Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-12-2005
Runby: 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
3634483 3380 161493 Anaeromyxobacter dehalogenans 2CP-C
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Anaeromyxobacter_dehalogenans 2CP-C
-------------------------------------------------------------------
Anaeromyxobacter dehalogenans 2CP-C, d-proteobacteria
Anaeromyxobacter dehalogenans, species, d-proteobacteria
Anaeromyxobacter, genus, d-proteobacteria
Cystobacterineae, suborder, d-proteobacteria
delta/epsilon subdivisions, subphylum, proteobacteria
Deltaproteobacteria, class, d-proteobacteria
Myxococcaceae, family, d-proteobacteria
Myxococcales (fruiting gliding bacteria), order, d-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 5002096
# phrap: 6497547
# db:
altered.
3380000
4959881 +/- 1273083
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 9105
Number of reads with percent X's >= 20%: 481 = 0.8%
Number of reads with percent X's >= 50%: 233 = 0.4%
Number of reads with percent X's >= 80%: 36 = 0.1%
Total reads in project: 59631
Total bp X'd : 572188
reads >= 20% >= 50% >= 80% screened
Nr with L09136 8137 244 116 24
Nr with pCC1Fos 599 1 0 0
Nr with pMCL200_JGI_XZX+XZK 369 236 117 12
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 10
Number of reads with percent X's >= 20%: 1 = 0.5%
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: 214
Total bp X'd : 842
reads >= 20% >= 50% >= 80% screened
Nr with L09136 7 0 0 0
Nr with pMCL200_JGI_XZX+XZK 3 1 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 8245837
C = 20846747
G = 20466915
T = 9776359
N = 172237
X = 572188
GC fraction = 0.69
Total = 60080283
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634483_fasta.screen.contigs
-------------------------------------------------------------------
A 634656
C 1893358
G 1871691
T 633357
N 55
fraction GC = 0.75
total bases = 5033117
Libraries and Reads
-------------------------------------------------------------------
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 AHZI reads.list > grep.reads.list.AHZI
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZI 4 500
-------------------------------------------------------------------
#Found 10122 total values totalling 29337391.0000. <2898.378878 +/- 1858.060326>
#Range: [ 900 - 173431 ]
#Most likely bin: [ 2500 - 3000 ] 5732 counts
#Median bin: [ 2500 - 3000 ] 5732 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 4 0.00 0.00 ]
| 1000 - 1500 : [ 68 0.01 0.01 ]
|X 1500 - 2000 : [ 110 0.01 0.02 ]
|XXXX 2000 - 2500 : [ 634 0.06 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 5732 0.57 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3457 0.34 0.99 ]
|X 3500 - 4000 : [ 112 0.01 1.00 ]
#...
| 5000 - 5500 : [ 1 0.00 1.00 ]
#...
| 6000 - 6500 : [ 1 0.00 1.00 ]
| 6500 - 7000 : [ 1 0.00 1.00 ]
#...
| 71500 - 72000 : [ 1 0.00 1.00 ]
#...
| 173000 - 173500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZK reads.list > grep.reads.list.AHZK
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZK 4 500
-------------------------------------------------------------------
#Found 9528 total values totalling 59046833.0000. <6197.190701 +/- 1668.564212>
#Range: [ 962 - 122036 ]
#Most likely bin: [ 6000 - 6500 ] 2477 counts
#Median bin: [ 6000 - 6500 ] 2477 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 3 0.00 0.00 ]
|X 1000 - 1500 : [ 78 0.01 0.01 ]
|X 1500 - 2000 : [ 81 0.01 0.02 ]
|X 2000 - 2500 : [ 85 0.01 0.03 ]
|XX 2500 - 3000 : [ 94 0.01 0.04 ]
|X 3000 - 3500 : [ 73 0.01 0.04 ]
|X 3500 - 4000 : [ 85 0.01 0.05 ]
|XX 4000 - 4500 : [ 127 0.01 0.07 ]
|XXXX 4500 - 5000 : [ 240 0.03 0.09 ]
|XXXXXXXXXX 5000 - 5500 : [ 608 0.06 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1617 0.17 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2477 0.26 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2072 0.22 0.80 ]
|XXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1293 0.14 0.94 ]
|XXXXXXXXX 7500 - 8000 : [ 548 0.06 1.00 ]
|X 8000 - 8500 : [ 42 0.00 1.00 ]
#...
