Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-12-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634491 5000 66219 Clostridium phytofermentans
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Clostridium_phytofermentans
-------------------------------------------------------------------
Clostridiales, order, eubacteria
Clostridia, class, eubacteria
Clostridium phytofermentans, species, eubacteria
Clostridiaceae, family, eubacteria
Clostridium, genus, eubacteria
Firmicutes (Gram-positive bacteria), phylum, eubacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4692186
# phrap: 4378516
# db:
altered.
5000000
4690234 +/- 253723
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 16122
Number of reads with percent X's >= 20%: 117 = 0.2%
Number of reads with percent X's >= 50%: 57 = 0.1%
Number of reads with percent X's >= 80%: 6 = 0.0%
Total reads in project: 66153
Total bp X'd : 623700
reads >= 20% >= 50% >= 80% screened
Nr with L09136 14015 85 41 1
Nr with pCC1Fos 2048 5 0 0
Nr with pMCL200_JGI_XZX+XZK 59 27 16 5
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 34
Number of reads with percent X's >= 20%: 0 = 0.0%
Number of reads with percent X's >= 50%: 0 = 0.0%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 164
Total bp X'd : 1226
reads >= 20% >= 50% >= 80% screened
Nr with L09136 12 0 0 0
Nr with pCC1Fos 21 0 0 0
Nr with pMCL200_JGI_XZX+XZK 1 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 19224797
C = 10914213
G = 10919255
T = 18957686
N = 312391
X = 623700
GC fraction = 0.36
Total = 60952042
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634491_fasta.screen.contigs
-------------------------------------------------------------------
A 1506451
C 866555
G 810886
T 1552826
N 360
fraction GC = 0.35
total bases = 4737078
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 AIAT reads.list > grep.reads.list.AIAT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAT 4 500
-------------------------------------------------------------------
#Found 15605 total values totalling 55567447.0000. <3560.874527 +/- 579.865174>
#Range: [ 764 - 10150 ]
#Most likely bin: [ 3000 - 3500 ] 5842 counts
#Median bin: [ 3500 - 4000 ] 4500 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 13 0.00 0.00 ]
| 1000 - 1500 : [ 73 0.00 0.01 ]
|X 1500 - 2000 : [ 101 0.01 0.01 ]
|X 2000 - 2500 : [ 214 0.01 0.03 ]
|XXXXXXXXXX 2500 - 3000 : [ 1390 0.09 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 5842 0.37 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 4500 0.29 0.78 ]
|XXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 2680 0.17 0.95 ]
|XXXXX 4500 - 5000 : [ 765 0.05 1.00 ]
| 5000 - 5500 : [ 20 0.00 1.00 ]
#...
| 9000 - 9500 : [ 4 0.00 1.00 ]
#...
| 10000 - 10500 : [ 3 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAU reads.list > grep.reads.list.AIAU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAU 4 500
-------------------------------------------------------------------
#Found 10623 total values totalling 69146523.0000. <6509.133296 +/- 837.323266>
#Range: [ 986 - 49326 ]
#Most likely bin: [ 6000 - 6500 ] 2745 counts
#Median bin: [ 6500 - 7000 ] 2667 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 13 0.00 0.00 ]
| 1500 - 2000 : [ 13 0.00 0.00 ]
| 2000 - 2500 : [ 20 0.00 0.00 ]
| 2500 - 3000 : [ 16 0.00 0.01 ]
| 3000 - 3500 : [ 16 0.00 0.01 ]
| 3500 - 4000 : [ 17 0.00 0.01 ]
| 4000 - 4500 : [ 12 0.00 0.01 ]
| 4500 - 5000 : [ 10 0.00 0.01 ]
|XX 5000 - 5500 : [ 125 0.01 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 2304 0.22 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2745 0.26 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2667 0.25 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1869 0.18 0.93 ]
|XXXXXXXXXXX 7500 - 8000 : [ 770 0.07 1.00 ]
| 8000 - 8500 : [ 23 0.00 1.00 ]
#...
| 10000 - 10500 : [ 1 0.00 1.00 ]
#...
| 49000 - 49500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAW reads.list > grep.reads.list.AIAW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAW 4 500
-------------------------------------------------------------------
#Found 819 total values totalling 29762045.0000. <36339.493284 +/- 3627.884596>
#Range: [ 24455 - 46741 ]
#Most likely bin: [ 33500 - 34000 ] 58 counts
#Median bin: [ 35500 - 36000 ] 41 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 24000 - 24500 : [ 1 0.00 0.00 ]
#...
|X 25500 - 26000 : [ 1 0.00 0.00 ]
#...
