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
3634481 3660 266 Paracoccus denitrificans
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Paracoccus_denitrificans
-------------------------------------------------------------------
Rhodobacterales, order, a-proteobacteria
Rhodobacteraceae, family, a-proteobacteria
Alphaproteobacteria, class, a-proteobacteria
Paracoccus denitrificans, species, a-proteobacteria
Paracoccus, genus, a-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 5180145
# phrap: 4846267
# db:
altered.
3660000
4562137 +/- 652307
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 22812
Number of reads with percent X's >= 20%: 143 = 0.2%
Number of reads with percent X's >= 50%: 71 = 0.1%
Number of reads with percent X's >= 80%: 6 = 0.0%
Total reads in project: 70861
Total bp X'd : 1158059
reads >= 20% >= 50% >= 80% screened
Nr with L09136 14370 84 42 2
Nr with pCC1Fos 1250 5 3 0
Nr with pMCL200_JGI_XZX+XZK 7192 54 26 4
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 6
Number of reads with percent X's >= 20%: 3 = 7.3%
Number of reads with percent X's >= 50%: 1 = 2.4%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 41
Total bp X'd : 1579
reads >= 20% >= 50% >= 80% screened
Nr with L09136 1 0 0 0
Nr with pMCL200_JGI_XZX+XZK 5 3 1 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 11488315
C = 21753380
G = 21831297
T = 11291138
N = 374073
X = 1158059
GC fraction = 0.64
Total = 67896262
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634481_fasta.screen.contigs
-------------------------------------------------------------------
A 867292
C 1738421
G 1725700
T 855359
N 102
fraction GC = 0.67
total bases = 5186874
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 AHZA reads.list > grep.reads.list.AHZA
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZA 4 500
-------------------------------------------------------------------
#Found 13523 total values totalling 49059075.0000. <3627.824817 +/- 10270.222702>
#Range: [ 970 - 595153 ]
#Most likely bin: [ 2500 - 3000 ] 4262 counts
#Median bin: [ 3000 - 3500 ] 3536 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 30 0.00 0.00 ]
|X 1500 - 2000 : [ 80 0.01 0.01 ]
|XXXXXXX 2000 - 2500 : [ 726 0.05 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 4262 0.32 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3536 0.26 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2558 0.19 0.83 ]
|XXXXXXXXXXXXXXX 4000 - 4500 : [ 1584 0.12 0.94 ]
|XXXXXX 4500 - 5000 : [ 644 0.05 0.99 ]
|X 5000 - 5500 : [ 72 0.01 1.00 ]
| 5500 - 6000 : [ 1 0.00 1.00 ]
| 6000 - 6500 : [ 1 0.00 1.00 ]
| 6500 - 7000 : [ 1 0.00 1.00 ]
#...
| 7500 - 8000 : [ 1 0.00 1.00 ]
#...
| 14500 - 15000 : [ 1 0.00 1.00 ]
#...
| 23000 - 23500 : [ 1 0.00 1.00 ]
#...
| 25000 - 25500 : [ 1 0.00 1.00 ]
| 25500 - 26000 : [ 2 0.00 1.00 ]
| 26000 - 26500 : [ 1 0.00 1.00 ]
#...
| 45500 - 46000 : [ 1 0.00 1.00 ]
#...
| 67500 - 68000 : [ 1 0.00 1.00 ]
#...
| 81500 - 82000 : [ 1 0.00 1.00 ]
#...
| 84500 - 85000 : [ 1 0.00 1.00 ]
#...
| 110000 - 110500 : [ 1 0.00 1.00 ]
| 110500 - 111000 : [ 1 0.00 1.00 ]
#...
| 117500 - 118000 : [ 1 0.00 1.00 ]
| 118000 - 118500 : [ 1 0.00 1.00 ]
#...
| 128000 - 128500 : [ 1 0.00 1.00 ]
#...
| 137000 - 137500 : [ 1 0.00 1.00 ]
#...
| 139000 - 139500 : [ 1 0.00 1.00 ]
#...
| 148000 - 148500 : [ 1 0.00 1.00 ]
#...
| 181500 - 182000 : [ 1 0.00 1.00 ]
#...
| 184000 - 184500 : [ 1 0.00 1.00 ]
#...
| 195500 - 196000 : [ 1 0.00 1.00 ]
#...
