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
3634497 3000 1757 Thermoanaerobacter ethanolicus
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Thermoanaerobacter_ethanolicus
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Thermoanaerobacteriaceae, family, eubacteria
Clostridia, class, eubacteria
Thermoanaerobacteriales, order, eubacteria
Thermoanaerobacter ethanolicus, species, eubacteria
Thermoanaerobacter, genus, eubacteria
Firmicutes (Gram-positive bacteria), phylum, eubacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3701503
# phrap: 2758283
# db:
altered.
3000000
3153262 +/- 400027
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 10138
Number of reads with percent X's >= 20%: 1846 = 4.3%
Number of reads with percent X's >= 50%: 1639 = 3.8%
Number of reads with percent X's >= 80%: 1392 = 3.2%
Total reads in project: 42885
Total bp X'd : 1861215
reads >= 20% >= 50% >= 80% screened
Nr with L09136 6127 464 356 234
Nr with LRS 51 50 42 35
Nr with pCC1Fos 2583 24 14 11
Nr with pMCL200_JGI_XZX+XZK 1377 1308 1227 1112
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 2667
Number of reads with percent X's >= 20%: 1483 = 15.4%
Number of reads with percent X's >= 50%: 1426 = 14.8%
Number of reads with percent X's >= 80%: 1334 = 13.9%
Total reads in project: 9617
Total bp X'd : 1398056
reads >= 20% >= 50% >= 80% screened
Nr with L09136 378 260 256 222
Nr with LRS 51 50 42 35
Nr with pCC1Fos 1068 20 13 11
Nr with pMCL200_JGI_XZX+XZK 1170 1153 1115 1066
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 12033638
C = 8407234
G = 7887340
T = 12430448
N = 398952
X = 1861215
GC fraction = 0.38
Total = 43018827
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634497_fasta.screen.contigs
-------------------------------------------------------------------
A 1147276
C 943170
G 910803
T 1166061
N 85725
fraction GC = 0.44
total bases = 4253035
Libraries and Reads
-------------------------------------------------------------------
Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
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-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBT reads.list > grep.reads.list.AIBT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBT 4 500
-------------------------------------------------------------------
#Found 5704 total values totalling 20172585.0000. <3536.568198 +/- 743.823226>
#Range: [ 818 - 22650 ]
#Most likely bin: [ 3500 - 4000 ] 1890 counts
#Median bin: [ 3500 - 4000 ] 1890 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 4 0.00 0.00 ]
|X 1000 - 1500 : [ 61 0.01 0.01 ]
|XX 1500 - 2000 : [ 117 0.02 0.03 ]
|XXXXX 2000 - 2500 : [ 214 0.04 0.07 ]
|XXXXXXXXXXXXXX 2500 - 3000 : [ 673 0.12 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1404 0.25 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1890 0.33 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1051 0.18 0.95 ]
|XXXXX 4500 - 5000 : [ 228 0.04 0.99 ]
|X 5000 - 5500 : [ 46 0.01 1.00 ]
| 5500 - 6000 : [ 12 0.00 1.00 ]
| 6000 - 6500 : [ 2 0.00 1.00 ]
#...
| 14000 - 14500 : [ 1 0.00 1.00 ]
#...
| 22500 - 23000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBU reads.list > grep.reads.list.AIBU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBU 4 500
-------------------------------------------------------------------
#Found 6345 total values totalling 43591806.0000. <6870.260993 +/- 1032.415430>
#Range: [ 939 - 26451 ]
#Most likely bin: [ 7000 - 7500 ] 1748 counts
#Median bin: [ 7000 - 7500 ] 1748 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
|X 1000 - 1500 : [ 24 0.00 0.00 ]
|X 1500 - 2000 : [ 37 0.01 0.01 ]
|X 2000 - 2500 : [ 29 0.00 0.01 ]
|X 2500 - 3000 : [ 33 0.01 0.02 ]
|X 3000 - 3500 : [ 22 0.00 0.02 ]
| 3500 - 4000 : [ 18 0.00 0.03 ]
|X 4000 - 4500 : [ 26 0.00 0.03 ]
|X 4500 - 5000 : [ 22 0.00 0.03 ]
|XX 5000 - 5500 : [ 72 0.01 0.04 ]
|XXXXXXXXX 5500 - 6000 : [ 391 0.06 0.11 ]
|XXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 894 0.14 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1544 0.24 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1748 0.28 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1133 0.18 0.94 ]
|XXXXXXXX 8000 - 8500 : [ 343 0.05 1.00 ]
| 8500 - 9000 : [ 6 0.00 1.00 ]
#...
| 10000 - 10500 : [ 1 0.00 1.00 ]
#...
| 26000 - 26500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBW reads.list > grep.reads.list.AIBW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBW 4 500
-------------------------------------------------------------------
#Found -1 total values totalling 0.0000. <-0.000000 +/- 0.000000>
#Range: [ - ]
#Most likely bin: [ 0 - 500 ] 1 counts
#Median bin: [ 0 - 500 ] counts
#Histogram Bins Count Fraction Cum_Fraction
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AYGG reads.list > grep.reads.list.AYGG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AYGG 4 500
-------------------------------------------------------------------
#Found 39 total values totalling 1262207.0000. <32364.282051 +/- 6113.821806>
#Range: [ 8138 - 41857 ]
#Most likely bin: [ 34000 - 34500 ] 6 counts
#Median bin: [ 34000 - 34500 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 8000 - 8500 : [ 1 0.03 0.03 ]
#...
|XXXXXXX 15500 - 16000 : [ 1 0.03 0.05 ]
#...