|X 27000 - 27500 : [ 2 0.00 0.00 ]
|X 27500 - 28000 : [ 2 0.00 0.01 ]
|X 28000 - 28500 : [ 1 0.00 0.01 ]
|XX 28500 - 29000 : [ 3 0.00 0.01 ]
|X 29000 - 29500 : [ 2 0.00 0.01 ]
|X 29500 - 30000 : [ 2 0.00 0.02 ]
|XXXX 30000 - 30500 : [ 6 0.01 0.02 ]
|XXXXXXXX 30500 - 31000 : [ 11 0.01 0.04 ]
|XXXXXXXX 31000 - 31500 : [ 12 0.01 0.05 ]
|XXXXXXXXXXXXXXXXXXXXX 31500 - 32000 : [ 30 0.04 0.09 ]
|XXXXXXXXXXXXXXXX 32000 - 32500 : [ 23 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 39 0.05 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 47 0.06 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 58 0.07 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 48 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 57 0.07 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 39 0.05 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 41 0.05 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 40 0.05 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 33 0.04 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 38 0.05 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 37 0.05 0.70 ]
|XXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 31 0.04 0.74 ]
|XXXXXXXXXXXXXXXX 38500 - 39000 : [ 23 0.03 0.77 ]
|XXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 30 0.04 0.80 ]
|XXXXXXXXXXXXXXXX 39500 - 40000 : [ 23 0.03 0.83 ]
|XXXXXXXXXXXXXXX 40000 - 40500 : [ 22 0.03 0.86 ]
|XXXXXXXXXXX 40500 - 41000 : [ 16 0.02 0.88 ]
|XXXXXXXXXXXXXXX 41000 - 41500 : [ 22 0.03 0.90 ]
|XXXXXXXXXX 41500 - 42000 : [ 15 0.02 0.92 ]
|XXXXXXXX 42000 - 42500 : [ 11 0.01 0.94 ]
|XXXXXX 42500 - 43000 : [ 9 0.01 0.95 ]
|XXXX 43000 - 43500 : [ 6 0.01 0.95 ]
|XXXXXXXXXX 43500 - 44000 : [ 14 0.02 0.97 ]
|XXXX 44000 - 44500 : [ 6 0.01 0.98 ]
|XXX 44500 - 45000 : [ 5 0.01 0.98 ]
|XXXX 45000 - 45500 : [ 6 0.01 0.99 ]
|XXX 45500 - 46000 : [ 5 0.01 1.00 ]
|X 46000 - 46500 : [ 1 0.00 1.00 ]
|X 46500 - 47000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep BIFI reads.list > grep.reads.list.BIFI
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BIFI 4 500
-------------------------------------------------------------------
#Found 351 total values totalling 12427454.0000. <35405.851852 +/- 3589.639428>
#Range: [ 21310 - 44492 ]
#Most likely bin: [ 36000 - 36500 ] 27 counts
#Median bin: [ 35500 - 36000 ] 23 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 21000 - 21500 : [ 1 0.00 0.00 ]
#...
|X 26000 - 26500 : [ 1 0.00 0.01 ]
|XXX 26500 - 27000 : [ 2 0.01 0.01 ]
|XXX 27000 - 27500 : [ 2 0.01 0.02 ]
|XXX 27500 - 28000 : [ 2 0.01 0.02 ]
|XXX 28000 - 28500 : [ 2 0.01 0.03 ]
|XXX 28500 - 29000 : [ 2 0.01 0.03 ]
|XXXXXXX 29000 - 29500 : [ 5 0.01 0.05 ]
|XXXXXXXXXX 29500 - 30000 : [ 7 0.02 0.07 ]
|XXXXXXXXXX 30000 - 30500 : [ 7 0.02 0.09 ]
|XXX 30500 - 31000 : [ 2 0.01 0.09 ]
|XXXXXXXXXXXXX 31000 - 31500 : [ 9 0.03 0.12 ]
|XXXXXXXXXXXXXXXX 31500 - 32000 : [ 11 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 15 0.04 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 23 0.07 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 18 0.05 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 17 0.05 0.36 ]
|XXXXXXXXXXXXX 34000 - 34500 : [ 9 0.03 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 18 0.05 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 22 0.06 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 23 0.07 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 27 0.08 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 18 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 19 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 17 0.05 0.79 ]
|XXXXXXXXXXXXXXX 38000 - 38500 : [ 10 0.03 0.82 ]
|XXXXXXXXXXXXXXX 38500 - 39000 : [ 10 0.03 0.85 ]
|XXXXXXXXXX 39000 - 39500 : [ 7 0.02 0.87 ]
|XXXXXXXXX 39500 - 40000 : [ 6 0.02 0.89 ]
|XXXX 40000 - 40500 : [ 3 0.01 0.90 ]
|XXXXXXXXXXXXX 40500 - 41000 : [ 9 0.03 0.92 ]
|XXXXXXXXXXXXXXX 41000 - 41500 : [ 10 0.03 0.95 ]
|XXXXXX 41500 - 42000 : [ 4 0.01 0.96 ]
|XXXX 42000 - 42500 : [ 3 0.01 0.97 ]
|XXXXXX 42500 - 43000 : [ 4 0.01 0.98 ]
|XXX 43000 - 43500 : [ 2 0.01 0.99 ]
|XXX 43500 - 44000 : [ 2 0.01 0.99 ]
|XXX 44000 - 44500 : [ 2 0.01 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIAU 6474 +- 783 (n=5405)
# AIAT 3415 +- 652 (n=7631)
# BIFI 35782 +- 3409 (n=179)
# AIAW 36238 +- 3512 (n=437)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634491_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
AIAT 40320 88 612 92 614 35789 99 616 100 630
