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
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Project Size(KB) TaxID GenusSpecies
3634474 2400 1096 Chlorobium phaeobacteroides
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Chlorobium_phaeobacteroides
-------------------------------------------------------------------
Chlorobium/Pelodictyon group, green sulfur bacteria
Chlorobiaceae, family, green sulfur bacteria
Chlorobiales, order, green sulfur bacteria
Chlorobia, class, green sulfur bacteria
Bacteroidetes/Chlorobi group, superphylum, eubacteria
Chlorobium phaeobacteroides, species, green sulfur bacteria
Chlorobium, genus, green sulfur bacteria
Chlorobi, phylum, green sulfur bacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3102486
# phrap: 2856185
# db:
altered.
2400000
2786223 +/- 291024
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 8575
Number of reads with percent X's >= 20%: 220 = 0.6%
Number of reads with percent X's >= 50%: 117 = 0.3%
Number of reads with percent X's >= 80%: 17 = 0.0%
Total reads in project: 39661
Total bp X'd : 415305
reads >= 20% >= 50% >= 80% screened
Nr with L09136 7992 85 42 11
Nr with pCC1Fos 323 12 5 0
Nr with pMCL200_JGI_XZX+XZK 260 123 70 6
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 5
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: 30
Total bp X'd : 185
reads >= 20% >= 50% >= 80% screened
Nr with L09136 4 0 0 0
Nr with pCC1Fos 1 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
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A = 9679653
C = 8993751
G = 8981554
T = 9446261
N = 161092
X = 415305
GC fraction = 0.48
Total = 37677616
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634474_fasta.screen.contigs
-------------------------------------------------------------------
A 812535
C 767463
G 737619
T 796002
N 667
fraction GC = 0.48
total bases = 3114286
Libraries and Reads
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Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
-------------------------------------------------------------------
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXX reads.list > grep.reads.list.AHXX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXX 4 500
-------------------------------------------------------------------
#Found 7663 total values totalling 25223258.0000. <3291.564400 +/- 3173.655173>
#Range: [ 697 - 158403 ]
#Most likely bin: [ 2500 - 3000 ] 2327 counts
#Median bin: [ 3000 - 3500 ] 1837 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
|X 1000 - 1500 : [ 40 0.01 0.01 ]
|X 1500 - 2000 : [ 73 0.01 0.01 ]
|XXXXXXXXXXXXXXXX 2000 - 2500 : [ 949 0.12 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2327 0.30 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1837 0.24 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1305 0.17 0.85 ]
|XXXXXXXXXXXXXX 4000 - 4500 : [ 804 0.10 0.96 ]
|XXXXX 4500 - 5000 : [ 299 0.04 1.00 ]
| 5000 - 5500 : [ 18 0.00 1.00 ]
#...
| 9000 - 9500 : [ 1 0.00 1.00 ]
#...
| 17000 - 17500 : [ 1 0.00 1.00 ]
#...
| 29000 - 29500 : [ 1 0.00 1.00 ]
| 29500 - 30000 : [ 1 0.00 1.00 ]
#...
| 36500 - 37000 : [ 1 0.00 1.00 ]
#...
| 63000 - 63500 : [ 1 0.00 1.00 ]
#...
| 95000 - 95500 : [ 1 0.00 1.00 ]
#...
| 129500 - 130000 : [ 1 0.00 1.00 ]
#...
| 140000 - 140500 : [ 1 0.00 1.00 ]
#...
| 158000 - 158500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXY reads.list > grep.reads.list.AHXY
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXY 4 500
-------------------------------------------------------------------
#Found 7283 total values totalling 50342508.0000. <6912.331182 +/- 1102.640760>
#Range: [ 295 - 18324 ]
#Most likely bin: [ 7000 - 7500 ] 1919 counts
#Median bin: [ 7000 - 7500 ] 1919 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
| 500 - 1000 : [ 12 0.00 0.00 ]
|X 1000 - 1500 : [ 41 0.01 0.01 ]
|X 1500 - 2000 : [ 41 0.01 0.01 ]
|X 2000 - 2500 : [ 29 0.00 0.02 ]
|X 2500 - 3000 : [ 45 0.01 0.02 ]
|X 3000 - 3500 : [ 55 0.01 0.03 ]
|X 3500 - 4000 : [ 32 0.00 0.04 ]
|X 4000 - 4500 : [ 45 0.01 0.04 ]
|X 4500 - 5000 : [ 38 0.01 0.05 ]
|X 5000 - 5500 : [ 32 0.00 0.05 ]
|XX 5500 - 6000 : [ 90 0.01 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1203 0.17 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1699 0.23 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1919 0.26 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1487 0.20 0.93 ]
|XXXXXXXXXXX 8000 - 8500 : [ 508 0.07 1.00 ]
| 8500 - 9000 : [ 3 0.00 1.00 ]
| 9000 - 9500 : [ 1 0.00 1.00 ]
| 9500 - 10000 : [ 1 0.00 1.00 ]
#...
