Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-12-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3640420 2600 NULL Marinobacter aquaeolei
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Marinobacter_aquaeolei
-------------------------------------------------------------------
Alteromonadales, order, g-proteobacteria
Alteromonadaceae, family, g-proteobacteria
Marinobacter hydrocarbonoclasticus, species, g-proteobacteria
Marinobacter, genus, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4685850
# phrap: 4304082
# db:
altered.
2600000
3863310 +/- 906789
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 9792
Number of reads with percent X's >= 20%: 147 = 0.3%
Number of reads with percent X's >= 50%: 78 = 0.2%
Number of reads with percent X's >= 80%: 20 = 0.0%
Total reads in project: 46391
Total bp X'd : 425959
reads >= 20% >= 50% >= 80% screened
Nr with L09136 8375 65 30 4
Nr with pCC1Fos 1324 0 0 0
Nr with pMCL200_JGI_XZX+XZK 93 82 48 16
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 1796
Number of reads with percent X's >= 20%: 1689 = 44.8%
Number of reads with percent X's >= 50%: 1660 = 44.0%
Number of reads with percent X's >= 80%: 1605 = 42.6%
Total reads in project: 3770
Total bp X'd : 1563705
reads >= 20% >= 50% >= 80% screened
Nr with L09136 962 906 896 863
Nr with LRS 22 22 22 22
Nr with pCC1Fos 51 4 1 1
Nr with pMCL200_JGI_XZX+XZK 761 757 741 719
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 10587704
C = 13434040
G = 13568359
T = 10234204
N = 425199
X = 2021473
GC fraction = 0.54
Total = 50270979
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3640420_fasta.screen.contigs
-------------------------------------------------------------------
A 1009432
C 1335922
G 1340522
T 1015723
N 402
fraction GC = 0.57
total bases = 4702001
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 ATST reads.list > grep.reads.list.ATST
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ATST 4 500
-------------------------------------------------------------------
#Found 9893 total values totalling 31467631.0000. <3180.797635 +/- 814.027558>
#Range: [ 625 - 79440 ]
#Most likely bin: [ 3000 - 3500 ] 7126 counts
#Median bin: [ 3000 - 3500 ] 7126 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 7 0.00 0.00 ]
| 1000 - 1500 : [ 16 0.00 0.00 ]
| 1500 - 2000 : [ 28 0.00 0.01 ]
| 2000 - 2500 : [ 27 0.00 0.01 ]
|XXXXXXXXXXX 2500 - 3000 : [ 1933 0.20 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 7126 0.72 0.92 ]
|XXXX 3500 - 4000 : [ 754 0.08 1.00 ]
#...
| 13000 - 13500 : [ 1 0.00 1.00 ]
#...
| 79000 - 79500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ATSU reads.list > grep.reads.list.ATSU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ATSU 4 500
-------------------------------------------------------------------
#Found 9833 total values totalling 52630374.0000. <5352.422862 +/- 1463.326134>
#Range: [ 986 - 98254 ]
#Most likely bin: [ 5000 - 5500 ] 4043 counts
#Median bin: [ 5000 - 5500 ] 4043 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
| 1000 - 1500 : [ 20 0.00 0.00 ]
| 1500 - 2000 : [ 20 0.00 0.00 ]
| 2000 - 2500 : [ 13 0.00 0.01 ]
| 2500 - 3000 : [ 15 0.00 0.01 ]
| 3000 - 3500 : [ 8 0.00 0.01 ]
| 3500 - 4000 : [ 12 0.00 0.01 ]
| 4000 - 4500 : [ 39 0.00 0.01 ]
|XXXXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 2160 0.22 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5000 - 5500 : [ 4043 0.41 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 2783 0.28 0.93 ]
|XXXXXXX 6000 - 6500 : [ 708 0.07 1.00 ]
#...
| 7000 - 7500 : [ 1 0.00 1.00 ]
#...
| 13000 - 13500 : [ 1 0.00 1.00 ]
#...
