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
3436113 7200 29543 Pelobacter propionicus
3436113 4000 29543 Pelobacter propionicus
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Pelobacter_propionicus
-------------------------------------------------------------------
Pelobacteraceae, family, d-proteobacteria
Desulfuromonadales, order, d-proteobacteria
delta/epsilon subdivisions, subphylum, proteobacteria
Pelobacter propionicus, species, d-proteobacteria
Deltaproteobacteria, class, d-proteobacteria
Pelobacter, genus, d-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4222850
# phrap: 4027013
# db:
altered.
7200000
4000000
4862465 +/- 1352313
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 52650
Number of reads with percent X's >= 20%: 1169 = 1.6%
Number of reads with percent X's >= 50%: 973 = 1.3%
Number of reads with percent X's >= 80%: 415 = 0.6%
Total reads in project: 72180
Total bp X'd : 4087115
reads >= 20% >= 50% >= 80% screened
Nr with L09136 13811 112 82 17
Nr with pCC1Fos 1659 0 0 0
Nr with pMCL200_JGI_XZX+XZK 37180 1057 891 398
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 3375
Number of reads with percent X's >= 20%: 2701 = 59.0%
Number of reads with percent X's >= 50%: 2622 = 57.3%
Number of reads with percent X's >= 80%: 2054 = 44.9%
Total reads in project: 4578
Total bp X'd : 2770204
reads >= 20% >= 50% >= 80% screened
Nr with L09136 97 4 4 1
Nr with LRS 53 53 52 47
Nr with pCC1Fos 23 4 3 0
Nr with pMCL200_JGI_XZX+XZK 3202 2640 2563 2006
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 15029695
C = 20416434
G = 19937217
T = 14866853
N = 487516
X = 7023408
GC fraction = 0.52
Total = 77761123
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436113_fasta.screen.contigs
-------------------------------------------------------------------
A 885847
C 1242746
G 1238895
T 891831
N 586
fraction GC = 0.58
total bases = 4259905
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 WBF reads.list > grep.reads.list.WBF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.WBF 4 500
-------------------------------------------------------------------
#Found 13555 total values totalling 43586892.0000. <3215.558244 +/- 753.185108>
#Range: [ 200 - 62288 ]
#Most likely bin: [ 2500 - 3000 ] 5303 counts
#Median bin: [ 3000 - 3500 ] 4054 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 9 0.00 0.00 ]
| 500 - 1000 : [ 2 0.00 0.00 ]
| 1000 - 1500 : [ 8 0.00 0.00 ]
| 1500 - 2000 : [ 34 0.00 0.00 ]
|XX 2000 - 2500 : [ 311 0.02 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 5303 0.39 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4054 0.30 0.72 ]
|XXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2527 0.19 0.90 ]
|XXXXXXXXX 4000 - 4500 : [ 1179 0.09 0.99 ]
|X 4500 - 5000 : [ 126 0.01 1.00 ]
#...
| 22000 - 22500 : [ 1 0.00 1.00 ]
#...
| 62000 - 62500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep WBL reads.list > grep.reads.list.WBL
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.WBL 4 500
-------------------------------------------------------------------
#Found 1778 total values totalling 11850809.0000. <6665.246907 +/- 1011.443197>
#Range: [ 277 - 10260 ]
#Most likely bin: [ 6500 - 7000 ] 492 counts
#Median bin: [ 6500 - 7000 ] 492 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 500 : [ 13 0.01 0.01 ]
#...
|X 1000 - 1500 : [ 7 0.00 0.01 ]
|X 1500 - 2000 : [ 8 0.00 0.02 ]
| 2000 - 2500 : [ 2 0.00 0.02 ]
| 2500 - 3000 : [ 6 0.00 0.02 ]
| 3000 - 3500 : [ 5 0.00 0.02 ]
|X 3500 - 4000 : [ 7 0.00 0.03 ]
| 4000 - 4500 : [ 1 0.00 0.03 ]
| 4500 - 5000 : [ 2 0.00 0.03 ]
| 5000 - 5500 : [ 3 0.00 0.03 ]
|XXXXXXXXXXXX 5500 - 6000 : [ 152 0.09 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 421 0.24 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 492 0.28 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 447 0.25 0.88 ]
|XXXXXXXXXXXXXXX 7500 - 8000 : [ 188 0.11 0.99 ]
|X 8000 - 8500 : [ 18 0.01 1.00 ]
| 8500 - 9000 : [ 1 0.00 1.00 ]
| 9000 - 9500 : [ 2 0.00 1.00 ]
| 9500 - 10000 : [ 1 0.00 1.00 ]
| 10000 - 10500 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep WBM reads.list > grep.reads.list.WBM
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.WBM 4 500
-------------------------------------------------------------------
#Found 754 total values totalling 27226422.0000. <36109.312997 +/- 3063.560679>
#Range: [ 19350 - 44924 ]
#Most likely bin: [ 35500 - 36000 ] 61 counts
#Median bin: [ 36000 - 36500 ] 58 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 19000 - 19500 : [ 1 0.00 0.00 ]
#...
|X 21500 - 22000 : [ 1 0.00 0.00 ]
|X 22000 - 22500 : [ 1 0.00 0.00 ]
#...
|X 23500 - 24000 : [ 1 0.00 0.01 ]
#...