AIAU 25344 96 789 98 766 24263 100 790 100 786
AIAW 5376 78 522 87 480 4433 95 528 100 574
BIFI 2304 62 423 79 364 1668 87 427 100 490
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIAT 17867 99 621 100 634 17922 98 612 100 626
AIAU 12131 100 788 100 785 12132 100 791 100 787
AIAW 2181 94 526 100 567 2252 95 531 100 581
BIFI 841 89 419 100 483 827 85 435 100 497
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634491_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
132 24263 12234 92.68 96.54 AIAU @
204 35789 18581 91.08 94.88 AIAT @
12 1668 921 76.75 79.95 BIFI @
28 4433 2409 86.04 89.62 AIAW @
] 66153 34145 90.81 cumulative total@@
LIBRARY PLATE ID COUNT [ AIAU 132 AIAT 204 BIFI 12 AIAW 28 ] for 376 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 3634491_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 66153 total values totalling 43743276.0000. <661.244025 +/- 193.389216>
#Range: [ 13 - 986 ]
#Most likely bin: [ 800 - 850 ] 12053 counts
#Median bin: [ 700 - 750 ] 8907 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 240 0.00 0.00 ]
|XXX 50 - 100 : [ 806 0.01 0.02 ]
|XXX 100 - 150 : [ 874 0.01 0.03 ]
|XXX 150 - 200 : [ 920 0.01 0.04 ]
|XXX 200 - 250 : [ 1022 0.02 0.06 ]
|XXXX 250 - 300 : [ 1268 0.02 0.08 ]
|XXXXX 300 - 350 : [ 1379 0.02 0.10 ]
|XXXXX 350 - 400 : [ 1462 0.02 0.12 ]
|XXXXXX 400 - 450 : [ 1698 0.03 0.15 ]
|XXXXXXX 450 - 500 : [ 2045 0.03 0.18 ]
|XXXXXXXXX 500 - 550 : [ 2592 0.04 0.22 ]
|XXXXXXXXXXX 550 - 600 : [ 3228 0.05 0.27 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 4784 0.07 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 6821 0.10 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8907 0.13 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 11027 0.17 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 12053 0.18 0.92 ]
|XXXXXXXXXXXXXXX 850 - 900 : [ 4655 0.07 0.99 ]
|X 900 - 950 : [ 360 0.01 1.00 ]
| 950 - 1000 : [ 12 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAT 3634491_fasta.screen.trimQ15.SaF > reads.trim15.AIAT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAT.rl 2 50
-------------------------------------------------------------------
#Found 35789 total values totalling 21767393.0000. <608.214619 +/- 181.970544>
#Range: [ 25 - 986 ]
#Most likely bin: [ 700 - 750 ] 6495 counts
#Median bin: [ 650 - 700 ] 5613 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 96 0.00 0.00 ]
|XXX 50 - 100 : [ 428 0.01 0.01 ]
|XXXX 100 - 150 : [ 570 0.02 0.03 ]
|XXXX 150 - 200 : [ 590 0.02 0.05 ]
|XXXX 200 - 250 : [ 718 0.02 0.07 ]
|XXXX 250 - 300 : [ 698 0.02 0.09 ]
|XXXXX 300 - 350 : [ 850 0.02 0.11 ]
|XXXXXX 350 - 400 : [ 1019 0.03 0.14 ]
|XXXXXXXX 400 - 450 : [ 1325 0.04 0.18 ]
|XXXXXXXXXX 450 - 500 : [ 1682 0.05 0.22 ]
|XXXXXXXXXXXXX 500 - 550 : [ 2120 0.06 0.28 ]
|XXXXXXXXXXXXXXXXX 550 - 600 : [ 2696 0.08 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 4021 0.11 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5613 0.16 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6495 0.18 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4156 0.12 0.92 ]
|XXXXXXXXX 800 - 850 : [ 1469 0.04 0.97 ]
|XXXXXX 850 - 900 : [ 994 0.03 0.99 ]
|X 900 - 950 : [ 237 0.01 1.00 ]
| 950 - 1000 : [ 12 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAU 3634491_fasta.screen.trimQ15.SaF > reads.trim15.AIAU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAU.rl 2 50
-------------------------------------------------------------------
#Found 24263 total values totalling 19111192.0000. <787.668137 +/- 104.254148>
#Range: [ 25 - 934 ]
#Most likely bin: [ 800 - 850 ] 10486 counts
#Median bin: [ 800 - 850 ] 10486 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 19 0.00 0.00 ]
| 50 - 100 : [ 49 0.00 0.00 ]
| 100 - 150 : [ 50 0.00 0.00 ]
| 150 - 200 : [ 58 0.00 0.01 ]
| 200 - 250 : [ 66 0.00 0.01 ]
| 250 - 300 : [ 85 0.00 0.01 ]
| 300 - 350 : [ 90 0.00 0.02 ]
| 350 - 400 : [ 110 0.00 0.02 ]
| 400 - 450 : [ 129 0.01 0.03 ]
| 450 - 500 : [ 124 0.01 0.03 ]
| 500 - 550 : [ 119 0.00 0.04 ]
|X 550 - 600 : [ 137 0.01 0.04 ]
|X 600 - 650 : [ 193 0.01 0.05 ]
|XX 650 - 700 : [ 489 0.02 0.07 ]
|XXXXXXX 700 - 750 : [ 1798 0.07 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6479 0.27 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 10486 0.43 0.84 ]