| 21500 - 22000 : [ 4 0.00 1.00 ]
| 22000 - 22500 : [ 2 0.00 1.00 ]
#...
| 95500 - 96000 : [ 1 0.00 1.00 ]
#...
| 98000 - 98500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ATSW reads.list > grep.reads.list.ATSW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ATSW 4 500
-------------------------------------------------------------------
#Found 598 total values totalling 20940501.0000. <35017.560201 +/- 3482.553716>
#Range: [ 21709 - 45397 ]
#Most likely bin: [ 34000 - 34500 ] 48 counts
#Median bin: [ 34500 - 35000 ] 29 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 21500 - 22000 : [ 1 0.00 0.00 ]
#...
|XX 23500 - 24000 : [ 2 0.00 0.01 ]
#...
|X 24500 - 25000 : [ 1 0.00 0.01 ]
|XX 25000 - 25500 : [ 3 0.01 0.01 ]
|XX 25500 - 26000 : [ 3 0.01 0.02 ]
|XX 26000 - 26500 : [ 2 0.00 0.02 ]
#...
|XX 27000 - 27500 : [ 2 0.00 0.02 ]
#...
|XX 28000 - 28500 : [ 2 0.00 0.03 ]
|XXXXXX 28500 - 29000 : [ 7 0.01 0.04 ]
|XX 29000 - 29500 : [ 2 0.00 0.04 ]
|XXXXXXXXX 29500 - 30000 : [ 11 0.02 0.06 ]
|XXXXXXXXXXXX 30000 - 30500 : [ 14 0.02 0.08 ]
|XXXXXXXXXXX 30500 - 31000 : [ 13 0.02 0.11 ]
|XXXXXXXXXXXXXXXXXXXX 31000 - 31500 : [ 24 0.04 0.15 ]
|XXXXXXXXXXXXXXXX 31500 - 32000 : [ 19 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 31 0.05 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 28 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 32 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 28 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 48 0.08 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 29 0.05 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 31 0.05 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 31 0.05 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 26 0.04 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 34 0.06 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 30 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 28 0.05 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 28 0.05 0.85 ]
|XXXXXXXXXXXX 38500 - 39000 : [ 14 0.02 0.88 ]
|XXXXXXXXXXX 39000 - 39500 : [ 13 0.02 0.90 ]
|XXXXXXXXXXXXX 39500 - 40000 : [ 16 0.03 0.92 ]
|XXXXXXXXXX 40000 - 40500 : [ 12 0.02 0.94 ]
|XXX 40500 - 41000 : [ 4 0.01 0.95 ]
|XXXXXXXX 41000 - 41500 : [ 9 0.02 0.97 ]
|XXXXXXXXXXX 41500 - 42000 : [ 13 0.02 0.99 ]
|XX 42000 - 42500 : [ 2 0.00 0.99 ]
#...
|XX 43000 - 43500 : [ 2 0.00 0.99 ]
|X 43500 - 44000 : [ 1 0.00 1.00 ]
#...
