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 in progress (or initial analysis of completed)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634477 3300 119484 Syntrophobacter fumaroxidans
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Syntrophobacter_fumaroxidans
-------------------------------------------------------------------
Syntrophobacteraceae, family, d-proteobacteria
Syntrophobacterales, order, d-proteobacteria
Syntrophobacter fumaroxidans, species, d-proteobacteria
delta/epsilon subdivisions, subphylum, proteobacteria
Syntrophobacter, genus, d-proteobacteria
Deltaproteobacteria, class, d-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4068050
# phrap: 3034020
# db:
altered.
3300000
3467356 +/- 438414
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 3282
Number of reads with percent X's >= 20%: 143 = 1.0%
Number of reads with percent X's >= 50%: 122 = 0.8%
Number of reads with percent X's >= 80%: 111 = 0.7%
Total reads in project: 14943
Total bp X'd : 230621
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3181 44 33 26
Nr with LRS 19 19 17 16
Nr with pMCL200_JGI_XZX+XZK 82 80 72 69
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 2828775
C = 4052350
G = 4090615
T = 2740001
N = 98341
X = 230621
GC fraction = 0.58
Total = 14040703
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634477_fasta.screen.contigs
-------------------------------------------------------------------
A 842045
C 1267787
G 1266968
T 845576
N 1193
fraction GC = 0.60
total bases = 4223569
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 AHYI reads.list > grep.reads.list.AHYI
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYI 4 500
-------------------------------------------------------------------
#Found 1435 total values totalling 4489570.0000. <3128.620209 +/- 467.597030>
#Range: [ 858 - 4240 ]
#Most likely bin: [ 2500 - 3000 ] 554 counts
#Median bin: [ 3000 - 3500 ] 518 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 3 0.00 0.00 ]
|X 1000 - 1500 : [ 11 0.01 0.01 ]
|X 1500 - 2000 : [ 8 0.01 0.02 ]
|XX 2000 - 2500 : [ 31 0.02 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 554 0.39 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 518 0.36 0.78 ]
|XXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 268 0.19 0.97 ]
|XXX 4000 - 4500 : [ 42 0.03 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYK reads.list > grep.reads.list.AHYK
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYK 4 500
-------------------------------------------------------------------
#Found 507 total values totalling 3253765.0000. <6417.682446 +/- 1119.388758>
#Range: [ 1385 - 8125 ]
#Most likely bin: [ 6000 - 6500 ] 168 counts
#Median bin: [ 6500 - 7000 ] 123 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1000 - 1500 : [ 3 0.01 0.01 ]
|X 1500 - 2000 : [ 6 0.01 0.02 ]
|X 2000 - 2500 : [ 5 0.01 0.03 ]
|X 2500 - 3000 : [ 5 0.01 0.04 ]
|X 3000 - 3500 : [ 5 0.01 0.05 ]
|X 3500 - 4000 : [ 4 0.01 0.06 ]
| 4000 - 4500 : [ 2 0.00 0.06 ]
| 4500 - 5000 : [ 1 0.00 0.06 ]
#...
