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
3634472 2400 1102 Prosthecochloris aestuarii
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Prosthecochloris_aestuarii
-------------------------------------------------------------------
Chlorobiaceae, family, green sulfur bacteria
Chlorobiales, order, green sulfur bacteria
Chlorobia, class, green sulfur bacteria
Bacteroidetes/Chlorobi group, superphylum, eubacteria
Prosthecochloris aestuarii, species, green sulfur bacteria
Prosthecochloris, genus, green sulfur bacteria
Chlorobi, phylum, green sulfur bacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2553339
# phrap: 2491784
# db:
altered.
2400000
2481707 +/- 63004
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 7401
Number of reads with percent X's >= 20%: 109 = 0.3%
Number of reads with percent X's >= 50%: 55 = 0.2%
Number of reads with percent X's >= 80%: 6 = 0.0%
Total reads in project: 35484
Total bp X'd : 323843
reads >= 20% >= 50% >= 80% screened
Nr with L09136 6849 77 38 2
Nr with pCC1Fos 499 1 0 0
Nr with pMCL200_JGI_XZX+XZK 53 31 17 4
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 23
Number of reads with percent X's >= 20%: 2 = 1.5%
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: 137
Total bp X'd : 1194
reads >= 20% >= 50% >= 80% screened
Nr with L09136 21 1 0 0
Nr with pCC1Fos 2 1 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 8454701
C = 8459911
G = 8441177
T = 8277656
N = 156478
X = 323843
GC fraction = 0.50
Total = 34113766
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634472_fasta.screen.contigs
-------------------------------------------------------------------
A 645595
C 643655
G 638507
T 635381
N 59
fraction GC = 0.50
total bases = 2563197
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 AHXO reads.list > grep.reads.list.AHXO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXO 4 500
-------------------------------------------------------------------
#Found 6466 total values totalling 23932413.0000. <3701.270182 +/- 512.628380>
#Range: [ 679 - 8290 ]
#Most likely bin: [ 3500 - 4000 ] 3066 counts
#Median bin: [ 3500 - 4000 ] 3066 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 9 0.00 0.00 ]
| 1000 - 1500 : [ 34 0.01 0.01 ]
|X 1500 - 2000 : [ 55 0.01 0.02 ]
|XX 2000 - 2500 : [ 129 0.02 0.04 ]
|XXX 2500 - 3000 : [ 205 0.03 0.07 ]
|XXXXXXXXXXXXXXXX 3000 - 3500 : [ 1199 0.19 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3066 0.47 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1678 0.26 0.99 ]
|X 4500 - 5000 : [ 90 0.01 1.00 ]
#...
| 8000 - 8500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXP reads.list > grep.reads.list.AHXP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXP 4 500
-------------------------------------------------------------------
#Found 7640 total values totalling 50028080.0000. <6548.178010 +/- 2028.202356>
#Range: [ 1013 - 107369 ]
#Most likely bin: [ 6000 - 6500 ] 1954 counts
#Median bin: [ 6500 - 7000 ] 1786 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1000 - 1500 : [ 25 0.00 0.00 ]
| 1500 - 2000 : [ 18 0.00 0.01 ]
|X 2000 - 2500 : [ 30 0.00 0.01 ]
|X 2500 - 3000 : [ 37 0.00 0.01 ]
|X 3000 - 3500 : [ 43 0.01 0.02 ]
|X 3500 - 4000 : [ 47 0.01 0.03 ]
|X 4000 - 4500 : [ 67 0.01 0.03 ]
|XX 4500 - 5000 : [ 116 0.02 0.05 ]
|XXXXX 5000 - 5500 : [ 233 0.03 0.08 ]
|XXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1018 0.13 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1954 0.26 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1786 0.23 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1361 0.18 0.88 ]
|XXXXXXXXXXXXXXX 7500 - 8000 : [ 754 0.10 0.98 ]
|XXX 8000 - 8500 : [ 138 0.02 1.00 ]
#...