| 18000 - 18500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXZ reads.list > grep.reads.list.AHXZ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXZ 4 500
-------------------------------------------------------------------
#Found 365 total values totalling 13431165.0000. <36797.712329 +/- 3619.686223>
#Range: [ 27096 - 47460 ]
#Most likely bin: [ 34000 - 34500 ] 23 counts
#Median bin: [ 36000 - 36500 ] 21 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 27000 - 27500 : [ 1 0.00 0.00 ]
#...
|XX 28500 - 29000 : [ 1 0.00 0.01 ]
|XX 29000 - 29500 : [ 1 0.00 0.01 ]
|XXX 29500 - 30000 : [ 2 0.01 0.01 ]
|XXX 30000 - 30500 : [ 2 0.01 0.02 ]
|XXXXXXXXXX 30500 - 31000 : [ 6 0.02 0.04 ]
|XXXXXXXXXXXXXX 31000 - 31500 : [ 8 0.02 0.06 ]
|XXXXXXXXX 31500 - 32000 : [ 5 0.01 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 15 0.04 0.11 ]
|XXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 11 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 17 0.05 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 17 0.05 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 23 0.06 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 21 0.06 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 15 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 17 0.05 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 21 0.06 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 23 0.06 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 13 0.04 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 14 0.04 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 18 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 17 0.05 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 15 0.04 0.78 ]
|XXXXXXXXXXXXXXXX 39500 - 40000 : [ 9 0.02 0.80 ]
|XXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 11 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 11 0.03 0.86 ]
|XXXXXXX 41000 - 41500 : [ 4 0.01 0.87 ]
|XXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 12 0.03 0.90 ]
|XXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 11 0.03 0.93 ]
|XXXXXXXXX 42500 - 43000 : [ 5 0.01 0.95 ]
|XXXXX 43000 - 43500 : [ 3 0.01 0.96 ]
|XXXXXXX 43500 - 44000 : [ 4 0.01 0.97 ]
|XXXXXXXXX 44000 - 44500 : [ 5 0.01 0.98 ]
|XXX 44500 - 45000 : [ 2 0.01 0.99 ]
|XX 45000 - 45500 : [ 1 0.00 0.99 ]
|XXX 45500 - 46000 : [ 2 0.01 0.99 ]
|XX 46000 - 46500 : [ 1 0.00 1.00 ]
#...
