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 in progress (or initial analysis of completed)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634491 5000 66219 Clostridium phytofermentans
-------------------------------------------------------------------
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: 4697468
# phrap: 4388559
# db:
altered.
5000000
4695342 +/- 249624
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 17330
Number of reads with percent X's >= 20%: 863 = 1.2%
Number of reads with percent X's >= 50%: 785 = 1.1%
Number of reads with percent X's >= 80%: 694 = 0.9%
Total reads in project: 73114
Total bp X'd : 1301901
reads >= 20% >= 50% >= 80% screened
Nr with L09136 14644 360 310 254
Nr with LRS 75 75 71 69
Nr with pCC1Fos 2159 19 9 4
Nr with pMCL200_JGI_XZX+XZK 452 409 395 367
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 1046
Number of reads with percent X's >= 20%: 725 = 12.0%
Number of reads with percent X's >= 50%: 711 = 11.7%
Number of reads with percent X's >= 80%: 676 = 11.1%
Total reads in project: 6063
Total bp X'd : 658493
reads >= 20% >= 50% >= 80% screened
Nr with L09136 480 259 255 241
Nr with LRS 75 75 71 69
Nr with pCC1Fos 101 10 7 4
Nr with pMCL200_JGI_XZX+XZK 390 381 378 362
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 21523997
C = 12953704
G = 12537634
T = 20998479
N = 538833
X = 1301904
GC fraction = 0.36
Total = 69854551
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634491_fasta.screen.contigs
-------------------------------------------------------------------
A 1509348
C 869078
G 812209
T 1555114
N 764
fraction GC = 0.35
total bases = 4746513
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 6472 +- 984 (n=5503)
# AIAT 3430 +- 642 (n=7986)
# BIFI 35472 +- 3708 (n=179)
# AIAW 36074 +- 4038 (n=453)
-------------------------------------------------------------------
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 40090 88 616 91 624
AIAU 25344 96 789 98 766 25344 95 790 98 782
AIAW 5376 78 522 87 480 5376 78 528 87 549
BIFI 2304 62 423 79 364 2304 63 427 80 453
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIAT 20228 87 620 90 629 19862 89 611 92 619
AIAU 12672 95 788 98 780 12672 96 791 98 784
AIAW 2688 76 525 86 544 2688 80 530 89 554
BIFI 1152 65 419 79 452 1152 61 435 80 454
-------------------------------------------------------------------
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 25344 12672 96.00 100.00 AIAU @
204 40090 19557 95.87 99.86 AIAT @
12 2304 1152 96.00 100.00 BIFI @
28 5376 2688 96.00 100.00 AIAW @
] 73114 36069 95.93 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 73114 total values totalling 43816805.0000. <599.294321 +/- 265.258276>
#Range: [ 0 - 986 ]
#Most likely bin: [ 800 - 850 ] 12053 counts
#Median bin: [ 700 - 750 ] 8907 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 6833 0.09 0.09 ]
|XXXX 50 - 100 : [ 1128 0.02 0.11 ]
|XXX 100 - 150 : [ 912 0.01 0.12 ]
|XXX 150 - 200 : [ 922 0.01 0.13 ]
|XXX 200 - 250 : [ 1024 0.01 0.15 ]
|XXXX 250 - 300 : [ 1269 0.02 0.17 ]
|XXXXX 300 - 350 : [ 1380 0.02 0.18 ]
|XXXXX 350 - 400 : [ 1462 0.02 0.20 ]
|XXXXXX 400 - 450 : [ 1698 0.02 0.23 ]
|XXXXXXX 450 - 500 : [ 2045 0.03 0.26 ]
|XXXXXXXXX 500 - 550 : [ 2592 0.04 0.29 ]
