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: Joel Martin
Description: analysis of libraries in progress (or initial analysis of completed)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
4002191 2700 2371 Xylella fastidiosa
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Xylella_fastidiosa
-------------------------------------------------------------------
Xanthomonadales, order, g-proteobacteria
Xanthomonadaceae, family, g-proteobacteria
Xylella fastidiosa, species, g-proteobacteria
Xylella, genus, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2422854
# phrap: 2382798
# db:
altered.
2700000
2501884 +/- 141040
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 6759
Number of reads with percent X's >= 20%: 127 = 0.3%
Number of reads with percent X's >= 50%: 71 = 0.2%
Number of reads with percent X's >= 80%: 9 = 0.0%
Total reads in project: 37424
Total bp X'd : 287109
reads >= 20% >= 50% >= 80% screened
Nr with L09136 6702 121 69 9
Nr with pMCL200_JGI_XZX+XZK 57 6 2 0
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 4
Number of reads with percent X's >= 20%: 0 = 0.0%
Number of reads with percent X's >= 50%: 0 = 0.0%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 41
Total bp X'd : 128
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3 0 0 0
Nr with pMCL200_JGI_XZX+XZK 1 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 9557673
C = 9894679
G = 9927346
T = 9136940
N = 241201
X = 287109
GC fraction = 0.51
Total = 39044948
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 4002191_fasta.screen.contigs
-------------------------------------------------------------------
A 623718
C 671842
G 583857
T 545168
N 55
fraction GC = 0.52
total bases = 2424640
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 BONP reads.list > grep.reads.list.BONP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BONP 4 500
-------------------------------------------------------------------
#Found 8342 total values totalling 26342265.0000. <3157.787701 +/- 4741.202343>
#Range: [ 330 - 224673 ]
#Most likely bin: [ 3000 - 3500 ] 3451 counts
#Median bin: [ 3000 - 3500 ] 3451 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
#...
| 1000 - 1500 : [ 32 0.00 0.00 ]
|X 1500 - 2000 : [ 68 0.01 0.01 ]
|XXXXXX 2000 - 2500 : [ 493 0.06 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 3379 0.41 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3451 0.41 0.89 ]
|XXXXXXXXXX 3500 - 4000 : [ 893 0.11 1.00 ]
| 4000 - 4500 : [ 5 0.00 1.00 ]
| 4500 - 5000 : [ 4 0.00 1.00 ]
| 5000 - 5500 : [ 2 0.00 1.00 ]
| 5500 - 6000 : [ 2 0.00 1.00 ]
| 6000 - 6500 : [ 1 0.00 1.00 ]
#...
| 19000 - 19500 : [ 1 0.00 1.00 ]
#...
| 20000 - 20500 : [ 1 0.00 1.00 ]
#...
| 34500 - 35000 : [ 1 0.00 1.00 ]
#...
| 43000 - 43500 : [ 1 0.00 1.00 ]
#...
| 45500 - 46000 : [ 1 0.00 1.00 ]
#...
| 66500 - 67000 : [ 1 0.00 1.00 ]
#...
| 127500 - 128000 : [ 1 0.00 1.00 ]
#...
| 186000 - 186500 : [ 1 0.00 1.00 ]
#...
| 200500 - 201000 : [ 1 0.00 1.00 ]
#...
| 202500 - 203000 : [ 1 0.00 1.00 ]
#...