|X 24500 - 25000 : [ 1 0.00 0.01 ]
#...
|X 25500 - 26000 : [ 1 0.00 0.01 ]
|X 26000 - 26500 : [ 1 0.00 0.01 ]
|X 26500 - 27000 : [ 1 0.00 0.01 ]
|X 27000 - 27500 : [ 2 0.00 0.01 ]
|X 27500 - 28000 : [ 1 0.00 0.01 ]
|X 28000 - 28500 : [ 1 0.00 0.02 ]
|X 28500 - 29000 : [ 1 0.00 0.02 ]
|XX 29000 - 29500 : [ 3 0.00 0.02 ]
|XX 29500 - 30000 : [ 3 0.00 0.03 ]
|XXXX 30000 - 30500 : [ 6 0.01 0.03 ]
|XXX 30500 - 31000 : [ 4 0.01 0.04 ]
|XXXX 31000 - 31500 : [ 6 0.01 0.05 ]
|XXXXXXXXXXXX 31500 - 32000 : [ 19 0.03 0.07 ]
|XXXXXXXXXX 32000 - 32500 : [ 16 0.02 0.09 ]
|XXXXXXXXXXXXXX 32500 - 33000 : [ 21 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 29 0.04 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 49 0.06 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 40 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 47 0.06 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 49 0.06 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 61 0.08 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 58 0.08 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 51 0.07 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 43 0.06 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 45 0.06 0.75 ]
|XXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 32 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 28 0.04 0.83 ]
|XXXXXXXXXXXXXXXX 39000 - 39500 : [ 25 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 39 0.05 0.91 ]
|XXXXXXXXXXX 40000 - 40500 : [ 17 0.02 0.93 ]
|XXXXXXXXXX 40500 - 41000 : [ 16 0.02 0.95 ]
|XXXXXXXXX 41000 - 41500 : [ 13 0.02 0.97 ]
|XXXXX 41500 - 42000 : [ 8 0.01 0.98 ]
|XXX 42000 - 42500 : [ 5 0.01 0.99 ]
|X 42500 - 43000 : [ 2 0.00 0.99 ]
|XX 43000 - 43500 : [ 3 0.00 1.00 ]
|X 43500 - 44000 : [ 1 0.00 1.00 ]
|X 44000 - 44500 : [ 1 0.00 1.00 ]
|X 44500 - 45000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AGKS reads.list > grep.reads.list.AGKS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AGKS 4 500
-------------------------------------------------------------------
#Found 9327 total values totalling 60715883.0000. <6509.690469 +/- 1022.568212>
#Range: [ 260 - 10911 ]
#Most likely bin: [ 6000 - 6500 ] 2231 counts
#Median bin: [ 6500 - 7000 ] 2128 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 3 0.00 0.00 ]
| 500 - 1000 : [ 10 0.00 0.00 ]
|X 1000 - 1500 : [ 37 0.00 0.01 ]
|X 1500 - 2000 : [ 64 0.01 0.01 ]
|X 2000 - 2500 : [ 58 0.01 0.02 ]
|X 2500 - 3000 : [ 53 0.01 0.02 ]
|X 3000 - 3500 : [ 54 0.01 0.03 ]
|X 3500 - 4000 : [ 35 0.00 0.03 ]
|X 4000 - 4500 : [ 34 0.00 0.04 ]
|X 4500 - 5000 : [ 29 0.00 0.04 ]
|XX 5000 - 5500 : [ 84 0.01 0.05 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1553 0.17 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2231 0.24 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2128 0.23 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1865 0.20 0.88 ]
|XXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 996 0.11 0.99 ]
|XX 8000 - 8500 : [ 90 0.01 1.00 ]
| 8500 - 9000 : [ 2 0.00 1.00 ]
#...
| 10500 - 11000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ZGJ reads.list > grep.reads.list.ZGJ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ZGJ 4 500
-------------------------------------------------------------------
#Found 2853 total values totalling 6474791.0000. <2269.467578 +/- 370.368243>
#Range: [ 1051 - 16701 ]
#Most likely bin: [ 2000 - 2500 ] 1726 counts
#Median bin: [ 2000 - 2500 ] 1726 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 3 0.00 0.00 ]
|XXXXXXXXXXXX 1500 - 2000 : [ 524 0.18 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 2500 : [ 1726 0.60 0.79 ]
|XXXXXXXXXXXXXX 2500 - 3000 : [ 599 0.21 1.00 ]
#...
| 16500 - 17000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# ZGI 2131 +- 678 (n=1116)
# AGKS 6030 +- 1610 (n=4861)
# WBM 35885 +- 3150 (n=386)
# ZGJ 2075 +- 252 (n=1408)
# WBF 3129 +- 549 (n=6832)
# WBL 6096 +- 1786 (n=962)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436113_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
AGKS 26208 -1 -1 96 721 22013 99 654 100 727
WBF 33984 -1 -1 96 655 30864 100 684 100 688
WBL 7680 -1 -1 93 729 4306 100 677 100 775
WBM 3840 -1 -1 97 683 3696 99 667 100 705
ZGI 7680 -1 -1 99 698 5060 100 654 100 706
ZGJ 15360 -1 -1 99 671 6241 100 605 100 658
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AGKS 11071 99 649 100 731 10942 99 660 100 723
WBF 15519 100 684 100 698 15345 100 684 100 678
WBL 2149 100 673 100 780 2157 99 681 100 771
WBM 1834 99 693 100 698 1862 99 642 100 713
ZGI 2524 100 652 100 713 2536 100 656 100 699
ZGJ 3120 100 606 100 666 3121 100 605 100 650
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436113_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 85863 42862 379.31 cumulative total @@
Only indicates plates present in input file.
