Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-13-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634475 2400 34090 Pelodictyon phaeoclathratiforme
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Pelodictyon_phaeoclathratiforme
-------------------------------------------------------------------
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
Pelodictyon phaeoclathratiforme, species, green sulfur bacteria
Pelodictyon, genus, green sulfur bacteria
Chlorobi, phylum, green sulfur bacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2982359
# phrap: 2898978
# db:
altered.
2400000
2760445 +/- 257136
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 7524
Number of reads with percent X's >= 20%: 1130 = 3.3%
Number of reads with percent X's >= 50%: 589 = 1.7%
Number of reads with percent X's >= 80%: 80 = 0.2%
Total reads in project: 34430
Total bp X'd : 835859
reads >= 20% >= 50% >= 80% screened
Nr with L09136 6277 240 96 14
Nr with pCC1Fos 311 166 54 0
Nr with pMCL200_JGI_XZX+XZK 936 724 439 66
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 4
Number of reads with percent X's >= 20%: 2 = 4.1%
Number of reads with percent X's >= 50%: 1 = 2.0%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 49
Total bp X'd : 1001
reads >= 20% >= 50% >= 80% screened
Nr with L09136 2 0 0 0
Nr with pMCL200_JGI_XZX+XZK 2 2 1 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 8310266
C = 7725886
G = 7700928
T = 8067937
N = 163883
X = 835859
GC fraction = 0.47
Total = 32804759
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634475_fasta.screen.contigs
-------------------------------------------------------------------
A 798158
C 744765
G 697542
T 759513
N 239
fraction GC = 0.48
total bases = 3000217
Libraries and Reads
-------------------------------------------------------------------
Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
-------------------------------------------------------------------
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYA reads.list > grep.reads.list.AHYA
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYA 4 500
-------------------------------------------------------------------
#Found 6389 total values totalling 20245228.0000. <3168.763187 +/- 1274.344871>
#Range: [ 611 - 88331 ]
#Most likely bin: [ 3000 - 3500 ] 2264 counts
#Median bin: [ 3000 - 3500 ] 2264 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 31 0.00 0.00 ]
|XXXX 1000 - 1500 : [ 219 0.03 0.04 ]
|XXXXX 1500 - 2000 : [ 265 0.04 0.08 ]
|XXXXXXX 2000 - 2500 : [ 415 0.06 0.15 ]
|XXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 1168 0.18 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2264 0.35 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1456 0.23 0.91 ]
|XXXXXXXXXX 4000 - 4500 : [ 551 0.09 1.00 ]
| 4500 - 5000 : [ 18 0.00 1.00 ]
| 5000 - 5500 : [ 1 0.00 1.00 ]
#...
| 88000 - 88500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYB reads.list > grep.reads.list.AHYB
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYB 4 500
-------------------------------------------------------------------
#Found 7318 total values totalling 40788278.0000. <5573.691992 +/- 1826.135757>
#Range: [ 638 - 8331 ]
#Most likely bin: [ 6000 - 6500 ] 1632 counts
#Median bin: [ 6000 - 6500 ] 1632 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 40 0.01 0.01 ]
|XXXXXXXX 1000 - 1500 : [ 340 0.05 0.05 ]
|XXXXXXX 1500 - 2000 : [ 286 0.04 0.09 ]
|XXXXX 2000 - 2500 : [ 215 0.03 0.12 ]
|XXXXX 2500 - 3000 : [ 185 0.03 0.15 ]
|XXXXX 3000 - 3500 : [ 196 0.03 0.17 ]
|XXXX 3500 - 4000 : [ 157 0.02 0.19 ]
|XXXX 4000 - 4500 : [ 179 0.02 0.22 ]
|XXXXX 4500 - 5000 : [ 203 0.03 0.25 ]
|XXXXXXX 5000 - 5500 : [ 302 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 933 0.13 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1632 0.22 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1365 0.19 0.82 ]
|XXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 872 0.12 0.94 ]
|XXXXXXXXX 7500 - 8000 : [ 368 0.05 0.99 ]
|X 8000 - 8500 : [ 45 0.01 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYC reads.list > grep.reads.list.AHYC
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYC 4 500
-------------------------------------------------------------------
#Found 207 total values totalling 7401921.0000. <35758.072464 +/- 3599.368844>
#Range: [ 593 - 44267 ]
#Most likely bin: [ 34500 - 35000 ] 20 counts
#Median bin: [ 35500 - 36000 ] 15 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 500 - 1000 : [ 1 0.00 0.00 ]
#...