|XXXXXXXXXXX 550 - 600 : [ 3228 0.04 0.33 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 4784 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 6821 0.09 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8907 0.12 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 11029 0.15 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 12053 0.16 0.93 ]
|XXXXXXXXXXXXXXX 850 - 900 : [ 4655 0.06 0.99 ]
|X 900 - 950 : [ 360 0.00 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 40090 total values totalling 21807721.0000. <543.969095 +/- 252.880009>
#Range: [ 0 - 986 ]
#Most likely bin: [ 700 - 750 ] 6495 counts
#Median bin: [ 600 - 650 ] 4021 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 4139 0.10 0.10 ]
|XXXX 50 - 100 : [ 651 0.02 0.12 ]
|XXXX 100 - 150 : [ 605 0.02 0.13 ]
|XXXX 150 - 200 : [ 590 0.01 0.15 ]
|XXXX 200 - 250 : [ 718 0.02 0.17 ]
|XXXX 250 - 300 : [ 698 0.02 0.18 ]
|XXXXX 300 - 350 : [ 850 0.02 0.21 ]
|XXXXXX 350 - 400 : [ 1019 0.03 0.23 ]
|XXXXXXXX 400 - 450 : [ 1325 0.03 0.26 ]
|XXXXXXXXXX 450 - 500 : [ 1682 0.04 0.31 ]
|XXXXXXXXXXXXX 500 - 550 : [ 2120 0.05 0.36 ]
|XXXXXXXXXXXXXXXXX 550 - 600 : [ 2696 0.07 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 4021 0.10 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5613 0.14 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6495 0.16 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4156 0.10 0.93 ]
|XXXXXXXXX 800 - 850 : [ 1469 0.04 0.97 ]
|XXXXXX 850 - 900 : [ 994 0.02 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 25344 total values totalling 19119769.0000. <754.410077 +/- 187.838932>
#Range: [ 0 - 934 ]
#Most likely bin: [ 800 - 850 ] 10486 counts
#Median bin: [ 800 - 850 ] 10486 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 0 - 50 : [ 1073 0.04 0.04 ]
| 50 - 100 : [ 74 0.00 0.05 ]
| 100 - 150 : [ 50 0.00 0.05 ]
| 150 - 200 : [ 58 0.00 0.05 ]
| 200 - 250 : [ 66 0.00 0.05 ]
| 250 - 300 : [ 85 0.00 0.06 ]
| 300 - 350 : [ 90 0.00 0.06 ]
| 350 - 400 : [ 110 0.00 0.06 ]
| 400 - 450 : [ 129 0.01 0.07 ]
| 450 - 500 : [ 124 0.00 0.07 ]
| 500 - 550 : [ 119 0.00 0.08 ]
|X 550 - 600 : [ 137 0.01 0.08 ]
|X 600 - 650 : [ 193 0.01 0.09 ]
|XX 650 - 700 : [ 489 0.02 0.11 ]
|XXXXXXX 700 - 750 : [ 1798 0.07 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6481 0.26 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 10486 0.41 0.85 ]
|XXXXXXXXXXXXXX 850 - 900 : [ 3659 0.14 1.00 ]
| 900 - 950 : [ 123 0.00 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 5376 total values totalling 2247783.0000. <418.114397 +/- 269.566341>
#Range: [ 0 - 849 ]
#Most likely bin: [ 0 - 50 ] 960 counts
#Median bin: [ 450 - 500 ] 196 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 960 0.18 0.18 ]
|XXXXXXXXX 50 - 100 : [ 207 0.04 0.22 ]
|XXXXXX 100 - 150 : [ 156 0.03 0.25 ]
|XXXXXXX 150 - 200 : [ 158 0.03 0.28 ]
|XXXXXX 200 - 250 : [ 152 0.03 0.30 ]
|XXXXXXXXX 250 - 300 : [ 218 0.04 0.34 ]
|XXXXXXXXXXXX 300 - 350 : [ 284 0.05 0.40 ]
|XXXXXXXXXXX 350 - 400 : [ 263 0.05 0.45 ]
|XXXXXXXXX 400 - 450 : [ 212 0.04 0.49 ]
|XXXXXXXX 450 - 500 : [ 196 0.04 0.52 ]
|XXXXXXXXXXXX 500 - 550 : [ 293 0.05 0.58 ]
|XXXXXXXXXXXXX 550 - 600 : [ 320 0.06 0.64 ]