Make no assumption regarding plates (not) present in project that do not appear above.
-------------------------------------------------------------------
trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3436113_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 72180 total values totalling 47841835.0000. <662.812898 +/- 122.887174>
#Range: [ 15 - 937 ]
#Most likely bin: [ 650 - 700 ] 18912 counts
#Median bin: [ 650 - 700 ] 18912 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 68 0.00 0.00 ]
| 50 - 100 : [ 178 0.00 0.00 ]
|XX 100 - 150 : [ 712 0.01 0.01 ]
|X 150 - 200 : [ 367 0.01 0.02 ]
|X 200 - 250 : [ 640 0.01 0.03 ]
|X 250 - 300 : [ 383 0.01 0.03 ]
|X 300 - 350 : [ 481 0.01 0.04 ]
|X 350 - 400 : [ 633 0.01 0.05 ]
|X 400 - 450 : [ 637 0.01 0.06 ]
|XX 450 - 500 : [ 742 0.01 0.07 ]
|XXX 500 - 550 : [ 1645 0.02 0.09 ]
|XXXXXXXXXX 550 - 600 : [ 4824 0.07 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 11652 0.16 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 18912 0.26 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 18149 0.25 0.83 ]
|XXXXXXXXXXXXXXXXXXX 750 - 800 : [ 9094 0.13 0.96 ]
|XXXXX 800 - 850 : [ 2559 0.04 0.99 ]
|X 850 - 900 : [ 484 0.01 1.00 ]
| 900 - 950 : [ 20 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for WBF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep WBF 3436113_fasta.screen.trimQ15.SaF > reads.trim15.WBF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.WBF.rl 2 50
-------------------------------------------------------------------
#Found 30864 total values totalling 21080950.0000. <683.027151 +/- 97.926468>
#Range: [ 18 - 937 ]
#Most likely bin: [ 650 - 700 ] 10076 counts
#Median bin: [ 650 - 700 ] 10076 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 21 0.00 0.00 ]
| 50 - 100 : [ 45 0.00 0.00 ]
| 100 - 150 : [ 80 0.00 0.00 ]
| 150 - 200 : [ 60 0.00 0.01 ]
|X 200 - 250 : [ 221 0.01 0.01 ]
| 250 - 300 : [ 76 0.00 0.02 ]
| 300 - 350 : [ 78 0.00 0.02 ]
| 350 - 400 : [ 113 0.00 0.02 ]
| 400 - 450 : [ 118 0.00 0.03 ]
|X 450 - 500 : [ 163 0.01 0.03 ]
|XX 500 - 550 : [ 413 0.01 0.04 ]
|XXXXXX 550 - 600 : [ 1392 0.05 0.09 ]
|XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 5072 0.16 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 10076 0.33 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7072 0.23 0.81 ]
|XXXXXXXXXXXXXX 750 - 800 : [ 3516 0.11 0.92 ]
|XXXXXXX 800 - 850 : [ 1859 0.06 0.98 ]
|XX 850 - 900 : [ 469 0.02 1.00 ]
| 900 - 950 : [ 20 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for WBL
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep WBL 3436113_fasta.screen.trimQ15.SaF > reads.trim15.WBL.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.WBL.rl 2 50
-------------------------------------------------------------------
#Found 4306 total values totalling 2904174.0000. <674.448212 +/- 180.753613>
#Range: [ 30 - 857 ]
#Most likely bin: [ 750 - 800 ] 1423 counts
#Median bin: [ 700 - 750 ] 1407 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 7 0.00 0.00 ]
| 50 - 100 : [ 12 0.00 0.00 ]
|XXXXXXX 100 - 150 : [ 237 0.06 0.06 ]
|X 150 - 200 : [ 22 0.01 0.06 ]
|XX 200 - 250 : [ 73 0.02 0.08 ]
|X 250 - 300 : [ 19 0.00 0.09 ]
|X 300 - 350 : [ 25 0.01 0.09 ]
|X 350 - 400 : [ 21 0.00 0.10 ]
|X 400 - 450 : [ 27 0.01 0.10 ]
|X 450 - 500 : [ 25 0.01 0.11 ]
|X 500 - 550 : [ 32 0.01 0.12 ]
|XX 550 - 600 : [ 63 0.01 0.13 ]
|XXXXX 600 - 650 : [ 164 0.04 0.17 ]
|XXXXXXXXXXXXXXX 650 - 700 : [ 525 0.12 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1407 0.33 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1423 0.33 0.95 ]
|XXXXXX 800 - 850 : [ 222 0.05 1.00 ]
| 850 - 900 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for WBM
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep WBM 3436113_fasta.screen.trimQ15.SaF > reads.trim15.WBM.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.WBM.rl 2 50
-------------------------------------------------------------------
#Found 3696 total values totalling 2447428.0000. <662.182900 +/- 156.632843>
#Range: [ 30 - 864 ]
#Most likely bin: [ 700 - 750 ] 1057 counts
#Median bin: [ 700 - 750 ] 1057 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 8 0.00 0.00 ]
|X 50 - 100 : [ 24 0.01 0.01 ]
|X 100 - 150 : [ 24 0.01 0.02 ]