|XXXXXXX 20500 - 21000 : [ 1 0.03 0.08 ]
#...
|XXXXXXX 25000 - 25500 : [ 1 0.03 0.10 ]
#...
|XXXXXXX 27000 - 27500 : [ 1 0.03 0.13 ]
#...
|XXXXXXX 28000 - 28500 : [ 1 0.03 0.15 ]
#...
|XXXXXXX 29000 - 29500 : [ 1 0.03 0.18 ]
|XXXXXXX 29500 - 30000 : [ 1 0.03 0.21 ]
#...
|XXXXXXX 30500 - 31000 : [ 1 0.03 0.23 ]
#...
|XXXXXXXXXXXXXXXXXXXX 31500 - 32000 : [ 3 0.08 0.31 ]
|XXXXXXXXXXXXX 32000 - 32500 : [ 2 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 3 0.08 0.44 ]
|XXXXXXX 33000 - 33500 : [ 1 0.03 0.46 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 6 0.15 0.62 ]
|XXXXXXXXXXXXX 34500 - 35000 : [ 2 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 3 0.08 0.74 ]
|XXXXXXXXXXXXX 35500 - 36000 : [ 2 0.05 0.79 ]
|XXXXXXX 36000 - 36500 : [ 1 0.03 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 4 0.10 0.92 ]
#...
|XXXXXXXXXXXXX 38500 - 39000 : [ 2 0.05 0.97 ]
#...
|XXXXXXX 41500 - 42000 : [ 1 0.03 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# WARNING: phrap4 - library AYGG in assembly w/o entry in constraints file
# AIBU 6806 +- 2168 (n=6363)
# AIBT 3470 +- 1483 (n=5743)
# AYGG 29355 +- 11182 (n=43)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634497_fasta.screen.trimQ15.SaF and database (md_run table)
* note J15 is Jazz trimmed length, Q20 is count of Quality 20+ bases
-------------------------------------------------------------------
DB |----J15---| |----Q20---| Fasta |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIBT 16896 84 580 91 575 16773 84 583 89 594
AIBU 16896 88 790 95 748 16896 88 791 95 786
AIBW 3072 14 371 28 116 3072 14 570 28 375
AYGG 6144 80 512 89 469 6144 81 522 90 522
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIBT 8390 84 579 89 591 8383 85 587 89 598
AIBU 8448 88 794 96 788 8448 88 788 94 784
AIBW 1536 1 364 15 122 1536 28 575 41 469
AYGG 3072 80 522 89 514 3072 81 523 90 531
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634497_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
88 16896 8448 96.00 100.00 AIBU @
88 16773 8430 95.80 99.79 AIBT @
16 3072 1536 96.00 100.00 AIBW @
32 6144 3072 96.00 100.00 AYGG @
] 42885 21486 95.92 cumulative total@@
LIBRARY PLATE ID COUNT [ AIBT 88 AIBU 88 AIBW 16 AYGG 32 ] for 224 total 96 well plate ids.
Only indicates plates present in input file.
Make no assumption regarding plates (not) present in project that do not appear above.
-------------------------------------------------------------------
trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3634497_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 42885 total values totalling 22925700.0000. <534.585519 +/- 307.494951>
#Range: [ 0 - 939 ]
#Most likely bin: [ 0 - 50 ] 7766 counts
#Median bin: [ 650 - 700 ] 3217 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 7766 0.18 0.18 ]
|XXXX 50 - 100 : [ 740 0.02 0.20 ]
|XXX 100 - 150 : [ 495 0.01 0.21 ]
|XXX 150 - 200 : [ 519 0.01 0.22 ]
|XXX 200 - 250 : [ 552 0.01 0.23 ]
|XXXX 250 - 300 : [ 762 0.02 0.25 ]
|XXXX 300 - 350 : [ 867 0.02 0.27 ]
|XXXXX 350 - 400 : [ 926 0.02 0.29 ]
|XXXXX 400 - 450 : [ 914 0.02 0.32 ]
|XXXXXX 450 - 500 : [ 1167 0.03 0.34 ]
|XXXXXXX 500 - 550 : [ 1434 0.03 0.38 ]
|XXXXXXXXX 550 - 600 : [ 1797 0.04 0.42 ]
|XXXXXXXXXXXX 600 - 650 : [ 2298 0.05 0.47 ]
|XXXXXXXXXXXXXXXXX 650 - 700 : [ 3217 0.08 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4446 0.10 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6333 0.15 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6438 0.15 0.95 ]
|XXXXXXXXXXX 850 - 900 : [ 2135 0.05 1.00 ]
| 900 - 950 : [ 79 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBT 3634497_fasta.screen.trimQ15.SaF > reads.trim15.AIBT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBT.rl 2 50
-------------------------------------------------------------------
#Found 16773 total values totalling 8298735.0000. <494.767483 +/- 258.645192>
#Range: [ 0 - 861 ]
#Most likely bin: [ 700 - 750 ] 2504 counts
#Median bin: [ 550 - 600 ] 1251 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2241 0.13 0.13 ]
|XXXXXX 50 - 100 : [ 367 0.02 0.16 ]
|XXXXX 100 - 150 : [ 288 0.02 0.17 ]
|XXXXX 150 - 200 : [ 296 0.02 0.19 ]
|XXXXX 200 - 250 : [ 338 0.02 0.21 ]
|XXXXXX 250 - 300 : [ 368 0.02 0.23 ]
|XXXXXXX 300 - 350 : [ 451 0.03 0.26 ]
|XXXXXXXXX 350 - 400 : [ 577 0.03 0.29 ]
|XXXXXXXXXX 400 - 450 : [ 634 0.04 0.33 ]
|XXXXXXXXXXXXX 450 - 500 : [ 807 0.05 0.38 ]
|XXXXXXXXXXXXXXXX 500 - 550 : [ 1003 0.06 0.44 ]
|XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1251 0.07 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1626 0.10 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2184 0.13 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2504 0.15 0.89 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1637 0.10 0.99 ]
|XXX 800 - 850 : [ 199 0.01 1.00 ]