| 220500 - 221000 : [ 1 0.00 1.00 ]
#...
| 387500 - 388000 : [ 1 0.00 1.00 ]
#...
| 564000 - 564500 : [ 1 0.00 1.00 ]
#...
| 565500 - 566000 : [ 1 0.00 1.00 ]
#...
| 595000 - 595500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZB reads.list > grep.reads.list.AHZB
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZB 4 500
-------------------------------------------------------------------
#Found 14719 total values totalling 114566079.0000. <7783.550445 +/- 7457.585385>
#Range: [ 824 - 588370 ]
#Most likely bin: [ 7500 - 8000 ] 3331 counts
#Median bin: [ 7500 - 8000 ] 3331 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
| 1000 - 1500 : [ 20 0.00 0.00 ]
| 1500 - 2000 : [ 37 0.00 0.00 ]
| 2000 - 2500 : [ 39 0.00 0.01 ]
| 2500 - 3000 : [ 33 0.00 0.01 ]
|X 3000 - 3500 : [ 50 0.00 0.01 ]
|X 3500 - 4000 : [ 56 0.00 0.02 ]
|X 4000 - 4500 : [ 73 0.00 0.02 ]
|X 4500 - 5000 : [ 106 0.01 0.03 ]
|XX 5000 - 5500 : [ 139 0.01 0.04 ]
|XXXX 5500 - 6000 : [ 331 0.02 0.06 ]
|XXXXXXXX 6000 - 6500 : [ 691 0.05 0.11 ]
|XXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1515 0.10 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 2746 0.19 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 3331 0.23 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 2572 0.17 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 1820 0.12 0.92 ]
|XXXXXXXXXXX 9000 - 9500 : [ 947 0.06 0.99 ]
|XX 9500 - 10000 : [ 194 0.01 1.00 ]
| 10000 - 10500 : [ 4 0.00 1.00 ]
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 12000 - 12500 : [ 1 0.00 1.00 ]
#...
| 13000 - 13500 : [ 1 0.00 1.00 ]
#...
| 30500 - 31000 : [ 1 0.00 1.00 ]
#...
| 36500 - 37000 : [ 1 0.00 1.00 ]
#...
| 55500 - 56000 : [ 1 0.00 1.00 ]
#...
| 145500 - 146000 : [ 1 0.00 1.00 ]
#...
| 223500 - 224000 : [ 1 0.00 1.00 ]
#...
| 269500 - 270000 : [ 1 0.00 1.00 ]
#...
| 322000 - 322500 : [ 1 0.00 1.00 ]
#...
| 343000 - 343500 : [ 1 0.00 1.00 ]
| 343500 - 344000 : [ 1 0.00 1.00 ]
#...
| 588000 - 588500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZC reads.list > grep.reads.list.AHZC
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZC 4 500
-------------------------------------------------------------------
#Found 1184 total values totalling 44802313.0000. <37839.791385 +/- 3450.017948>
#Range: [ 27015 - 46453 ]
#Most likely bin: [ 36500 - 37000 ] 72 counts
#Median bin: [ 37500 - 38000 ] 68 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 27000 - 27500 : [ 3 0.00 0.00 ]
|X 27500 - 28000 : [ 1 0.00 0.00 ]
#...
