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
3634492 2400 1663 Arthrobacter sp.
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Arthrobacter_sp.
-------------------------------------------------------------------
Actinobacteria, phylum, actinobacteria
Micrococcineae, suborder, high GC Gram+
Actinobacteridae, subclass, high GC Gram+
Actinomycetales, order, high GC Gram+
Actinobacteria (class) (high G+C Gram-positive bacteria), class, high GC Gram+
Arthrobacter sp., species, high GC Gram+
Arthrobacter, genus, high GC Gram+
Micrococcaceae, family, high GC Gram+
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 5001639
# phrap: 4904706
# db:
altered.
2400000
4102115 +/- 1204227
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 13202
Number of reads with percent X's >= 20%: 220 = 0.3%
Number of reads with percent X's >= 50%: 122 = 0.2%
Number of reads with percent X's >= 80%: 15 = 0.0%
Total reads in project: 76909
Total bp X'd : 590073
reads >= 20% >= 50% >= 80% screened
Nr with L09136 12394 165 97 11
Nr with pCC1Fos 718 1 0 0
Nr with pMCL200_JGI_XZX+XZK 90 54 25 4
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 8
Number of reads with percent X's >= 20%: 3 = 7.1%
Number of reads with percent X's >= 50%: 2 = 4.8%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 42
Total bp X'd : 1958
reads >= 20% >= 50% >= 80% screened
Nr with pCC1Fos 5 0 0 0
Nr with pMCL200_JGI_XZX+XZK 3 3 2 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 13298105
C = 23899618
G = 24170415
T = 12926634
N = 386433
X = 590073
GC fraction = 0.64
Total = 75271278
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634492_fasta.screen.contigs
-------------------------------------------------------------------
A 862849
C 1641448
G 1636224
T 870886
N 192
fraction GC = 0.65
total bases = 5011599
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 AOWA reads.list > grep.reads.list.AOWA
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOWA 4 500
-------------------------------------------------------------------
#Found 15581 total values totalling 116847676.0000. <7499.369488 +/- 11317.626537>
#Range: [ 855 - 677334 ]
#Most likely bin: [ 7000 - 7500 ] 5418 counts
#Median bin: [ 7000 - 7500 ] 5418 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
| 1000 - 1500 : [ 11 0.00 0.00 ]
| 1500 - 2000 : [ 20 0.00 0.00 ]
| 2000 - 2500 : [ 20 0.00 0.00 ]
| 2500 - 3000 : [ 26 0.00 0.01 ]
| 3000 - 3500 : [ 31 0.00 0.01 ]
| 3500 - 4000 : [ 24 0.00 0.01 ]
| 4000 - 4500 : [ 26 0.00 0.01 ]
| 4500 - 5000 : [ 17 0.00 0.01 ]
| 5000 - 5500 : [ 20 0.00 0.01 ]
| 5500 - 6000 : [ 55 0.00 0.02 ]
|XXXX 6000 - 6500 : [ 530 0.03 0.05 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 5199 0.33 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 5418 0.35 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 3080 0.20 0.93 ]
|XXXXXXXX 8000 - 8500 : [ 1052 0.07 1.00 ]
| 8500 - 9000 : [ 26 0.00 1.00 ]
| 9000 - 9500 : [ 1 0.00 1.00 ]
#...
| 17500 - 18000 : [ 1 0.00 1.00 ]
#...
| 34000 - 34500 : [ 1 0.00 1.00 ]
#...
| 47500 - 48000 : [ 1 0.00 1.00 ]
#...
| 50500 - 51000 : [ 1 0.00 1.00 ]
#...
| 69000 - 69500 : [ 1 0.00 1.00 ]
#...
| 103500 - 104000 : [ 1 0.00 1.00 ]
#...
| 107500 - 108000 : [ 1 0.00 1.00 ]
#...
| 116000 - 116500 : [ 1 0.00 1.00 ]
#...
| 123500 - 124000 : [ 1 0.00 1.00 ]
#...
| 132000 - 132500 : [ 1 0.00 1.00 ]
#...
| 175500 - 176000 : [ 1 0.00 1.00 ]
#...
| 198000 - 198500 : [ 1 0.00 1.00 ]
#...
| 217500 - 218000 : [ 1 0.00 1.00 ]
#...
| 245000 - 245500 : [ 1 0.00 1.00 ]
#...
| 256500 - 257000 : [ 1 0.00 1.00 ]
#...