|XX 47000 - 47500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHXX 3122 +- 891 (n=3835)
# AHXZ 36355 +- 4774 (n=165)
# AHXY 6735 +- 1273 (n=3423)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634474_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
AHXX 19200 -1 -1 99 756 19195 97 744 98 749
AHXY 23424 -1 -1 92 616 23230 79 575 85 579
AHXZ 3072 -1 -1 73 350 3072 61 519 73 476
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHXX 9596 97 733 98 748 9599 97 755 98 751
AHXY 11397 70 557 79 553 11833 88 589 92 600
AHXZ 1536 66 541 76 499 1536 56 494 70 451
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634474_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
100 18713 9438 94.38 98.31 AHXX @
120 18886 10683 89.03 92.73 AHXY @
16 2062 1167 72.94 75.98 AHXZ @
] 39661 21288 90.20 cumulative total@@
LIBRARY PLATE ID COUNT [ AHXX 100 AHXY 120 AHXZ 16 ] for 236 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 3634474_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 45497 total values totalling 25555708.0000. <561.700947 +/- 279.553015>
#Range: [ 0 - 933 ]
#Most likely bin: [ 750 - 800 ] 8901 counts
#Median bin: [ 650 - 700 ] 3675 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 5598 0.12 0.12 ]
|XXXX 50 - 100 : [ 953 0.02 0.14 ]
|XXXX 100 - 150 : [ 780 0.02 0.16 ]
|XXX 150 - 200 : [ 674 0.01 0.18 ]
|XXX 200 - 250 : [ 705 0.02 0.19 ]
|XXX 250 - 300 : [ 762 0.02 0.21 ]
|XXXX 300 - 350 : [ 842 0.02 0.23 ]
|XXXX 350 - 400 : [ 897 0.02 0.25 ]
|XXXXX 400 - 450 : [ 1054 0.02 0.27 ]
|XXXXXX 450 - 500 : [ 1257 0.03 0.30 ]
|XXXXXXX 500 - 550 : [ 1661 0.04 0.33 ]
|XXXXXXXXXX 550 - 600 : [ 2194 0.05 0.38 ]
|XXXXXXXXXXXXX 600 - 650 : [ 2817 0.06 0.44 ]
|XXXXXXXXXXXXXXXXX 650 - 700 : [ 3675 0.08 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5966 0.13 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8901 0.20 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5879 0.13 0.98 ]
|XXXX 850 - 900 : [ 870 0.02 1.00 ]
| 900 - 950 : [ 12 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXX 3634474_fasta.screen.trimQ15.SaF > reads.trim15.AHXX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXX.rl 2 50
-------------------------------------------------------------------
#Found 19195 total values totalling 13894567.0000. <723.863871 +/- 162.251045>
#Range: [ 0 - 933 ]
#Most likely bin: [ 750 - 800 ] 6564 counts
#Median bin: [ 750 - 800 ] 6564 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 0 - 50 : [ 464 0.02 0.02 ]
| 50 - 100 : [ 56 0.00 0.03 ]
| 100 - 150 : [ 79 0.00 0.03 ]
|X 150 - 200 : [ 83 0.00 0.04 ]
| 200 - 250 : [ 72 0.00 0.04 ]
|X 250 - 300 : [ 93 0.00 0.04 ]
|X 300 - 350 : [ 104 0.01 0.05 ]
|X 350 - 400 : [ 131 0.01 0.06 ]
|X 400 - 450 : [ 133 0.01 0.06 ]
|X 450 - 500 : [ 148 0.01 0.07 ]
|X 500 - 550 : [ 209 0.01 0.08 ]
|XX 550 - 600 : [ 310 0.02 0.10 ]
|XXX 600 - 650 : [ 537 0.03 0.13 ]
|XXXXXXXX 650 - 700 : [ 1289 0.07 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3627 0.19 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6564 0.34 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4553 0.24 0.96 ]
|XXXX 850 - 900 : [ 732 0.04 1.00 ]
| 900 - 950 : [ 11 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXY 3634474_fasta.screen.trimQ15.SaF > reads.trim15.AHXY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXY.rl 2 50
-------------------------------------------------------------------