| 10000 - 10500 : [ 1 0.00 1.00 ]
#...
| 19500 - 20000 : [ 1 0.00 1.00 ]
#...
| 21000 - 21500 : [ 1 0.00 1.00 ]
| 21500 - 22000 : [ 1 0.00 1.00 ]
#...
| 122000 - 122500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZN reads.list > grep.reads.list.AHZN
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZN 4 500
-------------------------------------------------------------------
#Found 323 total values totalling 13416145.0000. <41536.052632 +/- 5851.748733>
#Range: [ 27098 - 125138 ]
#Most likely bin: [ 40000 - 40500 ] 25 counts
#Median bin: [ 41500 - 42000 ] 14 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 27000 - 27500 : [ 1 0.00 0.00 ]
#...
|XX 31500 - 32000 : [ 1 0.00 0.01 ]
|XX 32000 - 32500 : [ 1 0.00 0.01 ]
|XXXXX 32500 - 33000 : [ 3 0.01 0.02 ]
|XXXXX 33000 - 33500 : [ 3 0.01 0.03 ]
#...
|XX 34000 - 34500 : [ 1 0.00 0.03 ]
|XXXXXXXXXXXXX 34500 - 35000 : [ 8 0.02 0.06 ]
|XX 35000 - 35500 : [ 1 0.00 0.06 ]
|XXXXXXXXXXX 35500 - 36000 : [ 7 0.02 0.08 ]
|XXXXXXXX 36000 - 36500 : [ 5 0.02 0.10 ]
|XXXXXXXX 36500 - 37000 : [ 5 0.02 0.11 ]
|XXXXXXXXXXX 37000 - 37500 : [ 7 0.02 0.13 ]
|XXXXXXXXXXXXXXXX 37500 - 38000 : [ 10 0.03 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 14 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 12 0.04 0.24 ]
|XXXXXXXXXXXXXX 39000 - 39500 : [ 9 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 20 0.06 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 25 0.08 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 16 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 12 0.04 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 14 0.04 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 20 0.06 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 21 0.07 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 15 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 20 0.06 0.78 ]
|XXXXXXXXXXXXXX 44000 - 44500 : [ 9 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXX 44500 - 45000 : [ 13 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXXXX 45000 - 45500 : [ 13 0.04 0.89 ]
|XXXXXXXXXXXXXXXXXXXXX 45500 - 46000 : [ 13 0.04 0.93 ]
|XXXXXXXXXXXXXXXXXX 46000 - 46500 : [ 11 0.03 0.96 ]
|XXXXXXXXXX 46500 - 47000 : [ 6 0.02 0.98 ]
|XXXXXX 47000 - 47500 : [ 4 0.01 0.99 ]
|XX 47500 - 48000 : [ 1 0.00 0.99 ]
#...
|XX 57500 - 58000 : [ 1 0.00 1.00 ]
#...