|X 44500 - 45000 : [ 1 0.00 1.00 ]
|X 45000 - 45500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# ATSW 35192 +- 3250 (n=306)
# ATSU 5263 +- 755 (n=4929)
# ATST 3041 +- 333 (n=5023)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3640420_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
ATST 23808 89 717 95 760 23674 89 718 94 732
ATSU 23808 93 759 97 727 23808 93 759 97 750
ATSW 3072 89 642 95 632 3072 89 644 95 662
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
ATST 11859 89 713 95 728 11815 90 722 94 735
ATSU 11904 93 756 97 745 11904 93 762 97 754
ATSW 1536 90 646 96 653 1536 88 643 95 670
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3640420_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
16 3072 1536 96.00 100.00 ATSW @
124 23808 11904 96.00 100.00 ATSU @
124 23674 11897 95.94 99.94 ATST @
] 50554 25337 95.97 cumulative total@@
LIBRARY PLATE ID COUNT [ ATSW 16 ATSU 124 ATST 124 ] for 264 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 3640420_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 50554 total values totalling 33767756.0000. <667.954188 +/- 246.889758>
#Range: [ 0 - 985 ]
#Most likely bin: [ 750 - 800 ] 11378 counts
#Median bin: [ 750 - 800 ] 11378 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 0 - 50 : [ 4194 0.08 0.08 ]
|X 50 - 100 : [ 373 0.01 0.09 ]
|X 100 - 150 : [ 302 0.01 0.10 ]
|X 150 - 200 : [ 273 0.01 0.10 ]
|X 200 - 250 : [ 306 0.01 0.11 ]
|X 250 - 300 : [ 335 0.01 0.11 ]
|X 300 - 350 : [ 388 0.01 0.12 ]
|XX 350 - 400 : [ 493 0.01 0.13 ]
|XX 400 - 450 : [ 558 0.01 0.14 ]
|XX 450 - 500 : [ 649 0.01 0.16 ]
|XXX 500 - 550 : [ 847 0.02 0.17 ]
|XXXXX 550 - 600 : [ 1340 0.03 0.20 ]
|XXXXXXXX 600 - 650 : [ 2278 0.05 0.24 ]
|XXXXXXXXXXXXX 650 - 700 : [ 3825 0.08 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7435 0.15 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 11378 0.23 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 9732 0.19 0.88 ]
|XXXXXXXXXXXXXXXX 850 - 900 : [ 4625 0.09 0.98 ]
|XXXX 900 - 950 : [ 1163 0.02 1.00 ]
| 950 - 1000 : [ 60 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATST
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ATST 3640420_fasta.screen.trimQ15.SaF > reads.trim15.ATST.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ATST.rl 2 50
-------------------------------------------------------------------
#Found 23674 total values totalling 15156089.0000. <640.199755 +/- 271.813301>
#Range: [ 0 - 985 ]
#Most likely bin: [ 800 - 850 ] 3628 counts
#Median bin: [ 700 - 750 ] 2453 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2359 0.10 0.10 ]
|XXX 50 - 100 : [ 232 0.01 0.11 ]
|XX 100 - 150 : [ 216 0.01 0.12 ]
|XX 150 - 200 : [ 176 0.01 0.13 ]
|XX 200 - 250 : [ 194 0.01 0.13 ]
|XX 250 - 300 : [ 200 0.01 0.14 ]
|XXX 300 - 350 : [ 231 0.01 0.15 ]
|XXX 350 - 400 : [ 303 0.01 0.17 ]
|XXXX 400 - 450 : [ 360 0.02 0.18 ]
|XXXXX 450 - 500 : [ 496 0.02 0.20 ]
|XXXXXXX 500 - 550 : [ 646 0.03 0.23 ]
|XXXXXXXXXXX 550 - 600 : [ 1007 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1703 0.07 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2233 0.09 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2453 0.10 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2503 0.11 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3628 0.15 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 850 - 900 : [ 3532 0.15 0.95 ]
|XXXXXXXXXXXXX 900 - 950 : [ 1142 0.05 1.00 ]
|X 950 - 1000 : [ 60 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATSU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ATSU 3640420_fasta.screen.trimQ15.SaF > reads.trim15.ATSU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ATSU.rl 2 50