|XX 24000 - 24500 : [ 1 0.00 0.01 ]
#...
|XX 28000 - 28500 : [ 1 0.00 0.01 ]
#...
|XXXX 31000 - 31500 : [ 2 0.01 0.02 ]
|XXXX 31500 - 32000 : [ 2 0.01 0.03 ]
|XXXXXXXXXX 32000 - 32500 : [ 5 0.02 0.06 ]
|XXXXXXXXXXXXXX 32500 - 33000 : [ 7 0.03 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 11 0.05 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 19 0.09 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 14 0.07 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 20 0.10 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 15 0.07 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 15 0.07 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 13 0.06 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 18 0.09 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 12 0.06 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 12 0.06 0.81 ]
|XXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 9 0.04 0.86 ]
|XXXXXXXXXXXX 38500 - 39000 : [ 6 0.03 0.88 ]
|XXXX 39000 - 39500 : [ 2 0.01 0.89 ]
|XXXXXXXXXXXXXXXX 39500 - 40000 : [ 8 0.04 0.93 ]
|XXXXXXXX 40000 - 40500 : [ 4 0.02 0.95 ]
|XXXX 40500 - 41000 : [ 2 0.01 0.96 ]
|XXXX 41000 - 41500 : [ 2 0.01 0.97 ]
|XX 41500 - 42000 : [ 1 0.00 0.98 ]
|XXXX 42000 - 42500 : [ 2 0.01 0.99 ]
|XX 42500 - 43000 : [ 1 0.00 0.99 ]
|XX 43000 - 43500 : [ 1 0.00 1.00 ]
#...
|XX 44000 - 44500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHYA 3000 +- 795 (n=3356)
# AHYB 5187 +- 2158 (n=3922)
# AHYC 35657 +- 2309 (n=96)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634475_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
AHYA 17280 -1 -1 94 689 17208 85 664 92 676
AHYB 26496 -1 -1 92 644 26299 69 636 90 649
AHYC 4608 -1 -1 65 200 4605 30 362 65 296
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHYA 8802 85 662 93 679 8406 84 666 91 673
AHYB 13384 67 629 90 644 12915 71 642 90 655
AHYC 2301 31 375 59 317 2304 30 349 71 279
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634475_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
88 14658 7393 84.01 87.51 AHYA @
136 18192 9441 69.42 72.31 AHYB @
24 1580 1058 44.08 45.92 AHYC @
] 34430 17892 72.15 cumulative total@@
LIBRARY PLATE ID COUNT [ AHYA 88 AHYB 136 AHYC 24 ] for 248 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 3634475_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 48112 total values totalling 21844560.0000. <454.035584 +/- 323.801481>
#Range: [ 0 - 957 ]
#Most likely bin: [ 0 - 50 ] 12742 counts
#Median bin: [ 600 - 650 ] 2836 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 12742 0.26 0.26 ]
|XXXX 50 - 100 : [ 1328 0.03 0.29 ]