| 9000 - 9500 : [ 6 0.00 1.00 ]
| 9500 - 10000 : [ 1 0.00 1.00 ]
#...
| 16500 - 17000 : [ 1 0.00 1.00 ]
#...
| 26000 - 26500 : [ 1 0.00 1.00 ]
#...
| 45500 - 46000 : [ 1 0.00 1.00 ]
#...
| 74000 - 74500 : [ 1 0.00 1.00 ]
#...
| 93000 - 93500 : [ 1 0.00 1.00 ]
#...
| 107000 - 107500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXS reads.list > grep.reads.list.AHXS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXS 4 500
-------------------------------------------------------------------
#Found 804 total values totalling 30476119.0000. <37905.620647 +/- 4015.954426>
#Range: [ 22362 - 47009 ]
#Most likely bin: [ 38500 - 39000 ] 41 counts
#Median bin: [ 38000 - 38500 ] 33 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 22000 - 22500 : [ 1 0.00 0.00 ]
#...
|XX 23000 - 23500 : [ 2 0.00 0.00 ]
#...
|XX 24000 - 24500 : [ 2 0.00 0.01 ]
|XX 24500 - 25000 : [ 2 0.00 0.01 ]
#...
|XX 25500 - 26000 : [ 2 0.00 0.01 ]
#...
|XX 26500 - 27000 : [ 2 0.00 0.01 ]
#...
|X 27500 - 28000 : [ 1 0.00 0.01 ]
|X 28000 - 28500 : [ 1 0.00 0.02 ]
|XXXXX 28500 - 29000 : [ 5 0.01 0.02 ]
#...
|XXXXX 29500 - 30000 : [ 5 0.01 0.03 ]
|XXX 30000 - 30500 : [ 3 0.00 0.03 ]
|XXXXXXXX 30500 - 31000 : [ 8 0.01 0.04 ]
|XXXXXXXXXXX 31000 - 31500 : [ 11 0.01 0.06 ]
|XXXXXXXXXX 31500 - 32000 : [ 10 0.01 0.07 ]
|XXXXXXXXXXXXX 32000 - 32500 : [ 13 0.02 0.08 ]
|XXXXXXXXXXXXXXXXX 32500 - 33000 : [ 17 0.02 0.11 ]
|XXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 19 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 20 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 28 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 26 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 38 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 35 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 38 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 38 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 38 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 32 0.04 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 33 0.04 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 41 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 32 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 26 0.03 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 38 0.05 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 36 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 38 0.05 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 40 0.05 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 25 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 20 0.02 0.90 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 28 0.03 0.94 ]
|XXXXXXXXX 43500 - 44000 : [ 9 0.01 0.95 ]
|XXXXXXXXXXXXXX 44000 - 44500 : [ 14 0.02 0.97 ]
|XXXXXXXXXXX 44500 - 45000 : [ 11 0.01 0.98 ]
|XXXXXXXXX 45000 - 45500 : [ 9 0.01 0.99 ]
|XXXXX 45500 - 46000 : [ 5 0.01 1.00 ]
|X 46000 - 46500 : [ 1 0.00 1.00 ]
#...