-------------------------------------------------------------------
#Found 23808 total values totalling 16840123.0000. <707.330435 +/- 209.111663>
#Range: [ 0 - 929 ]
#Most likely bin: [ 750 - 800 ] 8290 counts
#Median bin: [ 750 - 800 ] 8290 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXX 0 - 50 : [ 1562 0.07 0.07 ]
| 50 - 100 : [ 77 0.00 0.07 ]
| 100 - 150 : [ 40 0.00 0.07 ]
| 150 - 200 : [ 60 0.00 0.07 ]
| 200 - 250 : [ 52 0.00 0.08 ]
| 250 - 300 : [ 39 0.00 0.08 ]
| 300 - 350 : [ 68 0.00 0.08 ]
| 350 - 400 : [ 86 0.00 0.08 ]
| 400 - 450 : [ 102 0.00 0.09 ]
| 450 - 500 : [ 99 0.00 0.09 ]
|X 500 - 550 : [ 153 0.01 0.10 ]
|X 550 - 600 : [ 239 0.01 0.11 ]
|XX 600 - 650 : [ 413 0.02 0.13 ]
|XXXXXX 650 - 700 : [ 1264 0.05 0.18 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4434 0.19 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8290 0.35 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5775 0.24 0.96 ]
|XXXXX 850 - 900 : [ 1038 0.04 1.00 ]
| 900 - 950 : [ 17 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATSW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ATSW 3640420_fasta.screen.trimQ15.SaF > reads.trim15.ATSW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ATSW.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 1771544.0000. <576.674479 +/- 261.821972>
#Range: [ 0 - 924 ]
#Most likely bin: [ 750 - 800 ] 585 counts
#Median bin: [ 650 - 700 ] 328 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXX 0 - 50 : [ 273 0.09 0.09 ]
|XXXX 50 - 100 : [ 64 0.02 0.11 ]
|XXX 100 - 150 : [ 46 0.01 0.12 ]
|XXX 150 - 200 : [ 37 0.01 0.14 ]
|XXXX 200 - 250 : [ 60 0.02 0.16 ]
|XXXXXXX 250 - 300 : [ 96 0.03 0.19 ]
|XXXXXX 300 - 350 : [ 89 0.03 0.22 ]
|XXXXXXX 350 - 400 : [ 104 0.03 0.25 ]
|XXXXXXX 400 - 450 : [ 96 0.03 0.28 ]
|XXXX 450 - 500 : [ 54 0.02 0.30 ]
|XXX 500 - 550 : [ 48 0.02 0.31 ]
|XXXXXX 550 - 600 : [ 94 0.03 0.35 ]
|XXXXXXXXXXX 600 - 650 : [ 162 0.05 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 328 0.11 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 548 0.18 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 585 0.19 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 329 0.11 0.98 ]
|XXXX 850 - 900 : [ 55 0.02 1.00 ]
| 900 - 950 : [ 4 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3640420
-------------------------------------------------------------------
ATST.000001.000100 pUC18.fa pUC18.fa LRS.fasta
ATST.000101.000200 pUC18.fa pUC18.fa LRS.fasta
ATSU.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
ATSU.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
ATSW.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
ATST.000001.000100 pUC18.fa pUC18.fa LRS.fasta
ATST.000101.000200 pUC18.fa pUC18.fa LRS.fasta
ATSU.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
ATSU.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
ATSW.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3640420_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3640420_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 46414 total values totalling 26437.1873. <0.569595 +/- 0.041605>
#Range: [ 0 - 0.8334 ]
#Most likely bin: [ 0.58 - 0.585 ] 2670 counts
#Median bin: [ 0.57 - 0.575 ] 2510 counts
#Entropy = 5.0359 bits
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.225 - 0.23 : [ 1 0.00 0.00 ]
#...
| 0.255 - 0.26 : [ 1 0.00 0.00 ]
#...
| 0.265 - 0.27 : [ 1 0.00 0.00 ]
#...
| 0.29 - 0.295 : [ 1 0.00 0.00 ]
#...
| 0.3 - 0.305 : [ 2 0.00 0.00 ]
| 0.305 - 0.31 : [ 1 0.00 0.00 ]
#...
| 0.32 - 0.325 : [ 2 0.00 0.00 ]
| 0.325 - 0.33 : [ 1 0.00 0.00 ]
| 0.33 - 0.335 : [ 2 0.00 0.00 ]
#...