| 850 - 900 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBU 3634497_fasta.screen.trimQ15.SaF > reads.trim15.AIBU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBU.rl 2 50
-------------------------------------------------------------------
#Found 16896 total values totalling 11739884.0000. <694.832150 +/- 270.787092>
#Range: [ 0 - 939 ]
#Most likely bin: [ 800 - 850 ] 6117 counts
#Median bin: [ 750 - 800 ] 4303 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXX 0 - 50 : [ 2012 0.12 0.12 ]
| 50 - 100 : [ 50 0.00 0.12 ]
| 100 - 150 : [ 33 0.00 0.12 ]
| 150 - 200 : [ 41 0.00 0.13 ]
| 200 - 250 : [ 30 0.00 0.13 ]
| 250 - 300 : [ 43 0.00 0.13 ]
| 300 - 350 : [ 38 0.00 0.13 ]
| 350 - 400 : [ 27 0.00 0.13 ]
| 400 - 450 : [ 41 0.00 0.14 ]
| 450 - 500 : [ 50 0.00 0.14 ]
| 500 - 550 : [ 46 0.00 0.14 ]
|X 550 - 600 : [ 79 0.00 0.15 ]
|X 600 - 650 : [ 116 0.01 0.15 ]
|XX 650 - 700 : [ 355 0.02 0.18 ]
|XXXXXXXXX 700 - 750 : [ 1310 0.08 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4303 0.25 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6117 0.36 0.87 ]
|XXXXXXXXXXXXXX 850 - 900 : [ 2126 0.13 1.00 ]
|X 900 - 950 : [ 79 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBW 3634497_fasta.screen.trimQ15.SaF > reads.trim15.AIBW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBW.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 272182.0000. <88.600911 +/- 208.663198>
#Range: [ 0 - 864 ]
#Most likely bin: [ 0 - 50 ] 2588 counts
#Median bin: [ 0 - 50 ] 2588 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2588 0.84 0.84 ]
|X 50 - 100 : [ 50 0.02 0.86 ]
| 100 - 150 : [ 15 0.00 0.86 ]
| 150 - 200 : [ 10 0.00 0.87 ]
| 200 - 250 : [ 11 0.00 0.87 ]
| 250 - 300 : [ 13 0.00 0.87 ]
| 300 - 350 : [ 17 0.01 0.88 ]
| 350 - 400 : [ 22 0.01 0.89 ]
| 400 - 450 : [ 22 0.01 0.89 ]
|X 450 - 500 : [ 45 0.01 0.91 ]
| 500 - 550 : [ 24 0.01 0.92 ]
| 550 - 600 : [ 26 0.01 0.93 ]
|X 600 - 650 : [ 41 0.01 0.94 ]
|X 650 - 700 : [ 42 0.01 0.95 ]
|X 700 - 750 : [ 59 0.02 0.97 ]
|X 750 - 800 : [ 57 0.02 0.99 ]
| 800 - 850 : [ 28 0.01 1.00 ]
| 850 - 900 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AYGG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AYGG 3634497_fasta.screen.trimQ15.SaF > reads.trim15.AYGG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AYGG.rl 2 50
-------------------------------------------------------------------
#Found 6144 total values totalling 2614899.0000. <425.602051 +/- 260.117150>
#Range: [ 0 - 886 ]
#Most likely bin: [ 0 - 50 ] 925 counts
#Median bin: [ 450 - 500 ] 265 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 925 0.15 0.15 ]
|XXXXXXXXXXXX 50 - 100 : [ 273 0.04 0.19 ]
|XXXXXXX 100 - 150 : [ 159 0.03 0.22 ]
|XXXXXXX 150 - 200 : [ 172 0.03 0.25 ]
|XXXXXXX 200 - 250 : [ 173 0.03 0.28 ]
|XXXXXXXXXXXXXXX 250 - 300 : [ 338 0.06 0.33 ]
|XXXXXXXXXXXXXXXX 300 - 350 : [ 361 0.06 0.39 ]
|XXXXXXXXXXXXX 350 - 400 : [ 300 0.05 0.44 ]
|XXXXXXXXX 400 - 450 : [ 217 0.04 0.47 ]
|XXXXXXXXXXX 450 - 500 : [ 265 0.04 0.52 ]
|XXXXXXXXXXXXXXXX 500 - 550 : [ 361 0.06 0.58 ]
|XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 441 0.07 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 515 0.08 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 636 0.10 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 573 0.09 0.93 ]
|XXXXXXXXXXXXXXX 750 - 800 : [ 336 0.05 0.98 ]
|XXXX 800 - 850 : [ 94 0.02 1.00 ]
| 850 - 900 : [ 5 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AYGH
trimt JAZZ trim 15 readlength histogram for AYGI
trimt JAZZ trim 15 readlength histogram for SCNB
trimt JAZZ trim 15 readlength histogram for BPBX
trimt JAZZ trim 15 readlength histogram for BPBY
trimt JAZZ trim 15 readlength histogram for BPBZ
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634497
-------------------------------------------------------------------
AIBT.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIBT.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIBU.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIBW.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AYGG.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AIBT.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIBT.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIBU.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIBW.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AYGG.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634497_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634497_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 35287 total values totalling 13822.0388. <0.391703 +/- 0.121956>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.34 - 0.345 ] 1472 counts
#Median bin: [ 0.35 - 0.355 ] 1410 counts
#Entropy = 5.8235 bits
| 0 - 0.005 : [ 15 4.25e-04 4.25e-04 15 ]
#...