|X 47000 - 47500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHXP 6459 +- 1213 (n=3918)
# AHXS 37959 +- 3904 (n=415)
# AHXO 3570 +- 557 (n=3322)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634472_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
AHXO 17664 -1 -1 96 686 17091 91 623 95 636
AHXP 18432 -1 -1 95 701 18432 92 751 95 740
AHXS 3072 -1 -1 95 541 3072 89 548 95 569
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHXO 8669 92 618 96 636 8422 90 629 94 637
AHXP 9216 91 747 94 736 9216 93 755 95 744
AHXS 1536 89 550 95 570 1536 88 547 95 568
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634472_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
16 2821 1487 92.94 96.81 AHXS @
83 15740 7584 91.37 95.18 AHXO @
96 16923 8604 89.62 93.36 AHXP @
] 35484 17675 90.64 cumulative total@@
LIBRARY PLATE ID COUNT [ AHXS 16 AHXO 83 AHXP 96 ] for 195 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 3634472_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 38595 total values totalling 23930813.0000. <620.049566 +/- 244.317638>
#Range: [ 0 - 963 ]
#Most likely bin: [ 750 - 800 ] 8708 counts
#Median bin: [ 700 - 750 ] 6593 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXX 0 - 50 : [ 2972 0.08 0.08 ]
|XX 50 - 100 : [ 450 0.01 0.09 ]
|XX 100 - 150 : [ 396 0.01 0.10 ]
|XX 150 - 200 : [ 377 0.01 0.11 ]
|XX 200 - 250 : [ 477 0.01 0.12 ]
|XXX 250 - 300 : [ 686 0.02 0.14 ]
|XXX 300 - 350 : [ 622 0.02 0.15 ]
|XXX 350 - 400 : [ 657 0.02 0.17 ]
|XXX 400 - 450 : [ 696 0.02 0.19 ]
|XXXX 450 - 500 : [ 792 0.02 0.21 ]
|XXXXX 500 - 550 : [ 988 0.03 0.24 ]
|XXXXXXX 550 - 600 : [ 1527 0.04 0.28 ]
|XXXXXXXXXXX 600 - 650 : [ 2318 0.06 0.34 ]
|XXXXXXXXXXXXXXXXXX 650 - 700 : [ 3912 0.10 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6593 0.17 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8708 0.23 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5542 0.14 0.98 ]
|XXXX 850 - 900 : [ 838 0.02 1.00 ]
| 900 - 950 : [ 40 0.00 1.00 ]
| 950 - 1000 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXO 3634472_fasta.screen.trimQ15.SaF > reads.trim15.AHXO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXO.rl 2 50
-------------------------------------------------------------------
#Found 17091 total values totalling 9721387.0000. <568.801533 +/- 242.866167>
#Range: [ 0 - 963 ]
#Most likely bin: [ 700 - 750 ] 2908 counts
#Median bin: [ 650 - 700 ] 2192 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXX 0 - 50 : [ 1251 0.07 0.07 ]
|XXXX 50 - 100 : [ 298 0.02 0.09 ]
|XXXX 100 - 150 : [ 287 0.02 0.11 ]
|XXXX 150 - 200 : [ 289 0.02 0.12 ]
|XXXXX 200 - 250 : [ 349 0.02 0.14 ]
|XXXXX 250 - 300 : [ 345 0.02 0.16 ]
|XXXXXX 300 - 350 : [ 411 0.02 0.19 ]
|XXXXXXX 350 - 400 : [ 491 0.03 0.22 ]
|XXXXXXX 400 - 450 : [ 544 0.03 0.25 ]
|XXXXXXXX 450 - 500 : [ 602 0.04 0.28 ]
|XXXXXXXXXX 500 - 550 : [ 711 0.04 0.33 ]
|XXXXXXXXXXXXXX 550 - 600 : [ 1019 0.06 0.39 ]
|XXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1407 0.08 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2192 0.13 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2908 0.17 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2551 0.15 0.92 ]
|XXXXXXXXXXXXXXXX 800 - 850 : [ 1165 0.07 0.98 ]
|XXX 850 - 900 : [ 232 0.01 1.00 ]
| 900 - 950 : [ 35 0.00 1.00 ]
| 950 - 1000 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXP 3634472_fasta.screen.trimQ15.SaF > reads.trim15.AHXP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXP.rl 2 50