|XXXXXXXXXXXXXX 850 - 900 : [ 3659 0.15 0.99 ]
| 900 - 950 : [ 123 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAW 3634491_fasta.screen.trimQ15.SaF > reads.trim15.AIAW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAW.rl 2 50
-------------------------------------------------------------------
#Found 4433 total values totalling 2233485.0000. <503.831491 +/- 214.738300>
#Range: [ 16 - 849 ]
#Most likely bin: [ 650 - 700 ] 593 counts
#Median bin: [ 550 - 600 ] 320 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 0 - 50 : [ 67 0.02 0.02 ]
|XXXXXXXXXXX 50 - 100 : [ 166 0.04 0.05 ]
|XXXXXXXXXX 100 - 150 : [ 153 0.03 0.09 ]
|XXXXXXXXXXX 150 - 200 : [ 156 0.04 0.12 ]
|XXXXXXXXXX 200 - 250 : [ 150 0.03 0.16 ]
|XXXXXXXXXXXXXXX 250 - 300 : [ 217 0.05 0.21 ]
|XXXXXXXXXXXXXXXXXXX 300 - 350 : [ 283 0.06 0.27 ]
|XXXXXXXXXXXXXXXXXX 350 - 400 : [ 263 0.06 0.33 ]
|XXXXXXXXXXXXXX 400 - 450 : [ 212 0.05 0.38 ]
|XXXXXXXXXXXXX 450 - 500 : [ 196 0.04 0.42 ]
|XXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 293 0.07 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 320 0.07 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 450 0.10 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 593 0.13 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 508 0.11 0.91 ]
|XXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 323 0.07 0.98 ]
|XXXXXX 800 - 850 : [ 83 0.02 1.00 ]
trimt JAZZ trim 15 readlength histogram for BIFI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep BIFI 3634491_fasta.screen.trimQ15.SaF > reads.trim15.BIFI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.BIFI.rl 2 50
-------------------------------------------------------------------
#Found 1668 total values totalling 631206.0000. <378.420863 +/- 231.193894>
#Range: [ 13 - 851 ]
#Most likely bin: [ 250 - 300 ] 268 counts
#Median bin: [ 300 - 350 ] 156 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 0 - 50 : [ 58 0.03 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 50 - 100 : [ 163 0.10 0.13 ]
|XXXXXXXXXXXXXXX 100 - 150 : [ 101 0.06 0.19 ]
|XXXXXXXXXXXXXXXXX 150 - 200 : [ 116 0.07 0.26 ]
|XXXXXXXXXXXXX 200 - 250 : [ 88 0.05 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 268 0.16 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXX 300 - 350 : [ 156 0.09 0.57 ]
|XXXXXXXXXX 350 - 400 : [ 70 0.04 0.61 ]
|XXXXX 400 - 450 : [ 32 0.02 0.63 ]
|XXXXXX 450 - 500 : [ 43 0.03 0.66 ]
|XXXXXXXXX 500 - 550 : [ 60 0.04 0.69 ]
|XXXXXXXXXXX 550 - 600 : [ 75 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXX 600 - 650 : [ 120 0.07 0.81 ]
|XXXXXXXXXXXXXXXXXXX 650 - 700 : [ 126 0.08 0.88 ]
|XXXXXXXXXXXXXXXX 700 - 750 : [ 106 0.06 0.95 ]
|XXXXXXXXXX 750 - 800 : [ 69 0.04 0.99 ]
|XX 800 - 850 : [ 15 0.01 1.00 ]
| 850 - 900 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634491
-------------------------------------------------------------------
AIAT.000001.000100 pUC18.fa LRS.fasta
AIAT.000101.000200 pUC18.fa LRS.fasta
AIAT.000201.000300 pUC18.fa LRS.fasta
AIAU.000001.000100 pMCL200.fa LRS.fasta
AIAU.000101.000200 pMCL200.fa LRS.fasta
AIAW.000001.000100 pCC1Fos.fa LRS.fasta
BIFI.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AIAT.000001.000100 pUC18.fa LRS.fasta
AIAT.000101.000200 pUC18.fa LRS.fasta
AIAT.000201.000300 pUC18.fa LRS.fasta
AIAU.000001.000100 pMCL200.fa LRS.fasta
AIAU.000101.000200 pMCL200.fa LRS.fasta
AIAW.000001.000100 pCC1Fos.fa LRS.fasta
BIFI.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634491_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634491_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 65913 total values totalling 23269.3798. <0.353032 +/- 0.043950>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.35 - 0.355 ] 3594 counts
#Median bin: [ 0.35 - 0.355 ] 3594 counts
#Entropy = 5.1209 bits
| 0 - 0.005 : [ 1 1.52e-05 1.52e-05 1 ]
#...
| 0.03 - 0.035 : [ 1 1.52e-05 3.03e-05 2 ]
#...
| 0.04 - 0.045 : [ 1 1.52e-05 4.55e-05 3 ]
#...
| 0.07 - 0.075 : [ 1 1.52e-05 6.07e-05 4 ]
#...
| 0.08 - 0.085 : [ 2 3.03e-05 9.10e-05 6 ]
#...
| 0.09 - 0.095 : [ 1 1.52e-05 1.06e-04 7 ]
#...
| 0.115 - 0.12 : [ 1 1.52e-05 1.21e-04 8 ]
| 0.12 - 0.125 : [ 1 1.52e-05 1.37e-04 9 ]
| 0.125 - 0.13 : [ 1 1.52e-05 1.52e-04 10 ]
#...
| 0.135 - 0.14 : [ 2 3.03e-05 1.82e-04 12 ]
| 0.14 - 0.145 : [ 4 6.07e-05 2.43e-04 16 ]
#...