|XXXXXXXXXXXXXXXXXXX 600 - 650 : [ 450 0.08 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 593 0.11 0.83 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 508 0.09 0.92 ]
|XXXXXXXXXXXXX 750 - 800 : [ 323 0.06 0.98 ]
|XXX 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 2304 total values totalling 641532.0000. <278.442708 +/- 254.907851>
#Range: [ 0 - 851 ]
#Most likely bin: [ 0 - 50 ] 661 counts
#Median bin: [ 200 - 250 ] 88 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 661 0.29 0.29 ]
|XXXXXXXXXXXX 50 - 100 : [ 196 0.09 0.37 ]
|XXXXXX 100 - 150 : [ 101 0.04 0.42 ]
|XXXXXXX 150 - 200 : [ 116 0.05 0.47 ]
|XXXXX 200 - 250 : [ 88 0.04 0.50 ]
|XXXXXXXXXXXXXXXX 250 - 300 : [ 268 0.12 0.62 ]
|XXXXXXXXX 300 - 350 : [ 156 0.07 0.69 ]
|XXXX 350 - 400 : [ 70 0.03 0.72 ]
|XX 400 - 450 : [ 32 0.01 0.73 ]
|XXX 450 - 500 : [ 43 0.02 0.75 ]
|XXXX 500 - 550 : [ 60 0.03 0.78 ]
|XXXXX 550 - 600 : [ 75 0.03 0.81 ]
|XXXXXXX 600 - 650 : [ 120 0.05 0.86 ]
|XXXXXXXX 650 - 700 : [ 126 0.05 0.92 ]
|XXXXXX 700 - 750 : [ 106 0.05 0.96 ]
|XXXX 750 - 800 : [ 69 0.03 0.99 ]
|X 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 27099 total values totalling 9541.7777. <0.352108 +/- 0.044769>
#Range: [ 0 - 0.6818 ]
#Most likely bin: [ 0.35 - 0.355 ] 1456 counts
#Median bin: [ 0.35 - 0.355 ] 1456 counts
#Entropy = 5.1604 bits
| 0 - 0.005 : [ 1 3.69e-05 3.69e-05 1 ]
#...
| 0.03 - 0.035 : [ 1 3.69e-05 7.38e-05 2 ]
#...
| 0.115 - 0.12 : [ 1 3.69e-05 1.11e-04 3 ]
| 0.12 - 0.125 : [ 1 3.69e-05 1.48e-04 4 ]
#...
| 0.13 - 0.135 : [ 1 3.69e-05 1.85e-04 5 ]
| 0.135 - 0.14 : [ 1 3.69e-05 2.21e-04 6 ]
| 0.14 - 0.145 : [ 2 7.38e-05 2.95e-04 8 ]
| 0.145 - 0.15 : [ 1 3.69e-05 3.32e-04 9 ]
| 0.15 - 0.155 : [ 1 3.69e-05 3.69e-04 10 ]
| 0.155 - 0.16 : [ 1 3.69e-05 4.06e-04 11 ]
| 0.16 - 0.165 : [ 4 1.48e-04 5.54e-04 15 ]
| 0.165 - 0.17 : [ 2 7.38e-05 6.27e-04 17 ]
| 0.17 - 0.175 : [ 5 1.85e-04 8.12e-04 22 ]
| 0.175 - 0.18 : [ 5 1.85e-04 9.96e-04 27 ]
| 0.18 - 0.185 : [ 10 3.69e-04 1.37e-03 37 ]
| 0.185 - 0.19 : [ 3 1.11e-04 1.48e-03 40 ]
| 0.19 - 0.195 : [ 6 2.21e-04 1.70e-03 46 ]
| 0.195 - 0.2 : [ 3 1.11e-04 1.81e-03 49 ]
| 0.2 - 0.205 : [ 9 3.32e-04 2.14e-03 58 ]
| 0.205 - 0.21 : [ 10 3.69e-04 2.51e-03 68 ]
| 0.21 - 0.215 : [ 16 5.90e-04 3.10e-03 84 ]
|X 0.215 - 0.22 : [ 20 7.38e-04 3.84e-03 104 ]
|X 0.22 - 0.225 : [ 22 8.12e-04 4.65e-03 126 ]
|X 0.225 - 0.23 : [ 27 9.96e-04 5.65e-03 153 ]
|X 0.23 - 0.235 : [ 29 1.07e-03 6.72e-03 182 ]
|X 0.235 - 0.24 : [ 36 1.33e-03 8.04e-03 218 ]
|XX 0.24 - 0.245 : [ 73 2.69e-03 1.07e-02 291 ]
|X 0.245 - 0.25 : [ 45 1.66e-03 1.24e-02 336 ]
|XXX 0.25 - 0.255 : [ 119 4.39e-03 1.68e-02 455 ]
|XXX 0.255 - 0.26 : [ 102 3.76e-03 2.06e-02 557 ]
|XXX 0.26 - 0.265 : [ 120 4.43e-03 2.50e-02 677 ]
|XXXXX 0.265 - 0.27 : [ 168 6.20e-03 3.12e-02 845 ]
|XXXXXX 0.27 - 0.275 : [ 230 8.49e-03 3.97e-02 1075 ]
|XXXXXXX 0.275 - 0.28 : [ 257 9.48e-03 4.92e-02 1332 ]
|XXXXXXXX 0.28 - 0.285 : [ 290 1.07e-02 5.99e-02 1622 ]
|XXXXXXXXXX 0.285 - 0.29 : [ 354 1.31e-02 7.29e-02 1976 ]
|XXXXXXXXXXXX 0.29 - 0.295 : [ 446 1.65e-02 8.94e-02 2422 ]
|XXXXXXXXXXXXX 0.295 - 0.3 : [ 485 1.79e-02 1.07e-01 2907 ]
|XXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 585 2.16e-02 1.29e-01 3492 ]
|XXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 664 2.45e-02 1.53e-01 4156 ]
|XXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 773 2.85e-02 1.82e-01 4929 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 838 3.09e-02 2.13e-01 5767 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 930 3.43e-02 2.47e-01 6697 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 1038 3.83e-02 2.85e-01 7735 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 1209 4.46e-02 3.30e-01 8944 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 1238 4.57e-02 3.76e-01 10182 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 1279 4.72e-02 4.23e-01 11461 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 1338 4.94e-02 4.72e-01 12799 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 1456 5.37e-02 5.26e-01 14255 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 1404 5.18e-02 5.78e-01 15659 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 1386 5.11e-02 6.29e-01 17045 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 1324 4.89e-02 6.78e-01 18369 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 1184 4.37e-02 7.22e-01 19553 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 1171 4.32e-02 7.65e-01 20724 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 1014 3.74e-02 8.02e-01 21738 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 925 3.41e-02 8.36e-01 22663 ]
|XXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 781 2.88e-02 8.65e-01 23444 ]
|XXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 608 2.24e-02 8.88e-01 24052 ]
|XXXXXXXXXXXXXXX 0.4 - 0.405 : [ 552 2.04e-02 9.08e-01 24604 ]
|XXXXXXXXXXXX 0.405 - 0.41 : [ 441 1.63e-02 9.24e-01 25045 ]
|XXXXXXXXX 0.41 - 0.415 : [ 313 1.16e-02 9.36e-01 25358 ]
|XXXXXXXX 0.415 - 0.42 : [ 296 1.09e-02 9.47e-01 25654 ]
|XXXXXX 0.42 - 0.425 : [ 229 8.45e-03 9.55e-01 25883 ]
|XXXXX 0.425 - 0.43 : [ 188 6.94e-03 9.62e-01 26071 ]
|XXXX 0.43 - 0.435 : [ 154 5.68e-03 9.68e-01 26225 ]
|XXXX 0.435 - 0.44 : [ 128 4.72e-03 9.72e-01 26353 ]
|XXX 0.44 - 0.445 : [ 98 3.62e-03 9.76e-01 26451 ]
|XX 0.445 - 0.45 : [ 81 2.99e-03 9.79e-01 26532 ]
|XX 0.45 - 0.455 : [ 68 2.51e-03 9.82e-01 26600 ]
|X 0.455 - 0.46 : [ 45 1.66e-03 9.83e-01 26645 ]
|X 0.46 - 0.465 : [ 47 1.73e-03 9.85e-01 26692 ]
|X 0.465 - 0.47 : [ 43 1.59e-03 9.87e-01 26735 ]
|X 0.47 - 0.475 : [ 46 1.70e-03 9.88e-01 26781 ]
|X 0.475 - 0.48 : [ 53 1.96e-03 9.90e-01 26834 ]
|X 0.48 - 0.485 : [ 31 1.14e-03 9.91e-01 26865 ]
|X 0.485 - 0.49 : [ 28 1.03e-03 9.92e-01 26893 ]
| 0.49 - 0.495 : [ 14 5.17e-04 9.93e-01 26907 ]
| 0.495 - 0.5 : [ 16 5.90e-04 9.94e-01 26923 ]
|X 0.5 - 0.505 : [ 26 9.59e-04 9.94e-01 26949 ]
| 0.505 - 0.51 : [ 14 5.17e-04 9.95e-01 26963 ]
| 0.51 - 0.515 : [ 16 5.90e-04 9.96e-01 26979 ]
|X 0.515 - 0.52 : [ 23 8.49e-04 9.96e-01 27002 ]
|X 0.52 - 0.525 : [ 24 8.86e-04 9.97e-01 27026 ]
|X 0.525 - 0.53 : [ 21 7.75e-04 9.98e-01 27047 ]
| 0.53 - 0.535 : [ 12 4.43e-04 9.99e-01 27059 ]
| 0.535 - 0.54 : [ 7 2.58e-04 9.99e-01 27066 ]
| 0.54 - 0.545 : [ 6 2.21e-04 9.99e-01 27072 ]
| 0.545 - 0.55 : [ 8 2.95e-04 9.99e-01 27080 ]
| 0.55 - 0.555 : [ 3 1.11e-04 9.99e-01 27083 ]
| 0.555 - 0.56 : [ 7 2.58e-04 1.00e+00 27090 ]
| 0.56 - 0.565 : [ 1 3.69e-05 1.00e+00 27091 ]
| 0.565 - 0.57 : [ 1 3.69e-05 1.00e+00 27092 ]
| 0.57 - 0.575 : [ 1 3.69e-05 1.00e+00 27093 ]
#...