|XXX 100 - 150 : [ 830 0.02 0.31 ]
|XX 150 - 200 : [ 705 0.01 0.32 ]
|XXX 200 - 250 : [ 808 0.02 0.34 ]
|XX 250 - 300 : [ 749 0.02 0.36 ]
|XX 300 - 350 : [ 706 0.01 0.37 ]
|XX 350 - 400 : [ 752 0.02 0.39 ]
|XXX 400 - 450 : [ 923 0.02 0.41 ]
|XXXX 450 - 500 : [ 1133 0.02 0.43 ]
|XXXX 500 - 550 : [ 1373 0.03 0.46 ]
|XXXXXX 550 - 600 : [ 1952 0.04 0.50 ]
|XXXXXXXXX 600 - 650 : [ 2836 0.06 0.56 ]
|XXXXXXXXXXXXX 650 - 700 : [ 4195 0.09 0.64 ]
|XXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6222 0.13 0.77 ]
|XXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6419 0.13 0.91 ]
|XXXXXXXXXXXX 800 - 850 : [ 3779 0.08 0.99 ]
|XX 850 - 900 : [ 606 0.01 1.00 ]
| 900 - 950 : [ 52 0.00 1.00 ]
| 950 - 1000 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYA
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYA 3634475_fasta.screen.trimQ15.SaF > reads.trim15.AHYA.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYA.rl 2 50
-------------------------------------------------------------------
#Found 17208 total values totalling 9679396.0000. <562.493956 +/- 278.337189>
#Range: [ 0 - 957 ]
#Most likely bin: [ 700 - 750 ] 3173 counts
#Median bin: [ 650 - 700 ] 2083 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2473 0.14 0.14 ]
|XX 50 - 100 : [ 190 0.01 0.15 ]
|XX 100 - 150 : [ 187 0.01 0.17 ]
|XX 150 - 200 : [ 188 0.01 0.18 ]
|XX 200 - 250 : [ 183 0.01 0.19 ]
|XXX 250 - 300 : [ 210 0.01 0.20 ]
|XXX 300 - 350 : [ 228 0.01 0.21 ]
|XXX 350 - 400 : [ 260 0.02 0.23 ]
|XXXX 400 - 450 : [ 313 0.02 0.25 ]
|XXXXX 450 - 500 : [ 406 0.02 0.27 ]
|XXXXXXX 500 - 550 : [ 523 0.03 0.30 ]
|XXXXXXXXXX 550 - 600 : [ 799 0.05 0.35 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 1230 0.07 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2083 0.12 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3173 0.18 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2875 0.17 0.89 ]
|XXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1553 0.09 0.98 ]
|XXXX 850 - 900 : [ 291 0.02 1.00 ]
|X 900 - 950 : [ 41 0.00 1.00 ]
| 950 - 1000 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYB
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYB 3634475_fasta.screen.trimQ15.SaF > reads.trim15.AHYB.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYB.rl 2 50
-------------------------------------------------------------------
#Found 26299 total values totalling 11564523.0000. <439.732423 +/- 329.145315>
#Range: [ 0 - 934 ]
#Most likely bin: [ 0 - 50 ] 7741 counts
#Median bin: [ 550 - 600 ] 1074 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 7741 0.29 0.29 ]