| 266500 - 267000 : [ 1 0.00 1.00 ]
#...
| 287500 - 288000 : [ 1 0.00 1.00 ]
#...
| 345500 - 346000 : [ 1 0.00 1.00 ]
#...
| 346500 - 347000 : [ 1 0.00 1.00 ]
#...
| 444000 - 444500 : [ 1 0.00 1.00 ]
#...
| 540500 - 541000 : [ 1 0.00 1.00 ]
#...
| 633500 - 634000 : [ 1 0.00 1.00 ]
#...
| 677000 - 677500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAX reads.list > grep.reads.list.AIAX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAX 4 500
-------------------------------------------------------------------
#Found 12851 total values totalling 53833866.0000. <4189.079916 +/- 13710.288780>
#Range: [ 755 - 740147 ]
#Most likely bin: [ 3500 - 4000 ] 4728 counts
#Median bin: [ 3500 - 4000 ] 4728 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 7 0.00 0.00 ]
| 1000 - 1500 : [ 37 0.00 0.00 ]
|X 1500 - 2000 : [ 61 0.00 0.01 ]
|X 2000 - 2500 : [ 67 0.01 0.01 ]
|XX 2500 - 3000 : [ 281 0.02 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4505 0.35 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 4728 0.37 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 2597 0.20 0.96 ]
|XXXX 4500 - 5000 : [ 521 0.04 1.00 ]
| 5000 - 5500 : [ 15 0.00 1.00 ]
#...
| 11500 - 12000 : [ 1 0.00 1.00 ]
#...
| 15500 - 16000 : [ 1 0.00 1.00 ]
#...
| 19500 - 20000 : [ 1 0.00 1.00 ]
#...
| 43500 - 44000 : [ 1 0.00 1.00 ]
#...
| 58000 - 58500 : [ 1 0.00 1.00 ]
#...
| 60000 - 60500 : [ 1 0.00 1.00 ]
#...
| 70500 - 71000 : [ 1 0.00 1.00 ]
#...
| 74000 - 74500 : [ 1 0.00 1.00 ]
#...
| 91000 - 91500 : [ 1 0.00 1.00 ]
#...
| 96500 - 97000 : [ 1 0.00 1.00 ]
#...
| 99500 - 100000 : [ 1 0.00 1.00 ]
#...
| 103000 - 103500 : [ 1 0.00 1.00 ]
#...
| 134000 - 134500 : [ 1 0.00 1.00 ]
#...
| 136500 - 137000 : [ 2 0.00 1.00 ]
#...
| 141500 - 142000 : [ 1 0.00 1.00 ]
#...
| 169000 - 169500 : [ 1 0.00 1.00 ]
#...
| 202500 - 203000 : [ 1 0.00 1.00 ]
#...
| 210500 - 211000 : [ 1 0.00 1.00 ]
#...
| 223000 - 223500 : [ 1 0.00 1.00 ]
#...
| 234000 - 234500 : [ 1 0.00 1.00 ]
#...
| 256000 - 256500 : [ 1 0.00 1.00 ]
#...
| 263500 - 264000 : [ 1 0.00 1.00 ]
#...
| 297500 - 298000 : [ 1 0.00 1.00 ]
#...
| 298500 - 299000 : [ 1 0.00 1.00 ]
#...
| 313500 - 314000 : [ 1 0.00 1.00 ]
#...
| 321000 - 321500 : [ 1 0.00 1.00 ]
#...
| 324000 - 324500 : [ 1 0.00 1.00 ]
#...
| 436000 - 436500 : [ 1 0.00 1.00 ]
#...
| 549500 - 550000 : [ 1 0.00 1.00 ]
#...
| 672500 - 673000 : [ 1 0.00 1.00 ]
#...