| 224500 - 225000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep BONS reads.list > grep.reads.list.BONS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BONS 4 500
-------------------------------------------------------------------
#Found 8638 total values totalling 69314717.0000. <8024.394188 +/- 2623.243848>
#Range: [ 1322 - 160380 ]
#Most likely bin: [ 7000 - 7500 ] 1638 counts
#Median bin: [ 7500 - 8000 ] 1543 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 3 0.00 0.00 ]
| 1500 - 2000 : [ 4 0.00 0.00 ]
| 2000 - 2500 : [ 5 0.00 0.00 ]
| 2500 - 3000 : [ 9 0.00 0.00 ]
| 3000 - 3500 : [ 8 0.00 0.00 ]
| 3500 - 4000 : [ 12 0.00 0.00 ]
| 4000 - 4500 : [ 19 0.00 0.01 ]
| 4500 - 5000 : [ 18 0.00 0.01 ]
|X 5000 - 5500 : [ 32 0.00 0.01 ]
|X 5500 - 6000 : [ 54 0.01 0.02 ]
|XXX 6000 - 6500 : [ 114 0.01 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1059 0.12 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1638 0.19 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1543 0.18 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1536 0.18 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 1121 0.13 0.83 ]
|XXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 767 0.09 0.92 ]
|XXXXXXXXXXX 9500 - 10000 : [ 454 0.05 0.97 ]
|XXXX 10000 - 10500 : [ 176 0.02 0.99 ]
|X 10500 - 11000 : [ 56 0.01 1.00 ]
| 11000 - 11500 : [ 7 0.00 1.00 ]
#...
| 74000 - 74500 : [ 1 0.00 1.00 ]
#...
| 156500 - 157000 : [ 1 0.00 1.00 ]
#...
| 160000 - 160500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# BONP 2876 +- 977 (n=4133)
# BONS 7946 +- 1059 (n=4371)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 4002191_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
BONP 22656 86 662 93 728 18537 97 687 100 721
BONS 19968 94 768 97 734 18887 100 768 100 761
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
BONP 9149 98 684 100 722 9388 97 689 100 720
BONS 9427 100 769 100 762 9460 100 767 100 759
-------------------------------------------------------------------
reads2plates summary
extracted from file: 4002191_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
100 18537 9259 92.59 96.45 BONP @
104 18887 9592 92.23 96.07 BONS @
] 37424 18851 92.41 cumulative total@@
LIBRARY PLATE ID COUNT [ BONP 100 BONS 104 ] for 204 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 4002191_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 37424 total values totalling 26873194.0000. <718.073803 +/- 191.944759>
#Range: [ 16 - 964 ]
#Most likely bin: [ 800 - 850 ] 10212 counts
#Median bin: [ 750 - 800 ] 8088 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 121 0.00 0.00 ]
|XX 50 - 100 : [ 452 0.01 0.02 ]
|XXX 100 - 150 : [ 642 0.02 0.03 ]
|XX 150 - 200 : [ 586 0.02 0.05 ]
|XX 200 - 250 : [ 485 0.01 0.06 ]
|XX 250 - 300 : [ 415 0.01 0.07 ]
|XX 300 - 350 : [ 408 0.01 0.08 ]
|XX 350 - 400 : [ 436 0.01 0.09 ]
|XX 400 - 450 : [ 499 0.01 0.11 ]
|XX 450 - 500 : [ 551 0.01 0.12 ]
|XX 500 - 550 : [ 608 0.02 0.14 ]
|XXX 550 - 600 : [ 814 0.02 0.16 ]
|XXXX 600 - 650 : [ 1140 0.03 0.19 ]
|XXXXXXXX 650 - 700 : [ 2053 0.05 0.25 ]
|XXXXXXXXXXXXXXXX 700 - 750 : [ 4040 0.11 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8088 0.22 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 10212 0.27 0.84 ]
|XXXXXXXXXXXXXXXXXXXX 850 - 900 : [ 5162 0.14 0.98 ]
|XXX 900 - 950 : [ 691 0.02 1.00 ]
| 950 - 1000 : [ 21 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for BONT
trimt JAZZ trim 15 readlength histogram for BONU
trimt JAZZ trim 15 readlength histogram for BONW