| 0.34 - 0.345 : [ 4 0.00 0.00 ]
| 0.345 - 0.35 : [ 1 0.00 0.00 ]
| 0.35 - 0.355 : [ 3 0.00 0.00 ]
| 0.355 - 0.36 : [ 2 0.00 0.00 ]
| 0.36 - 0.365 : [ 8 0.00 0.00 ]
| 0.365 - 0.37 : [ 3 0.00 0.00 ]
| 0.37 - 0.375 : [ 2 0.00 0.00 ]
| 0.375 - 0.38 : [ 5 0.00 0.00 ]
| 0.38 - 0.385 : [ 8 0.00 0.00 ]
| 0.385 - 0.39 : [ 14 0.00 0.00 ]
| 0.39 - 0.395 : [ 14 0.00 0.00 ]
| 0.395 - 0.4 : [ 14 0.00 0.00 ]
| 0.4 - 0.405 : [ 19 0.00 0.00 ]
| 0.405 - 0.41 : [ 26 0.00 0.00 ]
| 0.41 - 0.415 : [ 13 0.00 0.00 ]
| 0.415 - 0.42 : [ 23 0.00 0.00 ]
| 0.42 - 0.425 : [ 26 0.00 0.00 ]
|X 0.425 - 0.43 : [ 35 0.00 0.01 ]
| 0.43 - 0.435 : [ 29 0.00 0.01 ]
|X 0.435 - 0.44 : [ 51 0.00 0.01 ]
|X 0.44 - 0.445 : [ 58 0.00 0.01 ]
|X 0.445 - 0.45 : [ 50 0.00 0.01 ]
|X 0.45 - 0.455 : [ 69 0.00 0.01 ]
|XX 0.455 - 0.46 : [ 114 0.00 0.01 ]
|XX 0.46 - 0.465 : [ 130 0.00 0.02 ]
|XXX 0.465 - 0.47 : [ 168 0.00 0.02 ]
|XXX 0.47 - 0.475 : [ 187 0.00 0.02 ]
|XXX 0.475 - 0.48 : [ 232 0.00 0.03 ]
|XXXX 0.48 - 0.485 : [ 279 0.01 0.03 ]
|XXXXX 0.485 - 0.49 : [ 329 0.01 0.04 ]
|XXXXXX 0.49 - 0.495 : [ 401 0.01 0.05 ]
|XXXXXXX 0.495 - 0.5 : [ 453 0.01 0.06 ]
|XXXXXXXXXX 0.5 - 0.505 : [ 639 0.01 0.07 ]
|XXXXXXXXXX 0.505 - 0.51 : [ 644 0.01 0.09 ]
|XXXXXXXXXX 0.51 - 0.515 : [ 681 0.01 0.10 ]
|XXXXXXXXXXX 0.515 - 0.52 : [ 760 0.02 0.12 ]
|XXXXXXXXXXXXX 0.52 - 0.525 : [ 848 0.02 0.14 ]
|XXXXXXXXXXXXXX 0.525 - 0.53 : [ 944 0.02 0.16 ]
|XXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1028 0.02 0.18 ]
|XXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1242 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1484 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1609 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1784 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1966 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 2213 0.05 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 2321 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 2510 0.05 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 2564 0.06 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 2670 0.06 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 2551 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 2369 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 2092 0.05 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 2146 0.05 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1788 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1565 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1311 0.03 0.92 ]
|XXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1065 0.02 0.94 ]
|XXXXXXXXXXXX 0.625 - 0.63 : [ 810 0.02 0.96 ]
|XXXXXXXXXX 0.63 - 0.635 : [ 646 0.01 0.97 ]
|XXXXXX 0.635 - 0.64 : [ 411 0.01 0.98 ]
|XXXXX 0.64 - 0.645 : [ 311 0.01 0.99 ]
|XXX 0.645 - 0.65 : [ 214 0.00 0.99 ]
|XX 0.65 - 0.655 : [ 131 0.00 0.99 ]
|X 0.655 - 0.66 : [ 82 0.00 1.00 ]
|X 0.66 - 0.665 : [ 60 0.00 1.00 ]
|X 0.665 - 0.67 : [ 55 0.00 1.00 ]
| 0.67 - 0.675 : [ 21 0.00 1.00 ]
| 0.675 - 0.68 : [ 20 0.00 1.00 ]
| 0.68 - 0.685 : [ 14 0.00 1.00 ]
| 0.685 - 0.69 : [ 17 0.00 1.00 ]
| 0.69 - 0.695 : [ 8 0.00 1.00 ]
| 0.695 - 0.7 : [ 6 0.00 1.00 ]
| 0.7 - 0.705 : [ 4 0.00 1.00 ]
| 0.705 - 0.71 : [ 4 0.00 1.00 ]
| 0.71 - 0.715 : [ 2 0.00 1.00 ]
#...