| 0.15 - 0.155 : [ 3 4.55e-05 2.88e-04 19 ]
| 0.155 - 0.16 : [ 2 3.03e-05 3.19e-04 21 ]
| 0.16 - 0.165 : [ 5 7.59e-05 3.94e-04 26 ]
| 0.165 - 0.17 : [ 2 3.03e-05 4.25e-04 28 ]
| 0.17 - 0.175 : [ 4 6.07e-05 4.85e-04 32 ]
| 0.175 - 0.18 : [ 6 9.10e-05 5.77e-04 38 ]
| 0.18 - 0.185 : [ 15 2.28e-04 8.04e-04 53 ]
| 0.185 - 0.19 : [ 8 1.21e-04 9.25e-04 61 ]
| 0.19 - 0.195 : [ 12 1.82e-04 1.11e-03 73 ]
| 0.195 - 0.2 : [ 3 4.55e-05 1.15e-03 76 ]
| 0.2 - 0.205 : [ 19 2.88e-04 1.44e-03 95 ]
| 0.205 - 0.21 : [ 14 2.12e-04 1.65e-03 109 ]
| 0.21 - 0.215 : [ 26 3.94e-04 2.05e-03 135 ]
| 0.215 - 0.22 : [ 35 5.31e-04 2.58e-03 170 ]
|X 0.22 - 0.225 : [ 50 7.59e-04 3.34e-03 220 ]
|X 0.225 - 0.23 : [ 63 9.56e-04 4.29e-03 283 ]
|X 0.23 - 0.235 : [ 62 9.41e-04 5.23e-03 345 ]
|X 0.235 - 0.24 : [ 63 9.56e-04 6.19e-03 408 ]
|X 0.24 - 0.245 : [ 132 2.00e-03 8.19e-03 540 ]
|X 0.245 - 0.25 : [ 110 1.67e-03 9.86e-03 650 ]
|XXX 0.25 - 0.255 : [ 235 3.57e-03 1.34e-02 885 ]
|XX 0.255 - 0.26 : [ 210 3.19e-03 1.66e-02 1095 ]
|XXX 0.26 - 0.265 : [ 250 3.79e-03 2.04e-02 1345 ]
|XXXX 0.265 - 0.27 : [ 358 5.43e-03 2.58e-02 1703 ]
|XXXXX 0.27 - 0.275 : [ 483 7.33e-03 3.32e-02 2186 ]
|XXXXXX 0.275 - 0.28 : [ 569 8.63e-03 4.18e-02 2755 ]
|XXXXXXX 0.28 - 0.285 : [ 673 1.02e-02 5.20e-02 3428 ]
|XXXXXXXXX 0.285 - 0.29 : [ 811 1.23e-02 6.43e-02 4239 ]
|XXXXXXXXXXXX 0.29 - 0.295 : [ 1061 1.61e-02 8.04e-02 5300 ]
|XXXXXXXXXXXXX 0.295 - 0.3 : [ 1148 1.74e-02 9.78e-02 6448 ]
|XXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 1449 2.20e-02 1.20e-01 7897 ]
|XXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 1558 2.36e-02 1.43e-01 9455 ]
|XXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 1829 2.77e-02 1.71e-01 11284 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 2044 3.10e-02 2.02e-01 13328 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 2285 3.47e-02 2.37e-01 15613 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 2584 3.92e-02 2.76e-01 18197 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 2885 4.38e-02 3.20e-01 21082 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 3019 4.58e-02 3.66e-01 24101 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 3233 4.90e-02 4.15e-01 27334 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 3341 5.07e-02 4.65e-01 30675 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 3594 5.45e-02 5.20e-01 34269 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 3488 5.29e-02 5.73e-01 37757 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 3489 5.29e-02 6.26e-01 41246 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 3353 5.09e-02 6.77e-01 44599 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 3026 4.59e-02 7.23e-01 47625 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 2858 4.34e-02 7.66e-01 50483 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 2564 3.89e-02 8.05e-01 53047 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 2285 3.47e-02 8.39e-01 55332 ]
|XXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 1856 2.82e-02 8.68e-01 57188 ]
|XXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 1413 2.14e-02 8.89e-01 58601 ]
|XXXXXXXXXXXXXXX 0.4 - 0.405 : [ 1339 2.03e-02 9.09e-01 59940 ]
|XXXXXXXXXXXX 0.405 - 0.41 : [ 1077 1.63e-02 9.26e-01 61017 ]
|XXXXXXXXX 0.41 - 0.415 : [ 800 1.21e-02 9.38e-01 61817 ]
|XXXXXXXX 0.415 - 0.42 : [ 704 1.07e-02 9.49e-01 62521 ]
|XXXXXX 0.42 - 0.425 : [ 528 8.01e-03 9.57e-01 63049 ]
|XXXXX 0.425 - 0.43 : [ 445 6.75e-03 9.63e-01 63494 ]