| 150 - 200 : [ 12 0.00 0.02 ]
|X 200 - 250 : [ 26 0.01 0.03 ]
|XX 250 - 300 : [ 63 0.02 0.04 ]
|XXXX 300 - 350 : [ 101 0.03 0.07 ]
|XXXXXX 350 - 400 : [ 165 0.04 0.11 ]
|XXX 400 - 450 : [ 87 0.02 0.14 ]
|XX 450 - 500 : [ 43 0.01 0.15 ]
|XXX 500 - 550 : [ 71 0.02 0.17 ]
|XXXXX 550 - 600 : [ 133 0.04 0.20 ]
|XXXXXXXX 600 - 650 : [ 199 0.05 0.26 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 560 0.15 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1057 0.29 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 879 0.24 0.93 ]
|XXXXXXXXX 800 - 850 : [ 234 0.06 1.00 ]
| 850 - 900 : [ 10 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AGKS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AGKS 3436113_fasta.screen.trimQ15.SaF > reads.trim15.AGKS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AGKS.rl 2 50
-------------------------------------------------------------------
#Found 22013 total values totalling 14330451.0000. <650.999455 +/- 145.141488>
#Range: [ 15 - 854 ]
#Most likely bin: [ 700 - 750 ] 7373 counts
#Median bin: [ 650 - 700 ] 5167 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 26 0.00 0.00 ]
| 50 - 100 : [ 90 0.00 0.01 ]
|XX 100 - 150 : [ 356 0.02 0.02 ]
|X 150 - 200 : [ 253 0.01 0.03 ]
|X 200 - 250 : [ 263 0.01 0.04 ]
|X 250 - 300 : [ 194 0.01 0.05 ]
|X 300 - 350 : [ 250 0.01 0.07 ]
|XX 350 - 400 : [ 306 0.01 0.08 ]
|XX 400 - 450 : [ 351 0.02 0.09 ]
|XX 450 - 500 : [ 389 0.02 0.11 ]
|XXX 500 - 550 : [ 574 0.03 0.14 ]
|XXXXX 550 - 600 : [ 944 0.04 0.18 ]
|XXXXXXXXXXXX 600 - 650 : [ 2193 0.10 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5167 0.23 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7373 0.33 0.85 ]
|XXXXXXXXXXXXXXXXX 750 - 800 : [ 3065 0.14 0.99 ]
|X 800 - 850 : [ 217 0.01 1.00 ]
| 850 - 900 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ZGJ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ZGJ 3436113_fasta.screen.trimQ15.SaF > reads.trim15.ZGJ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ZGJ.rl 2 50
-------------------------------------------------------------------
#Found 6241 total values totalling 3775761.0000. <604.992950 +/- 78.282372>
#Range: [ 43 - 806 ]
#Most likely bin: [ 600 - 650 ] 2075 counts
#Median bin: [ 600 - 650 ] 2075 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 1 0.00 0.00 ]
| 50 - 100 : [ 3 0.00 0.00 ]
| 100 - 150 : [ 9 0.00 0.00 ]
| 150 - 200 : [ 13 0.00 0.00 ]
|X 200 - 250 : [ 48 0.01 0.01 ]
| 250 - 300 : [ 25 0.00 0.02 ]
| 300 - 350 : [ 22 0.00 0.02 ]
| 350 - 400 : [ 24 0.00 0.02 ]
|X 400 - 450 : [ 38 0.01 0.03 ]
|XX 450 - 500 : [ 102 0.02 0.05 ]
|XXXXXXXXXX 500 - 550 : [ 500 0.08 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1921 0.31 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2075 0.33 0.77 ]
|XXXXXXXXXXXXXXXXXXX 650 - 700 : [ 989 0.16 0.92 ]
|XXXXXXXX 700 - 750 : [ 427 0.07 0.99 ]
|X 750 - 800 : [ 43 0.01 1.00 ]
| 800 - 850 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436113
-------------------------------------------------------------------
AGKS.000001.000100 pMCL200.fa.4 LRS.fasta
AGKS.000101.000200 pMCL200.fa.4 LRS.fasta
WBF.000001.000100 pUC18.fa.4 LRS.fasta
WBF.000101.000200 pUC.fasta LRS.fasta
WBF.000201.000300 pUC.fasta LRS.fasta
WBL.000001.000100 pMCL200.fa.4 LRS.fasta
WBM.000001.000100 pCC1Fos.fa.4 LRS.fasta
ZGI.000001.000100 pMCL200.fasta LRS.fasta
ZGJ.000001.000100 pMCL200.fasta ../SCREENME_TOO.fasta LRS.fasta
AGKS.000001.000100 pMCL200.fa.4 LRS.fasta
AGKS.000101.000200 pMCL200.fa.4 LRS.fasta
WBF.000001.000100 pUC18.fa.4 LRS.fasta
WBF.000101.000200 pUC.fasta LRS.fasta
WBF.000201.000300 pUC.fasta LRS.fasta
WBL.000001.000100 pMCL200.fa.4 LRS.fasta
WBM.000001.000100 pCC1Fos.fa.4 LRS.fasta
ZGI.000001.000100 pMCL200.fasta LRS.fasta
ZGJ.000001.000100 pMCL200.fasta ../SCREENME_TOO.fasta LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436113_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436113_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 72534 total values totalling 42198.2458. <0.581772 +/- 0.066920>
#Range: [ 0 - 0.8723 ]
#Most likely bin: [ 0.62 - 0.625 ] 3060 counts
#Median bin: [ 0.595 - 0.6 ] 2570 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.05 - 0.055 : [ 1 0.00 0.00 ]
#...