| 0.025 - 0.03 : [ 1 2.83e-05 4.53e-04 16 ]
#...
| 0.04 - 0.045 : [ 1 2.83e-05 4.82e-04 17 ]
#...
| 0.07 - 0.075 : [ 2 5.67e-05 5.38e-04 19 ]
#...
| 0.085 - 0.09 : [ 1 2.83e-05 5.67e-04 20 ]
#...
| 0.095 - 0.1 : [ 1 2.83e-05 5.95e-04 21 ]
#...
| 0.105 - 0.11 : [ 1 2.83e-05 6.23e-04 22 ]
| 0.11 - 0.115 : [ 1 2.83e-05 6.52e-04 23 ]
| 0.115 - 0.12 : [ 3 8.50e-05 7.37e-04 26 ]
#...
| 0.125 - 0.13 : [ 1 2.83e-05 7.65e-04 27 ]
| 0.13 - 0.135 : [ 1 2.83e-05 7.93e-04 28 ]
| 0.135 - 0.14 : [ 2 5.67e-05 8.50e-04 30 ]
| 0.14 - 0.145 : [ 1 2.83e-05 8.79e-04 31 ]
| 0.145 - 0.15 : [ 1 2.83e-05 9.07e-04 32 ]
| 0.15 - 0.155 : [ 1 2.83e-05 9.35e-04 33 ]
| 0.155 - 0.16 : [ 2 5.67e-05 9.92e-04 35 ]
| 0.16 - 0.165 : [ 3 8.50e-05 1.08e-03 38 ]
| 0.165 - 0.17 : [ 1 2.83e-05 1.11e-03 39 ]
| 0.17 - 0.175 : [ 3 8.50e-05 1.19e-03 42 ]
| 0.175 - 0.18 : [ 3 8.50e-05 1.28e-03 45 ]
| 0.18 - 0.185 : [ 3 8.50e-05 1.36e-03 48 ]
| 0.185 - 0.19 : [ 1 2.83e-05 1.39e-03 49 ]
| 0.19 - 0.195 : [ 7 1.98e-04 1.59e-03 56 ]
| 0.195 - 0.2 : [ 1 2.83e-05 1.62e-03 57 ]
| 0.2 - 0.205 : [ 14 3.97e-04 2.01e-03 71 ]
| 0.205 - 0.21 : [ 8 2.27e-04 2.24e-03 79 ]
| 0.21 - 0.215 : [ 4 1.13e-04 2.35e-03 83 ]
| 0.215 - 0.22 : [ 15 4.25e-04 2.78e-03 98 ]
| 0.22 - 0.225 : [ 7 1.98e-04 2.98e-03 105 ]
|X 0.225 - 0.23 : [ 19 5.38e-04 3.51e-03 124 ]
|X 0.23 - 0.235 : [ 24 6.80e-04 4.19e-03 148 ]
|X 0.235 - 0.24 : [ 42 1.19e-03 5.38e-03 190 ]
|X 0.24 - 0.245 : [ 33 9.35e-04 6.32e-03 223 ]
|X 0.245 - 0.25 : [ 48 1.36e-03 7.68e-03 271 ]
|XXXX 0.25 - 0.255 : [ 135 3.83e-03 1.15e-02 406 ]
|XXXX 0.255 - 0.26 : [ 135 3.83e-03 1.53e-02 541 ]
|XXXXX 0.26 - 0.265 : [ 167 4.73e-03 2.01e-02 708 ]
|XXXXXX 0.265 - 0.27 : [ 212 6.01e-03 2.61e-02 920 ]
|XXXXXXXXX 0.27 - 0.275 : [ 333 9.44e-03 3.55e-02 1253 ]
|XXXXXXXXXXXX 0.275 - 0.28 : [ 432 1.22e-02 4.78e-02 1685 ]
|XXXXXXXXXXXXXX 0.28 - 0.285 : [ 523 1.48e-02 6.26e-02 2208 ]
|XXXXXXXXXXXXXXXXX 0.285 - 0.29 : [ 635 1.80e-02 8.06e-02 2843 ]
|XXXXXXXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 755 2.14e-02 1.02e-01 3598 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.295 - 0.3 : [ 811 2.30e-02 1.25e-01 4409 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 919 2.60e-02 1.51e-01 5328 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 1026 2.91e-02 1.80e-01 6354 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 1126 3.19e-02 2.12e-01 7480 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 1207 3.42e-02 2.46e-01 8687 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 1363 3.86e-02 2.85e-01 10050 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 1426 4.04e-02 3.25e-01 11476 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 1451 4.11e-02 3.66e-01 12927 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 1410 4.00e-02 4.06e-01 14337 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 1472 4.17e-02 4.48e-01 15809 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 1447 4.10e-02 4.89e-01 17256 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 1410 4.00e-02 5.29e-01 18666 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 1380 3.91e-02 5.68e-01 20046 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 1272 3.60e-02 6.04e-01 21318 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 1131 3.21e-02 6.36e-01 22449 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 1056 2.99e-02 6.66e-01 23505 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 983 2.79e-02 6.94e-01 24488 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 831 2.35e-02 7.18e-01 25319 ]
|XXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 764 2.17e-02 7.39e-01 26083 ]
|XXXXXXXXXXXXXXX 0.39 - 0.395 : [ 546 1.55e-02 7.55e-01 26629 ]
|XXXXXXXXXXXX 0.395 - 0.4 : [ 452 1.28e-02 7.67e-01 27081 ]
|XXXXXXXXXXXXX 0.4 - 0.405 : [ 462 1.31e-02 7.81e-01 27543 ]
|XXXXXXXXX 0.405 - 0.41 : [ 340 9.64e-03 7.90e-01 27883 ]
|XXXXXXX 0.41 - 0.415 : [ 258 7.31e-03 7.97e-01 28141 ]
|XXXXXXX 0.415 - 0.42 : [ 243 6.89e-03 8.04e-01 28384 ]
|XXXXX 0.42 - 0.425 : [ 191 5.41e-03 8.10e-01 28575 ]
|XXXXX 0.425 - 0.43 : [ 172 4.87e-03 8.15e-01 28747 ]
|XXXX 0.43 - 0.435 : [ 152 4.31e-03 8.19e-01 28899 ]
|XXX 0.435 - 0.44 : [ 127 3.60e-03 8.23e-01 29026 ]
|XXX 0.44 - 0.445 : [ 99 2.81e-03 8.25e-01 29125 ]
|XX 0.445 - 0.45 : [ 76 2.15e-03 8.28e-01 29201 ]
|X 0.45 - 0.455 : [ 53 1.50e-03 8.29e-01 29254 ]
|XX 0.455 - 0.46 : [ 64 1.81e-03 8.31e-01 29318 ]
|XX 0.46 - 0.465 : [ 63 1.79e-03 8.33e-01 29381 ]
|XX 0.465 - 0.47 : [ 57 1.62e-03 8.34e-01 29438 ]
|X 0.47 - 0.475 : [ 55 1.56e-03 8.36e-01 29493 ]
|X 0.475 - 0.48 : [ 55 1.56e-03 8.37e-01 29548 ]
|XX 0.48 - 0.485 : [ 59 1.67e-03 8.39e-01 29607 ]
|X 0.485 - 0.49 : [ 54 1.53e-03 8.41e-01 29661 ]
|X 0.49 - 0.495 : [ 38 1.08e-03 8.42e-01 29699 ]
|X 0.495 - 0.5 : [ 31 8.79e-04 8.43e-01 29730 ]
|XX 0.5 - 0.505 : [ 62 1.76e-03 8.44e-01 29792 ]
|X 0.505 - 0.51 : [ 49 1.39e-03 8.46e-01 29841 ]
|X 0.51 - 0.515 : [ 39 1.11e-03 8.47e-01 29880 ]
|X 0.515 - 0.52 : [ 49 1.39e-03 8.48e-01 29929 ]
|X 0.52 - 0.525 : [ 34 9.64e-04 8.49e-01 29963 ]
|X 0.525 - 0.53 : [ 40 1.13e-03 8.50e-01 30003 ]
|X 0.53 - 0.535 : [ 46 1.30e-03 8.52e-01 30049 ]
|X 0.535 - 0.54 : [ 55 1.56e-03 8.53e-01 30104 ]
|X 0.54 - 0.545 : [ 46 1.30e-03 8.54e-01 30150 ]
|XX 0.545 - 0.55 : [ 70 1.98e-03 8.56e-01 30220 ]
|XX 0.55 - 0.555 : [ 91 2.58e-03 8.59e-01 30311 ]
|XX 0.555 - 0.56 : [ 73 2.07e-03 8.61e-01 30384 ]
|XX 0.56 - 0.565 : [ 83 2.35e-03 8.63e-01 30467 ]
|XX 0.565 - 0.57 : [ 80 2.27e-03 8.66e-01 30547 ]
|XX 0.57 - 0.575 : [ 65 1.84e-03 8.68e-01 30612 ]
|XX 0.575 - 0.58 : [ 69 1.96e-03 8.69e-01 30681 ]
|XX 0.58 - 0.585 : [ 62 1.76e-03 8.71e-01 30743 ]
|X 0.585 - 0.59 : [ 51 1.45e-03 8.73e-01 30794 ]
|XX 0.59 - 0.595 : [ 65 1.84e-03 8.75e-01 30859 ]
|X 0.595 - 0.6 : [ 47 1.33e-03 8.76e-01 30906 ]
|XX 0.6 - 0.605 : [ 70 1.98e-03 8.78e-01 30976 ]
|XX 0.605 - 0.61 : [ 77 2.18e-03 8.80e-01 31053 ]
|XX 0.61 - 0.615 : [ 69 1.96e-03 8.82e-01 31122 ]
|XX 0.615 - 0.62 : [ 92 2.61e-03 8.85e-01 31214 ]
|XX 0.62 - 0.625 : [ 83 2.35e-03 8.87e-01 31297 ]
|XXX 0.625 - 0.63 : [ 113 3.20e-03 8.90e-01 31410 ]
|XXXX 0.63 - 0.635 : [ 132 3.74e-03 8.94e-01 31542 ]
|XXXX 0.635 - 0.64 : [ 147 4.17e-03 8.98e-01 31689 ]
|XXXX 0.64 - 0.645 : [ 161 4.56e-03 9.03e-01 31850 ]
|XXXXX 0.645 - 0.65 : [ 185 5.24e-03 9.08e-01 32035 ]