#Found 23230 total values totalling 10663836.0000. <459.054498 +/- 283.571687>
#Range: [ 0 - 904 ]
#Most likely bin: [ 0 - 50 ] 4130 counts
#Median bin: [ 550 - 600 ] 1713 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 4130 0.18 0.18 ]
|XXXXXXX 50 - 100 : [ 705 0.03 0.21 ]
|XXXXXX 100 - 150 : [ 590 0.03 0.23 ]
|XXXXX 150 - 200 : [ 508 0.02 0.26 ]
|XXXXX 200 - 250 : [ 559 0.02 0.28 ]
|XXXXXX 250 - 300 : [ 573 0.02 0.30 ]
|XXXXXX 300 - 350 : [ 652 0.03 0.33 ]
|XXXXXXX 350 - 400 : [ 693 0.03 0.36 ]
|XXXXXXXX 400 - 450 : [ 823 0.04 0.40 ]
|XXXXXXXXX 450 - 500 : [ 976 0.04 0.44 ]
|XXXXXXXXXXXXX 500 - 550 : [ 1307 0.06 0.50 ]
|XXXXXXXXXXXXXXXXX 550 - 600 : [ 1713 0.07 0.57 ]
|XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2099 0.09 0.66 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2189 0.09 0.75 ]
|XXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2106 0.09 0.84 ]
|XXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2190 0.09 0.94 ]
|XXXXXXXXXXXX 800 - 850 : [ 1285 0.06 0.99 ]
|X 850 - 900 : [ 131 0.01 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXZ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXZ 3634474_fasta.screen.trimQ15.SaF > reads.trim15.AHXZ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXZ.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 997305.0000. <324.643555 +/- 290.987393>
#Range: [ 0 - 881 ]
#Most likely bin: [ 0 - 50 ] 1004 counts
#Median bin: [ 250 - 300 ] 96 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1004 0.33 0.33 ]
|XXXXXXXX 50 - 100 : [ 192 0.06 0.39 ]
|XXXX 100 - 150 : [ 111 0.04 0.43 ]
|XXX 150 - 200 : [ 83 0.03 0.45 ]
|XXX 200 - 250 : [ 74 0.02 0.48 ]
|XXXX 250 - 300 : [ 96 0.03 0.51 ]
|XXX 300 - 350 : [ 86 0.03 0.54 ]
|XXX 350 - 400 : [ 73 0.02 0.56 ]
|XXXX 400 - 450 : [ 98 0.03 0.59 ]
|XXXXX 450 - 500 : [ 133 0.04 0.63 ]
|XXXXXX 500 - 550 : [ 145 0.05 0.68 ]
|XXXXXXX 550 - 600 : [ 171 0.06 0.74 ]
|XXXXXXX 600 - 650 : [ 181 0.06 0.80 ]
|XXXXXXXX 650 - 700 : [ 197 0.06 0.86 ]
|XXXXXXXXX 700 - 750 : [ 233 0.08 0.94 ]
|XXXXXX 750 - 800 : [ 147 0.05 0.98 ]
|XX 800 - 850 : [ 41 0.01 1.00 ]
| 850 - 900 : [ 7 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634474
-------------------------------------------------------------------
AHXX.000001.000100 pUC18.fa LRS.fasta
AHXX.000101.000200 pUC18.fa LRS.fasta
AHXY.000001.000100 pMCL200.fa LRS.fasta
AHXY.000101.000200 pMCL200.fa LRS.fasta
AHXZ.000001.000100 pCC1Fos.fa LRS.fasta
AHXX.000001.000100 pUC18.fa LRS.fasta
AHXX.000101.000200 pUC18.fa LRS.fasta
AHXY.000001.000100 pMCL200.fa LRS.fasta
AHXY.000101.000200 pMCL200.fa LRS.fasta
AHXZ.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634474_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634474_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 39476 total values totalling 19049.2148. <0.482552 +/- 0.053861>
#Range: [ 0.0889 - 0.7391 ]
#Most likely bin: [ 0.5 - 0.505 ] 1882 counts
#Median bin: [ 0.485 - 0.49 ] 1846 counts
| 0.085 - 0.09 : [ 1 0.00 0.00 ]
#...
| 0.16 - 0.165 : [ 1 0.00 0.00 ]
| 0.165 - 0.17 : [ 1 0.00 0.00 ]
| 0.17 - 0.175 : [ 2 0.00 0.00 ]
#...
| 0.185 - 0.19 : [ 1 0.00 0.00 ]
#...
| 0.195 - 0.2 : [ 1 0.00 0.00 ]
#...
| 0.205 - 0.21 : [ 1 0.00 0.00 ]
| 0.21 - 0.215 : [ 1 0.00 0.00 ]
| 0.215 - 0.22 : [ 3 0.00 0.00 ]
| 0.22 - 0.225 : [ 4 0.00 0.00 ]
| 0.225 - 0.23 : [ 2 0.00 0.00 ]
#...
