ]
#...
|XXXXXX 16.5 - 17 : [ 4 0.03 0.94 ]
#...
|XXXXXX 18 - 18.5 : [ 4 0.03 0.97 ]
|XX 18.5 - 19 : [ 1 0.01 0.97 ]
|XX 19 - 19.5 : [ 1 0.01 0.98 ]
#...
|XX 20 - 20.5 : [ 1 0.01 0.99 ]
#...
|XX 31.5 - 32 : [ 1 0.01 0.99 ]
#...
|XX 110.5 - 111 : [ 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 159 2 reads 1159 bases = 1.22 +- 0.41 = 0.78 +- 0.41
Contig 160 2 reads 507 bases = 1.39 +- 0.49 = 1.39 +- 0.49
Contig 162 4 reads 1977 bases = 1.84 +- 0.48 = 1.84 +- 0.48
Contig 158 2 reads 530 bases = 2.00 +- 0.00 = 2.00 +- 0.00
Contig 169 9 reads 2675 bases = 2.76 +- 1.71 = 0.92 +- 1.38
Contig 164 4 reads 1103 bases = 3.17 +- 1.02 = 1.71 +- 0.87
Contig 166 6 reads 1373 bases = 3.67 +- 2.04 = -0.06 +- 1.04
Contig 163 4 reads 889 bases = 3.82 +- 0.48 = 3.82 +- 0.48
Contig 168 7 reads 1485 bases = 4.23 +- 2.39 = 0.73 +- 0.88
Contig 167 7 reads 1486 bases = 4.40 +- 2.06 = 1.91 +- 0.71
Contig 192 34 reads 6464 bases = 4.44 +- 2.10 = 0.20 +- 3.70
Contig 183 17 reads 2482 bases = 4.45 +- 3.14 = 0.59 +- 1.82
Contig 165 5 reads 635 bases = 4.75 +- 0.54 = 0.79 +- 0.47
Contig 173 11 reads 1779 bases = 4.79 +- 3.36 = 2.05 +- 0.90
Contig 186 23 reads 3826 bases = 5.14 +- 2.58 = 0.98 +- 3.28
Contig 179 15 reads 2519 bases = 5.24 +- 3.65 = 5.24 +- 3.65
Contig 171 10 reads 1515 bases = 5.30 +- 2.21 = 0.03 +- 1.04
Contig 202 44 reads 6784 bases = 5.34 +- 3.06 = 3.05 +- 2.23
Contig 172 11 reads 1545 bases = 5.66 +- 2.02 = 3.54 +- 2.54
Contig 213 57 reads 8679 bases = 5.76 +- 3.24 = 0.07 +- 2.11
Contig 235 219 reads 11377 bases = 16.81 +- 16.75 = 1.05 +- 3.30
Contig 249 401 reads 19445 bases = 18.12 +- 10.98 = 1.32 +- 5.55
Contig 282 1065 reads 50516 bases = 18.23 +- 9.83 = 1.32 +- 10.27
Contig 214 60 reads 2738 bases = 18.32 +- 14.20 = 3.66 +- 5.91
Contig 216 69 reads 3308 bases = 18.46 +- 11.28 = 4.76 +- 5.29
Contig 208 48 reads 2220 bases = 18.93 +- 19.33 = 17.26 +- 18.62
Contig 212 56 reads 2553 bases = 19.08 +- 10.47 = 3.51 +- 4.02
Contig 206 47 reads 1924 bases = 19.18 +- 11.58 = 2.35 +- 3.92
Contig 194 35 reads 1423 bases = 19.40 +- 12.29 = 19.40 +- 12.29
Contig 222 101 reads 4379 bases = 20.10 +- 16.59 = 1.68 +- 4.35
Contig 195 37 reads 1150 bases = 27.34 +- 11.10 = 27.34 +- 11.10
Contig 196 38 reads 1182 bases = 28.11 +- 13.28 = 28.11 +- 13.28
Contig 201 44 reads 1228 bases = 28.51 +- 14.21 = 28.51 +- 14.21
Contig 200 42 reads 1221 bases = 29.04 +- 14.78 = 29.04 +- 14.78
Contig 215 65 reads 1563 bases = 31.02 +- 22.66 = 30.16 +- 21.84
Contig 205 47 reads 1297 bases = 31.05 +- 16.93 = 31.05 +- 16.93
Contig 231 178 reads 4984 bases = 31.86 +- 16.68 = 3.88 +- 5.26
Contig 210 51 reads 1197 bases = 36.68 +- 17.70 = 36.68 +- 17.70
Contig 219 79 reads 1675 bases = 41.34 +- 31.93 = 41.34 +- 31.93
Contig 295 1397 reads 10510 bases = 110.76 +- 118.44 = 5.01 +- 26.31
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 5637
HQ Discrepant reads = 119
Chimeric reads = 442
Suspect alignments = 1288
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 3.57 SUN/Ultra-2/3
Equivalent to Phil Green's version 0.990329
Score matrix (set by value of penalty: -2)
A C G T N X
A 1 -2 -2 -2 0 -3
C -2 1 -2 -2 0 -3
G -2 -2 1 -2 0 -3
T -2 -2 -2 1 0 -3
N 0 0 0 0 0 0
X -3 -3 -3 -3 0 -3
gap_init: -4
gap_ext: -3
ins_gap_ext: -3
del_gap_ext: -3
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 30
maxmatch: 55
max_group_size: 20
minscore: 55
bandwidth: 14
indexwordsize: 10
vector_bound: 20
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 13
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -5
confirm_score: 30
node_seg: 48
node_space: 24
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/microbe4/3634480/edit_dir.14Jun04.QD