|XXXXX 0.65 - 0.655 : [ 180 5.10e-03 9.13e-01 32215 ]
|XXXXX 0.655 - 0.66 : [ 195 5.53e-03 9.18e-01 32410 ]
|XXXXXX 0.66 - 0.665 : [ 203 5.75e-03 9.24e-01 32613 ]
|XXXXX 0.665 - 0.67 : [ 200 5.67e-03 9.30e-01 32813 ]
|XXXXXX 0.67 - 0.675 : [ 235 6.66e-03 9.37e-01 33048 ]
|XXXXXX 0.675 - 0.68 : [ 223 6.32e-03 9.43e-01 33271 ]
|XXXXXX 0.68 - 0.685 : [ 203 5.75e-03 9.49e-01 33474 ]
|XXXXXX 0.685 - 0.69 : [ 207 5.87e-03 9.54e-01 33681 ]
|XXXXXXX 0.69 - 0.695 : [ 249 7.06e-03 9.62e-01 33930 ]
|XXXXXX 0.695 - 0.7 : [ 210 5.95e-03 9.67e-01 34140 ]
|XXXXX 0.7 - 0.705 : [ 188 5.33e-03 9.73e-01 34328 ]
|XXXXX 0.705 - 0.71 : [ 169 4.79e-03 9.78e-01 34497 ]
|XXXX 0.71 - 0.715 : [ 135 3.83e-03 9.81e-01 34632 ]
|XXX 0.715 - 0.72 : [ 115 3.26e-03 9.85e-01 34747 ]
|XX 0.72 - 0.725 : [ 91 2.58e-03 9.87e-01 34838 ]
|XXX 0.725 - 0.73 : [ 102 2.89e-03 9.90e-01 34940 ]
|XX 0.73 - 0.735 : [ 78 2.21e-03 9.92e-01 35018 ]
|X 0.735 - 0.74 : [ 50 1.42e-03 9.94e-01 35068 ]
|X 0.74 - 0.745 : [ 37 1.05e-03 9.95e-01 35105 ]
|X 0.745 - 0.75 : [ 20 5.67e-04 9.95e-01 35125 ]
|X 0.75 - 0.755 : [ 27 7.65e-04 9.96e-01 35152 ]
|X 0.755 - 0.76 : [ 24 6.80e-04 9.97e-01 35176 ]
| 0.76 - 0.765 : [ 13 3.68e-04 9.97e-01 35189 ]
| 0.765 - 0.77 : [ 7 1.98e-04 9.97e-01 35196 ]
| 0.77 - 0.775 : [ 9 2.55e-04 9.98e-01 35205 ]
| 0.775 - 0.78 : [ 5 1.42e-04 9.98e-01 35210 ]
| 0.78 - 0.785 : [ 11 3.12e-04 9.98e-01 35221 ]
| 0.785 - 0.79 : [ 4 1.13e-04 9.98e-01 35225 ]
| 0.79 - 0.795 : [ 3 8.50e-05 9.98e-01 35228 ]
| 0.795 - 0.8 : [ 2 5.67e-05 9.98e-01 35230 ]
| 0.8 - 0.805 : [ 6 1.70e-04 9.99e-01 35236 ]
| 0.805 - 0.81 : [ 4 1.13e-04 9.99e-01 35240 ]
| 0.81 - 0.815 : [ 8 2.27e-04 9.99e-01 35248 ]
| 0.815 - 0.82 : [ 4 1.13e-04 9.99e-01 35252 ]
| 0.82 - 0.825 : [ 5 1.42e-04 9.99e-01 35257 ]
| 0.825 - 0.83 : [ 5 1.42e-04 9.99e-01 35262 ]
| 0.83 - 0.835 : [ 2 5.67e-05 9.99e-01 35264 ]
| 0.835 - 0.84 : [ 1 2.83e-05 9.99e-01 35265 ]
| 0.84 - 0.845 : [ 1 2.83e-05 9.99e-01 35266 ]
| 0.845 - 0.85 : [ 2 5.67e-05 9.99e-01 35268 ]
| 0.85 - 0.855 : [ 2 5.67e-05 1.00e+00 35270 ]
| 0.855 - 0.86 : [ 1 2.83e-05 1.00e+00 35271 ]
| 0.86 - 0.865 : [ 1 2.83e-05 1.00e+00 35272 ]
| 0.865 - 0.87 : [ 1 2.83e-05 1.00e+00 35273 ]
| 0.87 - 0.875 : [ 1 2.83e-05 1.00e+00 35274 ]
| 0.875 - 0.88 : [ 1 2.83e-05 1.00e+00 35275 ]
#...
| 0.89 - 0.895 : [ 2 5.67e-05 1.00e+00 35277 ]
| 0.895 - 0.9 : [ 1 2.83e-05 1.00e+00 35278 ]
#...
| 0.905 - 0.91 : [ 1 2.83e-05 1.00e+00 35279 ]
#...
| 0.915 - 0.92 : [ 3 8.50e-05 1.00e+00 35282 ]
#...
| 0.955 - 0.96 : [ 1 2.83e-05 1.00e+00 35283 ]
#...
| 0.965 - 0.97 : [ 1 2.83e-05 1.00e+00 35284 ]
#...
| 1 - 1.005 : [ 3 8.50e-05 1.00e+00 35287 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 1656. 393 reads; 30371 bp (untrimmed), 30338 (trimmed).
Contig 1657. 412 reads; 30286 bp (untrimmed), 30213 (trimmed).
Contig 1658. 418 reads; 44642 bp (untrimmed), 44585 (trimmed).
Contig 1659. 441 reads; 31600 bp (untrimmed), 31504 (trimmed).
Contig 1660. 456 reads; 32259 bp (untrimmed), 32156 (trimmed).
Contig 1661. 456 reads; 34007 bp (untrimmed), 33796 (trimmed).
Contig 1662. 479 reads; 30244 bp (untrimmed), 30160 (trimmed).