|X 28500 - 29000 : [ 1 0.00 0.00 ]
|XX 29000 - 29500 : [ 4 0.00 0.01 ]
|XX 29500 - 30000 : [ 4 0.00 0.01 ]
|XX 30000 - 30500 : [ 4 0.00 0.01 ]
|XXXX 30500 - 31000 : [ 8 0.01 0.02 ]
|XXXXXXXXX 31000 - 31500 : [ 16 0.01 0.03 ]
|XXX 31500 - 32000 : [ 6 0.01 0.04 ]
|XXXXXXXXX 32000 - 32500 : [ 16 0.01 0.05 ]
|XXXXXXXXXXX 32500 - 33000 : [ 20 0.02 0.07 ]
|XXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 32 0.03 0.10 ]
|XXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 36 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 47 0.04 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 50 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 61 0.05 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 62 0.05 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 47 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 72 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 64 0.05 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 68 0.06 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 65 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 69 0.06 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 67 0.06 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 48 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 50 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 40 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 37 0.03 0.84 ]
|XXXXXXXXXXXXXXXX 41500 - 42000 : [ 29 0.02 0.87 ]
|XXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 35 0.03 0.90 ]
|XXXXXXXXXXXXXX 42500 - 43000 : [ 26 0.02 0.92 ]
|XXXXXXXXXXXXXXXXX 43000 - 43500 : [ 30 0.03 0.94 ]
|XXXXXXXXX 43500 - 44000 : [ 17 0.01 0.96 ]
|XXXXXXXXX 44000 - 44500 : [ 17 0.01 0.97 ]
|XXXXX 44500 - 45000 : [ 9 0.01 0.98 ]
|XXXXXX 45000 - 45500 : [ 10 0.01 0.99 ]
|XXX 45500 - 46000 : [ 6 0.01 0.99 ]
|XXXX 46000 - 46500 : [ 7 0.01 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHZB 7553 +- 1196 (n=7441)
# AHZC 37646 +- 3538 (n=591)
# AHZA 3205 +- 823 (n=6810)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634481_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
AHZA 33792 -1 -1 99 732 32465 99 706 100 714
AHZB 38016 -1 -1 96 694 34809 99 676 100 688
AHZC 3840 -1 -1 96 622 3587 99 636 100 661
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHZA 16571 99 692 100 709 15894 99 720 100 720
AHZB 17623 99 683 100 699 17186 99 669 100 677
AHZC 1817 99 643 100 666 1770 98 628 100 656
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634481_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
172 32465 16187 94.11 98.03 AHZA @
196 34809 17694 90.28 94.04 AHZB @
20 3587 1878 93.90 97.81 AHZC @
] 70861 35759 92.16 cumulative total@@
LIBRARY PLATE ID COUNT [ AHZA 172 AHZB 196 AHZC 20 ] for 388 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 3634481_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 70861 total values totalling 48385952.0000. <682.829088 +/- 164.430928>
#Range: [ 15 - 927 ]
#Most likely bin: [ 750 - 800 ] 15479 counts
#Median bin: [ 700 - 750 ] 12232 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 121 0.00 0.00 ]
|X 50 - 100 : [ 450 0.01 0.01 ]
|X 100 - 150 : [ 573 0.01 0.02 ]
|XX 150 - 200 : [ 686 0.01 0.03 ]
|XX 200 - 250 : [ 778 0.01 0.04 ]
|XX 250 - 300 : [ 912 0.01 0.05 ]
|XXX 300 - 350 : [ 1067 0.02 0.06 ]
|XXX 350 - 400 : [ 1190 0.02 0.08 ]
|XXXX 400 - 450 : [ 1389 0.02 0.10 ]
|XXXX 450 - 500 : [ 1682 0.02 0.12 ]
|XXXXXX 500 - 550 : [ 2373 0.03 0.16 ]
|XXXXXXXX 550 - 600 : [ 3256 0.05 0.20 ]
|XXXXXXXXXXXXX 600 - 650 : [ 4918 0.07 0.27 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 8071 0.11 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 12232 0.17 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 15479 0.22 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 13016 0.18 0.96 ]
|XXXXXXX 850 - 900 : [ 2618 0.04 1.00 ]
| 900 - 950 : [ 50 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZA
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZA 3634481_fasta.screen.trimQ15.SaF > reads.trim15.AHZA.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZA.rl 2 50
-------------------------------------------------------------------
#Found 32465 total values totalling 22796244.0000. <702.179085 +/- 157.992103>
#Range: [ 15 - 927 ]
#Most likely bin: [ 750 - 800 ] 7501 counts
