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
3634470 2400 1096 Chlorobium phaeobacteroides
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Chlorobium_phaeobacteroides
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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: 6092876
# phrap: 4402039
# db:
altered.
2400000
4298305 +/- 1509393
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 7538
Number of reads with percent X's >= 20%: 61 = 0.2%
Number of reads with percent X's >= 50%: 34 = 0.1%
Number of reads with percent X's >= 80%: 9 = 0.0%
Total reads in project: 34717
Total bp X'd : 315305
reads >= 20% >= 50% >= 80% screened
Nr with L09136 7042 28 18 1
Nr with pCC1Fos 447 1 0 0
Nr with pMCL200_JGI_XZX+XZK 49 32 16 8
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 1411
Number of reads with percent X's >= 20%: 856 = 18.7%
Number of reads with percent X's >= 50%: 839 = 18.3%
Number of reads with percent X's >= 80%: 769 = 16.8%
Total reads in project: 4589
Total bp X'd : 763456
reads >= 20% >= 50% >= 80% screened
Nr with L09136 869 345 341 304
Nr with LRS 54 53 53 53
Nr with pCC1Fos 24 4 2 0
Nr with pMCL200_JGI_XZX+XZK 464 454 443 412
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Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 9591802
C = 8482077
G = 8417365
T = 9305770
N = 259203
X = 1087537
GC fraction = 0.45
Total = 37143754
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634470_fasta.screen.contigs
-------------------------------------------------------------------
A 1786367
C 1426022
G 1399585
T 1765407
N 2870
fraction GC = 0.44
total bases = 6380251
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
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Command: /usr/xpg4/bin/grep AHXF reads.list > grep.reads.list.AHXF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXF 4 500
-------------------------------------------------------------------
#Found 5221 total values totalling 18032300.0000. <3453.801954 +/- 3768.472939>
#Range: [ 450 - 273933 ]
#Most likely bin: [ 3000 - 3500 ] 2604 counts
#Median bin: [ 3000 - 3500 ] 2604 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
| 500 - 1000 : [ 3 0.00 0.00 ]
| 1000 - 1500 : [ 10 0.00 0.00 ]
| 1500 - 2000 : [ 11 0.00 0.00 ]
| 2000 - 2500 : [ 11 0.00 0.01 ]
|XXXXXXXXX 2500 - 3000 : [ 606 0.12 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2604 0.50 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1687 0.32 0.94 ]
|XXXX 4000 - 4500 : [ 279 0.05 1.00 ]
| 4500 - 5000 : [ 1 0.00 1.00 ]
#...
| 5500 - 6000 : [ 1 0.00 1.00 ]
#...
| 7000 - 7500 : [ 2 0.00 1.00 ]
| 7500 - 8000 : [ 1 0.00 1.00 ]
| 8000 - 8500 : [ 1 0.00 1.00 ]
#...
| 12000 - 12500 : [ 2 0.00 1.00 ]
#...
| 273500 - 274000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXG reads.list > grep.reads.list.AHXG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXG 4 500
-------------------------------------------------------------------
#Found 4613 total values totalling 30325141.0000. <6573.843703 +/- 805.970398>
#Range: [ 815 - 20428 ]
#Most likely bin: [ 6000 - 6500 ] 1499 counts
#Median bin: [ 6500 - 7000 ] 1186 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 6 0.00 0.00 ]
| 1500 - 2000 : [ 8 0.00 0.00 ]
| 2000 - 2500 : [ 10 0.00 0.01 ]
| 2500 - 3000 : [ 13 0.00 0.01 ]
| 3000 - 3500 : [ 7 0.00 0.01 ]
| 3500 - 4000 : [ 9 0.00 0.01 ]
| 4000 - 4500 : [ 14 0.00 0.01 ]
|X 4500 - 5000 : [ 19 0.00 0.02 ]
|X 5000 - 5500 : [ 34 0.01 0.03 ]
|XXXXXXXXXXXXXXX 5500 - 6000 : [ 579 0.13 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1499 0.32 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1186 0.26 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 836 0.18 0.92 ]
|XXXXXXXXX 7500 - 8000 : [ 353 0.08 0.99 ]
|X 8000 - 8500 : [ 28 0.01 1.00 ]
#...