| 0.235 - 0.24 : [ 5 0.00 0.00 ]
| 0.24 - 0.245 : [ 2 0.00 0.00 ]
| 0.245 - 0.25 : [ 5 0.00 0.00 ]
| 0.25 - 0.255 : [ 19 0.00 0.00 ]
| 0.255 - 0.26 : [ 19 0.00 0.00 ]
| 0.26 - 0.265 : [ 16 0.00 0.00 ]
|X 0.265 - 0.27 : [ 27 0.00 0.00 ]
|X 0.27 - 0.275 : [ 35 0.00 0.00 ]
|X 0.275 - 0.28 : [ 40 0.00 0.00 ]
|X 0.28 - 0.285 : [ 48 0.00 0.01 ]
|X 0.285 - 0.29 : [ 49 0.00 0.01 ]
|X 0.29 - 0.295 : [ 62 0.00 0.01 ]
|X 0.295 - 0.3 : [ 61 0.00 0.01 ]
|X 0.3 - 0.305 : [ 59 0.00 0.01 ]
|XX 0.305 - 0.31 : [ 85 0.00 0.01 ]
|XX 0.31 - 0.315 : [ 78 0.00 0.02 ]
|X 0.315 - 0.32 : [ 70 0.00 0.02 ]
|X 0.32 - 0.325 : [ 44 0.00 0.02 ]
|X 0.325 - 0.33 : [ 57 0.00 0.02 ]
|X 0.33 - 0.335 : [ 59 0.00 0.02 ]
|X 0.335 - 0.34 : [ 59 0.00 0.02 ]
|X 0.34 - 0.345 : [ 50 0.00 0.02 ]
|X 0.345 - 0.35 : [ 63 0.00 0.03 ]
|X 0.35 - 0.355 : [ 55 0.00 0.03 ]
|X 0.355 - 0.36 : [ 67 0.00 0.03 ]
|XX 0.36 - 0.365 : [ 75 0.00 0.03 ]
|XX 0.365 - 0.37 : [ 108 0.00 0.03 ]
|XX 0.37 - 0.375 : [ 91 0.00 0.04 ]
|XXX 0.375 - 0.38 : [ 119 0.00 0.04 ]
|XXX 0.38 - 0.385 : [ 133 0.00 0.04 ]
|XXXX 0.385 - 0.39 : [ 177 0.00 0.05 ]
|XXXX 0.39 - 0.395 : [ 194 0.00 0.05 ]
|XXXX 0.395 - 0.4 : [ 196 0.00 0.06 ]
|XXXXXX 0.4 - 0.405 : [ 284 0.01 0.06 ]
|XXXXXXX 0.405 - 0.41 : [ 336 0.01 0.07 ]
|XXXXXXXX 0.41 - 0.415 : [ 386 0.01 0.08 ]
|XXXXXXXXX 0.415 - 0.42 : [ 444 0.01 0.09 ]
|XXXXXXXXXXX 0.42 - 0.425 : [ 500 0.01 0.11 ]
|XXXXXXXXXXXXX 0.425 - 0.43 : [ 605 0.02 0.12 ]
|XXXXXXXXXXXXXXX 0.43 - 0.435 : [ 718 0.02 0.14 ]
|XXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 833 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 971 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 1101 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 1231 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 1396 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 1520 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 1563 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 1670 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 1706 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 1798 0.05 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1846 0.05 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1829 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1521 0.04 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1882 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1587 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1588 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1440 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1298 0.03 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1133 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 938 0.02 0.87 ]
|XXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 814 0.02 0.89 ]
|XXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 754 0.02 0.91 ]
|XXXXXXXXXXXXX 0.545 - 0.55 : [ 610 0.02 0.93 ]
|XXXXXXXXXXX 0.55 - 0.555 : [ 537 0.01 0.94 ]