| 740000 - 740500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAY reads.list > grep.reads.list.AIAY
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAY 4 500
-------------------------------------------------------------------
#Found 2616 total values totalling 20324043.0000. <7769.129587 +/- 12913.428476>
#Range: [ 235 - 480416 ]
#Most likely bin: [ 7000 - 7500 ] 586 counts
#Median bin: [ 7000 - 7500 ] 586 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 3 0.00 0.00 ]
| 500 - 1000 : [ 1 0.00 0.00 ]
|X 1000 - 1500 : [ 9 0.00 0.00 ]
|X 1500 - 2000 : [ 12 0.00 0.01 ]
|X 2000 - 2500 : [ 10 0.00 0.01 ]
|X 2500 - 3000 : [ 10 0.00 0.02 ]
|X 3000 - 3500 : [ 11 0.00 0.02 ]
|X 3500 - 4000 : [ 16 0.01 0.03 ]
|X 4000 - 4500 : [ 12 0.00 0.03 ]
|X 4500 - 5000 : [ 14 0.01 0.04 ]
|X 5000 - 5500 : [ 18 0.01 0.04 ]
|XXX 5500 - 6000 : [ 49 0.02 0.06 ]
|XXXXXXXXXXXXXXXX 6000 - 6500 : [ 237 0.09 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 498 0.19 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 586 0.22 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 520 0.20 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 359 0.14 0.90 ]
|XXXXXXXXXXXX 8500 - 9000 : [ 169 0.06 0.97 ]
|XXXXX 9000 - 9500 : [ 74 0.03 1.00 ]
| 9500 - 10000 : [ 1 0.00 1.00 ]
#...
| 18000 - 18500 : [ 1 0.00 1.00 ]
#...
| 36500 - 37000 : [ 1 0.00 1.00 ]
#...
| 131000 - 131500 : [ 1 0.00 1.00 ]
#...
| 144500 - 145000 : [ 1 0.00 1.00 ]
#...
| 252000 - 252500 : [ 1 0.00 1.00 ]
#...
| 345000 - 345500 : [ 1 0.00 1.00 ]
#...
| 480000 - 480500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAZ reads.list > grep.reads.list.AIAZ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAZ 4 500
-------------------------------------------------------------------
#Found 722 total values totalling 28150011.0000. <38988.934903 +/- 3343.073278>
#Range: [ 22451 - 46236 ]
#Most likely bin: [ 40500 - 41000 ] 50 counts
#Median bin: [ 39000 - 39500 ] 38 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 22000 - 22500 : [ 1 0.00 0.00 ]
#...
|X 28000 - 28500 : [ 1 0.00 0.00 ]
|XX 28500 - 29000 : [ 3 0.00 0.01 ]
#...
|X 30000 - 30500 : [ 1 0.00 0.01 ]
#...
|XX 31000 - 31500 : [ 3 0.00 0.01 ]
|XXX 31500 - 32000 : [ 4 0.01 0.02 ]
|XX 32000 - 32500 : [ 2 0.00 0.02 ]
|XXXXXX 32500 - 33000 : [ 8 0.01 0.03 ]
|XXXXXXXXXX 33000 - 33500 : [ 12 0.02 0.05 ]
|XXXXXXXXXX 33500 - 34000 : [ 12 0.02 0.07 ]
|XXXXXXX 34000 - 34500 : [ 9 0.01 0.08 ]
|XXXXXXXXXXXXXXXX 34500 - 35000 : [ 20 0.03 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 29 0.04 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 33 0.05 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 29 0.04 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 38 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 45 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 36 0.05 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 39 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 31 0.04 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 38 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 37 0.05 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 37 0.05 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 50 0.07 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 27 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 31 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 25 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 29 0.04 0.87 ]
|XXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 25 0.03 0.91 ]
|XXXXXXXXXXXXX 43500 - 44000 : [ 16 0.02 0.93 ]
|XXXXXXXXXXXXXX 44000 - 44500 : [ 17 0.02 0.95 ]
|XXXXXXXXXXXXXX 44500 - 45000 : [ 17 0.02 0.98 ]
|XXXXXXXX 45000 - 45500 : [ 10 0.01 0.99 ]
|XXXXX 45500 - 46000 : [ 6 0.01 1.00 ]
|X 46000 - 46500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIAZ 38759 +- 3222 (n=345)
# AOWA 7110 +- 774 (n=7759)
# AIAY 7186 +- 1485 (n=1286)
# AIAX 3543 +- 540 (n=6553)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634492_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
AIAX 35712 -1 -1 95 686 1329 88 696 90 709