| 9000 - 9500 : [ 3 0.00 1.00 ]
| 9500 - 10000 : [ 1 0.00 1.00 ]
| 10000 - 10500 : [ 3 0.00 1.00 ]
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 16000 - 16500 : [ 2 0.00 1.00 ]
#...
| 20000 - 20500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXH reads.list > grep.reads.list.AHXH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXH 4 500
-------------------------------------------------------------------
#Found 231 total values totalling 8653353.0000. <37460.402597 +/- 4857.006944>
#Range: [ 1116 - 46731 ]
#Most likely bin: [ 37000 - 37500 ] 14 counts
#Median bin: [ 37000 - 37500 ] 14 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 1000 - 1500 : [ 1 0.00 0.00 ]
#...
|XXX 11500 - 12000 : [ 1 0.00 0.01 ]
#...
|XXX 29000 - 29500 : [ 1 0.00 0.01 ]
#...
|XXXXXX 30000 - 30500 : [ 2 0.01 0.02 ]
#...
|XXXXXXXXXXXXXX 31000 - 31500 : [ 5 0.02 0.04 ]
|XXXXXXXXX 31500 - 32000 : [ 3 0.01 0.06 ]
|XXXXXXXXXXXXXXXXX 32000 - 32500 : [ 6 0.03 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 9 0.04 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 11 0.05 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 10 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 12 0.05 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 10 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 8 0.03 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 8 0.03 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 10 0.04 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 8 0.03 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 14 0.06 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 8 0.03 0.55 ]
|XXXXXXXXXXXXXX 38000 - 38500 : [ 5 0.02 0.57 ]
|XXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 7 0.03 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 13 0.06 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 8 0.03 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 10 0.04 0.74 ]
|XXXXXXXXXXX 40500 - 41000 : [ 4 0.02 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 10 0.04 0.80 ]
|XXXXXXXXXXXXXX 41500 - 42000 : [ 5 0.02 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 12 0.05 0.87 ]
|XXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 7 0.03 0.90 ]
|XXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 8 0.03 0.94 ]
|XXX 43500 - 44000 : [ 1 0.00 0.94 ]
|XXXXXXXXXXXXXXXXX 44000 - 44500 : [ 6 0.03 0.97 ]
|XXXXXXXXX 44500 - 45000 : [ 3 0.01 0.98 ]
#...
|XXXXXXXXX 45500 - 46000 : [ 3 0.01 0.99 ]
|XXX 46000 - 46500 : [ 1 0.00 1.00 ]
|XXX 46500 - 47000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHXG 6504 +- 945 (n=2315)
# AHXH 37311 +- 4465 (n=128)
# AHXF 3259 +- 454 (n=2641)
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Library / Read Quality summary
extracted from 3634470_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
AHXF 18432 89 608 94 624 18309 90 608 94 615
AHXG 17664 97 769 97 747 17664 94 776 97 768
AHXH 3072 87 658 94 640 3072 87 666 94 682
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHXF 9160 90 611 94 620 9149 90 606 93 610
AHXG 8832 94 775 98 767 8832 94 777 97 769
