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 in progress (or initial analysis of completed)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634503 4500 196162 Nocardioides sp.
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Nocardioides_sp.
-------------------------------------------------------------------
Actinobacteria, phylum, actinobacteria
Nocardioidaceae, family, high GC Gram+
Propionibacterineae, suborder, high GC Gram+
Actinobacteridae, subclass, high GC Gram+
Nocardioides sp., species, high GC Gram+
Actinomycetales, order, high GC Gram+
Nocardioides, genus, high GC Gram+
Actinobacteria (class) (high G+C Gram-positive bacteria), class, high GC Gram+
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3989176
# phrap: 2867085
# db:
altered.
4500000
3785420 +/- 682026
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 3368
Number of reads with percent X's >= 20%: 318 = 2.1%
Number of reads with percent X's >= 50%: 288 = 1.9%
Number of reads with percent X's >= 80%: 256 = 1.7%
Total reads in project: 15332
Total bp X'd : 396949
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3098 65 56 42
Nr with LRS 20 20 20 20
Nr with pMCL200_JGI_XZX+XZK 250 233 212 194
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 434
Number of reads with percent X's >= 20%: 295 = 18.2%
Number of reads with percent X's >= 50%: 276 = 17.1%
Number of reads with percent X's >= 80%: 254 = 15.7%
Total reads in project: 1618
Total bp X'd : 267923
reads >= 20% >= 50% >= 80% screened
Nr with L09136 185 53 48 41
Nr with LRS 20 20 20 20
Nr with pMCL200_JGI_XZX+XZK 229 222 208 193
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 2288620
C = 4847823
G = 4781192
T = 2308785
N = 121958
X = 396949
GC fraction = 0.65
Total = 14745327
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634503_fasta.screen.contigs
-------------------------------------------------------------------
A 647745
C 1561606
G 1556078
T 656165
N 2038
fraction GC = 0.70
total bases = 4423632
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 AICT reads.list > grep.reads.list.AICT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICT 4 500
-------------------------------------------------------------------
#Found 1086 total values totalling 3452344.0000. <3178.953959 +/- 211.267628>
#Range: [ 1051 - 3762 ]
#Most likely bin: [ 3000 - 3500 ] 865 counts
#Median bin: [ 3000 - 3500 ] 865 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 2 0.00 0.00 ]
| 1500 - 2000 : [ 3 0.00 0.00 ]
| 2000 - 2500 : [ 1 0.00 0.01 ]
|XXXXXXXX 2500 - 3000 : [ 177 0.16 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 865 0.80 0.97 ]
|XX 3500 - 4000 : [ 38 0.03 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICU reads.list > grep.reads.list.AICU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICU 4 500
-------------------------------------------------------------------
#Found 280 total values totalling 1875149.0000. <6696.960714 +/- 1310.788561>
#Range: [ 990 - 8615 ]
#Most likely bin: [ 6500 - 7000 ] 64 counts
#Median bin: [ 6500 - 7000 ] 64 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 1 0.00 0.00 ]
|XX 1000 - 1500 : [ 3 0.01 0.01 ]
|XXX 1500 - 2000 : [ 5 0.02 0.03 ]
|X 2000 - 2500 : [ 2 0.01 0.04 ]
|X 2500 - 3000 : [ 1 0.00 0.04 ]
|XX 3000 - 3500 : [ 3 0.01 0.05 ]
|X 3500 - 4000 : [ 1 0.00 0.06 ]
#...