| 0.59 - 0.595 : [ 2 7.38e-05 1.00e+00 27095 ]
| 0.595 - 0.6 : [ 1 3.69e-05 1.00e+00 27096 ]
#...
| 0.605 - 0.61 : [ 1 3.69e-05 1.00e+00 27097 ]
#...
| 0.645 - 0.65 : [ 1 3.69e-05 1.00e+00 27098 ]
#...
| 0.68 - 0.685 : [ 1 3.69e-05 1.00e+00 27099 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 283. 786 reads; 39900 bp (untrimmed), 39420 (trimmed).
Contig 284. 788 reads; 53003 bp (untrimmed), 52973 (trimmed).
Contig 285. 831 reads; 68900 bp (untrimmed), 68794 (trimmed).
Contig 286. 864 reads; 55148 bp (untrimmed), 55048 (trimmed).
Contig 287. 929 reads; 63574 bp (untrimmed), 63550 (trimmed).
Contig 288. 971 reads; 62135 bp (untrimmed), 62053 (trimmed).
Contig 289. 1023 reads; 58804 bp (untrimmed), 58757 (trimmed).
Contig 290. 1107 reads; 53173 bp (untrimmed), 52812 (trimmed).
Contig 291. 1125 reads; 73337 bp (untrimmed), 73105 (trimmed).
Contig 292. 1129 reads; 51615 bp (untrimmed), 51412 (trimmed).
Contig 293. 1156 reads; 61240 bp (untrimmed), 60999 (trimmed).
Contig 294. 1186 reads; 74585 bp (untrimmed), 74584 (trimmed).
Contig 295. 1190 reads; 67014 bp (untrimmed), 66907 (trimmed).
Contig 296. 1221 reads; 67754 bp (untrimmed), 67374 (trimmed).
Contig 297. 1256 reads; 90895 bp (untrimmed), 90692 (trimmed).
Contig 298. 1339 reads; 91566 bp (untrimmed), 91260 (trimmed).
Contig 299. 1392 reads; 85229 bp (untrimmed), 85110 (trimmed).
Contig 300. 1410 reads; 69499 bp (untrimmed), 69447 (trimmed).
Contig 301. 1412 reads; 91712 bp (untrimmed), 91685 (trimmed).
Contig 302. 1452 reads; 69336 bp (untrimmed), 69305 (trimmed).
Contig 303. 1479 reads; 96288 bp (untrimmed), 95964 (trimmed).
Contig 304. 1558 reads; 94754 bp (untrimmed), 94738 (trimmed).
Contig 305. 1609 reads; 85623 bp (untrimmed), 85617 (trimmed).
Contig 306. 1858 reads; 114749 bp (untrimmed), 114526 (trimmed).
Contig 307. 2289 reads; 129069 bp (untrimmed), 129038 (trimmed).
Contig 308. 2436 reads; 145287 bp (untrimmed), 145212 (trimmed).
Contig 309. 2872 reads; 174045 bp (untrimmed), 173737 (trimmed).