AHXH 1536 88 682 94 683 1536 87 650 94 680
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634470_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
96 18309 9200 95.83 99.83 AHXF @
92 17664 8832 96.00 100.00 AHXG @
16 3072 1536 96.00 100.00 AHXH @
] 39045 19568 95.92 cumulative total@@
LIBRARY PLATE ID COUNT [ AHXF 96 AHXG 92 AHXH 16 ] 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 3634470_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 39045 total values totalling 24724410.0000. <633.228582 +/- 239.936905>
#Range: [ 0 - 947 ]
#Most likely bin: [ 750 - 800 ] 7879 counts
#Median bin: [ 700 - 750 ] 6188 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 0 - 50 : [ 2940 0.08 0.08 ]
|XX 50 - 100 : [ 370 0.01 0.08 ]
|XX 100 - 150 : [ 320 0.01 0.09 ]
|XX 150 - 200 : [ 298 0.01 0.10 ]
|XX 200 - 250 : [ 360 0.01 0.11 ]
|XX 250 - 300 : [ 418 0.01 0.12 ]
|XXX 300 - 350 : [ 495 0.01 0.13 ]
|XXX 350 - 400 : [ 642 0.02 0.15 ]
|XXXX 400 - 450 : [ 751 0.02 0.17 ]
|XXXXX 450 - 500 : [ 963 0.02 0.19 ]
|XXXXXX 500 - 550 : [ 1183 0.03 0.22 ]
|XXXXXXXX 550 - 600 : [ 1577 0.04 0.26 ]
|XXXXXXXXXXXX 600 - 650 : [ 2386 0.06 0.33 ]
|XXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3945 0.10 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6188 0.16 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 7879 0.20 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6751 0.17 0.96 ]
|XXXXXXXX 850 - 900 : [ 1528 0.04 1.00 ]
| 900 - 950 : [ 51 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXF 3634470_fasta.screen.trimQ15.SaF > reads.trim15.AHXF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXF.rl 2 50
-------------------------------------------------------------------
#Found 18309 total values totalling 10033163.0000. <547.990770 +/- 233.124747>
#Range: [ 0 - 860 ]
#Most likely bin: [ 700 - 750 ] 3483 counts
#Median bin: [ 600 - 650 ] 2013 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXX 0 - 50 : [ 1599 0.09 0.09 ]
|XXX 50 - 100 : [ 266 0.01 0.10 ]
|XXX 100 - 150 : [ 245 0.01 0.12 ]
|XXX 150 - 200 : [ 222 0.01 0.13 ]
|XXX 200 - 250 : [ 286 0.02 0.14 ]
|XXXX 250 - 300 : [ 323 0.02 0.16 ]
|XXXXX 300 - 350 : [ 392 0.02 0.18 ]
|XXXXXX 350 - 400 : [ 503 0.03 0.21 ]
|XXXXXXX 400 - 450 : [ 629 0.03 0.24 ]
|XXXXXXXXXX 450 - 500 : [ 832 0.05 0.29 ]
|XXXXXXXXXXX 500 - 550 : [ 995 0.05 0.34 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 1317 0.07 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2013 0.11 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2984 0.16 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3483 0.19 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1982 0.11 0.99 ]
|XXX 800 - 850 : [ 234 0.01 1.00 ]
| 850 - 900 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXG 3634470_fasta.screen.trimQ15.SaF > reads.trim15.AHXG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXG.rl 2 50
-------------------------------------------------------------------
#Found 17664 total values totalling 12891676.0000. <729.827672 +/- 200.742796>
#Range: [ 0 - 916 ]
#Most likely bin: [ 800 - 850 ] 6019 counts