|XXXX 0.43 - 0.435 : [ 329 4.99e-03 9.68e-01 63823 ]
|XXX 0.435 - 0.44 : [ 284 4.31e-03 9.73e-01 64107 ]
|XXX 0.44 - 0.445 : [ 244 3.70e-03 9.76e-01 64351 ]
|XX 0.445 - 0.45 : [ 221 3.35e-03 9.80e-01 64572 ]
|XX 0.45 - 0.455 : [ 168 2.55e-03 9.82e-01 64740 ]
|X 0.455 - 0.46 : [ 122 1.85e-03 9.84e-01 64862 ]
|X 0.46 - 0.465 : [ 97 1.47e-03 9.86e-01 64959 ]
|X 0.465 - 0.47 : [ 97 1.47e-03 9.87e-01 65056 ]
|X 0.47 - 0.475 : [ 114 1.73e-03 9.89e-01 65170 ]
|X 0.475 - 0.48 : [ 107 1.62e-03 9.90e-01 65277 ]
|X 0.48 - 0.485 : [ 81 1.23e-03 9.92e-01 65358 ]
|X 0.485 - 0.49 : [ 66 1.00e-03 9.93e-01 65424 ]
| 0.49 - 0.495 : [ 33 5.01e-04 9.93e-01 65457 ]
| 0.495 - 0.5 : [ 33 5.01e-04 9.94e-01 65490 ]
| 0.5 - 0.505 : [ 43 6.52e-04 9.94e-01 65533 ]
| 0.505 - 0.51 : [ 35 5.31e-04 9.95e-01 65568 ]
| 0.51 - 0.515 : [ 30 4.55e-04 9.95e-01 65598 ]
|X 0.515 - 0.52 : [ 53 8.04e-04 9.96e-01 65651 ]
|X 0.52 - 0.525 : [ 49 7.43e-04 9.97e-01 65700 ]
|X 0.525 - 0.53 : [ 45 6.83e-04 9.97e-01 65745 ]
| 0.53 - 0.535 : [ 27 4.10e-04 9.98e-01 65772 ]
| 0.535 - 0.54 : [ 17 2.58e-04 9.98e-01 65789 ]
| 0.54 - 0.545 : [ 13 1.97e-04 9.98e-01 65802 ]
| 0.545 - 0.55 : [ 16 2.43e-04 9.99e-01 65818 ]
| 0.55 - 0.555 : [ 12 1.82e-04 9.99e-01 65830 ]
| 0.555 - 0.56 : [ 24 3.64e-04 9.99e-01 65854 ]
| 0.56 - 0.565 : [ 14 2.12e-04 9.99e-01 65868 ]
| 0.565 - 0.57 : [ 6 9.10e-05 9.99e-01 65874 ]
| 0.57 - 0.575 : [ 3 4.55e-05 9.99e-01 65877 ]
| 0.575 - 0.58 : [ 2 3.03e-05 9.99e-01 65879 ]
| 0.58 - 0.585 : [ 3 4.55e-05 1.00e+00 65882 ]
| 0.585 - 0.59 : [ 1 1.52e-05 1.00e+00 65883 ]
| 0.59 - 0.595 : [ 6 9.10e-05 1.00e+00 65889 ]
#...
| 0.6 - 0.605 : [ 2 3.03e-05 1.00e+00 65891 ]
| 0.605 - 0.61 : [ 4 6.07e-05 1.00e+00 65895 ]
#...
| 0.615 - 0.62 : [ 1 1.52e-05 1.00e+00 65896 ]
| 0.62 - 0.625 : [ 1 1.52e-05 1.00e+00 65897 ]
| 0.625 - 0.63 : [ 1 1.52e-05 1.00e+00 65898 ]
#...
| 0.645 - 0.65 : [ 2 3.03e-05 1.00e+00 65900 ]
#...
| 0.66 - 0.665 : [ 1 1.52e-05 1.00e+00 65901 ]
| 0.665 - 0.67 : [ 2 3.03e-05 1.00e+00 65903 ]
| 0.67 - 0.675 : [ 1 1.52e-05 1.00e+00 65904 ]
#...
| 0.68 - 0.685 : [ 1 1.52e-05 1.00e+00 65905 ]
#...
| 0.735 - 0.74 : [ 1 1.52e-05 1.00e+00 65906 ]
#...
| 0.755 - 0.76 : [ 2 3.03e-05 1.00e+00 65908 ]
#...
| 0.765 - 0.77 : [ 1 1.52e-05 1.00e+00 65909 ]
#...
| 0.78 - 0.785 : [ 2 3.03e-05 1.00e+00 65911 ]
#...
| 1 - 1.005 : [ 2 3.03e-05 1.00e+00 65913 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 271. 747 reads; 56869 bp (untrimmed), 56714 (trimmed).
Contig 272. 773 reads; 53003 bp (untrimmed), 52973 (trimmed).
Contig 273. 774 reads; 39900 bp (untrimmed), 39420 (trimmed).
Contig 274. 816 reads; 68900 bp (untrimmed), 68794 (trimmed).
Contig 275. 853 reads; 55148 bp (untrimmed), 55048 (trimmed).
Contig 276. 909 reads; 63574 bp (untrimmed), 63550 (trimmed).
Contig 277. 965 reads; 62135 bp (untrimmed), 62053 (trimmed).
Contig 278. 1008 reads; 58804 bp (untrimmed), 58757 (trimmed).
Contig 279. 1088 reads; 53173 bp (untrimmed), 52812 (trimmed).
Contig 280. 1096 reads; 73337 bp (untrimmed), 73105 (trimmed).
Contig 281. 1113 reads; 51615 bp (untrimmed), 51412 (trimmed).
Contig 282. 1171 reads; 67014 bp (untrimmed), 66907 (trimmed).
Contig 283. 1180 reads; 74585 bp (untrimmed), 74584 (trimmed).
Contig 284. 1194 reads; 67754 bp (untrimmed), 67374 (trimmed).
Contig 285. 1238 reads; 90895 bp (untrimmed), 90692 (trimmed).
Contig 286. 1311 reads; 91566 bp (untrimmed), 91260 (trimmed).
Contig 287. 1375 reads; 85229 bp (untrimmed), 85110 (trimmed).