trimt JAZZ trim 15 readlength histogram for BONP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep BONP 4002191_fasta.screen.trimQ15.SaF > reads.trim15.BONP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.BONP.rl 2 50
-------------------------------------------------------------------
#Found 18537 total values totalling 12429142.0000. <670.504505 +/- 229.769429>
#Range: [ 20 - 964 ]
#Most likely bin: [ 800 - 850 ] 3892 counts
#Median bin: [ 750 - 800 ] 3264 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 95 0.01 0.01 ]
|XXXX 50 - 100 : [ 386 0.02 0.03 ]
|XXXXXX 100 - 150 : [ 585 0.03 0.06 ]
|XXXXX 150 - 200 : [ 514 0.03 0.09 ]
|XXXX 200 - 250 : [ 394 0.02 0.11 ]
|XXX 250 - 300 : [ 321 0.02 0.12 ]
|XXX 300 - 350 : [ 308 0.02 0.14 ]
|XXX 350 - 400 : [ 287 0.02 0.16 ]
|XXX 400 - 450 : [ 330 0.02 0.17 ]
|XXXX 450 - 500 : [ 368 0.02 0.19 ]
|XXXX 500 - 550 : [ 414 0.02 0.22 ]
|XXXXXX 550 - 600 : [ 563 0.03 0.25 ]
|XXXXXXXX 600 - 650 : [ 740 0.04 0.29 ]
|XXXXXXXXXXXX 650 - 700 : [ 1200 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1993 0.11 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3264 0.18 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3892 0.21 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 850 - 900 : [ 2415 0.13 0.97 ]
|XXXXX 900 - 950 : [ 449 0.02 1.00 ]
| 950 - 1000 : [ 19 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for BONS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep BONS 4002191_fasta.screen.trimQ15.SaF > reads.trim15.BONS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.BONS.rl 2 50
-------------------------------------------------------------------
#Found 18887 total values totalling 14444052.0000. <764.761582 +/- 129.562853>
#Range: [ 16 - 960 ]
#Most likely bin: [ 800 - 850 ] 6320 counts
#Median bin: [ 750 - 800 ] 4824 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 26 0.00 0.00 ]
| 50 - 100 : [ 66 0.00 0.00 ]
| 100 - 150 : [ 57 0.00 0.01 ]
| 150 - 200 : [ 72 0.00 0.01 ]
|X 200 - 250 : [ 91 0.00 0.02 ]
|X 250 - 300 : [ 94 0.00 0.02 ]
|X 300 - 350 : [ 100 0.01 0.03 ]
|X 350 - 400 : [ 149 0.01 0.03 ]
|X 400 - 450 : [ 169 0.01 0.04 ]
|X 450 - 500 : [ 183 0.01 0.05 ]
|X 500 - 550 : [ 194 0.01 0.06 ]
|XX 550 - 600 : [ 251 0.01 0.08 ]
|XXX 600 - 650 : [ 400 0.02 0.10 ]
|XXXXX 650 - 700 : [ 853 0.05 0.14 ]
|XXXXXXXXXXXXX 700 - 750 : [ 2047 0.11 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4824 0.26 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6320 0.33 0.84 ]
|XXXXXXXXXXXXXXXXX 850 - 900 : [ 2747 0.15 0.99 ]
|XX 900 - 950 : [ 242 0.01 1.00 ]
| 950 - 1000 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 4002191
-------------------------------------------------------------------
BONP.000001.000100 pUC18.fa pUC18.fa LRS.fasta
BONP.000101.000200 pUC18.fa pUC18.fa LRS.fasta
BONS.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
BONS.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
BONP.000001.000100 pUC18.fa pUC18.fa LRS.fasta
BONP.000101.000200 pUC18.fa pUC18.fa LRS.fasta
BONS.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
BONS.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.4002191_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.4002191_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 37298 total values totalling 19286.3407. <0.517088 +/- 0.057083>
#Range: [ 0 - 0.7949 ]
#Most likely bin: [ 0.525 - 0.53 ] 1652 counts
#Median bin: [ 0.52 - 0.525 ] 1578 counts
#Entropy = 5.4870 bits
| 0 - 0.005 : [ 1 2.68e-05 2.68e-05 1 ]
#...