#Median bin: [ 750 - 800 ] 5451 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 0 - 50 : [ 1024 0.06 0.06 ]
| 50 - 100 : [ 36 0.00 0.06 ]
| 100 - 150 : [ 30 0.00 0.06 ]
| 150 - 200 : [ 31 0.00 0.06 ]
| 200 - 250 : [ 37 0.00 0.07 ]
| 250 - 300 : [ 40 0.00 0.07 ]
| 300 - 350 : [ 36 0.00 0.07 ]
| 350 - 400 : [ 45 0.00 0.07 ]
| 400 - 450 : [ 35 0.00 0.07 ]
| 450 - 500 : [ 51 0.00 0.08 ]
| 500 - 550 : [ 71 0.00 0.08 ]
|X 550 - 600 : [ 126 0.01 0.09 ]
|XX 600 - 650 : [ 239 0.01 0.10 ]
|XXXXX 650 - 700 : [ 727 0.04 0.14 ]
|XXXXXXXXXXXXXXXX 700 - 750 : [ 2346 0.13 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5451 0.31 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6019 0.34 0.93 ]
|XXXXXXXXX 850 - 900 : [ 1300 0.07 1.00 ]
| 900 - 950 : [ 20 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXH 3634470_fasta.screen.trimQ15.SaF > reads.trim15.AHXH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXH.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 1799571.0000. <585.797852 +/- 277.278298>
#Range: [ 0 - 947 ]
#Most likely bin: [ 800 - 850 ] 498 counts
#Median bin: [ 700 - 750 ] 359 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 317 0.10 0.10 ]
|XXXXX 50 - 100 : [ 68 0.02 0.13 ]
|XXXX 100 - 150 : [ 45 0.01 0.14 ]
|XXXX 150 - 200 : [ 45 0.01 0.15 ]
|XXX 200 - 250 : [ 37 0.01 0.17 ]
|XXXX 250 - 300 : [ 55 0.02 0.18 ]
|XXXXX 300 - 350 : [ 67 0.02 0.21 ]
|XXXXXXXX 350 - 400 : [ 94 0.03 0.24 ]
|XXXXXXX 400 - 450 : [ 87 0.03 0.27 ]
|XXXXXX 450 - 500 : [ 80 0.03 0.29 ]
|XXXXXXXXX 500 - 550 : [ 117 0.04 0.33 ]
|XXXXXXXXXXX 550 - 600 : [ 134 0.04 0.37 ]
|XXXXXXXXXXX 600 - 650 : [ 134 0.04 0.42 ]
|XXXXXXXXXXXXXXXXXXX 650 - 700 : [ 234 0.08 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 359 0.12 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 446 0.15 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 498 0.16 0.92 ]
|XXXXXXXXXXXXXXXXXX 850 - 900 : [ 224 0.07 0.99 ]
|XX 900 - 950 : [ 31 0.01 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634470
-------------------------------------------------------------------
AHXF.000001.000100 pUC18.fa LRS.fasta
AHXF.000101.000200 pUC18.fa LRS.fasta
AHXG.000001.000100 pMCL200.fa LRS.fasta
AHXG.000101.000200 pMCL200.fa LRS.fasta
AHXH.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AHXF.000001.000100 pUC18.fa LRS.fasta
AHXF.000101.000200 pUC18.fa LRS.fasta
AHXG.000001.000100 pMCL200.fa LRS.fasta
AHXG.000101.000200 pMCL200.fa LRS.fasta
AHXH.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634470_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634470_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 36171 total values totalling 16932.8862. <0.468134 +/- 0.059482>
#Range: [ 0 - 0.78 ]
#Most likely bin: [ 0.49 - 0.495 ] 1508 counts
#Median bin: [ 0.475 - 0.48 ] 1336 counts
#Entropy = 5.5670 bits
| 0 - 0.005 : [ 3 0.00 0.00 ]
#...
| 0.16 - 0.165 : [ 1 0.00 0.00 ]
#...
| 0.19 - 0.195 : [ 1 0.00 0.00 ]
#...
| 0.2 - 0.205 : [ 1 0.00 0.00 ]
| 0.205 - 0.21 : [ 2 0.00 0.00 ]
| 0.21 - 0.215 : [ 1 0.00 0.00 ]
#...
| 0.22 - 0.225 : [ 1 0.00 0.00 ]
| 0.225 - 0.23 : [ 1 0.00 0.00 ]
#...