|XX 125000 - 125500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHZN 41189 +- 3573 (n=167)
# AHZI 2763 +- 417 (n=6040)
# AHZK 6078 +- 1276 (n=4928)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634483_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
AHZI 34944 -1 -1 91 563 34876 84 612 88 604
AHZK 35712 -1 -1 87 494 35712 78 571 88 563
AHZN 3840 -1 -1 56 250 3840 48 450 56 441
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHZI 17241 84 612 89 609 17635 83 613 87 598
AHZK 18048 83 579 91 587 17664 72 562 84 537
AHZN 1920 40 438 50 420 1920 56 458 63 457
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634483_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
20 1977 1344 67.20 70.00 AHZN @
136 29257 12531 92.14 95.98 AHZI @
160 28397 14045 87.78 91.44 AHZK @
] 59631 27920 88.35 cumulative total@@
LIBRARY PLATE ID COUNT [ AHZN 20 AHZI 136 AHZK 160 ] for 316 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 3634483_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 74428 total values totalling 34855244.0000. <468.308217 +/- 292.889771>
#Range: [ 0 - 933 ]
#Most likely bin: [ 0 - 50 ] 13475 counts
#Median bin: [ 550 - 600 ] 3426 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 13475 0.18 0.18 ]
|XXXXXX 50 - 100 : [ 2092 0.03 0.21 ]
|XXXXX 100 - 150 : [ 1621 0.02 0.23 ]
|XXXXX 150 - 200 : [ 1631 0.02 0.25 ]
|XXXXX 200 - 250 : [ 1768 0.02 0.28 ]
|XXXXXXX 250 - 300 : [ 2446 0.03 0.31 ]
|XXXXXXXXXX 300 - 350 : [ 3215 0.04 0.35 ]
|XXXXXXX 350 - 400 : [ 2353 0.03 0.38 ]
|XXXXXX 400 - 450 : [ 2145 0.03 0.41 ]
|XXXXXX 450 - 500 : [ 2143 0.03 0.44 ]
|XXXXXXXX 500 - 550 : [ 2701 0.04 0.48 ]
|XXXXXXXXXX 550 - 600 : [ 3426 0.05 0.52 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 5062 0.07 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 7320 0.10 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8924 0.12 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8793 0.12 0.93 ]
|XXXXXXXXXXXXXX 800 - 850 : [ 4633 0.06 0.99 ]
|XX 850 - 900 : [ 668 0.01 1.00 ]
| 900 - 950 : [ 12 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZI 3634483_fasta.screen.trimQ15.SaF > reads.trim15.AHZI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZI.rl 2 50
-------------------------------------------------------------------
#Found 34876 total values totalling 17982924.0000. <515.624613 +/- 283.328199>
#Range: [ 0 - 933 ]
#Most likely bin: [ 750 - 800 ] 4996 counts
#Median bin: [ 600 - 650 ] 2524 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 4829 0.14 0.14 ]
|XXXXXXX 50 - 100 : [ 841 0.02 0.16 ]
|XXXXXX 100 - 150 : [ 764 0.02 0.18 ]
|XXXXXX 150 - 200 : [ 782 0.02 0.21 ]
|XXXXXX 200 - 250 : [ 796 0.02 0.23 ]
|XXXXXXX 250 - 300 : [ 895 0.03 0.26 ]
|XXXXXXXX 300 - 350 : [ 1018 0.03 0.28 ]
|XXXXXXX 350 - 400 : [ 933 0.03 0.31 ]
|XXXXXXX 400 - 450 : [ 926 0.03 0.34 ]
|XXXXXXXX 450 - 500 : [ 975 0.03 0.37 ]
|XXXXXXXXXX 500 - 550 : [ 1291 0.04 0.40 ]
|XXXXXXXXXXXXX 550 - 600 : [ 1618 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2524 0.07 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3761 0.11 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4561 0.13 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4996 0.14 0.90 ]
|XXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2911 0.08 0.99 ]
|XXXX 850 - 900 : [ 446 0.01 1.00 ]
| 900 - 950 : [ 9 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZK
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZK 3634483_fasta.screen.trimQ15.SaF > reads.trim15.AHZK.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZK.rl 2 50
-------------------------------------------------------------------
#Found 35712 total values totalling 16018590.0000. <448.549227 +/- 290.146038>
#Range: [ 0 - 911 ]
#Most likely bin: [ 0 - 50 ] 6824 counts
#Median bin: [ 500 - 550 ] 1309 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 6824 0.19 0.19 ]
|XXXXXX 50 - 100 : [ 1084 0.03 0.22 ]
|XXXX 100 - 150 : [ 755 0.02 0.24 ]
|XXXX 150 - 200 : [ 745 0.02 0.26 ]
|XXXXX 200 - 250 : [ 870 0.02 0.29 ]
|XXXXXXXX 250 - 300 : [ 1331 0.04 0.33 ]
|XXXXXXXXXXXX 300 - 350 : [ 2070 0.06 0.38 ]
|XXXXXXX 350 - 400 : [ 1267 0.04 0.42 ]
|XXXXXX 400 - 450 : [ 1034 0.03 0.45 ]
|XXXXXX 450 - 500 : [ 1056 0.03 0.48 ]
|XXXXXXXX 500 - 550 : [ 1309 0.04 0.51 ]
|XXXXXXXXXX 550 - 600 : [ 1697 0.05 0.56 ]
|XXXXXXXXXXXXXX 600 - 650 : [ 2388 0.07 0.63 ]
|XXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3407 0.10 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4227 0.12 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3723 0.10 0.95 ]
|XXXXXXXXXX 800 - 850 : [ 1701 0.05 0.99 ]
|X 850 - 900 : [ 221 0.01 1.00 ]
| 900 - 950 : [ 3 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZN
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZN 3634483_fasta.screen.trimQ15.SaF > reads.trim15.AHZN.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZN.rl 2 50
-------------------------------------------------------------------
#Found 3840 total values totalling 853730.0000. <222.325521 +/- 257.349440>
#Range: [ 0 - 859 ]
#Most likely bin: [ 0 - 50 ] 1822 counts
#Median bin: [ 50 - 100 ] 167 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1822 0.47 0.47 ]
|XXXX 50 - 100 : [ 167 0.04 0.52 ]
|XX 100 - 150 : [ 102 0.03 0.54 ]
|XX 150 - 200 : [ 104 0.03 0.57 ]
|XX 200 - 250 : [ 102 0.03 0.60 ]
|XXXXX 250 - 300 : [ 220 0.06 0.66 ]
|XXX 300 - 350 : [ 127 0.03 0.69 ]
|XXX 350 - 400 : [ 153 0.04 0.73 ]
|XXXX 400 - 450 : [ 185 0.05 0.78 ]
|XX 450 - 500 : [ 112 0.03 0.81 ]
|XX 500 - 550 : [ 101 0.03 0.83 ]
|XX 550 - 600 : [ 111 0.03 0.86 ]
|XXX 600 - 650 : [ 150 0.04 0.90 ]
|XXX 650 - 700 : [ 152 0.04 0.94 ]
|XXX 700 - 750 : [ 136 0.04 0.97 ]
|XX 750 - 800 : [ 74 0.02 0.99 ]
| 800 - 850 : [ 21 0.01 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634483
-------------------------------------------------------------------
AHZI.000001.000100 pUC18.fa LRS.fasta
AHZI.000101.000200 pUC18.fa LRS.fasta
AHZK.000001.000100 pMCL200.fa LRS.fasta
AHZK.000101.000200 pMCL200.fa LRS.fasta
AHZN.000001.000100 pCC1Fos.fa LRS.fasta
AHZI.000001.000100 pUC18.fa LRS.fasta
AHZI.000101.000200 pUC18.fa LRS.fasta
AHZK.000001.000100 pMCL200.fa LRS.fasta
AHZK.000101.000200 pMCL200.fa LRS.fasta
AHZN.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634483_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634483_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 59229 total values totalling 43899.3768. <0.741180 +/- 0.049838>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.75 - 0.755 ] 2774 counts
#Median bin: [ 0.74 - 0.745 ] 2455 counts
#Entropy = 5.3365 bits
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.34 - 0.345 : [ 1 0.00 0.00 ]
| 0.345 - 0.35 : [ 1 0.00 0.00 ]
#...
| 0.395 - 0.4 : [ 1 0.00 0.00 ]
#...
| 0.42 - 0.425 : [ 2 0.00 0.00 ]
| 0.425 - 0.43 : [ 2 0.00 0.00 ]
#...
| 0.465 - 0.47 : [ 1 0.00 0.00 ]
#...
| 0.48 - 0.485 : [ 3 0.00 0.00 ]
#...
| 0.5 - 0.505 : [ 6 0.00 0.00 ]
#...