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIAX 671 87 683 90 699 658 88 709 90 720
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634492_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
192 35321 17827 92.85 96.72 AOWA @
184 32853 16740 90.98 94.77 AIAX @
40 6252 3372 84.30 87.81 AIAY @
16 2483 1455 90.94 94.73 AIAZ @
] 76909 39394 91.19 cumulative total@@
LIBRARY PLATE ID COUNT [ AOWA 192 AIAX 184 AIAY 40 AIAZ 16 ] for 432 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 3634492_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 1329 total values totalling 811737.0000. <610.787810 +/- 259.801702>
#Range: [ 0 - 882 ]
#Most likely bin: [ 750 - 800 ] 360 counts
#Median bin: [ 700 - 750 ] 253 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXX 0 - 50 : [ 160 0.12 0.12 ]
| 50 - 100 : [ 4 0.00 0.12 ]
| 100 - 150 : [ 3 0.00 0.13 ]
|X 150 - 200 : [ 11 0.01 0.13 ]
|X 200 - 250 : [ 8 0.01 0.14 ]
|X 250 - 300 : [ 11 0.01 0.15 ]
|X 300 - 350 : [ 8 0.01 0.15 ]
|XX 350 - 400 : [ 21 0.02 0.17 ]
|XXX 400 - 450 : [ 27 0.02 0.19 ]
|XXX 450 - 500 : [ 24 0.02 0.21 ]
|XXX 500 - 550 : [ 23 0.02 0.23 ]
|XXXXX 550 - 600 : [ 48 0.04 0.26 ]
|XXXXXXX 600 - 650 : [ 67 0.05 0.31 ]
|XXXXXXXXXXXXXXXXX 650 - 700 : [ 149 0.11 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 253 0.19 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 360 0.27 0.89 ]
|XXXXXXXXXXXXXXX 800 - 850 : [ 139 0.10 0.99 ]
|X 850 - 900 : [ 13 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOWA
trimt JAZZ trim 15 readlength histogram for AIAX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAX 3634492_fasta.screen.trimQ15.SaF > reads.trim15.AIAX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAX.rl 2 50
-------------------------------------------------------------------
#Found 1329 total values totalling 811737.0000. <610.787810 +/- 259.801702>
#Range: [ 0 - 882 ]
#Most likely bin: [ 750 - 800 ] 360 counts
#Median bin: [ 700 - 750 ] 253 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXX 0 - 50 : [ 160 0.12 0.12 ]
| 50 - 100 : [ 4 0.00 0.12 ]
| 100 - 150 : [ 3 0.00 0.13 ]
|X 150 - 200 : [ 11 0.01 0.13 ]
|X 200 - 250 : [ 8 0.01 0.14 ]
|X 250 - 300 : [ 11 0.01 0.15 ]
|X 300 - 350 : [ 8 0.01 0.15 ]
|XX 350 - 400 : [ 21 0.02 0.17 ]
|XXX 400 - 450 : [ 27 0.02 0.19 ]
|XXX 450 - 500 : [ 24 0.02 0.21 ]
|XXX 500 - 550 : [ 23 0.02 0.23 ]
|XXXXX 550 - 600 : [ 48 0.04 0.26 ]
|XXXXXXX 600 - 650 : [ 67 0.05 0.31 ]
|XXXXXXXXXXXXXXXXX 650 - 700 : [ 149 0.11 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 253 0.19 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 360 0.27 0.89 ]
|XXXXXXXXXXXXXXX 800 - 850 : [ 139 0.10 0.99 ]
|X 850 - 900 : [ 13 0.01 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAY
trimt JAZZ trim 15 readlength histogram for AIAZ
trimt JAZZ trim 15 readlength histogram for AZOW
trimt JAZZ trim 15 readlength histogram for AZOX
trimt JAZZ trim 15 readlength histogram for AZOY
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634492
-------------------------------------------------------------------
AIAX.000001.000100 pUC18.fa LRS.fasta
AIAX.000101.000200 pUC18.fa LRS.fasta
AIAX.000201.000300 pUC18.fa LRS.fasta
AIAY.000001.000100 pMCL200.fa.4 LRS.fasta
AIAZ.000001.000100 pCC1Fos.fa LRS.fasta
AOWA.000001.000100 pMCL200.fa LRS.fasta
AOWA.000101.000200 pMCL200.fa LRS.fasta
AIAX.000001.000100 pUC18.fa LRS.fasta
AIAX.000101.000200 pUC18.fa LRS.fasta
AIAX.000201.000300 pUC18.fa LRS.fasta
AIAY.000001.000100 pMCL200.fa.4 LRS.fasta
AIAZ.000001.000100 pCC1Fos.fa LRS.fasta
AOWA.000001.000100 pMCL200.fa LRS.fasta
AOWA.000101.000200 pMCL200.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634492_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634492_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 76748 total values totalling 50136.9734. <0.653267 +/- 0.037807>
#Range: [ 0.2258 - 1 ]
#Most likely bin: [ 0.66 - 0.665 ] 4738 counts
#Median bin: [ 0.655 - 0.66 ] 4726 counts
| 0.225 - 0.23 : [ 1 0.00 0.00 ]
#...