| 0.03 - 0.035 : [ 1 2.68e-05 5.36e-05 2 ]
#...
| 0.135 - 0.14 : [ 1 2.68e-05 8.04e-05 3 ]
#...
| 0.185 - 0.19 : [ 1 2.68e-05 1.07e-04 4 ]
| 0.19 - 0.195 : [ 1 2.68e-05 1.34e-04 5 ]
#...
| 0.21 - 0.215 : [ 1 2.68e-05 1.61e-04 6 ]
| 0.215 - 0.22 : [ 1 2.68e-05 1.88e-04 7 ]
| 0.22 - 0.225 : [ 4 1.07e-04 2.95e-04 11 ]
| 0.225 - 0.23 : [ 2 5.36e-05 3.49e-04 13 ]
| 0.23 - 0.235 : [ 1 2.68e-05 3.75e-04 14 ]
| 0.235 - 0.24 : [ 3 8.04e-05 4.56e-04 17 ]
#...
| 0.245 - 0.25 : [ 4 1.07e-04 5.63e-04 21 ]
| 0.25 - 0.255 : [ 3 8.04e-05 6.43e-04 24 ]
| 0.255 - 0.26 : [ 4 1.07e-04 7.51e-04 28 ]
| 0.26 - 0.265 : [ 3 8.04e-05 8.31e-04 31 ]
| 0.265 - 0.27 : [ 2 5.36e-05 8.85e-04 33 ]
| 0.27 - 0.275 : [ 4 1.07e-04 9.92e-04 37 ]
| 0.275 - 0.28 : [ 9 2.41e-04 1.23e-03 46 ]
| 0.28 - 0.285 : [ 6 1.61e-04 1.39e-03 52 ]
| 0.285 - 0.29 : [ 13 3.49e-04 1.74e-03 65 ]
| 0.29 - 0.295 : [ 9 2.41e-04 1.98e-03 74 ]
| 0.295 - 0.3 : [ 16 4.29e-04 2.41e-03 90 ]
| 0.3 - 0.305 : [ 18 4.83e-04 2.90e-03 108 ]
|X 0.305 - 0.31 : [ 23 6.17e-04 3.51e-03 131 ]
| 0.31 - 0.315 : [ 13 3.49e-04 3.86e-03 144 ]
| 0.315 - 0.32 : [ 15 4.02e-04 4.26e-03 159 ]
|X 0.32 - 0.325 : [ 25 6.70e-04 4.93e-03 184 ]
|X 0.325 - 0.33 : [ 27 7.24e-04 5.66e-03 211 ]
|X 0.33 - 0.335 : [ 40 1.07e-03 6.73e-03 251 ]
|X 0.335 - 0.34 : [ 44 1.18e-03 7.91e-03 295 ]
|X 0.34 - 0.345 : [ 52 1.39e-03 9.30e-03 347 ]
|X 0.345 - 0.35 : [ 55 1.47e-03 1.08e-02 402 ]
|X 0.35 - 0.355 : [ 61 1.64e-03 1.24e-02 463 ]
|XX 0.355 - 0.36 : [ 76 2.04e-03 1.45e-02 539 ]
|XX 0.36 - 0.365 : [ 93 2.49e-03 1.69e-02 632 ]
|XX 0.365 - 0.37 : [ 101 2.71e-03 1.97e-02 733 ]
|XX 0.37 - 0.375 : [ 87 2.33e-03 2.20e-02 820 ]
|XX 0.375 - 0.38 : [ 94 2.52e-03 2.45e-02 914 ]
|XXX 0.38 - 0.385 : [ 112 3.00e-03 2.75e-02 1026 ]
|XXX 0.385 - 0.39 : [ 140 3.75e-03 3.13e-02 1166 ]
|XXX 0.39 - 0.395 : [ 134 3.59e-03 3.49e-02 1300 ]
|XXX 0.395 - 0.4 : [ 141 3.78e-03 3.86e-02 1441 ]
|XXXX 0.4 - 0.405 : [ 174 4.67e-03 4.33e-02 1615 ]
|XXXXX 0.405 - 0.41 : [ 207 5.55e-03 4.88e-02 1822 ]
|XXXXX 0.41 - 0.415 : [ 217 5.82e-03 5.47e-02 2039 ]
|XXXXX 0.415 - 0.42 : [ 227 6.09e-03 6.08e-02 2266 ]
|XXXXXX 0.42 - 0.425 : [ 256 6.86e-03 6.76e-02 2522 ]
|XXXXXXX 0.425 - 0.43 : [ 280 7.51e-03 7.51e-02 2802 ]
|XXXXXXX 0.43 - 0.435 : [ 296 7.94e-03 8.31e-02 3098 ]
|XXXXXXXX 0.435 - 0.44 : [ 336 9.01e-03 9.21e-02 3434 ]
|XXXXXXXXX 0.44 - 0.445 : [ 362 9.71e-03 1.02e-01 3796 ]
|XXXXXXXXXX 0.445 - 0.45 : [ 406 1.09e-02 1.13e-01 4202 ]
|XXXXXXXXXXX 0.45 - 0.455 : [ 441 1.18e-02 1.24e-01 4643 ]