| 0.235 - 0.24 : [ 2 0.00 0.00 ]
| 0.24 - 0.245 : [ 3 0.00 0.00 ]
| 0.245 - 0.25 : [ 5 0.00 0.00 ]
| 0.25 - 0.255 : [ 5 0.00 0.00 ]
| 0.255 - 0.26 : [ 2 0.00 0.00 ]
| 0.26 - 0.265 : [ 8 0.00 0.00 ]
| 0.265 - 0.27 : [ 11 0.00 0.00 ]
| 0.27 - 0.275 : [ 12 0.00 0.00 ]
|X 0.275 - 0.28 : [ 28 0.00 0.00 ]
| 0.28 - 0.285 : [ 17 0.00 0.00 ]
|X 0.285 - 0.29 : [ 26 0.00 0.00 ]
|X 0.29 - 0.295 : [ 36 0.00 0.00 ]
|X 0.295 - 0.3 : [ 23 0.00 0.01 ]
|X 0.3 - 0.305 : [ 56 0.00 0.01 ]
|XX 0.305 - 0.31 : [ 57 0.00 0.01 ]
|XX 0.31 - 0.315 : [ 83 0.00 0.01 ]
|XX 0.315 - 0.32 : [ 88 0.00 0.01 ]
|XXX 0.32 - 0.325 : [ 101 0.00 0.02 ]
|XXX 0.325 - 0.33 : [ 98 0.00 0.02 ]
|XXXX 0.33 - 0.335 : [ 145 0.00 0.02 ]
|XXXX 0.335 - 0.34 : [ 153 0.00 0.03 ]
|XXXX 0.34 - 0.345 : [ 165 0.00 0.03 ]
|XXXX 0.345 - 0.35 : [ 169 0.00 0.04 ]
|XXXXXX 0.35 - 0.355 : [ 235 0.01 0.04 ]
|XXXXXXX 0.355 - 0.36 : [ 248 0.01 0.05 ]
|XXXXXXX 0.36 - 0.365 : [ 257 0.01 0.06 ]
|XXXXXXXX 0.365 - 0.37 : [ 312 0.01 0.07 ]
|XXXXXXXXX 0.37 - 0.375 : [ 337 0.01 0.07 ]
|XXXXXXXXXX 0.375 - 0.38 : [ 381 0.01 0.08 ]
|XXXXXXXXXXX 0.38 - 0.385 : [ 419 0.01 0.10 ]
|XXXXXXXXXXXXX 0.385 - 0.39 : [ 476 0.01 0.11 ]
|XXXXXXXXXXXXX 0.39 - 0.395 : [ 507 0.01 0.12 ]
|XXXXXXXXXXXXXX 0.395 - 0.4 : [ 545 0.02 0.14 ]
|XXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 635 0.02 0.16 ]
|XXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 595 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 665 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 673 0.02 0.21 ]
|XXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 630 0.02 0.23 ]
|XXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 718 0.02 0.25 ]
|XXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 714 0.02 0.27 ]
|XXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 761 0.02 0.29 ]
|XXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 809 0.02 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 904 0.02 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 922 0.03 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 988 0.03 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 1079 0.03 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 1129 0.03 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 1335 0.04 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 1336 0.04 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 1425 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1411 0.04 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1508 0.04 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1392 0.04 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1507 0.04 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1394 0.04 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1300 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1125 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1001 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 875 0.02 0.88 ]
|XXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 717 0.02 0.90 ]
|XXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 642 0.02 0.92 ]
|XXXXXXXXXXXXXX 0.54 - 0.545 : [ 523 0.01 0.93 ]
|XXXXXXXXXXX 0.545 - 0.55 : [ 419 0.01 0.94 ]
|XXXXXXXXX 0.55 - 0.555 : [ 335 0.01 0.95 ]
|XXXXXXXX 0.555 - 0.56 : [ 283 0.01 0.96 ]
|XXXXXX 0.56 - 0.565 : [ 221 0.01 0.97 ]
|XXXXX 0.565 - 0.57 : [ 203 0.01 0.97 ]
|XXXX 0.57 - 0.575 : [ 162 0.00 0.98 ]
|XXXXX 0.575 - 0.58 : [ 178 0.00 0.98 ]
|XXX 0.58 - 0.585 : [ 126 0.00 0.99 ]
|XX 0.585 - 0.59 : [ 89 0.00 0.99 ]
|XX 0.59 - 0.595 : [ 71 0.00 0.99 ]
|X 0.595 - 0.6 : [ 52 0.00 0.99 ]
|X 0.6 - 0.605 : [ 51 0.00 0.99 ]
|X 0.605 - 0.61 : [ 41 0.00 0.99 ]
|X 0.61 - 0.615 : [ 36 0.00 1.00 ]
|X 0.615 - 0.62 : [ 34 0.00 1.00 ]
|X 0.62 - 0.625 : [ 22 0.00 1.00 ]
|X 0.625 - 0.63 : [ 23 0.00 1.00 ]
|X 0.63 - 0.635 : [ 24 0.00 1.00 ]
| 0.635 - 0.64 : [ 15 0.00 1.00 ]
| 0.64 - 0.645 : [ 9 0.00 1.00 ]
| 0.645 - 0.65 : [ 9 0.00 1.00 ]
| 0.65 - 0.655 : [ 8 0.00 1.00 ]
| 0.655 - 0.66 : [ 6 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 : [ 1 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 : [ 2 0.00 1.00 ]
#...