| 0.35 - 0.355 : [ 1 0.00 0.00 ]
| 0.355 - 0.36 : [ 1 0.00 0.00 ]
#...
| 0.375 - 0.38 : [ 1 0.00 0.00 ]
#...
| 0.385 - 0.39 : [ 5 0.00 0.00 ]
#...
| 0.4 - 0.405 : [ 1 0.00 0.00 ]
| 0.405 - 0.41 : [ 1 0.00 0.00 ]
| 0.41 - 0.415 : [ 1 0.00 0.00 ]
| 0.415 - 0.42 : [ 5 0.00 0.00 ]
| 0.42 - 0.425 : [ 2 0.00 0.00 ]
| 0.425 - 0.43 : [ 3 0.00 0.00 ]
| 0.43 - 0.435 : [ 6 0.00 0.00 ]
| 0.435 - 0.44 : [ 2 0.00 0.00 ]
| 0.44 - 0.445 : [ 3 0.00 0.00 ]
| 0.445 - 0.45 : [ 6 0.00 0.00 ]
| 0.45 - 0.455 : [ 7 0.00 0.00 ]
| 0.455 - 0.46 : [ 7 0.00 0.00 ]
| 0.46 - 0.465 : [ 6 0.00 0.00 ]
| 0.465 - 0.47 : [ 6 0.00 0.00 ]
| 0.47 - 0.475 : [ 7 0.00 0.00 ]
| 0.475 - 0.48 : [ 13 0.00 0.00 ]
| 0.48 - 0.485 : [ 16 0.00 0.00 ]
| 0.485 - 0.49 : [ 16 0.00 0.00 ]
| 0.49 - 0.495 : [ 18 0.00 0.00 ]
| 0.495 - 0.5 : [ 8 0.00 0.00 ]
| 0.5 - 0.505 : [ 24 0.00 0.00 ]
| 0.505 - 0.51 : [ 23 0.00 0.00 ]
| 0.51 - 0.515 : [ 28 0.00 0.00 ]
| 0.515 - 0.52 : [ 51 0.00 0.00 ]
| 0.52 - 0.525 : [ 53 0.00 0.00 ]
|X 0.525 - 0.53 : [ 72 0.00 0.01 ]
|X 0.53 - 0.535 : [ 86 0.00 0.01 ]
|X 0.535 - 0.54 : [ 135 0.00 0.01 ]
|X 0.54 - 0.545 : [ 136 0.00 0.01 ]
|X 0.545 - 0.55 : [ 159 0.00 0.01 ]
|XX 0.55 - 0.555 : [ 230 0.00 0.01 ]
|XX 0.555 - 0.56 : [ 265 0.00 0.02 ]
|XXX 0.56 - 0.565 : [ 314 0.00 0.02 ]
|XXX 0.565 - 0.57 : [ 354 0.00 0.03 ]
|XXXX 0.57 - 0.575 : [ 487 0.01 0.03 ]
|XXXXX 0.575 - 0.58 : [ 548 0.01 0.04 ]
|XXXXXX 0.58 - 0.585 : [ 652 0.01 0.05 ]
|XXXXXX 0.585 - 0.59 : [ 717 0.01 0.06 ]
|XXXXXXX 0.59 - 0.595 : [ 851 0.01 0.07 ]
|XXXXXXXX 0.595 - 0.6 : [ 928 0.01 0.08 ]
|XXXXXXXXXX 0.6 - 0.605 : [ 1240 0.02 0.10 ]
|XXXXXXXXXXXX 0.605 - 0.61 : [ 1453 0.02 0.12 ]
|XXXXXXXXXXXXXX 0.61 - 0.615 : [ 1691 0.02 0.14 ]
|XXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1926 0.03 0.16 ]
|XXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 2290 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 2732 0.04 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 3151 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 3458 0.05 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 3914 0.05 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 4179 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 4445 0.06 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 4726 0.06 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 4738 0.06 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 4582 0.06 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 4358 0.06 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 4015 0.05 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 3401 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 3153 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 2590 0.03 0.89 ]
|XXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 2061 0.03 0.92 ]
|XXXXXXXXXXXXXXX 0.7 - 0.705 : [ 1725 0.02 0.94 ]
|XXXXXXXXXXX 0.705 - 0.71 : [ 1319 0.02 0.96 ]
|XXXXXXXX 0.71 - 0.715 : [ 995 0.01 0.97 ]
|XXXXXX 0.715 - 0.72 : [ 747 0.01 0.98 ]
|XXXX 0.72 - 0.725 : [ 480 0.01 0.99 ]
|XXX 0.725 - 0.73 : [ 308 0.00 0.99 ]
|XX 0.73 - 0.735 : [ 238 0.00 0.99 ]
|X 0.735 - 0.74 : [ 151 0.00 0.99 ]
|X 0.74 - 0.745 : [ 107 0.00 1.00 ]
|X 0.745 - 0.75 : [ 78 0.00 1.00 ]
|X 0.75 - 0.755 : [ 69 0.00 1.00 ]
| 0.755 - 0.76 : [ 39 0.00 1.00 ]
| 0.76 - 0.765 : [ 24 0.00 1.00 ]
| 0.765 - 0.77 : [ 20 0.00 1.00 ]
| 0.77 - 0.775 : [ 15 0.00 1.00 ]
| 0.775 - 0.78 : [ 16 0.00 1.00 ]
| 0.78 - 0.785 : [ 11 0.00 1.00 ]
| 0.785 - 0.79 : [ 11 0.00 1.00 ]
| 0.79 - 0.795 : [ 5 0.00 1.00 ]
| 0.795 - 0.8 : [ 3 0.00 1.00 ]
| 0.8 - 0.805 : [ 8 0.00 1.00 ]
| 0.805 - 0.81 : [ 5 0.00 1.00 ]
| 0.81 - 0.815 : [ 3 0.00 1.00 ]
| 0.815 - 0.82 : [ 1 0.00 1.00 ]
| 0.82 - 0.825 : [ 2 0.00 1.00 ]
| 0.825 - 0.83 : [ 2 0.00 1.00 ]
| 0.83 - 0.835 : [ 1 0.00 1.00 ]
| 0.835 - 0.84 : [ 1 0.00 1.00 ]
| 0.84 - 0.845 : [ 1 0.00 1.00 ]
| 0.845 - 0.85 : [ 1 0.00 1.00 ]
#...
| 0.865 - 0.87 : [ 1 0.00 1.00 ]
#...
| 0.94 - 0.945 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 21. 490 reads; 39290 bp (untrimmed), 38553 (trimmed).
Contig 22. 501 reads; 29457 bp (untrimmed), 29279 (trimmed).
Contig 23. 537 reads; 36076 bp (untrimmed), 35759 (trimmed).
Contig 24. 588 reads; 55311 bp (untrimmed), 55297 (trimmed).
Contig 25. 701 reads; 59682 bp (untrimmed), 59659 (trimmed).
Contig 26. 727 reads; 35864 bp (untrimmed), 35840 (trimmed).
Contig 27. 754 reads; 40571 bp (untrimmed), 40217 (trimmed).
Contig 28. 788 reads; 50675 bp (untrimmed), 49686 (trimmed).
Contig 29. 897 reads; 65227 bp (untrimmed), 65119 (trimmed).
Contig 30. 935 reads; 97877 bp (untrimmed), 97364 (trimmed).
Contig 31. 957 reads; 85713 bp (untrimmed), 85377 (trimmed).
Contig 32. 1031 reads; 97857 bp (untrimmed), 97724 (trimmed).
Contig 33. 1073 reads; 54114 bp (untrimmed), 53952 (trimmed).
Contig 34. 1214 reads; 104653 bp (untrimmed), 104383 (trimmed).
Contig 35. 1421 reads; 130711 bp (untrimmed), 130710 (trimmed).
Contig 36. 1536 reads; 86459 bp (untrimmed), 86428 (trimmed).
Contig 37. 1584 reads; 79943 bp (untrimmed), 79778 (trimmed).
Contig 38. 1605 reads; 108901 bp (untrimmed), 108882 (trimmed).
Contig 39. 1758 reads; 115917 bp (untrimmed), 115895 (trimmed).
Contig 40. 2751 reads; 159318 bp (untrimmed), 159196 (trimmed).
Contig 41. 3160 reads; 299250 bp (untrimmed), 298465 (trimmed).
Contig 42. 4796 reads; 231185 bp (untrimmed), 231140 (trimmed).