|XXXXXXXXX 0.555 - 0.56 : [ 412 0.01 0.95 ]
|XXXXXXX 0.56 - 0.565 : [ 317 0.01 0.96 ]
|XXXXX 0.565 - 0.57 : [ 255 0.01 0.96 ]
|XXXXX 0.57 - 0.575 : [ 213 0.01 0.97 ]
|XXXX 0.575 - 0.58 : [ 167 0.00 0.97 ]
|XXXX 0.58 - 0.585 : [ 195 0.00 0.98 ]
|XXX 0.585 - 0.59 : [ 157 0.00 0.98 ]
|XXX 0.59 - 0.595 : [ 129 0.00 0.99 ]
|XX 0.595 - 0.6 : [ 91 0.00 0.99 ]
|XX 0.6 - 0.605 : [ 73 0.00 0.99 ]
|XX 0.605 - 0.61 : [ 78 0.00 0.99 ]
|X 0.61 - 0.615 : [ 57 0.00 0.99 ]
|X 0.615 - 0.62 : [ 58 0.00 1.00 ]
|X 0.62 - 0.625 : [ 40 0.00 1.00 ]
|X 0.625 - 0.63 : [ 36 0.00 1.00 ]
| 0.63 - 0.635 : [ 19 0.00 1.00 ]
| 0.635 - 0.64 : [ 19 0.00 1.00 ]
| 0.64 - 0.645 : [ 12 0.00 1.00 ]
| 0.645 - 0.65 : [ 7 0.00 1.00 ]
| 0.65 - 0.655 : [ 10 0.00 1.00 ]
| 0.655 - 0.66 : [ 11 0.00 1.00 ]
| 0.66 - 0.665 : [ 3 0.00 1.00 ]
| 0.665 - 0.67 : [ 9 0.00 1.00 ]
| 0.67 - 0.675 : [ 1 0.00 1.00 ]
| 0.675 - 0.68 : [ 7 0.00 1.00 ]
| 0.68 - 0.685 : [ 2 0.00 1.00 ]
| 0.685 - 0.69 : [ 5 0.00 1.00 ]
| 0.69 - 0.695 : [ 2 0.00 1.00 ]
| 0.695 - 0.7 : [ 1 0.00 1.00 ]
| 0.7 - 0.705 : [ 1 0.00 1.00 ]
| 0.705 - 0.71 : [ 1 0.00 1.00 ]
| 0.71 - 0.715 : [ 1 0.00 1.00 ]
#...
| 0.72 - 0.725 : [ 1 0.00 1.00 ]
| 0.725 - 0.73 : [ 1 0.00 1.00 ]
#...
| 0.735 - 0.74 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 63. 486 reads; 40641 bp (untrimmed), 40599 (trimmed).
Contig 64. 498 reads; 37073 bp (untrimmed), 36691 (trimmed).
Contig 65. 528 reads; 13776 bp (untrimmed), 13759 (trimmed).
Contig 66. 543 reads; 46554 bp (untrimmed), 46503 (trimmed).
Contig 67. 547 reads; 40028 bp (untrimmed), 39771 (trimmed).
Contig 68. 549 reads; 46981 bp (untrimmed), 46565 (trimmed).
Contig 69. 552 reads; 46317 bp (untrimmed), 46182 (trimmed).
Contig 70. 579 reads; 38606 bp (untrimmed), 38595 (trimmed).
Contig 71. 603 reads; 38995 bp (untrimmed), 38917 (trimmed).
Contig 72. 670 reads; 49823 bp (untrimmed), 49653 (trimmed).
Contig 73. 692 reads; 55222 bp (untrimmed), 55205 (trimmed).
Contig 74. 987 reads; 65274 bp (untrimmed), 65245 (trimmed).
Contig 75. 1052 reads; 85957 bp (untrimmed), 85915 (trimmed).
Contig 76. 1097 reads; 81674 bp (untrimmed), 81566 (trimmed).
Contig 77. 1110 reads; 93210 bp (untrimmed), 93189 (trimmed).
Contig 78. 1121 reads; 81337 bp (untrimmed), 81309 (trimmed).
Contig 79. 1141 reads; 71159 bp (untrimmed), 71007 (trimmed).
Contig 80. 1181 reads; 82417 bp (untrimmed), 82401 (trimmed).
Contig 81. 1471 reads; 108243 bp (untrimmed), 108234 (trimmed).
Contig 82. 1545 reads; 116513 bp (untrimmed), 116478 (trimmed).
Contig 83. 1666 reads; 125309 bp (untrimmed), 124938 (trimmed).
Contig 84. 1699 reads; 129380 bp (untrimmed), 129364 (trimmed).
Contig 85. 1794 reads; 135147 bp (untrimmed), 135093 (trimmed).
Contig 86. 1901 reads; 156132 bp (untrimmed), 156109 (trimmed).
Contig 87. 2076 reads; 139799 bp (untrimmed), 139721 (trimmed).
Contig 88. 2286 reads; 162474 bp (untrimmed), 161946 (trimmed).
Contig 89. 2459 reads; 205960 bp (untrimmed), 205803 (trimmed).