Contig 288. 1436 reads; 69336 bp (untrimmed), 69305 (trimmed).
Contig 289. 1463 reads; 96288 bp (untrimmed), 95964 (trimmed).
Contig 290. 1491 reads; 77206 bp (untrimmed), 77154 (trimmed).
Contig 291. 1538 reads; 94754 bp (untrimmed), 94738 (trimmed).
Contig 292. 1590 reads; 85623 bp (untrimmed), 85617 (trimmed).
Contig 293. 1835 reads; 114749 bp (untrimmed), 114526 (trimmed).
Contig 294. 2261 reads; 129069 bp (untrimmed), 129038 (trimmed).
Contig 295. 2404 reads; 145287 bp (untrimmed), 145212 (trimmed).
Contig 296. 2530 reads; 151988 bp (untrimmed), 151916 (trimmed).
Contig 297. 2822 reads; 174206 bp (untrimmed), 173737 (trimmed).
--------------------------------------------------------------
Totals 65989 reads; 4737078 bp (untrimmed), 4692186 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4728250 bases = 11.84 +- 6.77 = 0.49 +- 5.71
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 285 total values totalling 1828.5800. <6.416070 +/- 4.604163>
#Range: [ 1.00 - 18.71 ]
#Most likely bin: [ 1.5 - 2 ] 28 counts
#Median bin: [ 4 - 4.5 ] 10 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 16 0.06 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 28 0.10 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 24 0.08 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 22 0.08 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 23 0.08 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 21 0.07 0.47 ]
|XXXXXXXXXXXXXX 4 - 4.5 : [ 10 0.04 0.51 ]
|XXXXXXXXXXXXX 4.5 - 5 : [ 9 0.03 0.54 ]
|XXXXXXXXXX 5 - 5.5 : [ 7 0.02 0.56 ]
|XXXXXXXXX 5.5 - 6 : [ 6 0.02 0.58 ]
|X 6 - 6.5 : [ 1 0.00 0.59 ]
|XXXXXXXXXXX 6.5 - 7 : [ 8 0.03 0.61 ]
|XXXXXXXXXX 7 - 7.5 : [ 7 0.02 0.64 ]
|XXXXXXX 7.5 - 8 : [ 5 0.02 0.66 ]
|XXXXXX 8 - 8.5 : [ 4 0.01 0.67 ]
|XXXXXXXXXX 8.5 - 9 : [ 7 0.02 0.69 ]
|XXXXXX 9 - 9.5 : [ 4 0.01 0.71 ]
|XXXXXXXXX 9.5 - 10 : [ 6 0.02 0.73 ]
|XXXXXXXXXXXXXX 10 - 10.5 : [ 10 0.04 0.76 ]
|XXXXXXXXXXX 10.5 - 11 : [ 8 0.03 0.79 ]
|XXXXXXXXXXX 11 - 11.5 : [ 8 0.03 0.82 ]
|XXXXXX 11.5 - 12 : [ 4 0.01 0.84 ]
|XXXX 12 - 12.5 : [ 3 0.01 0.85 ]
|XXXXXXXXX 12.5 - 13 : [ 6 0.02 0.87 ]
|XXXXXXXXXXXXX 13 - 13.5 : [ 9 0.03 0.90 ]
|XXXXXXXXXXX 13.5 - 14 : [ 8 0.03 0.93 ]
|XXXXXX 14 - 14.5 : [ 4 0.01 0.94 ]
|XXXXXXX 14.5 - 15 : [ 5 0.02 0.96 ]
|X 15 - 15.5 : [ 1 0.00 0.96 ]
|XXXXXX 15.5 - 16 : [ 4 0.01 0.98 ]
|X 16 - 16.5 : [ 1 0.00 0.98 ]
|XXX 16.5 - 17 : [ 2 0.01 0.99 ]
|X 17 - 17.5 : [ 1 0.00 0.99 ]
|X 17.5 - 18 : [ 1 0.00 0.99 ]
|X 18 - 18.5 : [ 1 0.00 1.00 ]
|X 18.5 - 19 : [ 1 0.00 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 171 total values totalling 1547.4000. <9.049123 +/- 4.129178>
#Range: [ 2.70 - 18.71 ]
#Most likely bin: [ 3.5 - 4 ] 14 counts
#Median bin: [ 9 - 9.5 ] 4 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 2.5 - 3 : [ 4 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 8 0.05 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 14 0.08 0.15 ]
|XXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 7 0.04 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 9 0.05 0.25 ]
|XXXXXXXXXXXXXXXXX 5 - 5.5 : [ 6 0.04 0.28 ]
|XXXXXXXXXXXXXXXXX 5.5 - 6 : [ 6 0.04 0.32 ]
|XXX 6 - 6.5 : [ 1 0.01 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 8 0.05 0.37 ]
|XXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 7 0.04 0.41 ]
|XXXXXXXXXXX 7.5 - 8 : [ 4 0.02 0.43 ]
|XXXXXXXXXXX 8 - 8.5 : [ 4 0.02 0.46 ]
|XXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 7 0.04 0.50 ]
|XXXXXXXXXXX 9 - 9.5 : [ 4 0.02 0.52 ]