| 0.72 - 0.725 : [ 4 0.00 1.00 ]
| 0.725 - 0.73 : [ 1 0.00 1.00 ]
#...
| 0.735 - 0.74 : [ 2 0.00 1.00 ]
| 0.74 - 0.745 : [ 2 0.00 1.00 ]
| 0.745 - 0.75 : [ 2 0.00 1.00 ]
| 0.75 - 0.755 : [ 1 0.00 1.00 ]
| 0.755 - 0.76 : [ 1 0.00 1.00 ]
| 0.76 - 0.765 : [ 1 0.00 1.00 ]
#...
| 0.78 - 0.785 : [ 1 0.00 1.00 ]
| 0.785 - 0.79 : [ 1 0.00 1.00 ]
| 0.79 - 0.795 : [ 3 0.00 1.00 ]
#...
| 0.815 - 0.82 : [ 1 0.00 1.00 ]
#...
| 0.83 - 0.835 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 105. 562 reads; 68363 bp (untrimmed), 68108 (trimmed).
Contig 106. 563 reads; 56655 bp (untrimmed), 56215 (trimmed).
Contig 107. 582 reads; 64124 bp (untrimmed), 64105 (trimmed).
Contig 108. 593 reads; 65450 bp (untrimmed), 65389 (trimmed).
Contig 109. 601 reads; 58331 bp (untrimmed), 58154 (trimmed).
Contig 110. 633 reads; 74535 bp (untrimmed), 74254 (trimmed).
Contig 111. 664 reads; 64364 bp (untrimmed), 64224 (trimmed).
Contig 112. 731 reads; 62376 bp (untrimmed), 62293 (trimmed).
Contig 113. 742 reads; 58282 bp (untrimmed), 58094 (trimmed).
Contig 114. 761 reads; 77487 bp (untrimmed), 77455 (trimmed).
Contig 115. 796 reads; 75884 bp (untrimmed), 75879 (trimmed).
Contig 116. 870 reads; 82761 bp (untrimmed), 82703 (trimmed).
Contig 117. 925 reads; 82771 bp (untrimmed), 82608 (trimmed).
Contig 118. 1012 reads; 101772 bp (untrimmed), 101735 (trimmed).
Contig 119. 1295 reads; 135931 bp (untrimmed), 135885 (trimmed).
Contig 120. 1315 reads; 124215 bp (untrimmed), 124101 (trimmed).
Contig 121. 1561 reads; 169859 bp (untrimmed), 169739 (trimmed).
Contig 122. 1584 reads; 158408 bp (untrimmed), 158240 (trimmed).
Contig 123. 1601 reads; 130051 bp (untrimmed), 130031 (trimmed).
Contig 124. 1661 reads; 145208 bp (untrimmed), 144956 (trimmed).
Contig 125. 1683 reads; 179172 bp (untrimmed), 179108 (trimmed).
Contig 126. 1737 reads; 156371 bp (untrimmed), 156152 (trimmed).
Contig 127. 1905 reads; 178824 bp (untrimmed), 178815 (trimmed).
Contig 128. 1991 reads; 157715 bp (untrimmed), 157589 (trimmed).
Contig 129. 2063 reads; 179389 bp (untrimmed), 179345 (trimmed).