--------------------------------------------------------------
Totals 67051 reads; 4746513 bp (untrimmed), 4697468 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4734185 bases = 11.90 +- 6.81 = 0.52 +- 5.73
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 290 total values totalling 1878.7900. <6.478586 +/- 4.637803>
#Range: [ 1.02 - 18.82 ]
#Most likely bin: [ 1.5 - 2 ] 30 counts
#Median bin: [ 4 - 4.5 ] 10 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 16 0.06 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 30 0.10 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 22 0.08 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 24 0.08 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 21 0.07 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 22 0.08 0.47 ]
|XXXXXXXXXXXXX 4 - 4.5 : [ 10 0.03 0.50 ]
|XXXXXXXXX 4.5 - 5 : [ 7 0.02 0.52 ]
|XXXXXXXXXXXX 5 - 5.5 : [ 9 0.03 0.56 ]
|XXXXXXXXX 5.5 - 6 : [ 7 0.02 0.58 ]
#...
|XXXXXXXXXXXX 6.5 - 7 : [ 9 0.03 0.61 ]
|XXXXXXXX 7 - 7.5 : [ 6 0.02 0.63 ]
|XXXXXXXX 7.5 - 8 : [ 6 0.02 0.65 ]
|XXXXXXX 8 - 8.5 : [ 5 0.02 0.67 ]
|XXXXXXXXX 8.5 - 9 : [ 7 0.02 0.69 ]
|XXXXX 9 - 9.5 : [ 4 0.01 0.71 ]
|XXXXXXXXX 9.5 - 10 : [ 7 0.02 0.73 ]
|XXXXXXXXXXXXX 10 - 10.5 : [ 10 0.03 0.77 ]
|XXXXXXXXX 10.5 - 11 : [ 7 0.02 0.79 ]
|XXXXXXXXXXX 11 - 11.5 : [ 8 0.03 0.82 ]
|XXXXX 11.5 - 12 : [ 4 0.01 0.83 ]
|XXXXX 12 - 12.5 : [ 4 0.01 0.84 ]
|XXXXXXXX 12.5 - 13 : [ 6 0.02 0.87 ]
|XXXXXXXXXXX 13 - 13.5 : [ 8 0.03 0.89 ]
|XXXXXXXXXXXXX 13.5 - 14 : [ 10 0.03 0.93 ]
|XXX 14 - 14.5 : [ 2 0.01 0.93 ]
|XXXXX 14.5 - 15 : [ 4 0.01 0.95 ]
|XXX 15 - 15.5 : [ 2 0.01 0.96 ]
|XXXXXXX 15.5 - 16 : [ 5 0.02 0.97 ]
|X 16 - 16.5 : [ 1 0.00 0.98 ]
|XXX 16.5 - 17 : [ 2 0.01 0.98 ]
|XXX 17 - 17.5 : [ 2 0.01 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 174 total values totalling 1586.7400. <9.119195 +/- 4.158740>
#Range: [ 2.70 - 18.82 ]
#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 ]
|XXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 7 0.04 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 8 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 7 0.04 0.32 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 9 0.05 0.37 ]
|XXXXXXXXXXXXXXXXX 7 - 7.5 : [ 6 0.03 0.40 ]
|XXXXXXXXXXXXXX 7.5 - 8 : [ 5 0.03 0.43 ]
|XXXXXXXXXXX 8 - 8.5 : [ 4 0.02 0.45 ]
|XXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 7 0.04 0.49 ]
|XXXXXXXXXXX 9 - 9.5 : [ 4 0.02 0.52 ]
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 7 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 9 0.05 0.61 ]
|XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 7 0.04 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 8 0.05 0.70 ]
|XXXXXXXXXXX 11.5 - 12 : [ 4 0.02 0.72 ]
|XXXXXXXXXXX 12 - 12.5 : [ 4 0.02 0.74 ]
|XXXXXXXXXXXXXXXXX 12.5 - 13 : [ 6 0.03 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 8 0.05 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 10 0.06 0.88 ]
|XXXXXX 14 - 14.5 : [ 2 0.01 0.89 ]