-------------------------------------------------------------------
#Found 18432 total values totalling 12702503.0000. <689.154894 +/- 224.368553>
#Range: [ 0 - 918 ]
#Most likely bin: [ 750 - 800 ] 5914 counts
#Median bin: [ 750 - 800 ] 5914 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 0 - 50 : [ 1466 0.08 0.08 ]
| 50 - 100 : [ 65 0.00 0.08 ]
| 100 - 150 : [ 38 0.00 0.09 ]
| 150 - 200 : [ 23 0.00 0.09 ]
| 200 - 250 : [ 45 0.00 0.09 ]
| 250 - 300 : [ 56 0.00 0.09 ]
| 300 - 350 : [ 63 0.00 0.10 ]
|X 350 - 400 : [ 84 0.00 0.10 ]
| 400 - 450 : [ 72 0.00 0.10 ]
|X 450 - 500 : [ 97 0.01 0.11 ]
|X 500 - 550 : [ 113 0.01 0.12 ]
|XX 550 - 600 : [ 265 0.01 0.13 ]
|XXXX 600 - 650 : [ 572 0.03 0.16 ]
|XXXXXXXXX 650 - 700 : [ 1346 0.07 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3314 0.18 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5914 0.32 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4305 0.23 0.97 ]
|XXXX 850 - 900 : [ 589 0.03 1.00 ]
| 900 - 950 : [ 5 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXS 3634472_fasta.screen.trimQ15.SaF > reads.trim15.AHXS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXS.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 1506923.0000. <490.534831 +/- 244.305857>
#Range: [ 0 - 883 ]
#Most likely bin: [ 650 - 700 ] 374 counts
#Median bin: [ 550 - 600 ] 243 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 255 0.08 0.08 ]
|XXXXXXXXX 50 - 100 : [ 87 0.03 0.11 ]
|XXXXXXXX 100 - 150 : [ 71 0.02 0.13 ]
|XXXXXXX 150 - 200 : [ 65 0.02 0.16 ]
|XXXXXXXXX 200 - 250 : [ 83 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 285 0.09 0.28 ]
|XXXXXXXXXXXXXXXX 300 - 350 : [ 148 0.05 0.32 ]
|XXXXXXXXX 350 - 400 : [ 82 0.03 0.35 ]
|XXXXXXXXX 400 - 450 : [ 80 0.03 0.38 ]
|XXXXXXXXXX 450 - 500 : [ 93 0.03 0.41 ]
|XXXXXXXXXXXXXXXXXX 500 - 550 : [ 164 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 243 0.08 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 339 0.11 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 374 0.12 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 371 0.12 0.89 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 243 0.08 0.97 ]
|XXXXXXXX 800 - 850 : [ 72 0.02 0.99 ]
|XX 850 - 900 : [ 17 0.01 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634472
-------------------------------------------------------------------
AHXO.000001.000100 pUC18.fa LRS.fasta
AHXO.000101.000200 pUC18.fa LRS.fasta
AHXP.000001.000100 pMCL200.fa LRS.fasta
AHXP.000101.000200 pMCL200.fa LRS.fasta
AHXS.000001.000100 pCC1Fos.fa LRS.fasta
AHXO.000001.000100 pUC18.fa LRS.fasta
AHXO.000101.000200 pUC18.fa LRS.fasta
AHXP.000001.000100 pMCL200.fa LRS.fasta
AHXP.000101.000200 pMCL200.fa LRS.fasta
AHXS.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634472_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634472_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 35387 total values totalling 17727.1586. <0.500951 +/- 0.046371>
#Range: [ 0.1667 - 0.7272 ]
#Most likely bin: [ 0.5 - 0.505 ] 2012 counts
#Median bin: [ 0.5 - 0.505 ] 2012 counts
| 0.165 - 0.17 : [ 1 0.00 0.00 ]
#...
| 0.175 - 0.18 : [ 1 0.00 0.00 ]
#...
| 0.2 - 0.205 : [ 1 0.00 0.00 ]
#...
| 0.21 - 0.215 : [ 1 0.00 0.00 ]
| 0.215 - 0.22 : [ 1 0.00 0.00 ]
| 0.22 - 0.225 : [ 1 0.00 0.00 ]
| 0.225 - 0.23 : [ 1 0.00 0.00 ]
| 0.23 - 0.235 : [ 4 0.00 0.00 ]
#...