|XX 50 - 100 : [ 461 0.02 0.31 ]
|XX 100 - 150 : [ 381 0.01 0.33 ]
|XX 150 - 200 : [ 387 0.01 0.34 ]
|XX 200 - 250 : [ 421 0.02 0.36 ]
|XX 250 - 300 : [ 396 0.02 0.37 ]
|XX 300 - 350 : [ 406 0.02 0.39 ]
|XX 350 - 400 : [ 444 0.02 0.40 ]
|XXX 400 - 450 : [ 555 0.02 0.43 ]
|XXX 450 - 500 : [ 662 0.03 0.45 ]
|XXXX 500 - 550 : [ 798 0.03 0.48 ]
|XXXXXX 550 - 600 : [ 1074 0.04 0.52 ]
|XXXXXXXX 600 - 650 : [ 1514 0.06 0.58 ]
|XXXXXXXXXX 650 - 700 : [ 2028 0.08 0.66 ]
|XXXXXXXXXXXXXXX 700 - 750 : [ 2978 0.11 0.77 ]
|XXXXXXXXXXXXXXXXXX 750 - 800 : [ 3508 0.13 0.90 ]
|XXXXXXXXXXX 800 - 850 : [ 2219 0.08 0.99 ]
|XX 850 - 900 : [ 315 0.01 1.00 ]
| 900 - 950 : [ 11 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYC
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYC 3634475_fasta.screen.trimQ15.SaF > reads.trim15.AHYC.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYC.rl 2 50
-------------------------------------------------------------------
#Found 4605 total values totalling 600641.0000. <130.432356 +/- 193.324376>
#Range: [ 0 - 826 ]
#Most likely bin: [ 0 - 50 ] 2528 counts
#Median bin: [ 0 - 50 ] 2528 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2528 0.55 0.55 ]
|XXXXXXXXXXX 50 - 100 : [ 677 0.15 0.70 ]
|XXXX 100 - 150 : [ 262 0.06 0.75 ]
|XX 150 - 200 : [ 130 0.03 0.78 ]
|XXX 200 - 250 : [ 204 0.04 0.83 ]
|XX 250 - 300 : [ 143 0.03 0.86 ]
|X 300 - 350 : [ 72 0.02 0.87 ]
|X 350 - 400 : [ 48 0.01 0.88 ]
|X 400 - 450 : [ 55 0.01 0.89 ]
|X 450 - 500 : [ 65 0.01 0.91 ]
|X 500 - 550 : [ 52 0.01 0.92 ]
|X 550 - 600 : [ 79 0.02 0.94 ]
|X 600 - 650 : [ 92 0.02 0.96 ]
|X 650 - 700 : [ 84 0.02 0.98 ]
|X 700 - 750 : [ 71 0.02 0.99 ]
|X 750 - 800 : [ 36 0.01 1.00 ]
| 800 - 850 : [ 7 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634475
-------------------------------------------------------------------
AHYA.000001.000100 pUC18.fa LRS.fasta
AHYB.000001.000100 pMCL200.fa LRS.fasta
AHYB.000101.000200 pMCL200.fa LRS.fasta
AHYC.000001.000100 pCC1Fos.fa LRS.fasta
AHYA.000001.000100 pUC18.fa LRS.fasta
AHYB.000001.000100 pMCL200.fa LRS.fasta
AHYB.000101.000200 pMCL200.fa LRS.fasta
AHYC.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634475_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634475_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 34167 total values totalling 16501.1873. <0.482957 +/- 0.053372>
#Range: [ 0.1142 - 0.7916 ]
#Most likely bin: [ 0.5 - 0.505 ] 1566 counts
#Median bin: [ 0.485 - 0.49 ] 1485 counts
| 0.11 - 0.115 : [ 1 0.00 0.00 ]
#...
| 0.17 - 0.175 : [ 1 0.00 0.00 ]
#...
| 0.18 - 0.185 : [ 1 0.00 0.00 ]
#...
| 0.19 - 0.195 : [ 1 0.00 0.00 ]
#...