Contig 1663. 494 reads; 31448 bp (untrimmed), 31352 (trimmed).
Contig 1664. 494 reads; 34328 bp (untrimmed), 34172 (trimmed).
Contig 1665. 532 reads; 45771 bp (untrimmed), 45477 (trimmed).
Contig 1666. 551 reads; 34694 bp (untrimmed), 34600 (trimmed).
Contig 1667. 558 reads; 41455 bp (untrimmed), 41314 (trimmed).
Contig 1668. 588 reads; 44871 bp (untrimmed), 44778 (trimmed).
Contig 1669. 589 reads; 45448 bp (untrimmed), 45360 (trimmed).
Contig 1670. 736 reads; 44090 bp (untrimmed), 43961 (trimmed).
Contig 1671. 776 reads; 64576 bp (untrimmed), 64532 (trimmed).
Contig 1672. 803 reads; 47909 bp (untrimmed), 47719 (trimmed).
Contig 1673. 832 reads; 69586 bp (untrimmed), 69478 (trimmed).
Contig 1674. 889 reads; 56412 bp (untrimmed), 56344 (trimmed).
Contig 1675. 893 reads; 58277 bp (untrimmed), 58239 (trimmed).
Contig 1676. 980 reads; 66496 bp (untrimmed), 66470 (trimmed).
Contig 1677. 983 reads; 60576 bp (untrimmed), 60486 (trimmed).
Contig 1678. 1142 reads; 54143 bp (untrimmed), 53994 (trimmed).
Contig 1679. 1232 reads; 64450 bp (untrimmed), 64408 (trimmed).
Contig 1680. 1538 reads; 104679 bp (untrimmed), 104604 (trimmed).
Contig 1681. 1578 reads; 101833 bp (untrimmed), 101819 (trimmed).
Contig 1682. 1911 reads; 131553 bp (untrimmed), 131422 (trimmed).
--------------------------------------------------------------
Totals 33268 reads; 4253035 bp (untrimmed), 3701503 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3890718 bases = 7.21 +- 6.76 = 0.58 +- 4.69
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 1242 total values totalling 2844.9000. <2.290580 +/- 2.580955>
#Range: [ 1.04 - 31.66 ]
#Most likely bin: [ 1 - 1.5 ] 503 counts
#Median bin: [ 1.5 - 2 ] 444 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 503 0.40 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 444 0.36 0.76 ]
|XXXXXXXXXX 2 - 2.5 : [ 129 0.10 0.87 ]
|XXX 2.5 - 3 : [ 39 0.03 0.90 ]
|XX 3 - 3.5 : [ 22 0.02 0.92 ]
| 3.5 - 4 : [ 6 0.00 0.92 ]
|X 4 - 4.5 : [ 7 0.01 0.93 ]
| 4.5 - 5 : [ 5 0.00 0.93 ]
| 5 - 5.5 : [ 6 0.00 0.93 ]
| 5.5 - 6 : [ 6 0.00 0.94 ]
|X 6 - 6.5 : [ 7 0.01 0.95 ]
| 6.5 - 7 : [ 2 0.00 0.95 ]
| 7 - 7.5 : [ 2 0.00 0.95 ]
| 7.5 - 8 : [ 6 0.00 0.95 ]
| 8 - 8.5 : [ 5 0.00 0.96 ]
| 8.5 - 9 : [ 2 0.00 0.96 ]
| 9 - 9.5 : [ 2 0.00 0.96 ]
| 9.5 - 10 : [ 4 0.00 0.96 ]
|X 10 - 10.5 : [ 7 0.01 0.97 ]
| 10.5 - 11 : [ 5 0.00 0.97 ]
| 11 - 11.5 : [ 4 0.00 0.98 ]
| 11.5 - 12 : [ 5 0.00 0.98 ]
| 12 - 12.5 : [ 3 0.00 0.98 ]
| 12.5 - 13 : [ 3 0.00 0.99 ]
| 13 - 13.5 : [ 4 0.00 0.99 ]
| 13.5 - 14 : [ 5 0.00 0.99 ]
#...
| 14.5 - 15 : [ 3 0.00 1.00 ]
#...
| 16 - 16.5 : [ 1 0.00 1.00 ]
#...
| 17 - 17.5 : [ 1 0.00 1.00 ]
#...
| 18 - 18.5 : [ 1 0.00 1.00 ]
#...
| 19 - 19.5 : [ 1 0.00 1.00 ]
#...
| 31 - 31.5 : [ 1 0.00 1.00 ]
| 31.5 - 32 : [ 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 106 total values totalling 926.8100. <8.743491 +/- 4.371429>
#Range: [ 2.40 - 31.14 ]
#Most likely bin: [ 3 - 3.5 ] 8 counts
#Median bin: [ 8 - 8.5 ] 5 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 2 - 2.5 : [ 1 0.01 0.01 ]
|XXXXXXXXXX 2.5 - 3 : [ 2 0.02 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 8 0.08 0.10 ]
|XXXXX 3.5 - 4 : [ 1 0.01 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 7 0.07 0.18 ]
|XXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 4 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 5 0.05 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 6 0.06 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 7 0.07 0.39 ]
|XXXXXXXXXX 6.5 - 7 : [ 2 0.02 0.41 ]
|XXXXX 7 - 7.5 : [ 1 0.01 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 6 0.06 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 5 0.05 0.52 ]
|XXXXXXXXXX 8.5 - 9 : [ 2 0.02 0.54 ]
|XXXXXXXXXX 9 - 9.5 : [ 2 0.02 0.56 ]
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 4 0.04 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 7 0.07 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 5 0.05 0.71 ]
|XXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 5 0.05 0.79 ]
|XXXXXXXXXXXXXXX 12 - 12.5 : [ 3 0.03 0.82 ]
|XXXXXXXXXXXXXXX 12.5 - 13 : [ 3 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 4 0.04 0.89 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 5 0.05 0.93 ]
#...