| 0.11 - 0.115 : [ 1 0.00 0.00 ]
#...
| 0.195 - 0.2 : [ 1 0.00 0.00 ]
#...
| 0.205 - 0.21 : [ 3 0.00 0.00 ]
#...
| 0.23 - 0.235 : [ 1 0.00 0.00 ]
#...
| 0.25 - 0.255 : [ 2 0.00 0.00 ]
| 0.255 - 0.26 : [ 4 0.00 0.00 ]
| 0.26 - 0.265 : [ 1 0.00 0.00 ]
#...
| 0.27 - 0.275 : [ 1 0.00 0.00 ]
| 0.275 - 0.28 : [ 3 0.00 0.00 ]
| 0.28 - 0.285 : [ 5 0.00 0.00 ]
| 0.285 - 0.29 : [ 5 0.00 0.00 ]
| 0.29 - 0.295 : [ 5 0.00 0.00 ]
| 0.295 - 0.3 : [ 6 0.00 0.00 ]
| 0.3 - 0.305 : [ 9 0.00 0.00 ]
| 0.305 - 0.31 : [ 10 0.00 0.00 ]
| 0.31 - 0.315 : [ 25 0.00 0.00 ]
| 0.315 - 0.32 : [ 21 0.00 0.00 ]
| 0.32 - 0.325 : [ 38 0.00 0.00 ]
| 0.325 - 0.33 : [ 30 0.00 0.00 ]
| 0.33 - 0.335 : [ 36 0.00 0.00 ]
|X 0.335 - 0.34 : [ 49 0.00 0.00 ]
|X 0.34 - 0.345 : [ 50 0.00 0.00 ]
|X 0.345 - 0.35 : [ 70 0.00 0.01 ]
|X 0.35 - 0.355 : [ 82 0.00 0.01 ]
|X 0.355 - 0.36 : [ 67 0.00 0.01 ]
|X 0.36 - 0.365 : [ 88 0.00 0.01 ]
|X 0.365 - 0.37 : [ 92 0.00 0.01 ]
|X 0.37 - 0.375 : [ 105 0.00 0.01 ]
|XX 0.375 - 0.38 : [ 124 0.00 0.01 ]
|XX 0.38 - 0.385 : [ 135 0.00 0.01 ]
|XX 0.385 - 0.39 : [ 124 0.00 0.02 ]
|XX 0.39 - 0.395 : [ 135 0.00 0.02 ]
|XX 0.395 - 0.4 : [ 134 0.00 0.02 ]
|XX 0.4 - 0.405 : [ 138 0.00 0.02 ]
|XX 0.405 - 0.41 : [ 162 0.00 0.02 ]
|XX 0.41 - 0.415 : [ 182 0.00 0.03 ]
|XX 0.415 - 0.42 : [ 182 0.00 0.03 ]
|XXX 0.42 - 0.425 : [ 204 0.00 0.03 ]
|XXX 0.425 - 0.43 : [ 223 0.00 0.04 ]
|XXXX 0.43 - 0.435 : [ 289 0.00 0.04 ]
|XXX 0.435 - 0.44 : [ 251 0.00 0.04 ]
|XXXX 0.44 - 0.445 : [ 284 0.00 0.05 ]
|XXXX 0.445 - 0.45 : [ 321 0.00 0.05 ]
|XXXX 0.45 - 0.455 : [ 328 0.00 0.06 ]
|XXXXX 0.455 - 0.46 : [ 346 0.00 0.06 ]
|XXXXX 0.46 - 0.465 : [ 404 0.01 0.07 ]
|XXXXXX 0.465 - 0.47 : [ 437 0.01 0.07 ]
|XXXXXX 0.47 - 0.475 : [ 435 0.01 0.08 ]
|XXXXXX 0.475 - 0.48 : [ 475 0.01 0.08 ]
|XXXXXXX 0.48 - 0.485 : [ 521 0.01 0.09 ]
|XXXXXXX 0.485 - 0.49 : [ 528 0.01 0.10 ]
|XXXXXXXX 0.49 - 0.495 : [ 606 0.01 0.11 ]
|XXXXXXXX 0.495 - 0.5 : [ 633 0.01 0.12 ]
|XXXXXXXXXXXXXX 0.5 - 0.505 : [ 1100 0.02 0.13 ]
|XXXXXXXXXX 0.505 - 0.51 : [ 783 0.01 0.14 ]
|XXXXXXXXXXX 0.51 - 0.515 : [ 836 0.01 0.15 ]
|XXXXXXXXXXXXX 0.515 - 0.52 : [ 975 0.01 0.17 ]
|XXXXXXXXXXXX 0.52 - 0.525 : [ 930 0.01 0.18 ]
|XXXXXXXXXXXXX 0.525 - 0.53 : [ 1000 0.01 0.19 ]
|XXXXXXXXXXXXXX 0.53 - 0.535 : [ 1044 0.01 0.21 ]
|XXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1143 0.02 0.22 ]
|XXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1189 0.02 0.24 ]
|XXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1238 0.02 0.26 ]
|XXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1290 0.02 0.27 ]
|XXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1402 0.02 0.29 ]
|XXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1475 0.02 0.31 ]
|XXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1581 0.02 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1798 0.02 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 2012 0.03 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 2173 0.03 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 2474 0.03 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 2640 0.04 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 2570 0.04 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 2901 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 2830 0.04 