| 0.695 - 0.7 : [ 2 0.00 1.00 ]
| 0.7 - 0.705 : [ 1 0.00 1.00 ]
| 0.705 - 0.71 : [ 1 0.00 1.00 ]
#...
| 0.72 - 0.725 : [ 1 0.00 1.00 ]
| 0.725 - 0.73 : [ 1 0.00 1.00 ]
#...
| 0.74 - 0.745 : [ 1 0.00 1.00 ]
#...
| 0.78 - 0.785 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 2070. 315 reads; 35360 bp (untrimmed), 35301 (trimmed).
Contig 2071. 316 reads; 34932 bp (untrimmed), 34760 (trimmed).
Contig 2072. 320 reads; 39483 bp (untrimmed), 39311 (trimmed).
Contig 2073. 321 reads; 34710 bp (untrimmed), 34551 (trimmed).
Contig 2074. 328 reads; 37538 bp (untrimmed), 37477 (trimmed).
Contig 2075. 329 reads; 34235 bp (untrimmed), 34033 (trimmed).
Contig 2076. 338 reads; 29797 bp (untrimmed), 29496 (trimmed).
Contig 2077. 371 reads; 39020 bp (untrimmed), 38794 (trimmed).
Contig 2078. 391 reads; 37386 bp (untrimmed), 37343 (trimmed).
Contig 2079. 432 reads; 44362 bp (untrimmed), 44340 (trimmed).
Contig 2080. 438 reads; 51432 bp (untrimmed), 51250 (trimmed).
Contig 2081. 483 reads; 34236 bp (untrimmed), 34145 (trimmed).
Contig 2082. 491 reads; 50281 bp (untrimmed), 50165 (trimmed).
Contig 2083. 503 reads; 45550 bp (untrimmed), 45513 (trimmed).
Contig 2084. 506 reads; 55459 bp (untrimmed), 55422 (trimmed).
Contig 2085. 512 reads; 46135 bp (untrimmed), 46094 (trimmed).
Contig 2086. 512 reads; 52534 bp (untrimmed), 52523 (trimmed).
Contig 2087. 568 reads; 57245 bp (untrimmed), 57202 (trimmed).
Contig 2088. 585 reads; 58859 bp (untrimmed), 58722 (trimmed).
Contig 2089. 605 reads; 61303 bp (untrimmed), 61182 (trimmed).
Contig 2090. 658 reads; 67648 bp (untrimmed), 67625 (trimmed).
Contig 2091. 667 reads; 77008 bp (untrimmed), 76962 (trimmed).
Contig 2092. 692 reads; 71479 bp (untrimmed), 71379 (trimmed).
Contig 2093. 784 reads; 64485 bp (untrimmed), 64330 (trimmed).
Contig 2094. 817 reads; 81753 bp (untrimmed), 81603 (trimmed).
Contig 2095. 1380 reads; 137495 bp (untrimmed), 137442 (trimmed).
Contig 2096. 3240 reads; 310978 bp (untrimmed), 310958 (trimmed).