| 0.24 - 0.245 : [ 1 0.00 0.00 ]
| 0.245 - 0.25 : [ 1 0.00 0.00 ]
| 0.25 - 0.255 : [ 5 0.00 0.00 ]
| 0.255 - 0.26 : [ 6 0.00 0.00 ]
| 0.26 - 0.265 : [ 1 0.00 0.00 ]
| 0.265 - 0.27 : [ 5 0.00 0.00 ]
| 0.27 - 0.275 : [ 6 0.00 0.00 ]
| 0.275 - 0.28 : [ 13 0.00 0.00 ]
| 0.28 - 0.285 : [ 18 0.00 0.00 ]
|X 0.285 - 0.29 : [ 31 0.00 0.00 ]
| 0.29 - 0.295 : [ 21 0.00 0.00 ]
| 0.295 - 0.3 : [ 21 0.00 0.00 ]
| 0.3 - 0.305 : [ 19 0.00 0.00 ]
| 0.305 - 0.31 : [ 23 0.00 0.01 ]
|X 0.31 - 0.315 : [ 34 0.00 0.01 ]
|X 0.315 - 0.32 : [ 40 0.00 0.01 ]
|X 0.32 - 0.325 : [ 26 0.00 0.01 ]
|X 0.325 - 0.33 : [ 34 0.00 0.01 ]
|X 0.33 - 0.335 : [ 36 0.00 0.01 ]
|X 0.335 - 0.34 : [ 30 0.00 0.01 ]
|X 0.34 - 0.345 : [ 34 0.00 0.01 ]
|X 0.345 - 0.35 : [ 35 0.00 0.01 ]
|X 0.35 - 0.355 : [ 31 0.00 0.01 ]
|X 0.355 - 0.36 : [ 39 0.00 0.01 ]
|X 0.36 - 0.365 : [ 41 0.00 0.02 ]
|X 0.365 - 0.37 : [ 48 0.00 0.02 ]
|X 0.37 - 0.375 : [ 50 0.00 0.02 ]
|X 0.375 - 0.38 : [ 58 0.00 0.02 ]
|X 0.38 - 0.385 : [ 47 0.00 0.02 ]
|X 0.385 - 0.39 : [ 56 0.00 0.02 ]
|XX 0.39 - 0.395 : [ 77 0.00 0.03 ]
|X 0.395 - 0.4 : [ 62 0.00 0.03 ]
|XX 0.4 - 0.405 : [ 106 0.00 0.03 ]
|XX 0.405 - 0.41 : [ 118 0.00 0.03 ]
|XXX 0.41 - 0.415 : [ 131 0.00 0.04 ]
|XXXX 0.415 - 0.42 : [ 185 0.01 0.04 ]
|XXXX 0.42 - 0.425 : [ 213 0.01 0.05 ]
|XXXXX 0.425 - 0.43 : [ 252 0.01 0.06 ]
|XXXXXX 0.43 - 0.435 : [ 314 0.01 0.06 ]
|XXXXXXX 0.435 - 0.44 : [ 372 0.01 0.07 ]
|XXXXXXXXX 0.44 - 0.445 : [ 438 0.01 0.09 ]
|XXXXXXXXXXX 0.445 - 0.45 : [ 552 0.02 0.10 ]
|XXXXXXXXXXXXX 0.45 - 0.455 : [ 651 0.02 0.12 ]
|XXXXXXXXXXXXXXX 0.455 - 0.46 : [ 778 0.02 0.14 ]
|XXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 877 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 948 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 1113 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 1280 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 1479 0.04 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1688 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1717 0.05 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1676 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 2012 0.06 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1979 0.06 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1915 0.05 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1867 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1720 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1600 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1426 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1223 0.03 0.84 ]
|XXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1068 0.03 0.87 ]
|XXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 861 0.02 0.89 ]
|XXXXXXXXXXXXXXX 0.55 - 0.555 : [ 761 0.02 0.91 ]
|XXXXXXXXXXXX 0.555 - 0.56 : [ 596 0.02 0.93 ]
|XXXXXXXXXXX 0.56 - 0.565 : [ 555 0.02 0.94 ]
|XXXXXXX 0.565 - 0.57 : [ 371 0.01 0.96 ]
|XXXXXX 0.57 - 0.575 : [ 305 0.01 0.96 ]
|XXXX 0.575 - 0.58 : [ 216 0.01 0.97 ]
|XXXX 0.58 - 0.585 : [ 214 0.01 0.98 ]
|XXX 0.585 - 0.59 : [ 157 0.00 0.98 ]
|XXX 0.59 - 0.595 : [ 156 0.00 0.98 ]
|XXX 0.595 - 0.6 : [ 130 0.00 0.99 ]
|XX 0.6 - 0.605 : [ 125 0.00 0.99 ]
|X 0.605 - 0.61 : [ 68 0.00 0.99 ]
|X 0.61 - 0.615 : [ 60 0.00 1.00 ]
|X 0.615 - 0.62 : [ 35 0.00 1.00 ]
|X 0.62 - 0.625 : [ 29 0.00 1.00 ]
| 0.625 - 0.63 : [ 21 0.00 1.00 ]
| 0.63 - 0.635 : [ 12 0.00 1.00 ]
| 0.635 - 0.64 : [ 6 0.00 1.00 ]
| 0.64 - 0.645 : [ 17 0.00 1.00 ]
| 0.645 - 0.65 : [ 10 0.00 1.00 ]
| 0.65 - 0.655 : [ 6 0.00 1.00 ]
| 0.655 - 0.66 : [ 2 0.00 1.00 ]
| 0.66 - 0.665 : [ 3 0.00 1.00 ]
| 0.665 - 0.67 : [ 2 0.00 1.00 ]
| 0.67 - 0.675 : [ 2 0.00 1.00 ]
| 0.675 - 0.68 : [ 2 0.00 1.00 ]
| 0.68 - 0.685 : [ 2 0.00 1.00 ]
| 0.685 - 0.69 : [ 1 0.00 1.00 ]
| 0.69 - 0.695 : [ 1 0.00 1.00 ]
| 0.695 - 0.7 : [ 1 0.00 1.00 ]
| 0.7 - 0.705 : [ 1 0.00 1.00 ]
#...
| 0.725 - 0.73 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 39. 210 reads; 24556 bp (untrimmed), 24371 (trimmed).
Contig 40. 323 reads; 27886 bp (untrimmed), 27843 (trimmed).
Contig 41. 349 reads; 29833 bp (untrimmed), 29804 (trimmed).
Contig 42. 365 reads; 27584 bp (untrimmed), 27457 (trimmed).
Contig 43. 535 reads; 48325 bp (untrimmed), 47999 (trimmed).
Contig 44. 566 reads; 40043 bp (untrimmed), 40016 (trimmed).
Contig 45. 584 reads; 36563 bp (untrimmed), 36516 (trimmed).
Contig 46. 627 reads; 44288 bp (untrimmed), 44020 (trimmed).
Contig 47. 739 reads; 57122 bp (untrimmed), 56842 (trimmed).
Contig 48. 795 reads; 55225 bp (untrimmed), 55010 (trimmed).
Contig 49. 802 reads; 62489 bp (untrimmed), 62265 (trimmed).
Contig 50. 809 reads; 51672 bp (untrimmed), 51638 (trimmed).
Contig 51. 952 reads; 69192 bp (untrimmed), 68731 (trimmed).
Contig 52. 1025 reads; 73080 bp (untrimmed), 72951 (trimmed).
Contig 53. 1044 reads; 85883 bp (untrimmed), 85769 (trimmed).
Contig 54. 1111 reads; 85319 bp (untrimmed), 85275 (trimmed).
Contig 55. 1121 reads; 65348 bp (untrimmed), 65304 (trimmed).
Contig 56. 1405 reads; 98181 bp (untrimmed), 98128 (trimmed).
Contig 57. 1409 reads; 93590 bp (untrimmed), 93433 (trimmed).
Contig 58. 1514 reads; 101861 bp (untrimmed), 101668 (trimmed).
Contig 59. 1553 reads; 109659 bp (untrimmed), 109463 (trimmed).
Contig 60. 1736 reads; 120397 bp (untrimmed), 120349 (trimmed).