|XXXXXXXXXXXXX 0.455 - 0.46 : [ 533 1.43e-02 1.39e-01 5176 ]
|XXXXXXXXXXXXX 0.46 - 0.465 : [ 555 1.49e-02 1.54e-01 5731 ]
|XXXXXXXXXXXXXXX 0.465 - 0.47 : [ 618 1.66e-02 1.70e-01 6349 ]
|XXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 712 1.91e-02 1.89e-01 7061 ]
|XXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 759 2.03e-02 2.10e-01 7820 ]
|XXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 859 2.30e-02 2.33e-01 8679 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 954 2.56e-02 2.58e-01 9633 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1040 2.79e-02 2.86e-01 10673 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1090 2.92e-02 3.15e-01 11763 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1451 3.89e-02 3.54e-01 13214 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1357 3.64e-02 3.91e-01 14571 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1525 4.09e-02 4.32e-01 16096 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1556 4.17e-02 4.73e-01 17652 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1578 4.23e-02 5.16e-01 19230 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1652 4.43e-02 5.60e-01 20882 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1596 4.28e-02 6.03e-01 22478 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1629 4.37e-02 6.46e-01 24107 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1533 4.11e-02 6.87e-01 25640 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1530 4.10e-02 7.28e-01 27170 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1343 3.60e-02 7.64e-01 28513 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1171 3.14e-02 7.96e-01 29684 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1129 3.03e-02 8.26e-01 30813 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 968 2.60e-02 8.52e-01 31781 ]
|XXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 849 2.28e-02 8.75e-01 32630 ]
|XXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 717 1.92e-02 8.94e-01 33347 ]
|XXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 663 1.78e-02 9.12e-01 34010 ]
|XXXXXXXXXXXXX 0.585 - 0.59 : [ 535 1.43e-02 9.26e-01 34545 ]
|XXXXXXXXXXXX 0.59 - 0.595 : [ 491 1.32e-02 9.39e-01 35036 ]
|XXXXXXXXXXX 0.595 - 0.6 : [ 437 1.17e-02 9.51e-01 35473 ]
|XXXXXXXXX 0.6 - 0.605 : [ 359 9.63e-03 9.61e-01 35832 ]
|XXXXXX 0.605 - 0.61 : [ 268 7.19e-03 9.68e-01 36100 ]
|XXXXXX 0.61 - 0.615 : [ 248 6.65e-03 9.75e-01 36348 ]
|XXXXX 0.615 - 0.62 : [ 218 5.84e-03 9.80e-01 36566 ]