|XXXXXXXXXXXX 5500 - 6000 : [ 50 0.10 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 168 0.33 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 123 0.24 0.73 ]
|XXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 84 0.17 0.90 ]
|XXXXXXXXXXXX 7500 - 8000 : [ 50 0.10 1.00 ]
| 8000 - 8500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHYK 6317 +- 1234 (n=248)
# AHYI 3001 +- 542 (n=729)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634477_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
AHYI 21504 93 615 96 643 7647 94 626 95 631
AHYK 17664 97 794 98 773 7296 97 788 98 780
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHYI 3824 93 624 95 632 3823 94 628 95 631
AHYK 3840 97 787 99 779 3456 96 790 98 781
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634477_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
40 7647 3831 95.78 99.77 AHYI @
40 7296 3840 96.00 100.00 AHYK @
] 14943 7671 95.89 cumulative total@@
LIBRARY PLATE ID COUNT [ AHYI 40 AHYK 40 ] for 80 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 3634477_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 14943 total values totalling 10055952.0000. <672.954025 +/- 201.211662>
#Range: [ 0 - 910 ]
#Most likely bin: [ 750 - 800 ] 3488 counts
#Median bin: [ 700 - 750 ] 2390 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXX 0 - 50 : [ 654 0.04 0.04 ]
|X 50 - 100 : [ 68 0.00 0.05 ]
|X 100 - 150 : [ 78 0.01 0.05 ]
|X 150 - 200 : [ 77 0.01 0.06 ]
|X 200 - 250 : [ 95 0.01 0.07 ]
|X 250 - 300 : [ 104 0.01 0.07 ]
|XX 300 - 350 : [ 138 0.01 0.08 ]
|XX 350 - 400 : [ 182 0.01 0.09 ]
|XXX 400 - 450 : [ 249 0.02 0.11 ]
|XXXX 450 - 500 : [ 334 0.02 0.13 ]
|XXXXXX 500 - 550 : [ 490 0.03 0.17 ]
|XXXXXXX 550 - 600 : [ 599 0.04 0.21 ]
|XXXXXXXXXXX 600 - 650 : [ 960 0.06 0.27 ]
|XXXXXXXXXXXXXXXX 650 - 700 : [ 1418 0.09 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2390 0.16 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3488 0.23 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3132 0.21 0.97 ]
|XXXXXX 850 - 900 : [ 483 0.03 1.00 ]
| 900 - 950 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYI 3634477_fasta.screen.trimQ15.SaF > reads.trim15.AHYI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYI.rl 2 50
-------------------------------------------------------------------
#Found 7647 total values totalling 4494777.0000. <587.783052 +/- 203.162987>
#Range: [ 0 - 850 ]
#Most likely bin: [ 700 - 750 ] 1684 counts
#Median bin: [ 650 - 700 ] 1280 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 0 - 50 : [ 424 0.06 0.06 ]
|X 50 - 100 : [ 53 0.01 0.06 ]
|XX 100 - 150 : [ 70 0.01 0.07 ]
|XX 150 - 200 : [ 75 0.01 0.08 ]
|XX 200 - 250 : [ 83 0.01 0.09 ]
|XX 250 - 300 : [ 98 0.01 0.11 ]
|XXX 300 - 350 : [ 132 0.02 0.12 ]
|XXXX 350 - 400 : [ 164 0.02 0.14 ]
|XXXXXX 400 - 450 : [ 233 0.03 0.17 ]
|XXXXXXXX 450 - 500 : [ 317 0.04 0.22 ]
|XXXXXXXXXXX 500 - 550 : [ 476 0.06 0.28 ]
|XXXXXXXXXXXXXX 550 - 600 : [ 579 0.08 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 911 0.12 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1280 0.17 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1684 0.22 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 955 0.12 0.99 ]
|XXX 800 - 850 : [ 112 0.01 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYK
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYK 3634477_fasta.screen.trimQ15.SaF > reads.trim15.AHYK.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYK.rl 2 50
-------------------------------------------------------------------
#Found 7296 total values totalling 5561175.0000. <762.222451 +/- 155.200435>
#Range: [ 0 - 910 ]
#Most likely bin: [ 800 - 850 ] 3020 counts
#Median bin: [ 750 - 800 ] 2533 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 0 - 50 : [ 230 0.03 0.03 ]
| 50 - 100 : [ 15 0.00 0.03 ]
| 100 - 150 : [ 8 0.00 0.03 ]
| 150 - 200 : [ 2 0.00 0.03 ]
| 200 - 250 : [ 12 0.00 0.04 ]
| 250 - 300 : [ 6 0.00 0.04 ]
| 300 - 350 : [ 6 0.00 0.04 ]
| 350 - 400 : [ 18 0.00 0.04 ]
| 400 - 450 : [ 16 0.00 0.04 ]
| 450 - 500 : [ 17 0.00 0.05 ]
| 500 - 550 : [ 14 0.00 0.05 ]
| 550 - 600 : [ 20 0.00 0.05 ]
|X 600 - 650 : [ 49 0.01 0.06 ]
|XX 650 - 700 : [ 138 0.02 0.08 ]
|XXXXXXXXX 700 - 750 : [ 706 0.10 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2533 0.35 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3020 0.41 0.93 ]
|XXXXXX 850 - 900 : [ 482 0.07 1.00 ]
| 900 - 950 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYN
trimt JAZZ trim 15 readlength histogram for AXNU
trimt JAZZ trim 15 readlength histogram for AXNW
trimt JAZZ trim 15 readlength histogram for AXNX
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634477
-------------------------------------------------------------------
AHYI.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHYI.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AHYK.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AHYN.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AXNW.000001.000100
AHYI.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHYI.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AHYK.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AHYN.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AXNW.000001.000100
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634477_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634477_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 14306 total values totalling 8587.0364. <0.600240 +/- 0.040973>
#Range: [ 0.1667 - 0.8696 ]
#Most likely bin: [ 0.605 - 0.61 ] 913 counts
#Median bin: [ 0.6 - 0.605 ] 833 counts
#Entropy = 4.9302 bits
| 0.165 - 0.17 : [ 1 0.00 0.00 ]
#...
| 0.26 - 0.265 : [ 1 0.00 0.00 ]
#...
| 0.27 - 0.275 : [ 1 0.00 0.00 ]
#...
| 0.28 - 0.285 : [ 2 0.00 0.00 ]
#...
| 0.29 - 0.295 : [ 2 0.00 0.00 ]
#...
| 0.305 - 0.31 : [ 2 0.00 0.00 ]
#...
| 0.32 - 0.325 : [ 3 0.00 0.00 ]
| 0.325 - 0.33 : [ 1 0.00 0.00 ]
#...
| 0.335 - 0.34 : [ 3 0.00 0.00 ]
| 0.34 - 0.345 : [ 1 0.00 0.00 ]
| 0.345 - 0.35 : [ 3 0.00 0.00 ]
#...
| 0.355 - 0.36 : [ 3 0.00 0.00 ]
| 0.36 - 0.365 : [ 1 0.00 0.00 ]
| 0.365 - 0.37 : [ 5 0.00 0.00 ]
| 0.37 - 0.375 : [ 2 0.00 0.00 ]
| 0.375 - 0.38 : [ 2 0.00 0.00 ]
| 0.38 - 0.385 : [ 3 0.00 0.00 ]
| 0.385 - 0.39 : [ 7 0.00 0.00 ]
| 0.39 - 0.395 : [ 6 0.00 0.00 ]
| 0.395 - 0.4 : [ 2 0.00 0.00 ]
| 0.4 - 0.405 : [ 6 0.00 0.00 ]
| 0.405 - 0.41 : [ 2 0.00 0.00 ]
| 0.41 - 0.415 : [ 3 0.00 0.00 ]
| 0.415 - 0.42 : [ 4 0.00 0.00 ]
| 0.42 - 0.425 : [ 8 0.00 0.01 ]
| 0.425 - 0.43 : [ 4 0.00 0.01 ]
| 0.43 - 0.435 : [ 6 0.00 0.01 ]