|XXXXXXXXXXX 5500 - 6000 : [ 17 0.06 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 63 0.23 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 64 0.23 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 51 0.18 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 52 0.19 0.94 ]
|XXXXXXXXXX 8000 - 8500 : [ 16 0.06 1.00 ]
|X 8500 - 9000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AICT 3047 +- 295 (n=532)
# AICU 6450 +- 1706 (n=142)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634503_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
AICT 30720 94 673 97 652 7652 92 609 95 613
AICU 36096 91 661 95 619 7680 90 654 95 640
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AICT 3829 92 600 95 606 3823 92 618 95 620
AICU 3840 91 663 96 650 3840 88 646 94 630
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634503_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
40 7652 3837 95.92 99.92 AICT @
40 7680 3840 96.00 100.00 AICU @
] 15332 7677 95.96 cumulative total@@
LIBRARY PLATE ID COUNT [ AICT 40 AICU 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 3634503_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 15332 total values totalling 8827722.0000. <575.771067 +/- 237.028738>
#Range: [ 0 - 908 ]
#Most likely bin: [ 700 - 750 ] 2657 counts
#Median bin: [ 650 - 700 ] 1995 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXX 0 - 50 : [ 1200 0.08 0.08 ]
|XXX 50 - 100 : [ 184 0.01 0.09 ]
|XX 100 - 150 : [ 161 0.01 0.10 ]
|XXX 150 - 200 : [ 193 0.01 0.11 ]
|XXXX 200 - 250 : [ 238 0.02 0.13 ]
|XXXX 250 - 300 : [ 298 0.02 0.15 ]
|XXXXX 300 - 350 : [ 341 0.02 0.17 ]
|XXXXXX 350 - 400 : [ 381 0.02 0.20 ]
|XXXXXXX 400 - 450 : [ 480 0.03 0.23 ]
|XXXXXXXXX 450 - 500 : [ 599 0.04 0.27 ]
|XXXXXXXXXXX 500 - 550 : [ 702 0.05 0.31 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 971 0.06 0.37 ]
|XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1375 0.09 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1995 0.13 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2657 0.17 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2343 0.15 0.92 ]
|XXXXXXXXXXXXXXXX 800 - 850 : [ 1076 0.07 0.99 ]
|XX 850 - 900 : [ 137 0.01 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICT 3634503_fasta.screen.trimQ15.SaF > reads.trim15.AICT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICT.rl 2 50
-------------------------------------------------------------------
#Found 7652 total values totalling 4313904.0000. <563.761631 +/- 220.006552>
#Range: [ 0 - 872 ]
#Most likely bin: [ 700 - 750 ] 1444 counts
#Median bin: [ 600 - 650 ] 785 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXX 0 - 50 : [ 491 0.06 0.06 ]
|XXX 50 - 100 : [ 93 0.01 0.08 ]
|XX 100 - 150 : [ 88 0.01 0.09 ]
|XXX 150 - 200 : [ 110 0.01 0.10 ]
|XXX 200 - 250 : [ 115 0.02 0.12 ]
|XXXX 250 - 300 : [ 155 0.02 0.14 ]
|XXXXX 300 - 350 : [ 181 0.02 0.16 ]
|XXXXXX 350 - 400 : [ 232 0.03 0.19 ]
|XXXXXXXX 400 - 450 : [ 284 0.04 0.23 ]
|XXXXXXXXXX 450 - 500 : [ 355 0.05 0.27 ]
|XXXXXXXXXXXX 500 - 550 : [ 445 0.06 0.33 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 591 0.08 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 785 0.10 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1155 0.15 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1444 0.19 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 930 0.12 0.97 ]
|XXXXX 800 - 850 : [ 193 0.03 1.00 ]
| 850 - 900 : [ 5 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICU 3634503_fasta.screen.trimQ15.SaF > reads.trim15.AICU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICU.rl 2 50
-------------------------------------------------------------------
#Found 7680 total values totalling 4513818.0000. <587.736719 +/- 252.283811>
#Range: [ 0 - 908 ]
#Most likely bin: [ 750 - 800 ] 1413 counts
#Median bin: [ 650 - 700 ] 840 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 709 0.09 0.09 ]
|XXX 50 - 100 : [ 91 0.01 0.10 ]
|XX 100 - 150 : [ 73 0.01 0.11 ]
|XX 150 - 200 : [ 83 0.01 0.12 ]
|XXX 200 - 250 : [ 123 0.02 0.14 ]
|XXXX 250 - 300 : [ 143 0.02 0.16 ]
|XXXXX 300 - 350 : [ 160 0.02 0.18 ]
|XXXX 350 - 400 : [ 149 0.02 0.20 ]
|XXXXXX 400 - 450 : [ 196 0.03 0.22 ]
|XXXXXXX 450 - 500 : [ 244 0.03 0.26 ]
|XXXXXXX 500 - 550 : [ 257 0.03 0.29 ]
|XXXXXXXXXXX 550 - 600 : [ 380 0.05 0.34 ]
|XXXXXXXXXXXXXXXXX 600 - 650 : [ 590 0.08 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 840 0.11 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1213 0.16 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1413 0.18 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 883 0.11 0.98 ]
|XXXX 850 - 900 : [ 132 0.02 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICW
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634503
-------------------------------------------------------------------
AICT.000001.000100 pUC18.fa LRS.fasta
AICT.000101.000200 pUC18.fa LRS.fasta
AICU.000001.000100 pMCL200.fa LRS.fasta
AICU.000101.000200 pMCL200.fa LRS.fasta
AICW.000001.000100 pCC1Fos.fa LRS.fasta
AICT.000001.000100 pUC18.fa LRS.fasta
AICT.000101.000200 pUC18.fa LRS.fasta
AICU.000001.000100 pMCL200.fa LRS.fasta
AICU.000101.000200 pMCL200.fa LRS.fasta
AICW.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634503_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634503_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 14135 total values totalling 10016.3727. <0.708622 +/- 0.040647>
#Range: [ 0.3333 - 0.909 ]
#Most likely bin: [ 0.725 - 0.73 ] 754 counts
#Median bin: [ 0.71 - 0.715 ] 725 counts
| 0.33 - 0.335 : [ 1 0.00 0.00 ]
#...