| 0.21 - 0.215 : [ 1 0.00 0.00 ]
| 0.215 - 0.22 : [ 1 0.00 0.00 ]
| 0.22 - 0.225 : [ 4 0.00 0.00 ]
| 0.225 - 0.23 : [ 2 0.00 0.00 ]
| 0.23 - 0.235 : [ 4 0.00 0.00 ]
| 0.235 - 0.24 : [ 2 0.00 0.00 ]
| 0.24 - 0.245 : [ 2 0.00 0.00 ]
| 0.245 - 0.25 : [ 3 0.00 0.00 ]
| 0.25 - 0.255 : [ 5 0.00 0.00 ]
| 0.255 - 0.26 : [ 6 0.00 0.00 ]
| 0.26 - 0.265 : [ 7 0.00 0.00 ]
| 0.265 - 0.27 : [ 8 0.00 0.00 ]
| 0.27 - 0.275 : [ 6 0.00 0.00 ]
| 0.275 - 0.28 : [ 16 0.00 0.00 ]
| 0.28 - 0.285 : [ 19 0.00 0.00 ]
|X 0.285 - 0.29 : [ 22 0.00 0.00 ]
|X 0.29 - 0.295 : [ 23 0.00 0.00 ]
|X 0.295 - 0.3 : [ 23 0.00 0.00 ]
|X 0.3 - 0.305 : [ 38 0.00 0.01 ]
|X 0.305 - 0.31 : [ 33 0.00 0.01 ]
|X 0.31 - 0.315 : [ 43 0.00 0.01 ]
|X 0.315 - 0.32 : [ 35 0.00 0.01 ]
|X 0.32 - 0.325 : [ 52 0.00 0.01 ]
|X 0.325 - 0.33 : [ 54 0.00 0.01 ]
|XX 0.33 - 0.335 : [ 61 0.00 0.01 ]
|XX 0.335 - 0.34 : [ 68 0.00 0.02 ]
|XX 0.34 - 0.345 : [ 84 0.00 0.02 ]
|XX 0.345 - 0.35 : [ 92 0.00 0.02 ]
|XX 0.35 - 0.355 : [ 77 0.00 0.02 ]
|XX 0.355 - 0.36 : [ 97 0.00 0.03 ]
|XXX 0.36 - 0.365 : [ 103 0.00 0.03 ]
|XXX 0.365 - 0.37 : [ 105 0.00 0.03 ]
|XXX 0.37 - 0.375 : [ 108 0.00 0.04 ]
|XXXX 0.375 - 0.38 : [ 141 0.00 0.04 ]
|XXXX 0.38 - 0.385 : [ 150 0.00 0.04 ]
|XXXX 0.385 - 0.39 : [ 148 0.00 0.05 ]
|XXXXX 0.39 - 0.395 : [ 191 0.01 0.05 ]
|XXXXXX 0.395 - 0.4 : [ 223 0.01 0.06 ]
|XXXXXXX 0.4 - 0.405 : [ 273 0.01 0.07 ]
|XXXXXXXX 0.405 - 0.41 : [ 310 0.01 0.08 ]
|XXXXXXXXXX 0.41 - 0.415 : [ 384 0.01 0.09 ]
|XXXXXXXXXX 0.415 - 0.42 : [ 391 0.01 0.10 ]
|XXXXXXXXXXXX 0.42 - 0.425 : [ 475 0.01 0.11 ]
|XXXXXXXXXXXXXX 0.425 - 0.43 : [ 563 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 693 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 775 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 829 0.02 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 983 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 1081 0.03 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 1150 0.03 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 1203 0.04 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 1317 0.04 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 1352 0.04 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 1513 0.04 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 1513 0.04 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1485 0.04 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1511 0.04 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1294 0.04 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1566 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1380 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1287 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1166 0.03 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1073 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 870 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 882 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 776 0.02 0.88 ]
|XXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 638 0.02 0.90 ]
|XXXXXXXXXXXXX 0.545 - 0.55 : [ 508 0.01 0.92 ]
|XXXXXXXXXXXX 0.55 - 0.555 : [ 453 0.01 0.93 ]
|XXXXXXXXXX 0.555 - 0.56 : [ 391 0.01 0.94 ]
|XXXXXXXXX 0.56 - 0.565 : [ 362 0.01 0.95 ]
|XXXXXXX 0.565 - 0.57 : [ 287 0.01 0.96 ]
|XXXXX 0.57 - 0.575 : [ 206 0.01 0.97 ]
|XXXX 0.575 - 0.58 : [ 173 0.01 0.97 ]
|XXXXX 0.58 - 0.585 : [ 178 0.01 0.98 ]
|XXXX 0.585 - 0.59 : [ 149 0.00 0.98 ]
|XXX 0.59 - 0.595 : [ 106 0.00 0.98 ]
|XXX 0.595 - 0.6 : [ 109 0.00 0.99 ]
|XXX 0.6 - 0.605 : [ 114 0.00 0.99 ]
|XXX 0.605 - 0.61 : [ 104 0.00 0.99 ]
|XX 0.61 - 0.615 : [ 69 0.00 1.00 ]
|X 0.615 - 0.62 : [ 48 0.00 1.00 ]
| 0.62 - 0.625 : [ 19 0.00 1.00 ]
|X 0.625 - 0.63 : [ 23 0.00 1.00 ]
| 0.63 - 0.635 : [ 12 0.00 1.00 ]
| 0.635 - 0.64 : [ 10 0.00 1.00 ]
| 0.64 - 0.645 : [ 7 0.00 1.00 ]
| 0.645 - 0.65 : [ 5 0.00 1.00 ]
| 0.65 - 0.655 : [ 8 0.00 1.00 ]
| 0.655 - 0.66 : [ 4 0.00 1.00 ]
#...