--------------------------------------------------------------
Totals 34456 reads; 6380251 bp (untrimmed), 6092876 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 6297387 bases = 4.69 +- 4.27 = 0.60 +- 2.39
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 2002 total values totalling 4461.6800. <2.228611 +/- 1.441477>
#Range: [ 1.04 - 15.99 ]
#Most likely bin: [ 1.5 - 2 ] 761 counts
#Median bin: [ 1.5 - 2 ] 761 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 439 0.22 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 761 0.38 0.60 ]
|XXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 386 0.19 0.79 ]
|XXXXXXXXXXX 2.5 - 3 : [ 201 0.10 0.89 ]
|XXXX 3 - 3.5 : [ 70 0.03 0.93 ]
|X 3.5 - 4 : [ 27 0.01 0.94 ]
|X 4 - 4.5 : [ 16 0.01 0.95 ]
| 4.5 - 5 : [ 7 0.00 0.95 ]
| 5 - 5.5 : [ 9 0.00 0.96 ]
| 5.5 - 6 : [ 6 0.00 0.96 ]
| 6 - 6.5 : [ 7 0.00 0.96 ]
| 6.5 - 7 : [ 6 0.00 0.97 ]
|X 7 - 7.5 : [ 11 0.01 0.97 ]
|X 7.5 - 8 : [ 12 0.01 0.98 ]
|X 8 - 8.5 : [ 13 0.01 0.98 ]
|X 8.5 - 9 : [ 11 0.01 0.99 ]
| 9 - 9.5 : [ 7 0.00 0.99 ]
| 9.5 - 10 : [ 7 0.00 1.00 ]
| 10 - 10.5 : [ 1 0.00 1.00 ]
| 10.5 - 11 : [ 1 0.00 1.00 ]
| 11 - 11.5 : [ 2 0.00 1.00 ]
#...
| 12 - 12.5 : [ 1 0.00 1.00 ]
#...
| 15.5 - 16 : [ 1 0.00 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 244 total values totalling 1172.6500. <4.805943 +/- 2.691902>
#Range: [ 1.73 - 15.99 ]
#Most likely bin: [ 2.5 - 3 ] 56 counts
#Median bin: [ 3 - 3.5 ] 26 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 1.5 - 2 : [ 5 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 38 0.16 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 56 0.23 0.41 ]
|XXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 26 0.11 0.51 ]
|XXXXXXXXX 3.5 - 4 : [ 13 0.05 0.57 ]
|XXXXXX 4 - 4.5 : [ 8 0.03 0.60 ]
|XXXX 4.5 - 5 : [ 6 0.02 0.62 ]
|XXXXXX 5 - 5.5 : [ 8 0.03 0.66 ]
|XXXX 5.5 - 6 : [ 5 0.02 0.68 ]
|XXXX 6 - 6.5 : [ 6 0.02 0.70 ]
|XXXX 6.5 - 7 : [ 6 0.02 0.73 ]
|XXXXXXXX 7 - 7.5 : [ 11 0.05 0.77 ]
|XXXXXXXXX 7.5 - 8 : [ 12 0.05 0.82 ]
|XXXXXXXXX 8 - 8.5 : [ 13 0.05 0.87 ]
|XXXXXXXX 8.5 - 9 : [ 11 0.05 0.92 ]
|XXXXX 9 - 9.5 : [ 7 0.03 0.95 ]
|XXXXX 9.5 - 10 : [ 7 0.03 0.98 ]
|X 10 - 10.5 : [ 1 0.00 0.98 ]
|X 10.5 - 11 : [ 1 0.00 0.98 ]
|X 11 - 11.5 : [ 2 0.01 0.99 ]
#...
|X 12 - 12.5 : [ 1 0.00 1.00 ]
#...