Contig 61. 2023 reads; 135242 bp (untrimmed), 134926 (trimmed).
Contig 62. 2339 reads; 152410 bp (untrimmed), 152242 (trimmed).
Contig 63. 2747 reads; 188344 bp (untrimmed), 188336 (trimmed).
Contig 64. 3167 reads; 216856 bp (untrimmed), 216744 (trimmed).
Contig 65. 4189 reads; 274498 bp (untrimmed), 274427 (trimmed).
--------------------------------------------------------------
Totals 35347 reads; 2563197 bp (untrimmed), 2553339 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2563197 bases = 12.37 +- 5.59 = 0.27 +- 4.62
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 65 total values totalling 493.2000. <7.587692 +/- 4.557932>
#Range: [ 1.19 - 15.34 ]
#Most likely bin: [ 12.5 - 13 ] 6 counts
#Median bin: [ 5.5 - 6 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 3 0.05 0.05 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 5 0.08 0.12 ]
|XXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 3 0.05 0.17 ]
|XXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 3 0.05 0.22 ]
|XXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 3 0.05 0.26 ]
|XXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 3 0.05 0.31 ]
|XXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 3 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 3 0.05 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 4 0.06 0.46 ]
|XXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 3 0.05 0.51 ]
#...
|XXXXXXX 6.5 - 7 : [ 1 0.02 0.52 ]
#...
|XXXXXXXXXXXXX 7.5 - 8 : [ 2 0.03 0.55 ]
#...
|XXXXXXX 9 - 9.5 : [ 1 0.02 0.57 ]
|XXXXXXXXXXXXX 9.5 - 10 : [ 2 0.03 0.60 ]
|XXXXXXX 10 - 10.5 : [ 1 0.02 0.62 ]
|XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 3 0.05 0.66 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 4 0.06 0.72 ]
|XXXXXXXXXXXXX 12 - 12.5 : [ 2 0.03 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 6 0.09 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 4 0.06 0.91 ]
|XXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 3 0.05 0.95 ]
|XXXXXXXXXXXXX 14 - 14.5 : [ 2 0.03 0.98 ]
#...
|XXXXXXX 15 - 15.5 : [ 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 439.7000. <9.993182 +/- 3.517166>
#Range: [ 3.06 - 15.34 ]
#Most likely bin: [ 12.5 - 13 ] 6 counts
#Median bin: [ 10.5 - 11 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 3 - 3.5 : [ 1 0.02 0.02 ]
#...
|XXXXXXX 4 - 4.5 : [ 1 0.02 0.05 ]
|XXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 3 0.07 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 4 0.09 0.20 ]
|XXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 3 0.07 0.27 ]
#...
|XXXXXXX 6.5 - 7 : [ 1 0.02 0.30 ]
#...
|XXXXXXXXXXXXX 7.5 - 8 : [ 2 0.05 0.34 ]
#...
|XXXXXXX 9 - 9.5 : [ 1 0.02 0.36 ]
|XXXXXXXXXXXXX 9.5 - 10 : [ 2 0.05 0.41 ]
|XXXXXXX 10 - 10.5 : [ 1 0.02 0.43 ]
|XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 3 0.07 0.50 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 4 0.09 0.59 ]
|XXXXXXXXXXXXX 12 - 12.5 : [ 2 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 6 0.14 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 4 0.09 0.86 ]
|XXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 3 0.07 0.93 ]
|XXXXXXXXXXXXX 14 - 14.5 : [ 2 0.05 0.98 ]
#...