| 0.51 - 0.515 : [ 5 0.00 0.00 ]
| 0.515 - 0.52 : [ 6 0.00 0.00 ]
| 0.52 - 0.525 : [ 4 0.00 0.00 ]
| 0.525 - 0.53 : [ 9 0.00 0.00 ]
| 0.53 - 0.535 : [ 10 0.00 0.00 ]
| 0.535 - 0.54 : [ 7 0.00 0.00 ]
| 0.54 - 0.545 : [ 10 0.00 0.00 ]
| 0.545 - 0.55 : [ 6 0.00 0.00 ]
| 0.55 - 0.555 : [ 8 0.00 0.00 ]
| 0.555 - 0.56 : [ 18 0.00 0.00 ]
| 0.56 - 0.565 : [ 26 0.00 0.00 ]
| 0.565 - 0.57 : [ 20 0.00 0.00 ]
| 0.57 - 0.575 : [ 31 0.00 0.00 ]
| 0.575 - 0.58 : [ 28 0.00 0.00 ]
|X 0.58 - 0.585 : [ 52 0.00 0.00 ]
|X 0.585 - 0.59 : [ 61 0.00 0.01 ]
|X 0.59 - 0.595 : [ 87 0.00 0.01 ]
|X 0.595 - 0.6 : [ 90 0.00 0.01 ]
|XX 0.6 - 0.605 : [ 106 0.00 0.01 ]
|XX 0.605 - 0.61 : [ 106 0.00 0.01 ]
|X 0.61 - 0.615 : [ 95 0.00 0.01 ]
|XX 0.615 - 0.62 : [ 119 0.00 0.02 ]
|XX 0.62 - 0.625 : [ 119 0.00 0.02 ]
|XXX 0.625 - 0.63 : [ 219 0.00 0.02 ]
|XXXX 0.63 - 0.635 : [ 251 0.00 0.03 ]
|XXXX 0.635 - 0.64 : [ 245 0.00 0.03 ]
|XXXX 0.64 - 0.645 : [ 270 0.00 0.03 ]
|XXXXX 0.645 - 0.65 : [ 323 0.01 0.04 ]
|XXXXX 0.65 - 0.655 : [ 380 0.01 0.05 ]
|XXXXXXX 0.655 - 0.66 : [ 452 0.01 0.05 ]
|XXXXXXX 0.66 - 0.665 : [ 511 0.01 0.06 ]
|XXXXXXXXX 0.665 - 0.67 : [ 657 0.01 0.07 ]
|XXXXXXXXXXX 0.67 - 0.675 : [ 762 0.01 0.09 ]
|XXXXXXXXXXXX 0.675 - 0.68 : [ 838 0.01 0.10 ]
|XXXXXXXXXXXXXXX 0.68 - 0.685 : [ 1072 0.02 0.12 ]
|XXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 1131 0.02 0.14 ]
|XXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 1343 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 1429 0.02 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 1678 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 1805 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 1966 0.03 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 2085 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 2114 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.725 - 0.73 : [ 2343 0.04 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.73 - 0.735 : [ 2450 0.04 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.735 - 0.74 : [ 2437 0.04 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.74 - 0.745 : [ 2455 0.04 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.745 - 0.75 : [ 2409 0.04 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.75 - 0.755 : [ 2774 0.05 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.755 - 0.76 : [ 2573 0.04 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.76 - 0.765 : [ 2536 0.04 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.765 - 0.77 : [ 2287 0.04 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.77 - 0.775 : [ 2130 0.04 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.775 - 0.78 : [ 2070 0.03 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.78 - 0.785 : [ 1891 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.785 - 0.79 : [ 1612 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXX 0.79 - 0.795 : [ 1439 0.02 0.88 ]