| 0.435 - 0.44 : [ 6 0.00 0.01 ]
| 0.44 - 0.445 : [ 4 0.00 0.01 ]
| 0.445 - 0.45 : [ 8 0.00 0.01 ]
| 0.45 - 0.455 : [ 10 0.00 0.01 ]
| 0.455 - 0.46 : [ 7 0.00 0.01 ]
|X 0.46 - 0.465 : [ 20 0.00 0.01 ]
|X 0.465 - 0.47 : [ 15 0.00 0.01 ]
|X 0.47 - 0.475 : [ 13 0.00 0.01 ]
| 0.475 - 0.48 : [ 11 0.00 0.01 ]
|X 0.48 - 0.485 : [ 23 0.00 0.01 ]
|X 0.485 - 0.49 : [ 31 0.00 0.02 ]
|X 0.49 - 0.495 : [ 32 0.00 0.02 ]
|X 0.495 - 0.5 : [ 32 0.00 0.02 ]
|XX 0.5 - 0.505 : [ 55 0.00 0.02 ]
|XX 0.505 - 0.51 : [ 41 0.00 0.03 ]
|XX 0.51 - 0.515 : [ 52 0.00 0.03 ]
|XXX 0.515 - 0.52 : [ 65 0.00 0.04 ]
|XXX 0.52 - 0.525 : [ 59 0.00 0.04 ]
|XXXX 0.525 - 0.53 : [ 84 0.01 0.05 ]
|XXXXX 0.53 - 0.535 : [ 105 0.01 0.05 ]
|XXXXXXX 0.535 - 0.54 : [ 150 0.01 0.06 ]
|XXXXXX 0.54 - 0.545 : [ 131 0.01 0.07 ]
|XXXXXXXXX 0.545 - 0.55 : [ 204 0.01 0.09 ]
|XXXXXXXXXX 0.55 - 0.555 : [ 218 0.02 0.10 ]
|XXXXXXXXXXX 0.555 - 0.56 : [ 260 0.02 0.12 ]
|XXXXXXXXXXXXXX 0.56 - 0.565 : [ 327 0.02 0.14 ]
|XXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 410 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 448 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 540 0.04 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 638 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 730 0.05 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 819 0.06 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 811 0.06 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 833 0.06 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 913 0.06 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 861 0.06 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 853 0.06 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 744 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 681 0.05 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 624 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 563 0.04 0.87 ]
|XXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 402 0.03 0.90 ]
|XXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 356 0.02 0.93 ]
|XXXXXXXXXXXXX 0.65 - 0.655 : [ 287 0.02 0.95 ]
|XXXXXXXXX 0.655 - 0.66 : [ 198 0.01 0.96 ]
|XXXXXXX 0.66 - 0.665 : [ 152 0.01 0.97 ]
|XXXXX 0.665 - 0.67 : [ 124 0.01 0.98 ]
|XXXX 0.67 - 0.675 : [ 89 0.01 0.99 ]
|XX 0.675 - 0.68 : [ 48 0.00 0.99 ]
|XX 0.68 - 0.685 : [ 42 0.00 0.99 ]
|X 0.685 - 0.69 : [ 30 0.00 1.00 ]
|X 0.69 - 0.695 : [ 27 0.00 1.00 ]
| 0.695 - 0.7 : [ 8 0.00 1.00 ]
| 0.7 - 0.705 : [ 7 0.00 1.00 ]
| 0.705 - 0.71 : [ 4 0.00 1.00 ]
| 0.71 - 0.715 : [ 4 0.00 1.00 ]
| 0.715 - 0.72 : [ 1 0.00 1.00 ]
| 0.72 - 0.725 : [ 2 0.00 1.00 ]
| 0.725 - 0.73 : [ 2 0.00 1.00 ]
| 0.73 - 0.735 : [ 1 0.00 1.00 ]
#...
| 0.76 - 0.765 : [ 1 0.00 1.00 ]
| 0.765 - 0.77 : [ 1 0.00 1.00 ]
#...
| 0.78 - 0.785 : [ 2 0.00 1.00 ]
#...
| 0.82 - 0.825 : [ 1 0.00 1.00 ]
#...
| 0.83 - 0.835 : [ 1 0.00 1.00 ]
#...
| 0.865 - 0.87 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 1290. 47 reads; 9022 bp (untrimmed), 8972 (trimmed).
Contig 1291. 48 reads; 12008 bp (untrimmed), 11605 (trimmed).
Contig 1292. 48 reads; 9943 bp (untrimmed), 9769 (trimmed).
Contig 1293. 48 reads; 10964 bp (untrimmed), 10477 (trimmed).
Contig 1294. 48 reads; 12225 bp (untrimmed), 12201 (trimmed).
Contig 1295. 48 reads; 12495 bp (untrimmed), 12237 (trimmed).