--------------------------------------------------------------
Totals 39631 reads; 3114286 bp (untrimmed), 3102486 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3111049 bases = 11.14 +- 6.22 = 0.40 +- 4.00
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 84 total values totalling 786.7300. <9.365833 +/- 4.092184>
#Range: [ 1.48 - 33.07 ]
#Most likely bin: [ 11.5 - 12 ] 11 counts
#Median bin: [ 10 - 10.5 ] 8 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 1 - 1.5 : [ 1 0.01 0.01 ]
|XXXXXXX 1.5 - 2 : [ 2 0.02 0.04 ]
|XXXXXXX 2 - 2.5 : [ 2 0.02 0.06 ]
|XXXX 2.5 - 3 : [ 1 0.01 0.07 ]
|XXXXXXX 3 - 3.5 : [ 2 0.02 0.10 ]
|XXXX 3.5 - 4 : [ 1 0.01 0.11 ]
|XXXXXXX 4 - 4.5 : [ 2 0.02 0.13 ]
|XXXX 4.5 - 5 : [ 1 0.01 0.14 ]
|XXXX 5 - 5.5 : [ 1 0.01 0.15 ]
|XXXX 5.5 - 6 : [ 1 0.01 0.17 ]
|XXXXXXXXXXX 6 - 6.5 : [ 3 0.04 0.20 ]
|XXXX 6.5 - 7 : [ 1 0.01 0.21 ]
|XXXXXXXXXXXXXXX 7 - 7.5 : [ 4 0.05 0.26 ]
|XXXXXXXXXXX 7.5 - 8 : [ 3 0.04 0.30 ]
|XXXXXXX 8 - 8.5 : [ 2 0.02 0.32 ]
|XXXXXXXXXXX 8.5 - 9 : [ 3 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 5 0.06 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 6 0.07 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 8 0.10 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 9 0.11 0.69 ]
|XXXXXXX 11 - 11.5 : [ 2 0.02 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 11 0.13 0.85 ]
|XXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 5 0.06 0.90 ]
|XXXXXXX 12.5 - 13 : [ 2 0.02 0.93 ]
|XXXXXXXXXXX 13 - 13.5 : [ 3 0.04 0.96 ]
|XXXX 13.5 - 14 : [ 1 0.01 0.98 ]
|XXXX 14 - 14.5 : [ 1 0.01 0.99 ]
#...
|XXXX 33 - 33.5 : [ 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 75 total values totalling 757.8000. <10.104000 +/- 3.574663>
#Range: [ 3.89 - 33.07 ]
#Most likely bin: [ 11.5 - 12 ] 11 counts
#Median bin: [ 10 - 10.5 ] 8 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 3.5 - 4 : [ 1 0.01 0.01 ]
|XXXXXXX 4 - 4.5 : [ 2 0.03 0.04 ]
|XXXX 4.5 - 5 : [ 1 0.01 0.05 ]
|XXXX 5 - 5.5 : [ 1 0.01 0.07 ]
|XXXX 5.5 - 6 : [ 1 0.01 0.08 ]
|XXXXXXXXXXX 6 - 6.5 : [ 3 0.04 0.12 ]
|XXXX 6.5 - 7 : [ 1 0.01 0.13 ]
|XXXXXXXXXXXXXXX 7 - 7.5 : [ 4 0.05 0.19 ]
|XXXXXXXXXXX 7.5 - 8 : [ 3 0.04 0.23 ]
|XXXXXXX 8 - 8.5 : [ 2 0.03 0.25 ]
|XXXXXXXXXXX 8.5 - 9 : [ 3 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 5 0.07 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 6 0.08 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 8 0.11 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 8 0.11 0.65 ]
|XXXXXXX 11 - 11.5 : [ 2 0.03 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 11 0.15 0.83 ]
|XXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 5 0.07 0.89 ]
|XXXXXXX 12.5 - 13 : [ 2 0.03 0.92 ]
|XXXXXXXXXXX 13 - 13.5 : [ 3 0.04 0.96 ]
|XXXX 13.5 - 14 : [ 1 0.01 0.97 ]
|XXXX 14 - 14.5 : [ 1 0.01 0.99 ]
#...