|X 15.5 - 16 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 591 2 reads 1827 bases = 1.04 +- 0.19 = 0.00 +- 0.98
Contig 100 2 reads 1683 bases = 1.05 +- 0.22 = 1.05 +- 0.22
Contig 106 2 reads 1680 bases = 1.05 +- 0.22 = 0.11 +- 0.97
Contig 161 2 reads 1439 bases = 1.05 +- 0.21 = 1.05 +- 0.21
Contig 400 2 reads 1756 bases = 1.05 +- 0.22 = 1.05 +- 0.22
Contig 534 2 reads 1212 bases = 1.05 +- 0.21 = -0.05 +- 0.98
Contig 285 2 reads 1778 bases = 1.06 +- 0.24 = 0.03 +- 0.97
Contig 330 2 reads 1199 bases = 1.06 +- 0.23 = 1.06 +- 0.23
Contig 332 2 reads 1789 bases = 1.06 +- 0.23 = 0.01 +- 0.97
Contig 362 2 reads 1528 bases = 1.06 +- 0.24 = 1.06 +- 0.24
Contig 472 2 reads 1607 bases = 1.06 +- 0.23 = 1.06 +- 0.23
Contig 486 2 reads 1091 bases = 1.06 +- 0.24 = 0.29 +- 0.93
Contig 510 2 reads 1781 bases = 1.06 +- 0.24 = -0.01 +- 0.97
Contig 514 2 reads 1292 bases = 1.06 +- 0.24 = -0.47 +- 0.84
Contig 236 2 reads 1853 bases = 1.07 +- 0.25 = -0.01 +- 0.97
Contig 368 2 reads 1402 bases = 1.07 +- 0.26 = 0.35 +- 0.90
Contig 501 2 reads 1742 bases = 1.07 +- 0.25 = 1.07 +- 0.25
Contig 619 2 reads 1910 bases = 1.07 +- 0.26 = 1.07 +- 0.26
Contig 203 2 reads 1550 bases = 1.08 +- 0.27 = -0.05 +- 0.96
Contig 213 2 reads 1549 bases = 1.08 +- 0.27 = 1.08 +- 0.27
Contig 2096 3240 reads 310978 bases = 9.03 +- 3.50 = 0.08 +- 3.19
Contig 2041 133 reads 12349 bases = 9.04 +- 3.23 = 2.11 +- 3.09
Contig 2042 134 reads 12674 bases = 9.10 +- 3.39 = 1.13 +- 4.50
Contig 2032 90 reads 8416 bases = 9.21 +- 4.52 = 0.07 +- 3.52
Contig 2035 101 reads 9705 bases = 9.22 +- 3.77 = 0.35 +- 3.33
Contig 2017 41 reads 3880 bases = 9.30 +- 3.67 = 2.45 +- 2.38
Contig 2083 503 reads 45550 bases = 9.42 +- 3.20 = 0.38 +- 3.26
Contig 2085 512 reads 46135 bases = 9.54 +- 6.10 = 0.68 +- 3.43
Contig 2059 245 reads 22380 bases = 9.55 +- 3.80 = 0.11 +- 3.55
Contig 2004 26 reads 2352 bases = 9.58 +- 6.53 = 0.68 +- 2.27
Contig 2049 188 reads 17272 bases = 9.59 +- 3.88 = 0.17 +- 3.51
Contig 2076 338 reads 29797 bases = 9.65 +- 3.25 = 1.09 +- 3.56
Contig 2058 243 reads 21383 bases = 9.89 +- 4.74 = 0.83 +- 4.42
Contig 2011 33 reads 2868 bases = 9.96 +- 4.71 = 0.97 +- 2.48
Contig 2065 280 reads 23949 bases = 10.11 +- 9.08 = 0.55 +- 3.78
Contig 2093 784 reads 64485 bases = 10.67 +- 8.81 = 0.62 +- 4.23
Contig 2046 159 reads 12267 bases = 11.07 +- 3.96 = 0.07 +- 4.24
Contig 2060 256 reads 18879 bases = 11.37 +- 3.81 = 0.91 +- 3.16
Contig 2081 483 reads 34236 bases = 12.04 +- 15.12 = 0.58 +- 4.42
Contig 2029 77 reads 4245 bases = 15.99 +- 12.88 = 0.76 +- 3.68
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 551
HQ Discrepant reads = 264
Chimeric reads = 117
Suspect alignments = 264
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 3.57 SUN/Ultra-2/3
Equivalent to Phil Green's version 0.990329
Score matrix (set by value of penalty: -2)
A C G T N X
A 1 -2 -2 -2 0 -3
C -2 1 -2 -2 0 -3
G -2 -2 1 -2 0 -3
T -2 -2 -2 1 0 -3
N 0 0 0 0 0 0
X -3 -3 -3 -3 0 -3
gap_init: -4
gap_ext: -3
ins_gap_ext: -3
del_gap_ext: -3
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 30
maxmatch: 55
max_group_size: 20
minscore: 55
bandwidth: 14
indexwordsize: 10
vector_bound: 20
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 13
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -5
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/microbe4/3634470/edit_dir.19Nov04.QD