|XXXXXXXXXXXXXXXXX 0.795 - 0.8 : [ 1159 0.02 0.90 ]
|XXXXXXXXXXXXXXXXX 0.8 - 0.805 : [ 1154 0.02 0.92 ]
|XXXXXXXXXXXXX 0.805 - 0.81 : [ 898 0.02 0.93 ]
|XXXXXXXXXXX 0.81 - 0.815 : [ 763 0.01 0.94 ]
|XXXXXXXXX 0.815 - 0.82 : [ 628 0.01 0.96 ]
|XXXXXXXX 0.82 - 0.825 : [ 543 0.01 0.96 ]
|XXXXXX 0.825 - 0.83 : [ 405 0.01 0.97 ]
|XXXXX 0.83 - 0.835 : [ 352 0.01 0.98 ]
|XXXX 0.835 - 0.84 : [ 268 0.00 0.98 ]
|XXX 0.84 - 0.845 : [ 197 0.00 0.99 ]
|XX 0.845 - 0.85 : [ 161 0.00 0.99 ]
|XX 0.85 - 0.855 : [ 147 0.00 0.99 ]
|X 0.855 - 0.86 : [ 101 0.00 0.99 ]
|X 0.86 - 0.865 : [ 94 0.00 0.99 ]
|X 0.865 - 0.87 : [ 77 0.00 0.99 ]
|X 0.87 - 0.875 : [ 46 0.00 1.00 ]
|X 0.875 - 0.88 : [ 54 0.00 1.00 ]
|X 0.88 - 0.885 : [ 42 0.00 1.00 ]
| 0.885 - 0.89 : [ 33 0.00 1.00 ]
| 0.89 - 0.895 : [ 18 0.00 1.00 ]
| 0.895 - 0.9 : [ 12 0.00 1.00 ]
| 0.9 - 0.905 : [ 16 0.00 1.00 ]
| 0.905 - 0.91 : [ 10 0.00 1.00 ]
| 0.91 - 0.915 : [ 15 0.00 1.00 ]
| 0.915 - 0.92 : [ 10 0.00 1.00 ]
| 0.92 - 0.925 : [ 5 0.00 1.00 ]
| 0.925 - 0.93 : [ 10 0.00 1.00 ]
| 0.93 - 0.935 : [ 5 0.00 1.00 ]
| 0.935 - 0.94 : [ 5 0.00 1.00 ]
| 0.94 - 0.945 : [ 3 0.00 1.00 ]
| 0.945 - 0.95 : [ 1 0.00 1.00 ]
| 0.95 - 0.955 : [ 4 0.00 1.00 ]
| 0.955 - 0.96 : [ 3 0.00 1.00 ]
| 0.96 - 0.965 : [ 3 0.00 1.00 ]
| 0.965 - 0.97 : [ 2 0.00 1.00 ]
| 0.97 - 0.975 : [ 2 0.00 1.00 ]
| 0.975 - 0.98 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 4 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 71. 746 reads; 60757 bp (untrimmed), 60565 (trimmed).
Contig 72. 785 reads; 64186 bp (untrimmed), 63918 (trimmed).
Contig 73. 807 reads; 70589 bp (untrimmed), 70538 (trimmed).
Contig 74. 850 reads; 73113 bp (untrimmed), 72787 (trimmed).
Contig 75. 895 reads; 82288 bp (untrimmed), 81975 (trimmed).
Contig 76. 950 reads; 83323 bp (untrimmed), 83195 (trimmed).
Contig 77. 1016 reads; 86437 bp (untrimmed), 85442 (trimmed).
Contig 78. 1025 reads; 87897 bp (untrimmed), 87667 (trimmed).
Contig 79. 1047 reads; 83163 bp (untrimmed), 83122 (trimmed).
Contig 80. 1143 reads; 96355 bp (untrimmed), 96153 (trimmed).
Contig 81. 1167 reads; 97960 bp (untrimmed), 97640 (trimmed).
Contig 82. 1350 reads; 123073 bp (untrimmed), 122579 (trimmed).
Contig 83. 1453 reads; 134180 bp (untrimmed), 133660 (trimmed).
Contig 84. 1453 reads; 127540 bp (untrimmed), 127035 (trimmed).
Contig 85. 1495 reads; 136389 bp (untrimmed), 135542 (trimmed).
Contig 86. 1628 reads; 139284 bp (untrimmed), 138967 (trimmed).
Contig 87. 1642 reads; 130661 bp (untrimmed), 130388 (trimmed).
Contig 88. 1663 reads; 131971 bp (untrimmed), 131874 (trimmed).
Contig 89. 1676 reads; 159607 bp (untrimmed), 159336 (trimmed).
Contig 90. 1813 reads; 135231 bp (untrimmed), 135120 (trimmed).