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 2959 0.04 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 3016 0.04 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 3060 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 2851 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 2519 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 2309 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 2100 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 1874 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 1605 0.02 0.91 ]
|XXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 1375 0.02 0.93 ]
|XXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 1242 0.02 0.95 ]
|XXXXXXXXXXXXX 0.665 - 0.67 : [ 1013 0.01 0.96 ]
|XXXXXXXXXXX 0.67 - 0.675 : [ 854 0.01 0.97 ]
|XXXXXXXX 0.675 - 0.68 : [ 616 0.01 0.98 ]
|XXXXX 0.68 - 0.685 : [ 398 0.01 0.99 ]
|XXXX 0.685 - 0.69 : [ 284 0.00 0.99 ]
|XXX 0.69 - 0.695 : [ 207 0.00 0.99 ]
|XX 0.695 - 0.7 : [ 144 0.00 1.00 ]
|X 0.7 - 0.705 : [ 112 0.00 1.00 ]
|X 0.705 - 0.71 : [ 72 0.00 1.00 ]
|X 0.71 - 0.715 : [ 53 0.00 1.00 ]
| 0.715 - 0.72 : [ 15 0.00 1.00 ]
| 0.72 - 0.725 : [ 12 0.00 1.00 ]
| 0.725 - 0.73 : [ 10 0.00 1.00 ]
| 0.73 - 0.735 : [ 9 0.00 1.00 ]
| 0.735 - 0.74 : [ 5 0.00 1.00 ]
| 0.74 - 0.745 : [ 4 0.00 1.00 ]
| 0.745 - 0.75 : [ 3 0.00 1.00 ]
| 0.75 - 0.755 : [ 2 0.00 1.00 ]
| 0.755 - 0.76 : [ 4 0.00 1.00 ]
| 0.76 - 0.765 : [ 2 0.00 1.00 ]
#...
| 0.77 - 0.775 : [ 2 0.00 1.00 ]
| 0.775 - 0.78 : [ 1 0.00 1.00 ]
#...
| 0.785 - 0.79 : [ 2 0.00 1.00 ]
#...
| 0.805 - 0.81 : [ 1 0.00 1.00 ]
#...
| 0.83 - 0.835 : [ 1 0.00 1.00 ]
#...
| 0.87 - 0.875 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 194. 804 reads; 49154 bp (untrimmed), 49036 (trimmed).
Contig 195. 818 reads; 58081 bp (untrimmed), 58081 (trimmed).
Contig 196. 889 reads; 52811 bp (untrimmed), 52805 (trimmed).
Contig 197. 915 reads; 57427 bp (untrimmed), 57413 (trimmed).
Contig 198. 925 reads; 58074 bp (untrimmed), 58074 (trimmed).
Contig 199. 945 reads; 63398 bp (untrimmed), 63328 (trimmed).
Contig 200. 1015 reads; 60966 bp (untrimmed), 60947 (trimmed).
Contig 201. 1052 reads; 67722 bp (untrimmed), 67722 (trimmed).
Contig 202. 1087 reads; 59222 bp (untrimmed), 59206 (trimmed).
Contig 203. 1154 reads; 59213 bp (untrimmed), 59106 (trimmed).
Contig 204. 1182 reads; 68243 bp (untrimmed), 68216 (trimmed).
Contig 205. 1220 reads; 73943 bp (untrimmed), 73630 (trimmed).
Contig 206. 1279 reads; 86784 bp (untrimmed), 86761 (trimmed).
Contig 207. 1318 reads; 73623 bp (untrimmed), 73620 (trimmed).
Contig 208. 1471 reads; 86222 bp (untrimmed), 85833 (trimmed).
Contig 209. 1510 reads; 85176 bp (untrimmed), 85172 (trimmed).
Contig 210. 1516 reads; 92618 bp (untrimmed), 92571 (trimmed).
Contig 211. 1677 reads; 77026 bp (untrimmed), 77026 (trimmed).
Contig 212. 1761 reads; 119122 bp (untrimmed), 119122 (trimmed).
Contig 213. 2063 reads; 98499 bp (untrimmed), 98338 (trimmed).
Contig 214. 2094 reads; 132476 bp (untrimmed), 132476 (trimmed).
Contig 215. 3115 reads; 155119 bp (untrimmed), 155066 (trimmed).
Contig 216. 3342 reads; 181836 bp (untrimmed), 181836 (trimmed).
Contig 217. 3774 reads; 207406 bp (untrimmed), 207157 (trimmed).
Contig 218. 3835 reads; 201998 bp (untrimmed), 201998 (trimmed).
Contig 219. 4461 reads; 211849 bp (untrimmed), 211849 (trimmed).