#Median bin: [ 750 - 800 ] 7501 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 32 0.00 0.00 ]
|X 50 - 100 : [ 147 0.00 0.01 ]
|X 100 - 150 : [ 212 0.01 0.01 ]
|X 150 - 200 : [ 281 0.01 0.02 ]
|XX 200 - 250 : [ 333 0.01 0.03 ]
|XX 250 - 300 : [ 326 0.01 0.04 ]
|XX 300 - 350 : [ 415 0.01 0.05 ]
|XXX 350 - 400 : [ 488 0.02 0.07 ]
|XXX 400 - 450 : [ 547 0.02 0.09 ]
|XXX 450 - 500 : [ 651 0.02 0.11 ]
|XXXXX 500 - 550 : [ 932 0.03 0.13 ]
|XXXXXXX 550 - 600 : [ 1265 0.04 0.17 ]
|XXXXXXXXXXX 600 - 650 : [ 2030 0.06 0.24 ]
|XXXXXXXXXXXXXXXXX 650 - 700 : [ 3225 0.10 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4826 0.15 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 7501 0.23 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7451 0.23 0.94 ]
|XXXXXXXXX 850 - 900 : [ 1761 0.05 1.00 ]
| 900 - 950 : [ 42 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZB
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZB 3634481_fasta.screen.trimQ15.SaF > reads.trim15.AHZB.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZB.rl 2 50
-------------------------------------------------------------------
#Found 34809 total values totalling 23339445.0000. <670.500302 +/- 166.996343>
#Range: [ 22 - 908 ]
#Most likely bin: [ 750 - 800 ] 7482 counts
#Median bin: [ 700 - 750 ] 6406 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 70 0.00 0.00 ]
|X 50 - 100 : [ 269 0.01 0.01 ]
|XX 100 - 150 : [ 318 0.01 0.02 ]
|XX 150 - 200 : [ 377 0.01 0.03 ]
|XX 200 - 250 : [ 397 0.01 0.04 ]
|XX 250 - 300 : [ 463 0.01 0.05 ]
|XXX 300 - 350 : [ 549 0.02 0.07 ]
|XXX 350 - 400 : [ 586 0.02 0.09 ]
|XXXX 400 - 450 : [ 764 0.02 0.11 ]
|XXXXX 450 - 500 : [ 971 0.03 0.14 ]
|XXXXXXX 500 - 550 : [ 1328 0.04 0.18 ]
|XXXXXXXXXX 550 - 600 : [ 1855 0.05 0.23 ]
|XXXXXXXXXXXXXX 600 - 650 : [ 2572 0.07 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4108 0.12 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6406 0.18 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 7482 0.21 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5433 0.16 0.98 ]
|XXXXX 850 - 900 : [ 853 0.02 1.00 ]
| 900 - 950 : [ 8 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZC
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZC 3634481_fasta.screen.trimQ15.SaF > reads.trim15.AHZC.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZC.rl 2 50
-------------------------------------------------------------------
#Found 3587 total values totalling 2250263.0000. <627.338444 +/- 172.142574>
#Range: [ 24 - 861 ]
#Most likely bin: [ 700 - 750 ] 1000 counts
#Median bin: [ 650 - 700 ] 738 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 19 0.01 0.01 ]
|X 50 - 100 : [ 34 0.01 0.01 ]
|XX 100 - 150 : [ 43 0.01 0.03 ]
|X 150 - 200 : [ 28 0.01 0.03 ]
|XX 200 - 250 : [ 48 0.01 0.05 ]
|XXXXX 250 - 300 : [ 123 0.03 0.08 ]
|XXXX 300 - 350 : [ 103 0.03 0.11 ]
|XXXXX 350 - 400 : [ 116 0.03 0.14 ]
|XXX 400 - 450 : [ 78 0.02 0.17 ]
|XX 450 - 500 : [ 60 0.02 0.18 ]
|XXXXX 500 - 550 : [ 113 0.03 0.21 ]
|XXXXX 550 - 600 : [ 136 0.04 0.25 ]
|XXXXXXXXXXXXX 600 - 650 : [ 316 0.09 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 738 0.21 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1000 0.28 0.82 ]
|XXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 496 0.14 0.96 ]
|XXXXX 800 - 850 : [ 132 0.04 1.00 ]
| 850 - 900 : [ 4 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634481
-------------------------------------------------------------------
AHZA.000001.000100 pUC18.fa LRS.fasta
AHZA.000101.000200 pUC18.fa LRS.fasta
AHZB.000001.000100 pMCL200.fa LRS.fasta
AHZB.000101.000200 pMCL200.fa LRS.fasta
AHZB.000201.000300 pMCL200.fa LRS.fasta
AHZC.000001.000100 pCC1Fos.fa.4 LRS.fasta
AHZA.000001.000100 pUC18.fa LRS.fasta
AHZA.000101.000200 pUC18.fa LRS.fasta
AHZB.000001.000100 pMCL200.fa LRS.fasta
AHZB.000101.000200 pMCL200.fa LRS.fasta
AHZB.000201.000300 pMCL200.fa LRS.fasta
AHZC.000001.000100 pCC1Fos.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634481_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634481_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 70721 total values totalling 47009.8994. <0.664723 +/- 0.043479>
#Range: [ 0 - 0.8837 ]
#Most likely bin: [ 0.67 - 0.675 ] 3920 counts
#Median bin: [ 0.665 - 0.67 ] 3754 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.25 - 0.255 : [ 1 0.00 0.00 ]
#...