Contig 1296. 49 reads; 10064 bp (untrimmed), 9981 (trimmed).
Contig 1297. 50 reads; 9042 bp (untrimmed), 9001 (trimmed).
Contig 1298. 50 reads; 11589 bp (untrimmed), 11542 (trimmed).
Contig 1299. 51 reads; 13817 bp (untrimmed), 13771 (trimmed).
Contig 1300. 52 reads; 14408 bp (untrimmed), 14360 (trimmed).
Contig 1301. 53 reads; 11653 bp (untrimmed), 11506 (trimmed).
Contig 1302. 53 reads; 15318 bp (untrimmed), 15265 (trimmed).
Contig 1303. 55 reads; 10418 bp (untrimmed), 10398 (trimmed).
Contig 1304. 55 reads; 14422 bp (untrimmed), 14228 (trimmed).
Contig 1305. 57 reads; 14340 bp (untrimmed), 14277 (trimmed).
Contig 1306. 58 reads; 13814 bp (untrimmed), 13756 (trimmed).
Contig 1307. 62 reads; 14850 bp (untrimmed), 14600 (trimmed).
Contig 1308. 62 reads; 11869 bp (untrimmed), 11800 (trimmed).
Contig 1309. 67 reads; 13661 bp (untrimmed), 13618 (trimmed).
Contig 1310. 67 reads; 14422 bp (untrimmed), 14302 (trimmed).
Contig 1311. 68 reads; 15451 bp (untrimmed), 15400 (trimmed).
Contig 1312. 70 reads; 20771 bp (untrimmed), 20567 (trimmed).
Contig 1313. 74 reads; 18660 bp (untrimmed), 18596 (trimmed).
Contig 1314. 77 reads; 13566 bp (untrimmed), 13546 (trimmed).
Contig 1315. 80 reads; 20453 bp (untrimmed), 20255 (trimmed).
Contig 1316. 100 reads; 25762 bp (untrimmed), 25648 (trimmed).
--------------------------------------------------------------
Totals 14062 reads; 4223569 bp (untrimmed), 4068050 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4216502 bases = 2.86 +- 1.56 = 0.66 +- 1.65
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 1307 total values totalling 3307.9000. <2.530910 +/- 0.798797>
#Range: [ 1.05 - 5.35 ]
#Most likely bin: [ 1.5 - 2 ] 289 counts
#Median bin: [ 2 - 2.5 ] 267 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 1 - 1.5 : [ 106 0.08 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 289 0.22 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 267 0.20 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 276 0.21 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 205 0.16 0.87 ]
|XXXXXXXXXXXXXXX 3.5 - 4 : [ 108 0.08 0.96 ]
|XXXXXX 4 - 4.5 : [ 40 0.03 0.99 ]
|XX 4.5 - 5 : [ 13 0.01 1.00 ]
| 5 - 5.5 : [ 3 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 482 total values totalling 1529.3800. <3.172988 +/- 0.620558>
#Range: [ 1.67 - 5.35 ]
#Most likely bin: [ 2.5 - 3 ] 145 counts
#Median bin: [ 3 - 3.5 ] 140 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 1.5 - 2 : [ 8 0.02 0.02 ]
|XXXXXXXXXXXXXXX 2 - 2.5 : [ 53 0.11 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 145 0.30 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 140 0.29 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 88 0.18 0.90 ]
|XXXXXXXXX 4 - 4.5 : [ 33 0.07 0.97 ]
|XXX 4.5 - 5 : [ 12 0.02 0.99 ]