Contig 220. 4594 reads; 23166 bp (untrimmed), 23158 (trimmed).
--------------------------------------------------------------
Totals 71917 reads; 4259905 bp (untrimmed), 4222850 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4244597 bases = 14.59 +- 15.70 = 0.40 +- 6.42
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 185 total values totalling 1783.2900. <9.639405 +/- 16.676160>
#Range: [ 1.04 - 165.26 ]
#Most likely bin: [ 1.5 - 2 ] 22 counts
#Median bin: [ 6.5 - 7 ] 4 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 21 0.11 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 22 0.12 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 12 0.06 0.30 ]
|XXXXXXXXXXX 2.5 - 3 : [ 6 0.03 0.33 ]
|XXXXXXXXX 3 - 3.5 : [ 5 0.03 0.36 ]
|XXXXXXXXXXX 3.5 - 4 : [ 6 0.03 0.39 ]
|XXXXX 4 - 4.5 : [ 3 0.02 0.41 ]
|XXXXX 4.5 - 5 : [ 3 0.02 0.42 ]
|XXXXX 5 - 5.5 : [ 3 0.02 0.44 ]
|XXXXXXXXX 5.5 - 6 : [ 5 0.03 0.46 ]
|XXXXX 6 - 6.5 : [ 3 0.02 0.48 ]
|XXXXXXX 6.5 - 7 : [ 4 0.02 0.50 ]
|XXXXXXXXX 7 - 7.5 : [ 5 0.03 0.53 ]
|XXXX 7.5 - 8 : [ 2 0.01 0.54 ]
|XXXX 8 - 8.5 : [ 2 0.01 0.55 ]
|XXXX 8.5 - 9 : [ 2 0.01 0.56 ]
|XXXX 9 - 9.5 : [ 2 0.01 0.57 ]
|XX 9.5 - 10 : [ 1 0.01 0.58 ]
|XXXXXXXXX 10 - 10.5 : [ 5 0.03 0.61 ]
|XXXXXXXXXXX 10.5 - 11 : [ 6 0.03 0.64 ]
|XXXXXXXXX 11 - 11.5 : [ 5 0.03 0.66 ]
|XXXXXXXXXXX 11.5 - 12 : [ 6 0.03 0.70 ]
|XXXXXXXXXXXXX 12 - 12.5 : [ 7 0.04 0.74 ]
|XXXXXXXXX 12.5 - 13 : [ 5 0.03 0.76 ]
|XXXXXXXXXXX 13 - 13.5 : [ 6 0.03 0.79 ]
|XXXXXXX 13.5 - 14 : [ 4 0.02 0.82 ]
|XXXXXXXXXXX 14 - 14.5 : [ 6 0.03 0.85 ]
|XXXXXXXXX 14.5 - 15 : [ 5 0.03 0.88 ]
|XXXXXXXXX 15 - 15.5 : [ 5 0.03 0.90 ]
|XXXXXXX 15.5 - 16 : [ 4 0.02 0.92 ]
|XXXX 16 - 16.5 : [ 2 0.01 0.94 ]
|XXXXX 16.5 - 17 : [ 3 0.02 0.95 ]
|XXXX 17 - 17.5 : [ 2 0.01 0.96 ]
|XX 17.5 - 18 : [ 1 0.01 0.97 ]
|XX 18 - 18.5 : [ 1 0.01 0.97 ]
|XX 18.5 - 19 : [ 1 0.01 0.98 ]
#...
|XX 45.5 - 46 : [ 1 0.01 0.98 ]
#...
|XX 59 - 59.5 : [ 1 0.01 0.99 ]
#...
|XX 141.5 - 142 : [ 1 0.01 0.99 ]
#...
|XX 165 - 165.5 : [ 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 112 total values totalling 1609.9500. <14.374554 +/- 20.006449>
#Range: [ 3.40 - 165.26 ]
#Most likely bin: [ 12 - 12.5 ] 7 counts
#Median bin: [ 11.5 - 12 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 3 - 3.5 : [ 2 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 5 0.04 0.06 ]
|XXXXXX 4 - 4.5 : [ 1 0.01 0.07 ]
|XXXXXXXXXXX 4.5 - 5 : [ 2 0.02 0.09 ]
|XXXXXXXXXXXXXXXXX 5 - 5.5 : [ 3 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 5 0.04 0.16 ]
|XXXXXXXXXXX 6 - 6.5 : [ 2 0.02 0.18 ]
|XXXXXXXXXXXXXXXXX 6.5 - 7 : [ 3 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 5 0.04 0.25 ]
|XXXXXX 7.5 - 8 : [ 1 0.01 0.26 ]
|XXXXXXXXXXX 8 - 8.5 : [ 2 0.02 0.28 ]
|XXXXXXXXXXX 8.5 - 9 : [ 2 0.02 0.29 ]
|XXXXXXXXXXX 9 - 9.5 : [ 2 0.02 0.31 ]
|XXXXXX 9.5 - 10 : [ 1 0.01 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 4 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 5 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 5 0.04 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 6 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 7 0.06 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 5 0.04 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 6 0.05 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 4 0.04 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 6 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 14.5 - 15 : [ 5 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15 - 15.5 : [ 5 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXX 15.5 - 16 : [ 4 0.04 0.88 ]
|XXXXXXXXXXX 16 - 16.5 : [ 2 0.02 0.89 ]
|XXXXXXXXXXXXXXXXX 16.5 - 17 : [ 3 0.03 0.92 ]
|XXXXXXXXXXX 17 - 17.5 : [ 2 0.02 0.94 ]
|XXXXXX 17.5 - 18 : [ 1 0.01 0.95 ]
|XXXXXX 18 - 18.5 : [ 1 0.01 0.96 ]
|XXXXXX 18.5 - 19 : [ 1 0.01 0.96 ]
#...