|XXXX 33 - 33.5 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 4 3 reads 1603 bases = 1.48 +- 0.50 = 1.48 +- 0.50
Contig 5 3 reads 1664 bases = 1.72 +- 0.70 = 1.72 +- 0.70
Contig 8 4 reads 1386 bases = 1.92 +- 0.89 = 0.98 +- 0.74
Contig 6 4 reads 1868 bases = 2.08 +- 0.81 = 2.08 +- 0.81
Contig 13 9 reads 3566 bases = 2.18 +- 0.89 = 0.65 +- 2.23
Contig 7 4 reads 1394 bases = 2.51 +- 1.18 = 2.51 +- 1.18
Contig 12 7 reads 2045 bases = 3.10 +- 1.86 = 2.21 +- 1.05
Contig 10 4 reads 1158 bases = 3.17 +- 1.07 = 3.17 +- 1.07
Contig 14 12 reads 2805 bases = 3.89 +- 2.24 = 1.30 +- 1.56
Contig 17 17 reads 3496 bases = 4.07 +- 1.84 = 1.93 +- 1.41
Contig 21 26 reads 5430 bases = 4.07 +- 2.07 = 0.62 +- 2.28
Contig 15 12 reads 2231 bases = 4.83 +- 2.03 = 1.42 +- 1.55
Contig 28 57 reads 9406 bases = 5.29 +- 2.61 = 1.25 +- 3.67
Contig 16 16 reads 2728 bases = 5.52 +- 2.01 = 2.71 +- 2.07
Contig 32 71 reads 10008 bases = 6.02 +- 3.26 = 1.37 +- 3.85
Contig 25 43 reads 6141 bases = 6.08 +- 2.15 = 1.31 +- 3.37
Contig 27 50 reads 7254 bases = 6.23 +- 2.84 = 0.71 +- 3.07
Contig 33 80 reads 10411 bases = 6.94 +- 2.44 = 0.14 +- 4.22
Contig 38 150 reads 17864 bases = 7.17 +- 3.65 = 0.16 +- 3.47
Contig 34 97 reads 11020 bases = 7.33 +- 4.15 = 1.66 +- 2.94
Contig 58 386 reads 29275 bases = 11.57 +- 3.83 = 0.00 +- 2.78
Contig 82 1545 reads 116513 bases = 11.57 +- 5.04 = 0.20 +- 4.29
Contig 84 1699 reads 129380 bases = 11.57 +- 3.54 = 0.21 +- 3.56
Contig 76 1097 reads 81674 bases = 11.70 +- 5.07 = 0.25 +- 3.87
Contig 64 498 reads 37073 bases = 11.72 +- 4.31 = 0.67 +- 3.42
Contig 23 34 reads 2472 bases = 11.74 +- 10.00 = 2.13 +- 2.43
Contig 81 1471 reads 108243 bases = 11.79 +- 8.05 = 0.01 +- 3.93
Contig 67 547 reads 40028 bases = 12.04 +- 5.08 = 0.00 +- 3.99
Contig 78 1121 reads 81337 bases = 12.08 +- 4.02 = 0.29 +- 3.89
Contig 36 129 reads 9334 bases = 12.25 +- 3.06 = 0.73 +- 4.07
Contig 88 2286 reads 162474 bases = 12.35 +- 4.25 = 0.35 +- 4.15
Contig 59 400 reads 28235 bases = 12.49 +- 7.72 = 0.15 +- 4.25
Contig 80 1181 reads 82417 bases = 12.59 +- 4.06 = 0.04 +- 3.72
Contig 56 350 reads 23864 bases = 12.85 +- 3.80 = 0.27 +- 3.05
Contig 87 2076 reads 139799 bases = 13.03 +- 4.27 = 0.24 +- 4.54
Contig 74 987 reads 65274 bases = 13.26 +- 4.15 = 0.75 +- 4.35
Contig 70 579 reads 38606 bases = 13.31 +- 4.77 = 0.18 +- 4.20
Contig 71 603 reads 38995 bases = 13.64 +- 4.93 = 0.75 +- 3.83
Contig 79 1141 reads 71159 bases = 14.05 +- 4.21 = 0.20 +- 4.27
Contig 65 528 reads 13776 bases = 33.07 +- 57.00 = 2.03 +- 5.16
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 320
HQ Discrepant reads = 40
Chimeric reads = 106
Suspect alignments = 286
-------------------------------------------------------------------
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/microbe3/3634474/edit_dir.05Aug04.QD