|XXX 0.62 - 0.625 : [ 139 3.73e-03 9.84e-01 36705 ]
|XXX 0.625 - 0.63 : [ 115 3.08e-03 9.87e-01 36820 ]
|XX 0.63 - 0.635 : [ 94 2.52e-03 9.90e-01 36914 ]
|XX 0.635 - 0.64 : [ 94 2.52e-03 9.92e-01 37008 ]
|XX 0.64 - 0.645 : [ 64 1.72e-03 9.94e-01 37072 ]
|X 0.645 - 0.65 : [ 34 9.12e-04 9.95e-01 37106 ]
|X 0.65 - 0.655 : [ 41 1.10e-03 9.96e-01 37147 ]
|X 0.655 - 0.66 : [ 32 8.58e-04 9.97e-01 37179 ]
|X 0.66 - 0.665 : [ 22 5.90e-04 9.97e-01 37201 ]
| 0.665 - 0.67 : [ 20 5.36e-04 9.98e-01 37221 ]
| 0.67 - 0.675 : [ 8 2.14e-04 9.98e-01 37229 ]
| 0.675 - 0.68 : [ 10 2.68e-04 9.98e-01 37239 ]
| 0.68 - 0.685 : [ 8 2.14e-04 9.99e-01 37247 ]
| 0.685 - 0.69 : [ 6 1.61e-04 9.99e-01 37253 ]
| 0.69 - 0.695 : [ 11 2.95e-04 9.99e-01 37264 ]
| 0.695 - 0.7 : [ 10 2.68e-04 9.99e-01 37274 ]
| 0.7 - 0.705 : [ 9 2.41e-04 1.00e+00 37283 ]
| 0.705 - 0.71 : [ 3 8.04e-05 1.00e+00 37286 ]
| 0.71 - 0.715 : [ 1 2.68e-05 1.00e+00 37287 ]
| 0.715 - 0.72 : [ 4 1.07e-04 1.00e+00 37291 ]
| 0.72 - 0.725 : [ 1 2.68e-05 1.00e+00 37292 ]
| 0.725 - 0.73 : [ 2 5.36e-05 1.00e+00 37294 ]
| 0.73 - 0.735 : [ 1 2.68e-05 1.00e+00 37295 ]
#...
| 0.74 - 0.745 : [ 1 2.68e-05 1.00e+00 37296 ]
#...
| 0.75 - 0.755 : [ 1 2.68e-05 1.00e+00 37297 ]
#...
| 0.79 - 0.795 : [ 1 2.68e-05 1.00e+00 37298 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
--------------------------------------------------------------
Contig 1. 2 reads; 1045 bp (untrimmed), 851 (trimmed).
Contig 2. 4 reads; 194 bp (untrimmed), 194 (trimmed).
Contig 3. 26 reads; 3322 bp (untrimmed), 3242 (trimmed).
Contig 4. 129 reads; 10808 bp (untrimmed), 10748 (trimmed).
Contig 5. 223 reads; 17872 bp (untrimmed), 17846 (trimmed).
Contig 6. 300 reads; 26183 bp (untrimmed), 26141 (trimmed).
Contig 7. 525 reads; 32682 bp (untrimmed), 32635 (trimmed).
Contig 8. 568 reads; 36933 bp (untrimmed), 36768 (trimmed).
Contig 9. 1451 reads; 96139 bp (untrimmed), 95953 (trimmed).
Contig 10. 1458 reads; 97719 bp (untrimmed), 97658 (trimmed).
Contig 11. 1584 reads; 86557 bp (untrimmed), 86505 (trimmed).
Contig 12. 1627 reads; 108757 bp (untrimmed), 108470 (trimmed).
Contig 13. 2245 reads; 143571 bp (untrimmed), 143510 (trimmed).
Contig 14. 4066 reads; 258608 bp (untrimmed), 258516 (trimmed).
Contig 15. 4481 reads; 285602 bp (untrimmed), 285465 (trimmed).
Contig 16. 4744 reads; 324115 bp (untrimmed), 323922 (trimmed).
Contig 17. 6466 reads; 408968 bp (untrimmed), 408919 (trimmed).
Contig 18. 7484 reads; 485565 bp (untrimmed), 485511 (trimmed).