|XXXXXXX 15 - 15.5 : [ 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 3 3 reads 1694 bases = 1.19 +- 0.40 = 0.94 +- 0.44
Contig 7 3 reads 2028 bases = 1.32 +- 0.47 = 0.57 +- 0.96
Contig 5 3 reads 1716 bases = 1.49 +- 0.67 = 0.45 +- 1.24
Contig 4 3 reads 1563 bases = 1.64 +- 0.72 = 0.64 +- 0.48
Contig 1 2 reads 1106 bases = 1.81 +- 0.39 = 0.02 +- 0.43
Contig 8 3 reads 1497 bases = 1.86 +- 0.79 = 1.86 +- 0.79
Contig 19 8 reads 3580 bases = 1.96 +- 1.01 = 0.38 +- 1.37
Contig 15 6 reads 1887 bases = 1.98 +- 0.95 = 1.62 +- 1.22
Contig 13 5 reads 2088 bases = 2.07 +- 0.80 = 2.07 +- 0.80
Contig 12 4 reads 1856 bases = 2.17 +- 0.76 = 1.18 +- 0.90
Contig 2 3 reads 1289 bases = 2.27 +- 0.79 = 0.73 +- 1.04
Contig 10 4 reads 1349 bases = 2.51 +- 1.15 = 2.51 +- 1.15
Contig 6 3 reads 1063 bases = 2.51 +- 0.70 = 0.75 +- 0.43
Contig 17 7 reads 2056 bases = 2.86 +- 1.54 = 1.40 +- 2.19
Contig 11 4 reads 1078 bases = 3.04 +- 1.19 = 1.25 +- 0.96
Contig 22 11 reads 2860 bases = 3.06 +- 1.81 = 0.69 +- 2.08
Contig 14 5 reads 1548 bases = 3.23 +- 1.39 = 3.23 +- 1.39
Contig 9 4 reads 1021 bases = 3.55 +- 0.98 = 1.73 +- 0.63
Contig 16 6 reads 1221 bases = 3.65 +- 1.29 = 2.44 +- 1.13
Contig 18 7 reads 1586 bases = 3.96 +- 1.83 = 3.96 +- 1.83
Contig 47 739 reads 57122 bases = 11.69 +- 4.97 = 0.02 +- 4.55
Contig 42 365 reads 27584 bases = 11.88 +- 4.46 = 0.75 +- 4.64
Contig 51 952 reads 69192 bases = 12.32 +- 5.49 = 0.24 +- 5.02
Contig 46 627 reads 44288 bases = 12.48 +- 4.95 = -0.09 +- 4.90
Contig 52 1025 reads 73080 bases = 12.55 +- 4.47 = 0.36 +- 4.81
Contig 59 1553 reads 109659 bases = 12.63 +- 4.25 = 0.04 +- 4.55
Contig 44 566 reads 40043 bases = 12.66 +- 5.04 = 0.99 +- 4.86
Contig 56 1405 reads 98181 bases = 12.79 +- 3.89 = 0.30 +- 4.33
Contig 60 1736 reads 120397 bases = 12.88 +- 4.68 = 0.45 +- 4.75
Contig 48 795 reads 55225 bases = 12.90 +- 4.88 = 0.43 +- 5.08
Contig 64 3167 reads 216856 bases = 13.00 +- 4.90 = 0.37 +- 4.71
Contig 63 2747 reads 188344 bases = 13.17 +- 4.96 = 0.01 +- 4.67
Contig 58 1514 reads 101861 bases = 13.41 +- 5.09 = 0.11 +- 4.67
Contig 61 2023 reads 135242 bases = 13.44 +- 9.17 = -0.07 +- 4.00
Contig 57 1409 reads 93590 bases = 13.55 +- 4.82 = 0.08 +- 4.73
Contig 65 4189 reads 274498 bases = 13.80 +- 5.22 = 0.15 +- 4.89
Contig 62 2339 reads 152410 bases = 13.82 +- 5.96 = 0.00 +- 4.21
Contig 50 809 reads 51672 bases = 14.10 +- 4.25 = 0.35 +- 4.03
Contig 45 584 reads 36563 bases = 14.21 +- 5.03 = 0.41 +- 5.09
Contig 55 1121 reads 65348 bases = 15.34 +- 5.56 = 0.07 +- 5.52
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 463
HQ Discrepant reads = 30
Chimeric reads = 122
Suspect alignments = 268
-------------------------------------------------------------------
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/microbe3/3634472/edit_dir.13Aug04.QD