| 0.4 - 0.405 : [ 1 0.00 0.00 ]
#...
| 0.41 - 0.415 : [ 1 0.00 0.00 ]
| 0.415 - 0.42 : [ 1 0.00 0.00 ]
#...
| 0.45 - 0.455 : [ 2 0.00 0.00 ]
| 0.455 - 0.46 : [ 1 0.00 0.00 ]
| 0.46 - 0.465 : [ 1 0.00 0.00 ]
| 0.465 - 0.47 : [ 1 0.00 0.00 ]
| 0.47 - 0.475 : [ 1 0.00 0.00 ]
| 0.475 - 0.48 : [ 1 0.00 0.00 ]
| 0.48 - 0.485 : [ 2 0.00 0.00 ]
| 0.485 - 0.49 : [ 1 0.00 0.00 ]
| 0.49 - 0.495 : [ 3 0.00 0.00 ]
#...
| 0.5 - 0.505 : [ 1 0.00 0.00 ]
#...
| 0.515 - 0.52 : [ 1 0.00 0.00 ]
| 0.52 - 0.525 : [ 2 0.00 0.00 ]
| 0.525 - 0.53 : [ 4 0.00 0.00 ]
| 0.53 - 0.535 : [ 2 0.00 0.00 ]
| 0.535 - 0.54 : [ 1 0.00 0.00 ]
| 0.54 - 0.545 : [ 4 0.00 0.00 ]
| 0.545 - 0.55 : [ 2 0.00 0.00 ]
| 0.55 - 0.555 : [ 6 0.00 0.00 ]
| 0.555 - 0.56 : [ 8 0.00 0.00 ]
| 0.56 - 0.565 : [ 1 0.00 0.00 ]
| 0.565 - 0.57 : [ 7 0.00 0.00 ]
| 0.57 - 0.575 : [ 4 0.00 0.00 ]
| 0.575 - 0.58 : [ 7 0.00 0.00 ]
|X 0.58 - 0.585 : [ 13 0.00 0.01 ]
| 0.585 - 0.59 : [ 6 0.00 0.01 ]
|X 0.59 - 0.595 : [ 16 0.00 0.01 ]
|X 0.595 - 0.6 : [ 22 0.00 0.01 ]
|X 0.6 - 0.605 : [ 28 0.00 0.01 ]
|XX 0.605 - 0.61 : [ 38 0.00 0.01 ]
|XX 0.61 - 0.615 : [ 41 0.00 0.02 ]
|XXX 0.615 - 0.62 : [ 53 0.00 0.02 ]
|XXXX 0.62 - 0.625 : [ 80 0.01 0.03 ]
|XXXXXX 0.625 - 0.63 : [ 116 0.01 0.03 ]
|XXXXXXX 0.63 - 0.635 : [ 129 0.01 0.04 ]
|XXXXXXX 0.635 - 0.64 : [ 132 0.01 0.05 ]
|XXXXXXXXX 0.64 - 0.645 : [ 175 0.01 0.06 ]
|XXXXXXXXX 0.645 - 0.65 : [ 178 0.01 0.08 ]
|XXXXXXXXXXXXX 0.65 - 0.655 : [ 236 0.02 0.09 ]
|XXXXXXXXXXXXXX 0.655 - 0.66 : [ 257 0.02 0.11 ]
|XXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 301 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 352 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 397 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 419 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 525 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 545 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 612 0.04 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 666 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 677 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 701 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 725 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 745 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 745 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.725 - 0.73 : [ 754 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.73 - 0.735 : [ 697 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.735 - 0.74 : [ 624 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.74 - 0.745 : [ 597 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.745 - 0.75 : [ 528 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.75 - 0.755 : [ 457 0.03 0.90 ]
|XXXXXXXXXXXXXXXXXXX 0.755 - 0.76 : [ 350 0.02 0.92 ]
|XXXXXXXXXXXXXXX 0.76 - 0.765 : [ 287 0.02 0.94 ]
|XXXXXXXXXXXXXX 0.765 - 0.77 : [ 256 0.02 0.96 ]
|XXXXXXXX 0.77 - 0.775 : [ 155 0.01 0.97 ]
|XXXXXXX 0.775 - 0.78 : [ 135 0.01 0.98 ]
|XXXXX 0.78 - 0.785 : [ 97 0.01 0.99 ]
|XXX 0.785 - 0.79 : [ 62 0.00 0.99 ]
|XX 0.79 - 0.795 : [ 32 0.00 0.99 ]
|X 0.795 - 0.8 : [ 26 0.00 0.99 ]
|X 0.8 - 0.805 : [ 14 0.00 1.00 ]
|X 0.805 - 0.81 : [ 15 0.00 1.00 ]
|X 0.81 - 0.815 : [ 12 0.00 1.00 ]
| 0.815 - 0.82 : [ 7 0.00 1.00 ]
| 0.82 - 0.825 : [ 3 0.00 1.00 ]
| 0.825 - 0.83 : [ 5 0.00 1.00 ]
| 0.83 - 0.835 : [ 4 0.00 1.00 ]
| 0.835 - 0.84 : [ 1 0.00 1.00 ]
| 0.84 - 0.845 : [ 4 0.00 1.00 ]
| 0.845 - 0.85 : [ 3 0.00 1.00 ]
| 0.85 - 0.855 : [ 2 0.00 1.00 ]
| 0.855 - 0.86 : [ 3 0.00 1.00 ]
#...
| 0.865 - 0.87 : [ 1 0.00 1.00 ]
#...
| 0.88 - 0.885 : [ 3 0.00 1.00 ]
| 0.885 - 0.89 : [ 1 0.00 1.00 ]
#...
| 0.9 - 0.905 : [ 1 0.00 1.00 ]
| 0.905 - 0.91 : [ 2 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 1840. 31 reads; 8037 bp (untrimmed), 7983 (trimmed).
Contig 1841. 32 reads; 6537 bp (untrimmed), 6436 (trimmed).
Contig 1842. 32 reads; 6823 bp (untrimmed), 6786 (trimmed).
Contig 1843. 33 reads; 7406 bp (untrimmed), 7295 (trimmed).
Contig 1844. 33 reads; 9369 bp (untrimmed), 9336 (trimmed).
Contig 1845. 35 reads; 6025 bp (untrimmed), 6023 (trimmed).
Contig 1846. 35 reads; 9586 bp (untrimmed), 8652 (trimmed).
Contig 1847. 36 reads; 8900 bp (untrimmed), 8848 (trimmed).
Contig 1848. 38 reads; 10107 bp (untrimmed), 9761 (trimmed).
Contig 1849. 38 reads; 11603 bp (untrimmed), 11402 (trimmed).
Contig 1850. 40 reads; 6475 bp (untrimmed), 6169 (trimmed).
Contig 1851. 41 reads; 9366 bp (untrimmed), 9366 (trimmed).
Contig 1852. 43 reads; 11013 bp (untrimmed), 10829 (trimmed).
Contig 1853. 47 reads; 11759 bp (untrimmed), 11759 (trimmed).
Contig 1854. 52 reads; 10399 bp (untrimmed), 10352 (trimmed).