| 0.32 - 0.325 : [ 1 0.00 0.00 ]
#...
| 0.335 - 0.34 : [ 1 0.00 0.00 ]
| 0.34 - 0.345 : [ 2 0.00 0.00 ]
#...
| 0.35 - 0.355 : [ 1 0.00 0.00 ]
#...
| 0.375 - 0.38 : [ 1 0.00 0.00 ]
#...
| 0.395 - 0.4 : [ 1 0.00 0.00 ]
| 0.4 - 0.405 : [ 1 0.00 0.00 ]
| 0.405 - 0.41 : [ 1 0.00 0.00 ]
#...
| 0.425 - 0.43 : [ 5 0.00 0.00 ]
| 0.43 - 0.435 : [ 5 0.00 0.00 ]
| 0.435 - 0.44 : [ 3 0.00 0.00 ]
| 0.44 - 0.445 : [ 15 0.00 0.00 ]
| 0.445 - 0.45 : [ 13 0.00 0.00 ]
| 0.45 - 0.455 : [ 10 0.00 0.00 ]
| 0.455 - 0.46 : [ 7 0.00 0.00 ]
| 0.46 - 0.465 : [ 8 0.00 0.00 ]
| 0.465 - 0.47 : [ 10 0.00 0.00 ]
| 0.47 - 0.475 : [ 11 0.00 0.00 ]
| 0.475 - 0.48 : [ 23 0.00 0.00 ]
| 0.48 - 0.485 : [ 20 0.00 0.00 ]
| 0.485 - 0.49 : [ 20 0.00 0.00 ]
| 0.49 - 0.495 : [ 25 0.00 0.00 ]
| 0.495 - 0.5 : [ 24 0.00 0.00 ]
| 0.5 - 0.505 : [ 37 0.00 0.00 ]
| 0.505 - 0.51 : [ 44 0.00 0.00 ]
|X 0.51 - 0.515 : [ 62 0.00 0.00 ]
|X 0.515 - 0.52 : [ 55 0.00 0.01 ]
|X 0.52 - 0.525 : [ 79 0.00 0.01 ]
|X 0.525 - 0.53 : [ 93 0.00 0.01 ]
|X 0.53 - 0.535 : [ 120 0.00 0.01 ]
|XX 0.535 - 0.54 : [ 149 0.00 0.01 ]
|XX 0.54 - 0.545 : [ 168 0.00 0.01 ]
|XX 0.545 - 0.55 : [ 172 0.00 0.02 ]
|XX 0.55 - 0.555 : [ 171 0.00 0.02 ]
|XX 0.555 - 0.56 : [ 214 0.00 0.02 ]
|XX 0.56 - 0.565 : [ 222 0.00 0.03 ]
|XXX 0.565 - 0.57 : [ 286 0.00 0.03 ]
|XXX 0.57 - 0.575 : [ 314 0.00 0.03 ]
|XXXX 0.575 - 0.58 : [ 377 0.01 0.04 ]
|XXXXX 0.58 - 0.585 : [ 465 0.01 0.05 ]
|XXXXX 0.585 - 0.59 : [ 514 0.01 0.05 ]
|XXXXXX 0.59 - 0.595 : [ 575 0.01 0.06 ]
|XXXXXXX 0.595 - 0.6 : [ 662 0.01 0.07 ]
|XXXXXXXX 0.6 - 0.605 : [ 832 0.01 0.08 ]
|XXXXXXXXXX 0.605 - 0.61 : [ 949 0.01 0.10 ]
|XXXXXXXXXXXX 0.61 - 0.615 : [ 1128 0.02 0.11 ]
|XXXXXXXXXXXXXX 0.615 - 0.62 : [ 1355 0.02 0.13 ]
|XXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1462 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 1755 0.02 0.18 ]
|XXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 2048 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 2316 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 2533 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 2964 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 3182 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 3647 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 3634 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 3754 0.05 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 3920 0.06 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 3836 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 3634 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 3470 0.05 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 3201 0.05 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 2804 0.04 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 2455 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 2151 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 1860 0.03 0.90 ]