|X 5 - 5.5 : [ 3 0.01 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 48 2 reads 1774 bases = 1.05 +- 0.22 = 1.05 +- 0.22
Contig 95 2 reads 1717 bases = 1.05 +- 0.23 = 0.10 +- 0.97
Contig 165 2 reads 1597 bases = 1.06 +- 0.24 = 1.06 +- 0.24
Contig 185 2 reads 1814 bases = 1.08 +- 0.27 = 1.08 +- 0.27
Contig 107 2 reads 1780 bases = 1.09 +- 0.28 = -0.07 +- 0.95
Contig 183 2 reads 1370 bases = 1.09 +- 0.29 = 1.09 +- 0.29
Contig 93 2 reads 1191 bases = 1.09 +- 0.28 = -0.14 +- 0.94
Contig 160 2 reads 1700 bases = 1.10 +- 0.30 = -0.05 +- 0.95
Contig 184 2 reads 1338 bases = 1.10 +- 0.29 = -0.24 +- 0.92
Contig 31 2 reads 1347 bases = 1.10 +- 0.30 = 1.10 +- 0.30
Contig 36 2 reads 1455 bases = 1.10 +- 0.29 = 1.10 +- 0.29
Contig 33 2 reads 1344 bases = 1.11 +- 0.31 = 0.24 +- 0.91
Contig 170 2 reads 1139 bases = 1.12 +- 0.33 = 1.12 +- 0.33
Contig 189 2 reads 1754 bases = 1.12 +- 0.32 = 1.12 +- 0.32
Contig 71 2 reads 1566 bases = 1.12 +- 0.32 = 1.12 +- 0.32
Contig 129 2 reads 1730 bases = 1.13 +- 0.34 = 1.13 +- 0.34
Contig 39 2 reads 1555 bases = 1.13 +- 0.34 = 1.13 +- 0.34
Contig 88 2 reads 1544 bases = 1.13 +- 0.34 = 0.30 +- 0.88
Contig 61 2 reads 1611 bases = 1.14 +- 0.34 = 1.14 +- 0.34
Contig 102 2 reads 1538 bases = 1.15 +- 0.36 = -0.14 +- 0.91
Contig 1309 67 reads 13661 bases = 4.40 +- 2.08 = 0.14 +- 2.42
Contig 1267 38 reads 7533 bases = 4.42 +- 1.94 = 0.29 +- 1.91
Contig 1290 47 reads 9022 bases = 4.45 +- 1.77 = 0.10 +- 2.60
Contig 1269 39 reads 7863 bases = 4.46 +- 2.07 = 0.24 +- 1.64
Contig 1303 55 reads 10418 bases = 4.51 +- 2.03 = 0.57 +- 2.50
Contig 902 11 reads 2275 bases = 4.60 +- 2.82 = 1.41 +- 1.52
Contig 717 7 reads 1245 bases = 4.62 +- 2.07 = 3.53 +- 1.22
Contig 1272 40 reads 7332 bases = 4.66 +- 2.41 = 1.18 +- 1.46
Contig 1215 29 reads 5326 bases = 4.71 +- 2.14 = 2.08 +- 1.57
Contig 1153 20 reads 3798 bases = 4.72 +- 2.13 = 0.12 +- 2.62
Contig 1011 14 reads 2696 bases = 4.81 +- 2.14 = 2.25 +- 1.40
Contig 1257 36 reads 5763 bases = 4.81 +- 2.06 = 0.95 +- 2.20
Contig 1297 50 reads 9042 bases = 4.84 +- 1.90 = 0.62 +- 1.94
Contig 1008 14 reads 2498 bases = 4.85 +- 2.30 = 1.18 +- 0.94
Contig 1268 38 reads 7257 bases = 4.85 +- 1.99 = 0.87 +- 1.89
Contig 999 14 reads 2430 bases = 4.88 +- 1.90 = 0.64 +- 1.86
Contig 1314 77 reads 13566 bases = 4.97 +- 1.73 = 0.34 +- 2.96
Contig 1167 21 reads 3779 bases = 5.18 +- 1.69 = 0.91 +- 1.60
Contig 1022 15 reads 2420 bases = 5.24 +- 2.70 = 0.22 +- 1.53
Contig 1113 18 reads 2909 bases = 5.35 +- 3.36 = 0.89 +- 1.12
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 73
HQ Discrepant reads = 253
Chimeric reads = 30
Suspect alignments = 38
-------------------------------------------------------------------
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/microbe4/3634477/edit_dir.10Nov04.QC