--------------------------------------------------------------
Totals 37383 reads; 2424640 bp (untrimmed), 2422854 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2424446 bases = 15.00 +- 4.98 = 0.22 +- 4.40
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 17 total values totalling 226.1800. <13.304706 +/- 3.739815>
#Range: [ 1.21 - 17.87 ]
#Most likely bin: [ 15 - 15.5 ] 4 counts
#Median bin: [ 14.5 - 15 ] 4 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 1 - 1.5 : [ 1 0.06 0.06 ]
#...
|XXXXXXXXXX 7.5 - 8 : [ 1 0.06 0.12 ]
#...
|XXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 2 0.12 0.24 ]
#...
|XXXXXXXXXX 12 - 12.5 : [ 1 0.06 0.29 ]
#...
|XXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 2 0.12 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 14.5 - 15 : [ 4 0.24 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15 - 15.5 : [ 4 0.24 0.88 ]
|XXXXXXXXXX 15.5 - 16 : [ 1 0.06 0.94 ]
#...
|XXXXXXXXXX 17.5 - 18 : [ 1 0.06 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 16 total values totalling 224.9700. <14.060625 +/- 2.268550>
#Range: [ 7.99 - 17.87 ]
#Most likely bin: [ 15 - 15.5 ] 4 counts
#Median bin: [ 14.5 - 15 ] 4 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 7.5 - 8 : [ 1 0.06 0.06 ]
#...
|XXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 2 0.12 0.19 ]
#...
|XXXXXXXXXX 12 - 12.5 : [ 1 0.06 0.25 ]
#...
|XXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 2 0.12 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 14.5 - 15 : [ 4 0.25 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15 - 15.5 : [ 4 0.25 0.88 ]
|XXXXXXXXXX 15.5 - 16 : [ 1 0.06 0.94 ]
#...
|XXXXXXXXXX 17.5 - 18 : [ 1 0.06 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 1 2 reads 1045 bases = 1.21 +- 0.41 = -0.79 +- 0.41
Contig 3 26 reads 3322 bases = 7.99 +- 4.28 = 5.43 +- 4.61
Contig 6 300 reads 26183 bases = 11.20 +- 3.76 = 1.08 +- 3.32
Contig 4 129 reads 10808 bases = 11.29 +- 3.99 = 3.68 +- 4.61
Contig 5 223 reads 17872 bases = 12.03 +- 4.57 = 0.29 +- 5.36
Contig 16 4744 reads 324115 bases = 14.25 +- 4.93 = -0.05 +- 4.28
Contig 12 1627 reads 108757 bases = 14.38 +- 4.99 = 0.36 +- 4.96
Contig 10 1458 reads 97719 bases = 14.58 +- 4.40 = 0.38 +- 4.51
Contig 9 1451 reads 96139 bases = 14.64 +- 4.98 = -0.08 +- 4.13
Contig 8 568 reads 36933 bases = 14.92 +- 4.92 = 0.73 +- 4.86
Contig 18 7484 reads 485565 bases = 14.98 +- 4.35 = 0.21 +- 4.24
Contig 13 2245 reads 143571 bases = 15.24 +- 4.42 = 0.44 +- 3.94
Contig 15 4481 reads 285602 bases = 15.24 +- 4.54 = 0.19 +- 4.21
Contig 14 4066 reads 258608 bases = 15.29 +- 4.58 = 0.28 +- 4.66
Contig 17 6466 reads 408968 bases = 15.42 +- 5.11 = 0.09 +- 4.45
Contig 7 525 reads 32682 bases = 15.65 +- 4.95 = 0.04 +- 4.73
Contig 11 1584 reads 86557 bases = 17.87 +- 8.72 = 0.26 +- 4.67
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 391
HQ Discrepant reads = 9
Chimeric reads = 72
Suspect alignments = 232
-------------------------------------------------------------------
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/microbe3/4002191/edit_dir.deleteme.20Nov05.QD