|XXXXXXXXXXXXXXX 0.715 - 0.72 : [ 1502 0.02 0.92 ]
|XXXXXXXXXXXX 0.72 - 0.725 : [ 1207 0.02 0.94 ]
|XXXXXXXXXX 0.725 - 0.73 : [ 991 0.01 0.96 ]
|XXXXXXXX 0.73 - 0.735 : [ 753 0.01 0.97 ]
|XXXXXX 0.735 - 0.74 : [ 609 0.01 0.97 ]
|XXXXX 0.74 - 0.745 : [ 508 0.01 0.98 ]
|XXX 0.745 - 0.75 : [ 290 0.00 0.99 ]
|XX 0.75 - 0.755 : [ 234 0.00 0.99 ]
|XX 0.755 - 0.76 : [ 175 0.00 0.99 ]
|X 0.76 - 0.765 : [ 141 0.00 0.99 ]
|X 0.765 - 0.77 : [ 95 0.00 1.00 ]
|X 0.77 - 0.775 : [ 84 0.00 1.00 ]
|X 0.775 - 0.78 : [ 53 0.00 1.00 ]
|X 0.78 - 0.785 : [ 53 0.00 1.00 ]
| 0.785 - 0.79 : [ 28 0.00 1.00 ]
| 0.79 - 0.795 : [ 27 0.00 1.00 ]
| 0.795 - 0.8 : [ 14 0.00 1.00 ]
| 0.8 - 0.805 : [ 17 0.00 1.00 ]
| 0.805 - 0.81 : [ 9 0.00 1.00 ]
| 0.81 - 0.815 : [ 12 0.00 1.00 ]
| 0.815 - 0.82 : [ 7 0.00 1.00 ]
| 0.82 - 0.825 : [ 2 0.00 1.00 ]
| 0.825 - 0.83 : [ 5 0.00 1.00 ]
| 0.83 - 0.835 : [ 6 0.00 1.00 ]
| 0.835 - 0.84 : [ 5 0.00 1.00 ]
| 0.84 - 0.845 : [ 1 0.00 1.00 ]
| 0.845 - 0.85 : [ 7 0.00 1.00 ]
| 0.85 - 0.855 : [ 3 0.00 1.00 ]
| 0.855 - 0.86 : [ 1 0.00 1.00 ]
#...
| 0.87 - 0.875 : [ 1 0.00 1.00 ]
#...
| 0.88 - 0.885 : [ 2 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 18. 582 reads; 46720 bp (untrimmed), 46658 (trimmed).
Contig 19. 681 reads; 47825 bp (untrimmed), 47780 (trimmed).
Contig 20. 700 reads; 28544 bp (untrimmed), 28337 (trimmed).
Contig 21. 812 reads; 67100 bp (untrimmed), 66943 (trimmed).
Contig 22. 948 reads; 74968 bp (untrimmed), 74816 (trimmed).
Contig 23. 973 reads; 70524 bp (untrimmed), 70300 (trimmed).
Contig 24. 1023 reads; 77844 bp (untrimmed), 77844 (trimmed).
Contig 25. 1079 reads; 74767 bp (untrimmed), 74702 (trimmed).
Contig 26. 1209 reads; 89789 bp (untrimmed), 89656 (trimmed).
Contig 27. 1470 reads; 103685 bp (untrimmed), 103432 (trimmed).
Contig 28. 1665 reads; 113555 bp (untrimmed), 113404 (trimmed).
Contig 29. 1819 reads; 117082 bp (untrimmed), 117035 (trimmed).
Contig 30. 1836 reads; 145189 bp (untrimmed), 145053 (trimmed).
Contig 31. 1865 reads; 137503 bp (untrimmed), 137031 (trimmed).
Contig 32. 1926 reads; 141452 bp (untrimmed), 141221 (trimmed).
Contig 33. 2006 reads; 132480 bp (untrimmed), 132395 (trimmed).