|XXXXXXXXXXXXXXX 14.5 - 15 : [ 3 0.03 0.96 ]
#...
|XXXXX 16 - 16.5 : [ 1 0.01 0.97 ]
#...
|XXXXX 18 - 18.5 : [ 1 0.01 0.98 ]
#...
|XXXXX 19 - 19.5 : [ 1 0.01 0.99 ]
#...
|XXXXX 31 - 31.5 : [ 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 1051 2 reads 1597 bases = 1.04 +- 0.20 = 1.04 +- 0.20
Contig 1073 2 reads 2203 bases = 1.04 +- 0.20 = -0.13 +- 0.97
Contig 549 2 reads 1908 bases = 1.04 +- 0.20 = -0.05 +- 0.98
Contig 879 2 reads 1816 bases = 1.04 +- 0.21 = -0.03 +- 0.98
Contig 980 2 reads 1926 bases = 1.04 +- 0.19 = -0.01 +- 0.98
Contig 1029 2 reads 1839 bases = 1.05 +- 0.23 = 1.05 +- 0.23
Contig 547 2 reads 1820 bases = 1.06 +- 0.24 = 0.00 +- 0.97
Contig 594 2 reads 1789 bases = 1.06 +- 0.24 = -0.02 +- 0.97
Contig 895 2 reads 1807 bases = 1.06 +- 0.23 = 0.01 +- 0.97
Contig 1011 2 reads 1842 bases = 1.07 +- 0.25 = 0.04 +- 0.96
Contig 517 2 reads 1685 bases = 1.07 +- 0.26 = 0.06 +- 0.96
Contig 937 2 reads 1640 bases = 1.07 +- 0.26 = 1.07 +- 0.26
Contig 659 2 reads 2022 bases = 1.08 +- 0.27 = -0.10 +- 0.95
Contig 978 2 reads 1774 bases = 1.08 +- 0.28 = -0.07 +- 0.95
Contig 1050 2 reads 1743 bases = 1.09 +- 0.29 = 1.09 +- 0.29
Contig 506 2 reads 2103 bases = 1.09 +- 0.29 = 0.15 +- 0.94
Contig 509 2 reads 1584 bases = 1.09 +- 0.29 = 1.09 +- 0.29
Contig 588 2 reads 1727 bases = 1.09 +- 0.29 = -0.02 +- 0.95
Contig 751 2 reads 1756 bases = 1.09 +- 0.28 = 0.01 +- 0.96
Contig 772 2 reads 1828 bases = 1.09 +- 0.29 = -0.02 +- 0.95
Contig 1680 1538 reads 104679 bases = 12.65 +- 5.07 = -0.19 +- 5.37
Contig 1682 1911 reads 131553 bases = 12.66 +- 5.44 = -0.08 +- 4.61
Contig 1616 73 reads 5171 bases = 13.04 +- 8.79 = 9.53 +- 5.69
Contig 1650 309 reads 20771 bases = 13.07 +- 6.59 = -0.32 +- 7.46
Contig 1681 1578 reads 101833 bases = 13.39 +- 5.52 = -0.53 +- 5.67
Contig 1675 893 reads 58277 bases = 13.47 +- 5.27 = 0.58 +- 4.69
Contig 1663 494 reads 31448 bases = 13.52 +- 6.74 = -0.37 +- 7.91
Contig 1662 479 reads 30244 bases = 13.75 +- 4.86 = 1.13 +- 4.54
Contig 1674 889 reads 56412 bases = 13.75 +- 5.63 = 0.09 +- 5.35
Contig 1677 983 reads 60576 bases = 13.96 +- 4.52 = 0.14 +- 5.02
Contig 1666 551 reads 34694 bases = 13.97 +- 4.39 = 0.03 +- 5.81
Contig 1670 736 reads 44090 bases = 14.54 +- 6.51 = 0.16 +- 7.12
Contig 1627 112 reads 5890 bases = 14.58 +- 15.56 = 14.58 +- 15.56
Contig 1672 803 reads 47909 bases = 14.60 +- 5.80 = -0.03 +- 5.27
Contig 1679 1232 reads 64450 bases = 16.42 +- 4.75 = 1.13 +- 5.39
Contig 1598 32 reads 1683 bases = 17.42 +- 11.04 = 17.42 +- 11.04
Contig 1678 1142 reads 54143 bases = 18.01 +- 8.56 = -0.06 +- 6.71
Contig 1604 44 reads 2115 bases = 19.00 +- 15.49 = 0.56 +- 2.63
Contig 1649 308 reads 8192 bases = 31.14 +- 31.16 = 31.14 +- 31.16
Contig 1605 46 reads 990 bases = 31.66 +- 14.21 = 31.66 +- 14.21
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 993
HQ Discrepant reads = 363
Chimeric reads = 56
Suspect alignments = 361
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 4.18 SUN Solaris 7,8
Score matrix /psf/QC/Applications/pphrap/matrix/score_matrix
A C G T N X
A 1 -2 -2 -2 0 0
C -2 1 -2 -2 0 0
G -2 -2 1 -2 0 0
T -2 -2 -2 1 0 0
N 0 0 0 0 0 0
X 0 0 0 0 0 0
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
File generated in /psf/project/microbe2/3634497/edit_dir.02Nov05.QC