Contig 91. 1945 reads; 158337 bp (untrimmed), 157972 (trimmed).
Contig 92. 1978 reads; 173837 bp (untrimmed), 173066 (trimmed).
Contig 93. 2054 reads; 160663 bp (untrimmed), 160412 (trimmed).
Contig 94. 2647 reads; 206819 bp (untrimmed), 206771 (trimmed).
Contig 95. 2697 reads; 199202 bp (untrimmed), 198380 (trimmed).
Contig 96. 3066 reads; 250850 bp (untrimmed), 250022 (trimmed).
Contig 97. 3574 reads; 282718 bp (untrimmed), 282688 (trimmed).
--------------------------------------------------------------
Totals 59417 reads; 5033117 bp (untrimmed), 5002096 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 5031923 bases = 9.82 +- 4.27 = 0.16 +- 3.65
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 95 total values totalling 815.9800. <8.589263 +/- 2.344486>
#Range: [ 1.62 - 14.45 ]
#Most likely bin: [ 9.5 - 10 ] 16 counts
#Median bin: [ 9 - 9.5 ] 11 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 1.5 - 2 : [ 2 0.02 0.02 ]
|XX 2 - 2.5 : [ 1 0.01 0.03 ]
|XX 2.5 - 3 : [ 1 0.01 0.04 ]
#...
|XXXXX 3.5 - 4 : [ 2 0.02 0.06 ]
|XXXXXXXX 4 - 4.5 : [ 3 0.03 0.09 ]
|XXXXX 4.5 - 5 : [ 2 0.02 0.12 ]
#...
|XX 5.5 - 6 : [ 1 0.01 0.13 ]
|XXXXXXXX 6 - 6.5 : [ 3 0.03 0.16 ]
|XXXXX 6.5 - 7 : [ 2 0.02 0.18 ]
|XXXXX 7 - 7.5 : [ 2 0.02 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 9 0.09 0.29 ]
|XXXXXXXXXX 8 - 8.5 : [ 4 0.04 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 12 0.13 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 11 0.12 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 16 0.17 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 9 0.09 0.84 ]
|XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 8 0.08 0.93 ]
|XXXXXXXX 11 - 11.5 : [ 3 0.03 0.96 ]
|XXXXX 11.5 - 12 : [ 2 0.02 0.98 ]
|XX 12 - 12.5 : [ 1 0.01 0.99 ]
#...
|XX 14 - 14.5 : [ 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 89 total values totalling 798.7600. <8.974831 +/- 1.850599>
#Range: [ 3.87 - 14.45 ]
#Most likely bin: [ 9.5 - 10 ] 16 counts
#Median bin: [ 9 - 9.5 ] 11 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 3.5 - 4 : [ 1 0.01 0.01 ]
|XXXXXXXX 4 - 4.5 : [ 3 0.03 0.04 ]
|XX 4.5 - 5 : [ 1 0.01 0.06 ]
#...
|XX 5.5 - 6 : [ 1 0.01 0.07 ]
|XXXXXXXX 6 - 6.5 : [ 3 0.03 0.10 ]
|XXXXX 6.5 - 7 : [ 2 0.02 0.12 ]
|XXXXX 7 - 7.5 : [ 2 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 9 0.10 0.25 ]
|XXXXXXXXXX 8 - 8.5 : [ 4 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 12 0.13 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 11 0.12 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 16 0.18 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 9 0.10 0.83 ]
|XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 8 0.09 0.92 ]
|XXXXXXXX 11 - 11.5 : [ 3 0.03 0.96 ]
|XXXXX 11.5 - 12 : [ 2 0.02 0.98 ]
|XX 12 - 12.5 : [ 1 0.01 0.99 ]
#...