Contig 34. 2300 reads; 170264 bp (untrimmed), 170209 (trimmed).
Contig 35. 2959 reads; 212324 bp (untrimmed), 212193 (trimmed).
Contig 36. 3166 reads; 242657 bp (untrimmed), 242537 (trimmed).
Contig 37. 3465 reads; 244055 bp (untrimmed), 243428 (trimmed).
Contig 38. 3473 reads; 240737 bp (untrimmed), 240704 (trimmed).
Contig 39. 3694 reads; 264567 bp (untrimmed), 264361 (trimmed).
Contig 40. 4325 reads; 339670 bp (untrimmed), 339462 (trimmed).
Contig 41. 4364 reads; 323800 bp (untrimmed), 323763 (trimmed).
Contig 42. 4375 reads; 349551 bp (untrimmed), 349505 (trimmed).
Contig 43. 6138 reads; 419269 bp (untrimmed), 419226 (trimmed).
Contig 44. 9355 reads; 710386 bp (untrimmed), 710100 (trimmed).
--------------------------------------------------------------
Totals 70820 reads; 5186874 bp (untrimmed), 5180145 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 5192766 bases = 11.94 +- 4.18 = 0.09 +- 3.74
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 49 total values totalling 491.7200. <10.035102 +/- 4.636101>
#Range: [ 1.35 - 21.60 ]
#Most likely bin: [ 11.5 - 12 ] 9 counts
#Median bin: [ 11.5 - 12 ] 9 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 1 - 1.5 : [ 1 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 6 0.12 0.14 ]
#...
|XXXX 2.5 - 3 : [ 1 0.02 0.16 ]
|XXXX 3 - 3.5 : [ 1 0.02 0.18 ]
#...
|XXXX 4 - 4.5 : [ 1 0.02 0.20 ]
|XXXX 4.5 - 5 : [ 1 0.02 0.22 ]
#...
|XXXXXXXXX 8.5 - 9 : [ 2 0.04 0.27 ]
#...
|XXXX 9.5 - 10 : [ 1 0.02 0.29 ]
|XXXX 10 - 10.5 : [ 1 0.02 0.31 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 3 0.06 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 6 0.12 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 9 0.18 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 6 0.12 0.80 ]
|XXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.08 0.88 ]
|XXXXXXXXXXXXX 13 - 13.5 : [ 3 0.06 0.94 ]
#...
|XXXX 14 - 14.5 : [ 1 0.02 0.96 ]
#...
|XXXX 21 - 21.5 : [ 1 0.02 0.98 ]
|XXXX 21.5 - 22 : [ 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 37 total values totalling 453.4500. <12.255405 +/- 2.462438>
#Range: [ 8.53 - 21.60 ]
#Most likely bin: [ 11.5 - 12 ] 9 counts
#Median bin: [ 11.5 - 12 ] 9 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 8.5 - 9 : [ 2 0.05 0.05 ]
#...
|XXXX 9.5 - 10 : [ 1 0.03 0.08 ]
|XXXX 10 - 10.5 : [ 1 0.03 0.11 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 3 0.08 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 5 0.14 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 9 0.24 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 6 0.16 0.73 ]
|XXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.11 0.84 ]
|XXXXXXXXXXXXX 13 - 13.5 : [ 3 0.08 0.92 ]
#...
|XXXX 14 - 14.5 : [ 1 0.03 0.95 ]
#...