Contig 130. 2512 reads; 225476 bp (untrimmed), 225388 (trimmed).
Contig 131. 2863 reads; 286259 bp (untrimmed), 286122 (trimmed).
--------------------------------------------------------------
Totals 46784 reads; 4702001 bp (untrimmed), 4685850 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4692186 bases = 9.29 +- 3.92 = 0.18 +- 3.49
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 118 total values totalling 869.3000. <7.366949 +/- 2.934054>
#Range: [ 1.32 - 13.72 ]
#Most likely bin: [ 8.5 - 9 ] 13 counts
#Median bin: [ 8 - 8.5 ] 11 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 1 - 1.5 : [ 1 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 7 0.06 0.07 ]
|XXXXXXXXXXXX 2 - 2.5 : [ 4 0.03 0.10 ]
|XXXXXXXXX 2.5 - 3 : [ 3 0.03 0.13 ]
|XXX 3 - 3.5 : [ 1 0.01 0.14 ]
|XXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 6 0.05 0.19 ]
|XXXXXXXXX 4 - 4.5 : [ 3 0.03 0.21 ]
|XXXXXXXXXXXX 4.5 - 5 : [ 4 0.03 0.25 ]
|XXXXXXXXXXXX 5 - 5.5 : [ 4 0.03 0.28 ]
|XXX 5.5 - 6 : [ 1 0.01 0.29 ]
|XXXXXXXXX 6 - 6.5 : [ 3 0.03 0.31 ]
|XXXXXXXXXXXX 6.5 - 7 : [ 4 0.03 0.35 ]
|XXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 6 0.05 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 9 0.08 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 11 0.09 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 13 0.11 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 7 0.06 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 11 0.09 0.83 ]
|XXXXXXXXXXXXXXX 10 - 10.5 : [ 5 0.04 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 10 0.08 0.96 ]
#...
|XXXXXX 11.5 - 12 : [ 2 0.02 0.97 ]
|XXXXXX 12 - 12.5 : [ 2 0.02 0.99 ]
#...
|XXX 13.5 - 14 : [ 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 97 total values totalling 803.7800. <8.286392 +/- 2.056213>
#Range: [ 3.25 - 12.32 ]
#Most likely bin: [ 8.5 - 9 ] 13 counts
#Median bin: [ 8.5 - 9 ] 13 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 3 - 3.5 : [ 1 0.01 0.01 ]
|XXXXXXXXX 3.5 - 4 : [ 3 0.03 0.04 ]
|XXXXXX 4 - 4.5 : [ 2 0.02 0.06 ]
|XXXXXXXXXXXX 4.5 - 5 : [ 4 0.04 0.10 ]
|XXXXXXXXXXXX 5 - 5.5 : [ 4 0.04 0.14 ]
|XXX 5.5 - 6 : [ 1 0.01 0.15 ]
|XXXXXX 6 - 6.5 : [ 2 0.02 0.18 ]
|XXXXXXXXXXXX 6.5 - 7 : [ 4 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 6 0.06 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 9 0.09 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 11 0.11 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 13 0.13 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 7 0.07 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 11 0.11 0.80 ]
|XXXXXXXXXXXXXXX 10 - 10.5 : [ 5 0.05 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 10 0.10 0.96 ]
#...