| 0.665 - 0.67 : [ 6 0.00 1.00 ]
| 0.67 - 0.675 : [ 4 0.00 1.00 ]
| 0.675 - 0.68 : [ 1 0.00 1.00 ]
| 0.68 - 0.685 : [ 3 0.00 1.00 ]
| 0.685 - 0.69 : [ 2 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 : [ 4 0.00 1.00 ]
| 0.705 - 0.71 : [ 3 0.00 1.00 ]
#...
| 0.72 - 0.725 : [ 1 0.00 1.00 ]
#...
| 0.79 - 0.795 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 80. 417 reads; 45093 bp (untrimmed), 44825 (trimmed).
Contig 81. 424 reads; 37128 bp (untrimmed), 37052 (trimmed).
Contig 82. 466 reads; 35476 bp (untrimmed), 35306 (trimmed).
Contig 83. 469 reads; 53259 bp (untrimmed), 53136 (trimmed).
Contig 84. 483 reads; 41620 bp (untrimmed), 41554 (trimmed).
Contig 85. 518 reads; 46275 bp (untrimmed), 46100 (trimmed).
Contig 86. 552 reads; 40381 bp (untrimmed), 40233 (trimmed).
Contig 87. 577 reads; 57504 bp (untrimmed), 57381 (trimmed).
Contig 88. 597 reads; 54934 bp (untrimmed), 54668 (trimmed).
Contig 89. 620 reads; 45312 bp (untrimmed), 45197 (trimmed).
Contig 90. 731 reads; 59667 bp (untrimmed), 59650 (trimmed).
Contig 91. 739 reads; 73099 bp (untrimmed), 72824 (trimmed).
Contig 92. 758 reads; 62716 bp (untrimmed), 62709 (trimmed).
Contig 93. 909 reads; 75437 bp (untrimmed), 75235 (trimmed).
Contig 94. 923 reads; 76749 bp (untrimmed), 76664 (trimmed).
Contig 95. 992 reads; 75609 bp (untrimmed), 75593 (trimmed).
Contig 96. 1005 reads; 87964 bp (untrimmed), 87958 (trimmed).
Contig 97. 1039 reads; 93821 bp (untrimmed), 93794 (trimmed).
Contig 98. 1062 reads; 78102 bp (untrimmed), 77613 (trimmed).
Contig 99. 1063 reads; 82357 bp (untrimmed), 82266 (trimmed).
Contig 100. 1128 reads; 107930 bp (untrimmed), 107910 (trimmed).
Contig 101. 1178 reads; 86079 bp (untrimmed), 86028 (trimmed).
Contig 102. 1277 reads; 100754 bp (untrimmed), 100714 (trimmed).
Contig 103. 1473 reads; 98202 bp (untrimmed), 98009 (trimmed).
Contig 104. 1707 reads; 148971 bp (untrimmed), 148887 (trimmed).