|XX 14 - 14.5 : [ 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 2 2 reads 697 bases = 1.62 +- 0.49 = 1.62 +- 0.49
Contig 5 4 reads 1424 bases = 1.72 +- 0.83 = 0.33 +- 1.02
Contig 3 3 reads 1012 bases = 2.49 +- 0.80 = 2.49 +- 0.80
Contig 8 7 reads 1761 bases = 2.86 +- 2.06 = -0.08 +- 1.09
Contig 6 5 reads 1066 bases = 3.57 +- 1.10 = 1.94 +- 0.83
Contig 10 18 reads 3602 bases = 3.87 +- 3.14 = 1.45 +- 2.14
Contig 13 29 reads 4756 bases = 4.07 +- 1.77 = -0.07 +- 2.48
Contig 9 12 reads 2317 bases = 4.08 +- 1.74 = 0.28 +- 2.25
Contig 11 18 reads 3086 bases = 4.26 +- 2.03 = 0.01 +- 2.65
Contig 16 40 reads 6146 bases = 4.77 +- 2.28 = 0.12 +- 2.22
Contig 7 6 reads 894 bases = 4.96 +- 1.25 = 4.96 +- 1.25
Contig 17 43 reads 5845 bases = 5.51 +- 2.10 = 1.55 +- 1.78
Contig 12 28 reads 3600 bases = 6.10 +- 4.74 = 0.51 +- 3.61
Contig 28 114 reads 12665 bases = 6.18 +- 2.12 = 0.30 +- 2.59
Contig 18 48 reads 6751 bases = 6.25 +- 3.33 = 0.98 +- 2.28
Contig 14 34 reads 4374 bases = 6.57 +- 2.86 = 1.55 +- 1.65
Contig 23 87 reads 9971 bases = 6.73 +- 2.97 = 0.05 +- 2.86
Contig 34 177 reads 20795 bases = 7.05 +- 2.70 = 0.39 +- 2.48
Contig 21 53 reads 5779 bases = 7.09 +- 3.01 = 0.82 +- 2.89
Contig 29 123 reads 13388 bases = 7.52 +- 3.58 = 0.52 +- 2.30
Contig 69 705 reads 54928 bases = 10.18 +- 3.68 = 0.08 +- 3.64
Contig 91 1945 reads 158337 bases = 10.21 +- 4.01 = 0.05 +- 3.61
Contig 79 1047 reads 83163 bases = 10.33 +- 3.91 = 0.22 +- 3.62
Contig 38 210 reads 16591 bases = 10.37 +- 3.57 = -0.07 +- 3.57
Contig 66 645 reads 52811 bases = 10.42 +- 4.18 = 0.23 +- 3.96
Contig 87 1642 reads 130661 bases = 10.51 +- 4.28 = -0.05 +- 3.79
Contig 94 2647 reads 206819 bases = 10.51 +- 4.35 = 0.20 +- 3.96
Contig 70 731 reads 59148 bases = 10.54 +- 4.53 = 0.27 +- 4.06
Contig 88 1663 reads 131971 bases = 10.57 +- 4.70 = 0.07 +- 4.05
Contig 50 338 reads 27013 bases = 10.61 +- 4.29 = 0.51 +- 3.97
Contig 97 3574 reads 282718 bases = 10.62 +- 3.84 = 0.07 +- 3.85
Contig 36 190 reads 14635 bases = 10.81 +- 5.27 = 0.78 +- 3.21
Contig 93 2054 reads 160663 bases = 10.86 +- 4.41 = 0.01 +- 3.97
Contig 62 548 reads 41347 bases = 11.00 +- 4.85 = 0.07 +- 4.20
Contig 68 705 reads 53660 bases = 11.19 +- 4.61 = 0.19 +- 3.20
Contig 37 201 reads 14652 bases = 11.42 +- 5.49 = 1.23 +- 5.10
Contig 90 1813 reads 135231 bases = 11.54 +- 5.16 = 0.07 +- 4.11
Contig 95 2697 reads 199202 bases = 11.96 +- 5.01 = 0.20 +- 4.03
Contig 51 355 reads 24455 bases = 12.39 +- 9.58 = 0.86 +- 3.18
Contig 47 311 reads 19604 bases = 14.45 +- 5.28 = 0.36 +- 5.44
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 863
HQ Discrepant reads = 91
Chimeric reads = 183
Suspect alignments = 227
-------------------------------------------------------------------
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/finished2/microbe/3634483/edit_dir.28Mar05.QD