|XXXXXX 11.5 - 12 : [ 2 0.02 0.98 ]
|XXXXXX 12 - 12.5 : [ 2 0.02 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 16 2 reads 1423 bases = 1.32 +- 0.47 = 1.32 +- 0.47
Contig 20 4 reads 2071 bases = 1.53 +- 0.52 = 0.17 +- 1.17
Contig 11 2 reads 1005 bases = 1.56 +- 0.50 = 1.56 +- 0.50
Contig 13 2 reads 834 bases = 1.76 +- 0.43 = -0.17 +- 0.46
Contig 12 2 reads 1096 bases = 1.77 +- 0.42 = 1.77 +- 0.42
Contig 14 2 reads 899 bases = 1.78 +- 0.42 = 1.78 +- 0.42
Contig 10 2 reads 1123 bases = 1.79 +- 0.41 = 0.03 +- 0.46
Contig 26 5 reads 2625 bases = 1.86 +- 0.61 = 1.86 +- 0.61
Contig 23 4 reads 1854 bases = 2.02 +- 0.75 = 2.02 +- 0.75
Contig 25 4 reads 1807 bases = 2.14 +- 0.65 = 1.12 +- 0.97
Contig 18 3 reads 1368 bases = 2.19 +- 0.87 = 0.61 +- 0.95
Contig 27 7 reads 2532 bases = 2.31 +- 1.22 = -0.10 +- 1.32
Contig 29 7 reads 2383 bases = 2.63 +- 1.63 = 1.13 +- 1.05
Contig 22 4 reads 1442 bases = 2.71 +- 1.19 = 2.71 +- 1.19
Contig 21 4 reads 1243 bases = 2.85 +- 1.14 = 2.85 +- 1.14
Contig 38 18 reads 5284 bases = 3.25 +- 1.41 = 1.45 +- 2.60
Contig 30 8 reads 1955 bases = 3.56 +- 1.23 = 2.81 +- 1.74
Contig 37 18 reads 4766 bases = 3.57 +- 1.38 = 0.10 +- 1.40
Contig 31 8 reads 1987 bases = 3.73 +- 1.93 = 3.73 +- 1.93
Contig 34 11 reads 2624 bases = 3.73 +- 1.44 = 2.70 +- 0.79
Contig 54 55 reads 4903 bases = 10.00 +- 4.04 = 0.22 +- 5.14
Contig 86 306 reads 28797 bases = 10.00 +- 4.58 = 0.21 +- 3.65
Contig 65 131 reads 10720 bases = 10.25 +- 3.46 = 1.14 +- 3.29
Contig 130 2512 reads 225476 bases = 10.29 +- 3.94 = 0.10 +- 3.50
Contig 126 1737 reads 156371 bases = 10.36 +- 3.95 = 0.08 +- 3.59
Contig 117 925 reads 82771 bases = 10.52 +- 4.33 = 0.14 +- 3.36
Contig 68 141 reads 12797 bases = 10.53 +- 5.69 = 0.99 +- 3.67
Contig 88 311 reads 27290 bases = 10.55 +- 2.96 = 0.09 +- 4.05
Contig 124 1661 reads 145208 bases = 10.64 +- 4.06 = 0.02 +- 3.74
Contig 102 437 reads 38816 bases = 10.65 +- 4.05 = 0.49 +- 3.51
Contig 95 385 reads 33655 bases = 10.70 +- 3.11 = 0.06 +- 3.48
Contig 129 2063 reads 179389 bases = 10.73 +- 3.95 = 0.10 +- 3.52
Contig 53 54 reads 4796 bases = 10.74 +- 4.14 = 0.65 +- 3.34
Contig 69 148 reads 12766 bases = 10.82 +- 3.98 = 0.32 +- 3.14
Contig 112 731 reads 62376 bases = 10.95 +- 4.02 = -0.04 +- 3.29
Contig 123 1601 reads 130051 bases = 11.53 +- 4.00 = -0.02 +- 4.14
Contig 128 1991 reads 157715 bases = 11.82 +- 5.47 = 0.10 +- 4.14
Contig 113 742 reads 58282 bases = 12.11 +- 5.26 = 0.11 +- 3.84
Contig 78 235 reads 18291 bases = 12.32 +- 4.27 = 0.14 +- 2.67
Contig 35 14 reads 635 bases = 13.72 +- 1.04 = 0.18 +- 1.07
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1067
HQ Discrepant reads = 83
Chimeric reads = 65
Suspect alignments = 325
-------------------------------------------------------------------
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/microbe4/3640420/edit_dir.10Mar05.QD