Contig 43. 5255 reads; 429973 bp (untrimmed), 429953 (trimmed).
Contig 44. 5525 reads; 349314 bp (untrimmed), 349300 (trimmed).
Contig 45. 5979 reads; 445935 bp (untrimmed), 445730 (trimmed).
Contig 46. 11431 reads; 577907 bp (untrimmed), 577234 (trimmed).
Contig 47. 14815 reads; 743286 bp (untrimmed), 743267 (trimmed).
--------------------------------------------------------------
Totals 76867 reads; 5011599 bp (untrimmed), 5001639 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 5010375 bases = 13.81 +- 6.36 = 0.13 +- 4.32
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 45 total values totalling 515.3900. <11.453111 +/- 3.807120>
#Range: [ 1.41 - 18.70 ]
#Most likely bin: [ 10 - 10.5 ] 7 counts
#Median bin: [ 10 - 10.5 ] 7 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXX 1 - 1.5 : [ 1 0.02 0.02 ]
#...
|XXXXXXXXXXX 5.5 - 6 : [ 2 0.04 0.07 ]
#...
|XXXXXX 7 - 7.5 : [ 1 0.02 0.09 ]
|XXXXXX 7.5 - 8 : [ 1 0.02 0.11 ]
|XXXXXX 8 - 8.5 : [ 1 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 4 0.09 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 5 0.11 0.33 ]
|XXXXXXXXXXXXXXXXX 9.5 - 10 : [ 3 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 7 0.16 0.56 ]
|XXXXXX 10.5 - 11 : [ 1 0.02 0.58 ]
|XXXXXXXXXXX 11 - 11.5 : [ 2 0.04 0.62 ]
#...
|XXXXXXXXXXX 12 - 12.5 : [ 2 0.04 0.67 ]
#...
|XXXXXXXXXXX 13 - 13.5 : [ 2 0.04 0.71 ]
|XXXXXX 13.5 - 14 : [ 1 0.02 0.73 ]
|XXXXXXXXXXX 14 - 14.5 : [ 2 0.04 0.78 ]
|XXXXXX 14.5 - 15 : [ 1 0.02 0.80 ]
#...
|XXXXXXXXXXX 15.5 - 16 : [ 2 0.04 0.84 ]
#...
|XXXXXX 16.5 - 17 : [ 1 0.02 0.87 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXX 17.5 - 18 : [ 4 0.09 0.96 ]
|XXXXXX 18 - 18.5 : [ 1 0.02 0.98 ]
|XXXXXX 18.5 - 19 : [ 1 0.02 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 44 total values totalling 513.9800. <11.681364 +/- 3.532578>
#Range: [ 5.83 - 18.70 ]
#Most likely bin: [ 10 - 10.5 ] 7 counts
#Median bin: [ 10 - 10.5 ] 7 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 5.5 - 6 : [ 2 0.05 0.05 ]
#...
|XXXXXX 7 - 7.5 : [ 1 0.02 0.07 ]
|XXXXXX 7.5 - 8 : [ 1 0.02 0.09 ]
|XXXXXX 8 - 8.5 : [ 1 0.02 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 4 0.09 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 5 0.11 0.32 ]
|XXXXXXXXXXXXXXXXX 9.5 - 10 : [ 3 0.07 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 7 0.16 0.55 ]
|XXXXXX 10.5 - 11 : [ 1 0.02 0.57 ]
|XXXXXXXXXXX 11 - 11.5 : [ 2 0.05 0.61 ]
#...
|XXXXXXXXXXX 12 - 12.5 : [ 2 0.05 0.66 ]
#...
|XXXXXXXXXXX 13 - 13.5 : [ 2 0.05 0.70 ]
|XXXXXX 13.5 - 14 : [ 1 0.02 0.73 ]
|XXXXXXXXXXX 14 - 14.5 : [ 2 0.05 0.77 ]
|XXXXXX 14.5 - 15 : [ 1 0.02 0.80 ]
#...
|XXXXXXXXXXX 15.5 - 16 : [ 2 0.05 0.84 ]
#...