|XXXXXXXXXXXXXXXXX 9.5 - 10 : [ 6 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 9 0.05 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 8 0.05 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 8 0.05 0.70 ]
|XXXXXXXXXXX 11.5 - 12 : [ 4 0.02 0.73 ]
|XXXXXXXXX 12 - 12.5 : [ 3 0.02 0.74 ]
|XXXXXXXXXXXXXXXXX 12.5 - 13 : [ 6 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 9 0.05 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 8 0.05 0.88 ]
|XXXXXXXXXXX 14 - 14.5 : [ 4 0.02 0.90 ]
|XXXXXXXXXXXXXX 14.5 - 15 : [ 5 0.03 0.93 ]
|XXX 15 - 15.5 : [ 1 0.01 0.94 ]
|XXXXXXXXXXX 15.5 - 16 : [ 4 0.02 0.96 ]
|XXX 16 - 16.5 : [ 1 0.01 0.96 ]
|XXXXXX 16.5 - 17 : [ 2 0.01 0.98 ]
|XXX 17 - 17.5 : [ 1 0.01 0.98 ]
|XXX 17.5 - 18 : [ 1 0.01 0.99 ]
|XXX 18 - 18.5 : [ 1 0.01 0.99 ]
|XXX 18.5 - 19 : [ 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 16 2 reads 682 bases = 1.00 +- 0.04 = 1.00 +- 0.04
Contig 38 2 reads 1044 bases = 1.08 +- 0.27 = 1.08 +- 0.27
Contig 15 2 reads 1172 bases = 1.17 +- 0.37 = 1.17 +- 0.37
Contig 40 2 reads 1593 bases = 1.17 +- 0.38 = 1.17 +- 0.38
Contig 32 2 reads 1261 bases = 1.25 +- 0.43 = -0.17 +- 0.85
Contig 37 2 reads 989 bases = 1.27 +- 0.45 = 1.27 +- 0.45
Contig 33 2 reads 1562 bases = 1.30 +- 0.46 = 1.30 +- 0.46
Contig 25 2 reads 1070 bases = 1.31 +- 0.46 = 1.31 +- 0.46
Contig 49 3 reads 1891 bases = 1.31 +- 0.46 = 0.50 +- 1.08
Contig 17 2 reads 1409 bases = 1.35 +- 0.48 = 1.35 +- 0.48
Contig 18 2 reads 1396 bases = 1.41 +- 0.49 = 1.41 +- 0.49
Contig 12 2 reads 1376 bases = 1.42 +- 0.49 = 1.42 +- 0.49
Contig 20 2 reads 1021 bases = 1.44 +- 0.50 = -0.56 +- 0.50
Contig 27 2 reads 951 bases = 1.44 +- 0.50 = -0.07 +- 0.75
Contig 24 2 reads 963 bases = 1.45 +- 0.50 = 1.45 +- 0.50
Contig 22 2 reads 997 bases = 1.49 +- 0.50 = 1.49 +- 0.50
Contig 31 2 reads 1081 bases = 1.53 +- 0.50 = 1.53 +- 0.50
Contig 21 2 reads 848 bases = 1.55 +- 0.50 = 1.55 +- 0.50
Contig 34 2 reads 1005 bases = 1.56 +- 0.50 = 1.56 +- 0.50
Contig 35 2 reads 1032 bases = 1.57 +- 0.50 = 1.57 +- 0.50
Contig 295 2404 reads 145287 bases = 14.19 +- 5.45 = 0.15 +- 5.26
Contig 266 702 reads 41058 bases = 14.29 +- 6.32 = 0.54 +- 5.25
Contig 256 559 reads 33124 bases = 14.39 +- 7.68 = 1.66 +- 6.87
Contig 278 1008 reads 58804 bases = 14.72 +- 7.04 = 0.47 +- 6.22
Contig 255 535 reads 30905 bases = 14.76 +- 9.10 = 0.31 +- 6.23
Contig 282 1171 reads 67014 bases = 14.76 +- 6.37 = 0.33 +- 6.91
Contig 294 2261 reads 129069 bases = 14.97 +- 6.49 = 0.16 +- 5.23
Contig 284 1194 reads 67754 bases = 14.98 +- 7.66 = 0.60 +- 6.46
Contig 244 406 reads 21773 bases = 15.46 +- 6.10 = 0.44 +- 6.65
Contig 292 1590 reads 85623 bases = 15.65 +- 8.83 = 0.55 +- 6.53
Contig 268 723 reads 39108 bases = 15.69 +- 6.18 = 0.81 +- 6.31
Contig 258 570 reads 30759 bases = 15.71 +- 6.99 = -0.03 +- 7.51
Contig 234 298 reads 15962 bases = 15.72 +- 6.91 = 1.91 +- 7.51
Contig 273 774 reads 39900 bases = 16.45 +- 8.31 = -0.07 +- 6.19
Contig 231 282 reads 14451 bases = 16.61 +- 5.92 = 0.58 +- 8.83
Contig 290 1491 reads 77206 bases = 16.63 +- 8.25 = 0.15 +- 6.96
Contig 279 1088 reads 53173 bases = 17.30 +- 6.42 = 0.47 +- 6.19
Contig 288 1436 reads 69336 bases = 17.83 +- 7.78 = 0.10 +- 7.48
Contig 235 300 reads 13911 bases = 18.09 +- 7.69 = 0.56 +- 9.49
Contig 281 1113 reads 51615 bases = 18.71 +- 10.53 = 1.32 +- 6.51
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 455
HQ Discrepant reads = 55
Chimeric reads = 52
Suspect alignments = 473
-------------------------------------------------------------------
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/microbe2/3634491/edit_dir.26Oct05.QD