|XXXXXXXXXXX 14.5 - 15 : [ 4 0.02 0.91 ]
|XXXXXX 15 - 15.5 : [ 2 0.01 0.93 ]
|XXXXXXXXXXXXXX 15.5 - 16 : [ 5 0.03 0.95 ]
|XXX 16 - 16.5 : [ 1 0.01 0.96 ]
|XXXXXX 16.5 - 17 : [ 2 0.01 0.97 ]
|XXXXXX 17 - 17.5 : [ 2 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 149 14 reads 682 bases = 1.02 +- 0.50 = -0.98 +- 0.50
Contig 27 2 reads 1593 bases = 1.17 +- 0.38 = 1.17 +- 0.38
Contig 34 2 reads 1172 bases = 1.17 +- 0.37 = 1.17 +- 0.37
Contig 57 3 reads 1041 bases = 1.18 +- 0.54 = 0.98 +- 0.17
Contig 22 2 reads 1261 bases = 1.25 +- 0.43 = -0.17 +- 0.85
Contig 39 2 reads 989 bases = 1.27 +- 0.45 = 1.27 +- 0.45
Contig 24 2 reads 1562 bases = 1.30 +- 0.46 = 1.30 +- 0.46
Contig 28 2 reads 1070 bases = 1.31 +- 0.46 = 1.31 +- 0.46
Contig 43 3 reads 1891 bases = 1.31 +- 0.46 = 0.50 +- 1.08
Contig 33 2 reads 1396 bases = 1.41 +- 0.49 = 1.41 +- 0.49
Contig 37 2 reads 1376 bases = 1.42 +- 0.49 = 1.42 +- 0.49
Contig 14 2 reads 951 bases = 1.44 +- 0.50 = -0.07 +- 0.75
Contig 20 2 reads 1021 bases = 1.44 +- 0.50 = -0.56 +- 0.50
Contig 36 2 reads 1057 bases = 1.48 +- 0.50 = 0.45 +- 0.56
Contig 19 2 reads 997 bases = 1.49 +- 0.50 = 1.49 +- 0.50
Contig 30 2 reads 1112 bases = 1.49 +- 0.50 = 1.49 +- 0.50
Contig 44 3 reads 1409 bases = 1.52 +- 0.70 = 1.52 +- 0.70
Contig 17 2 reads 1081 bases = 1.53 +- 0.50 = 1.53 +- 0.50
Contig 13 2 reads 848 bases = 1.55 +- 0.50 = 1.55 +- 0.50
Contig 25 2 reads 1005 bases = 1.56 +- 0.50 = 1.56 +- 0.50
Contig 277 712 reads 41058 bases = 14.36 +- 6.33 = 0.48 +- 5.29
Contig 267 567 reads 33124 bases = 14.50 +- 7.64 = 1.66 +- 6.92
Contig 289 1023 reads 58804 bases = 14.83 +- 7.08 = 0.52 +- 6.28
Contig 295 1190 reads 67014 bases = 14.84 +- 6.39 = 0.37 +- 6.96
Contig 266 548 reads 30905 bases = 14.94 +- 9.06 = 0.40 +- 6.32
Contig 307 2289 reads 129069 bases = 15.03 +- 6.50 = 0.17 +- 5.25
Contig 296 1221 reads 67754 bases = 15.09 +- 7.65 = 0.59 +- 6.54
Contig 255 413 reads 21773 bases = 15.50 +- 6.10 = 0.42 +- 6.62
Contig 305 1609 reads 85623 bases = 15.72 +- 8.84 = 0.51 +- 6.58
Contig 279 728 reads 39108 bases = 15.73 +- 6.23 = 0.82 +- 6.34
Contig 246 302 reads 15962 bases = 15.85 +- 7.03 = 1.88 +- 7.60
Contig 269 585 reads 30759 bases = 15.88 +- 7.08 = 0.06 +- 7.52
Contig 293 1156 reads 61240 bases = 16.04 +- 8.83 = 0.63 +- 6.07
Contig 283 786 reads 39900 bases = 16.53 +- 8.33 = -0.04 +- 6.21
Contig 242 286 reads 14451 bases = 16.71 +- 5.90 = 0.54 +- 8.88
Contig 300 1410 reads 69499 bases = 17.39 +- 8.36 = 0.28 +- 7.19
Contig 290 1107 reads 53173 bases = 17.46 +- 6.53 = 0.46 +- 6.17
Contig 302 1452 reads 69336 bases = 17.91 +- 7.80 = 0.06 +- 7.52
Contig 245 301 reads 13911 bases = 18.04 +- 7.54 = 0.50 +- 9.27
Contig 292 1129 reads 51615 bases = 18.82 +- 10.67 = 1.36 +- 6.49
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 455
HQ Discrepant reads = 86
Chimeric reads = 63
Suspect alignments = 477
-------------------------------------------------------------------
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.06Oct05.QC