|XXXX 21 - 21.5 : [ 1 0.03 0.97 ]
|XXXX 21.5 - 22 : [ 1 0.03 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 14 2 reads 984 bases = 1.35 +- 0.48 = -0.65 +- 0.48
Contig 18 2 reads 637 bases = 1.50 +- 0.50 = 0.43 +- 0.56
Contig 9 2 reads 1007 bases = 1.70 +- 0.46 = -0.05 +- 0.55
Contig 19 2 reads 1030 bases = 1.89 +- 0.31 = 1.89 +- 0.31
Contig 10 2 reads 790 bases = 1.95 +- 0.22 = -0.05 +- 0.22
Contig 13 2 reads 527 bases = 1.96 +- 0.20 = -0.04 +- 0.20
Contig 22 2 reads 757 bases = 1.98 +- 0.14 = -0.02 +- 0.14
Contig 24 3 reads 634 bases = 2.72 +- 0.56 = 2.72 +- 0.56
Contig 26 6 reads 1786 bases = 3.01 +- 0.38 = 0.07 +- 1.03
Contig 25 6 reads 1278 bases = 4.20 +- 1.77 = 2.78 +- 1.33
Contig 27 8 reads 1475 bases = 4.71 +- 1.91 = 3.51 +- 1.18
Contig 31 38 reads 3748 bases = 8.53 +- 3.72 = -0.15 +- 1.91
Contig 33 78 reads 7565 bases = 8.82 +- 2.96 = 0.51 +- 2.34
Contig 37 361 reads 32605 bases = 9.52 +- 3.39 = 0.60 +- 3.54
Contig 45 824 reads 67100 bases = 10.38 +- 3.44 = 0.27 +- 3.48
Contig 46 966 reads 74968 bases = 10.81 +- 4.09 = 0.21 +- 3.85
Contig 41 583 reads 46720 bases = 10.87 +- 4.16 = 0.19 +- 3.66
Contig 65 4416 reads 349551 bases = 10.87 +- 3.90 = 0.02 +- 3.62
Contig 63 4379 reads 339670 bases = 11.25 +- 3.71 = 0.03 +- 3.63
Contig 29 22 reads 554 bases = 11.30 +- 1.57 = -0.10 +- 1.00
Contig 50 1220 reads 89789 bases = 11.83 +- 3.83 = 0.06 +- 3.61
Contig 56 2319 reads 170264 bases = 11.84 +- 3.79 = -0.01 +- 3.81
Contig 42 631 reads 45930 bases = 11.91 +- 4.36 = 0.57 +- 2.99
Contig 47 984 reads 70527 bases = 11.94 +- 4.18 = 0.20 +- 3.78
Contig 55 2027 reads 141505 bases = 12.00 +- 3.80 = 0.12 +- 3.88
Contig 59 2978 reads 212324 bases = 12.08 +- 3.86 = 0.06 +- 3.87
Contig 34 80 reads 5527 bases = 12.22 +- 4.62 = 2.35 +- 4.31
Contig 62 3716 reads 264567 bases = 12.29 +- 4.98 = 0.06 +- 3.86
Contig 49 1092 reads 74767 bases = 12.35 +- 3.71 = -0.02 +- 3.82
Contig 35 204 reads 14583 bases = 12.44 +- 4.01 = -0.05 +- 2.51
Contig 61 3483 reads 244055 bases = 12.50 +- 3.92 = 0.12 +- 3.57
Contig 43 689 reads 47825 bases = 12.53 +- 3.81 = 0.25 +- 3.33
Contig 58 2774 reads 187433 bases = 12.84 +- 4.53 = -0.02 +- 3.99
Contig 66 6183 reads 419270 bases = 12.92 +- 4.16 = 0.02 +- 3.92
Contig 51 1346 reads 90260 bases = 13.08 +- 4.65 = 0.11 +- 4.52
Contig 54 2014 reads 132480 bases = 13.28 +- 4.31 = 0.13 +- 3.58
Contig 40 556 reads 35840 bases = 13.43 +- 3.75 = 0.47 +- 3.28
Contig 52 1385 reads 86546 bases = 14.04 +- 4.10 = -0.02 +- 4.14
Contig 32 71 reads 2537 bases = 21.25 +- 15.37 = 1.60 +- 5.72
Contig 44 707 reads 28544 bases = 21.60 +- 6.45 = 0.63 +- 4.62
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 50
Chimeric reads = 102
Suspect alignments = 265
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 3.57 SUN/Ultra-2/3
Equivalent to Phil Green's version 0.990329
Score matrix (set by value of penalty: -2)
A C G T N X
A 1 -2 -2 -2 0 -3
C -2 1 -2 -2 0 -3
G -2 -2 1 -2 0 -3
T -2 -2 -2 1 0 -3
N 0 0 0 0 0 0
X -3 -3 -3 -3 0 -3
gap_init: -4
gap_ext: -3
ins_gap_ext: -3
del_gap_ext: -3
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 30
maxmatch: 55
max_group_size: 20
minscore: 55
bandwidth: 14
indexwordsize: 10
vector_bound: 20
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 13
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -5
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/microbe2/3634481/edit_dir.04Jun07.QD