|XXXXXX 16.5 - 17 : [ 1 0.02 0.86 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXX 17.5 - 18 : [ 4 0.09 0.95 ]
|XXXXXX 18 - 18.5 : [ 1 0.02 0.98 ]
|XXXXXX 18.5 - 19 : [ 1 0.02 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 2 3 reads 1368 bases = 1.41 +- 0.72 = 1.41 +- 0.72
Contig 4 15 reads 2019 bases = 5.83 +- 1.72 = -0.50 +- 2.80
Contig 8 59 reads 8720 bases = 5.89 +- 2.42 = 0.90 +- 2.43
Contig 5 19 reads 2227 bases = 7.34 +- 5.62 = 1.98 +- 1.14
Contig 13 285 reads 34257 bases = 7.57 +- 2.89 = 0.12 +- 2.82
Contig 11 271 reads 29084 bases = 8.31 +- 2.73 = 0.10 +- 2.81
Contig 30 935 reads 97877 bases = 8.57 +- 2.86 = 0.05 +- 2.90
Contig 6 25 reads 2288 bases = 8.66 +- 5.89 = 2.03 +- 3.37
Contig 19 478 reads 48931 bases = 8.83 +- 3.36 = 0.04 +- 3.03
Contig 14 286 reads 29086 bases = 8.95 +- 2.97 = 0.01 +- 3.33
Contig 20 490 reads 48640 bases = 9.01 +- 2.96 = 0.14 +- 3.36
Contig 10 172 reads 16433 bases = 9.03 +- 3.59 = 0.20 +- 3.05
Contig 16 360 reads 36019 bases = 9.09 +- 3.51 = 0.05 +- 2.84
Contig 12 273 reads 26663 bases = 9.20 +- 3.62 = 0.16 +- 3.44
Contig 24 588 reads 55311 bases = 9.49 +- 3.81 = 0.35 +- 3.66
Contig 32 1031 reads 97857 bases = 9.54 +- 3.52 = 0.04 +- 3.10
Contig 41 3160 reads 299250 bases = 9.60 +- 3.37 = 0.13 +- 3.46
Contig 35 1421 reads 130711 bases = 9.83 +- 3.34 = 0.15 +- 3.23
Contig 31 957 reads 85713 bases = 10.08 +- 3.73 = 0.03 +- 3.32
Contig 7 47 reads 3760 bases = 10.08 +- 4.53 = 1.50 +- 4.38
Contig 25 701 reads 59682 bases = 10.55 +- 3.95 = 0.29 +- 3.62
Contig 43 5255 reads 429973 bases = 11.00 +- 3.86 = 0.12 +- 3.67
Contig 21 490 reads 39290 bases = 11.21 +- 4.28 = 0.28 +- 3.57
Contig 45 5979 reads 445935 bases = 12.10 +- 3.85 = 0.03 +- 3.97
Contig 29 897 reads 65227 bases = 12.41 +- 3.71 = 0.14 +- 4.17
Contig 23 537 reads 36076 bases = 13.29 +- 4.88 = 1.05 +- 4.15
Contig 38 1605 reads 108901 bases = 13.32 +- 3.89 = 0.50 +- 4.16
Contig 39 1758 reads 115917 bases = 13.64 +- 4.36 = 0.40 +- 3.88
Contig 28 788 reads 50675 bases = 14.05 +- 5.14 = 0.40 +- 4.36
Contig 44 5525 reads 349314 bases = 14.17 +- 4.03 = 0.10 +- 4.16
Contig 22 501 reads 29457 bases = 14.96 +- 3.97 = 0.18 +- 4.98
Contig 40 2751 reads 159318 bases = 15.52 +- 4.35 = 0.12 +- 4.29
Contig 36 1536 reads 86459 bases = 15.89 +- 4.23 = 0.14 +- 4.85
Contig 27 754 reads 40571 bases = 16.80 +- 4.01 = 0.26 +- 3.80
Contig 37 1584 reads 79943 bases = 17.80 +- 5.00 = 0.17 +- 5.57
Contig 46 11431 reads 577907 bases = 17.81 +- 4.85 = 0.02 +- 5.05
Contig 47 14815 reads 743286 bases = 17.91 +- 6.55 = 0.01 +- 4.97
Contig 33 1073 reads 54114 bases = 17.94 +- 6.25 = 0.31 +- 5.01
Contig 26 727 reads 35864 bases = 18.45 +- 5.14 = 1.52 +- 5.23
Contig 42 4796 reads 231185 bases = 18.70 +- 13.61 = 0.18 +- 6.23
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 795
HQ Discrepant reads = 23
Chimeric reads = 113
Suspect alignments = 597
-------------------------------------------------------------------
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/microbe3/3634492/edit_dir.22Jul04.QD