Contig 105. 1812 reads; 153290 bp (untrimmed), 153245 (trimmed).
Contig 106. 3765 reads; 297391 bp (untrimmed), 297053 (trimmed).
--------------------------------------------------------------
Totals 34381 reads; 3000217 bp (untrimmed), 2982359 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2996804 bases = 9.81 +- 5.12 = 0.30 +- 3.72
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 99 total values totalling 778.6300. <7.864949 +/- 4.945691>
#Range: [ 1.56 - 39.89 ]
#Most likely bin: [ 8.5 - 9 ] 9 counts
#Median bin: [ 8 - 8.5 ] 5 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 8 0.08 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 7 0.07 0.15 ]
|XXXXXXXXX 2.5 - 3 : [ 2 0.02 0.17 ]
|XXXXXXXXX 3 - 3.5 : [ 2 0.02 0.19 ]
|XXXXXXXXXXXXX 3.5 - 4 : [ 3 0.03 0.22 ]
|XXXXXXXXXXXXX 4 - 4.5 : [ 3 0.03 0.25 ]
|XXXXXXXXXXXXX 4.5 - 5 : [ 3 0.03 0.28 ]
|XXXXXXXXX 5 - 5.5 : [ 2 0.02 0.30 ]
|XXXX 5.5 - 6 : [ 1 0.01 0.31 ]
|XXXXXXXXX 6 - 6.5 : [ 2 0.02 0.33 ]
|XXXXXXXXX 6.5 - 7 : [ 2 0.02 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 7 0.07 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 5 0.05 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 5 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 9 0.09 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 6 0.06 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 8 0.08 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 8 0.08 0.84 ]
|XXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 4 0.04 0.88 ]
|XXXXXXXXXXXXX 11 - 11.5 : [ 3 0.03 0.91 ]
|XXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 4 0.04 0.95 ]
#...
|XXXX 13 - 13.5 : [ 1 0.01 0.96 ]
|XXXX 13.5 - 14 : [ 1 0.01 0.97 ]
#...
|XXXX 18.5 - 19 : [ 1 0.01 0.98 ]
#...
|XXXX 23 - 23.5 : [ 1 0.01 0.99 ]
#...
|XXXX 39.5 - 40 : [ 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 72 total values totalling 625.4500. <8.686806 +/- 2.016498>
#Range: [ 3.86 - 13.10 ]
#Most likely bin: [ 8.5 - 9 ] 9 counts
#Median bin: [ 8.5 - 9 ] 9 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 3.5 - 4 : [ 1 0.01 0.01 ]
|XXXXXXXXX 4 - 4.5 : [ 2 0.03 0.04 ]
|XXXXXXXXXXXXX 4.5 - 5 : [ 3 0.04 0.08 ]
|XXXX 5 - 5.5 : [ 1 0.01 0.10 ]
|XXXX 5.5 - 6 : [ 1 0.01 0.11 ]
|XXXXXXXXX 6 - 6.5 : [ 2 0.03 0.14 ]
|XXXXXXXXX 6.5 - 7 : [ 2 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 7 0.10 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 5 0.07 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 5 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 9 0.12 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 6 0.08 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 8 0.11 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 8 0.11 0.83 ]
|XXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 4 0.06 0.89 ]
|XXXXXXXXXXXXX 11 - 11.5 : [ 3 0.04 0.93 ]
|XXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 4 0.06 0.99 ]
#...