|XXXXXX 45.5 - 46 : [ 1 0.01 0.97 ]
#...
|XXXXXX 59 - 59.5 : [ 1 0.01 0.98 ]
#...
|XXXXXX 141.5 - 142 : [ 1 0.01 0.99 ]
#...
|XXXXXX 165 - 165.5 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 54 2 reads 1601 bases = 1.04 +- 0.21 = 1.04 +- 0.21
Contig 53 2 reads 2016 bases = 1.06 +- 0.23 = 1.06 +- 0.23
Contig 16 2 reads 1790 bases = 1.09 +- 0.29 = 1.09 +- 0.29
Contig 32 2 reads 1972 bases = 1.09 +- 0.29 = 1.09 +- 0.29
Contig 27 2 reads 1408 bases = 1.14 +- 0.35 = 1.14 +- 0.35
Contig 45 2 reads 1138 bases = 1.16 +- 0.37 = 0.84 +- 0.37
Contig 55 2 reads 1647 bases = 1.18 +- 0.39 = 1.18 +- 0.39
Contig 29 2 reads 2136 bases = 1.20 +- 0.40 = 0.01 +- 0.89
Contig 62 3 reads 1359 bases = 1.24 +- 0.56 = 0.33 +- 1.10
Contig 46 2 reads 791 bases = 1.26 +- 0.44 = 0.10 +- 0.85
Contig 17 2 reads 1381 bases = 1.29 +- 0.45 = 0.17 +- 0.83
Contig 41 2 reads 1719 bases = 1.29 +- 0.45 = 0.15 +- 0.83
Contig 61 3 reads 1058 bases = 1.30 +- 0.71 = 1.00 +- 0.00
Contig 22 2 reads 1595 bases = 1.31 +- 0.46 = 1.31 +- 0.46
Contig 24 2 reads 1361 bases = 1.32 +- 0.47 = 1.32 +- 0.47
Contig 18 2 reads 1465 bases = 1.37 +- 0.48 = 0.28 +- 0.74
Contig 44 2 reads 1707 bases = 1.38 +- 0.49 = 0.05 +- 0.79
Contig 77 4 reads 1986 bases = 1.42 +- 0.73 = 1.42 +- 0.73
Contig 21 2 reads 1311 bases = 1.44 +- 0.50 = 0.32 +- 0.67
Contig 68 3 reads 1705 bases = 1.46 +- 0.50 = 1.46 +- 0.50
Contig 204 1182 reads 68243 bases = 15.32 +- 4.80 = 0.72 +- 4.40
Contig 211 1677 reads 77026 bases = 15.33 +- 6.38 = 0.05 +- 5.32
Contig 207 1318 reads 73623 bases = 15.61 +- 6.32 = 0.17 +- 4.88
Contig 209 1510 reads 85176 bases = 15.71 +- 4.47 = 0.42 +- 4.95
Contig 202 1087 reads 59222 bases = 15.84 +- 6.77 = 0.32 +- 5.34
Contig 217 3774 reads 207406 bases = 15.85 +- 6.21 = 0.01 +- 4.86
Contig 216 3342 reads 181836 bases = 16.00 +- 10.54 = 0.40 +- 5.82
Contig 137 88 reads 4523 bases = 16.48 +- 6.15 = 6.05 +- 5.50
Contig 177 525 reads 27943 bases = 16.51 +- 6.45 = 0.23 +- 4.90
Contig 218 3835 reads 201998 bases = 16.60 +- 8.55 = 0.24 +- 5.66
Contig 133 72 reads 3744 bases = 16.69 +- 10.73 = 6.29 +- 8.12
Contig 203 1154 reads 59213 bases = 17.13 +- 6.75 = 0.47 +- 5.36
Contig 215 3115 reads 155119 bases = 17.36 +- 10.96 = 0.88 +- 9.79
Contig 191 763 reads 38291 bases = 17.68 +- 5.96 = 0.85 +- 4.75
Contig 213 2063 reads 98499 bases = 18.21 +- 6.40 = 0.11 +- 6.34
Contig 219 4461 reads 211849 bases = 18.60 +- 5.38 = 0.15 +- 5.75
Contig 182 547 reads 10663 bases = 45.56 +- 10.90 = 0.61 +- 6.76
Contig 150 151 reads 2073 bases = 59.07 +- 58.26 = 0.07 +- 10.03
Contig 171 382 reads 2213 bases = 141.61 +- 108.51 = 5.08 +- 17.54
Contig 220 4594 reads 23166 bases = 165.26 +- 98.26 = 0.72 +- 46.92
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 3938
HQ Discrepant reads = 76
Chimeric reads = 71
Suspect alignments = 599
-------------------------------------------------------------------
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/microbe2/3436113/edit_dir.29Jan04.QD