|XXXX 13 - 13.5 : [ 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 6 2 reads 687 bases = 1.56 +- 0.50 = 1.56 +- 0.50
Contig 25 9 reads 703 bases = 1.64 +- 0.54 = -1.62 +- 0.56
Contig 4 2 reads 625 bases = 1.66 +- 0.47 = 1.66 +- 0.47
Contig 17 4 reads 1091 bases = 1.69 +- 0.68 = 0.40 +- 0.52
Contig 7 3 reads 1288 bases = 1.69 +- 0.84 = 1.69 +- 0.84
Contig 12 4 reads 1865 bases = 1.77 +- 0.65 = 0.90 +- 0.75
Contig 5 2 reads 697 bases = 1.88 +- 0.33 = 1.88 +- 0.33
Contig 18 5 reads 1767 bases = 1.95 +- 0.77 = 0.09 +- 1.25
Contig 10 3 reads 1359 bases = 2.02 +- 0.82 = 0.68 +- 1.14
Contig 11 3 reads 1301 bases = 2.04 +- 0.81 = 2.04 +- 0.81
Contig 9 3 reads 1387 bases = 2.13 +- 0.81 = 0.74 +- 0.84
Contig 15 4 reads 798 bases = 2.16 +- 0.93 = 1.69 +- 0.46
Contig 14 4 reads 1232 bases = 2.21 +- 0.89 = 2.21 +- 0.89
Contig 27 9 reads 3486 bases = 2.31 +- 0.91 = 0.34 +- 1.99
Contig 20 6 reads 631 bases = 2.38 +- 0.60 = 2.37 +- 0.61
Contig 24 8 reads 1691 bases = 2.69 +- 1.13 = 0.93 +- 0.84
Contig 8 3 reads 763 bases = 2.93 +- 0.34 = 0.93 +- 0.34
Contig 42 47 reads 659 bases = 3.04 +- 2.06 = -2.91 +- 2.18
Contig 22 7 reads 1288 bases = 3.45 +- 1.55 = 1.63 +- 0.65
Contig 26 9 reads 1962 bases = 3.65 +- 1.88 = 0.96 +- 1.27
Contig 105 1812 reads 153290 bases = 10.28 +- 3.78 = 0.30 +- 3.20
Contig 93 909 reads 75437 bases = 10.31 +- 3.58 = 0.10 +- 3.78
Contig 90 731 reads 59667 bases = 10.35 +- 4.34 = 0.43 +- 3.91
Contig 92 758 reads 62716 bases = 10.46 +- 3.65 = 0.17 +- 4.31
Contig 78 380 reads 31605 bases = 10.50 +- 3.32 = 0.66 +- 3.27
Contig 70 284 reads 23129 bases = 10.79 +- 4.43 = 0.50 +- 3.45
Contig 106 3765 reads 297391 bases = 10.82 +- 4.68 = 0.05 +- 3.70
Contig 102 1277 reads 100754 bases = 10.91 +- 4.16 = 0.11 +- 3.83
Contig 99 1063 reads 82357 bases = 11.06 +- 3.94 = 0.24 +- 3.80
Contig 95 992 reads 75609 bases = 11.23 +- 4.09 = 0.28 +- 3.90
Contig 82 466 reads 35476 bases = 11.37 +- 4.46 = 0.10 +- 4.29
Contig 89 620 reads 45312 bases = 11.59 +- 3.61 = 0.15 +- 3.11
Contig 98 1062 reads 78102 bases = 11.70 +- 16.99 = -0.01 +- 3.82
Contig 101 1178 reads 86079 bases = 11.76 +- 5.34 = 0.31 +- 3.58
Contig 86 552 reads 40381 bases = 11.87 +- 6.15 = 0.18 +- 4.39
Contig 103 1473 reads 98202 bases = 13.10 +- 4.83 = 0.18 +- 3.88
Contig 36 26 reads 694 bases = 13.53 +- 5.42 = 13.50 +- 5.42
Contig 35 26 reads 593 bases = 18.54 +- 4.42 = 18.52 +- 4.43
Contig 38 32 reads 702 bases = 23.11 +- 8.69 = 23.10 +- 8.69
Contig 45 64 reads 884 bases = 39.89 +- 26.17 = 39.89 +- 26.17
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 2687
HQ Discrepant reads = 56
Chimeric reads = 171
Suspect alignments = 302
-------------------------------------------------------------------
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/microbe3/3634475/edit_dir.16Aug04.QD