Contig 1855. 53 reads; 9558 bp (untrimmed), 8854 (trimmed).
Contig 1856. 56 reads; 12790 bp (untrimmed), 12498 (trimmed).
Contig 1857. 65 reads; 12320 bp (untrimmed), 12013 (trimmed).
Contig 1858. 72 reads; 15668 bp (untrimmed), 15646 (trimmed).
Contig 1859. 75 reads; 9031 bp (untrimmed), 8970 (trimmed).
Contig 1860. 88 reads; 20514 bp (untrimmed), 20371 (trimmed).
Contig 1861. 92 reads; 14058 bp (untrimmed), 13695 (trimmed).
Contig 1862. 99 reads; 19497 bp (untrimmed), 19474 (trimmed).
Contig 1863. 134 reads; 26208 bp (untrimmed), 25950 (trimmed).
Contig 1864. 149 reads; 27133 bp (untrimmed), 27056 (trimmed).
Contig 1865. 160 reads; 28135 bp (untrimmed), 27865 (trimmed).
Contig 1866. 246 reads; 45752 bp (untrimmed), 45502 (trimmed).
--------------------------------------------------------------
Totals 13714 reads; 4423632 bp (untrimmed), 3989176 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4410066 bases = 2.57 +- 1.53 = 0.65 +- 1.48
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 1844 total values totalling 4164.8000. <2.258568 +/- 0.760923>
#Range: [ 1.06 - 7.31 ]
#Most likely bin: [ 1.5 - 2 ] 555 counts
#Median bin: [ 2 - 2.5 ] 419 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 255 0.14 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 555 0.30 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 419 0.23 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 308 0.17 0.83 ]
|XXXXXXXXXXXX 3 - 3.5 : [ 173 0.09 0.93 ]
|XXXXXXX 3.5 - 4 : [ 95 0.05 0.98 ]
|X 4 - 4.5 : [ 17 0.01 0.99 ]
|X 4.5 - 5 : [ 15 0.01 1.00 ]
| 5 - 5.5 : [ 4 0.00 1.00 ]
| 5.5 - 6 : [ 2 0.00 1.00 ]
#...
| 7 - 7.5 : [ 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 353 total values totalling 1091.3700. <3.091700 +/- 0.704947>
#Range: [ 1.67 - 7.31 ]
#Most likely bin: [ 2.5 - 3 ] 112 counts
#Median bin: [ 3 - 3.5 ] 94 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 1.5 - 2 : [ 7 0.02 0.02 ]
|XXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 56 0.16 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 112 0.32 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 94 0.27 0.76 ]
|XXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 56 0.16 0.92 ]
|XXXX 4 - 4.5 : [ 11 0.03 0.95 ]
|XXXX 4.5 - 5 : [ 12 0.03 0.99 ]
|X 5 - 5.5 : [ 3 0.01 0.99 ]
| 5.5 - 6 : [ 1 0.00 1.00 ]
#...
| 7 - 7.5 : [ 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 364 2 reads 1858 bases = 1.06 +- 0.24 = 0.04 +- 0.97
Contig 243 2 reads 1525 bases = 1.07 +- 0.26 = 1.07 +- 0.26
Contig 78 2 reads 1561 bases = 1.07 +- 0.25 = -0.30 +- 0.92
Contig 115 2 reads 1257 bases = 1.08 +- 0.27 = 1.08 +- 0.27
Contig 126 2 reads 1944 bases = 1.08 +- 0.27 = -0.06 +- 0.96
Contig 220 2 reads 1858 bases = 1.08 +- 0.27 = 0.05 +- 0.96
Contig 86 2 reads 1475 bases = 1.08 +- 0.27 = -0.04 +- 0.96
Contig 111 2 reads 1409 bases = 1.09 +- 0.28 = 1.09 +- 0.28
Contig 143 2 reads 2063 bases = 1.09 +- 0.29 = 0.11 +- 0.95
Contig 206 2 reads 1978 bases = 1.09 +- 0.28 = 1.09 +- 0.28
Contig 278 2 reads 1021 bases = 1.09 +- 0.29 = -0.56 +- 0.77
Contig 231 2 reads 1443 bases = 1.10 +- 0.30 = 0.12 +- 0.94
Contig 296 2 reads 1618 bases = 1.10 +- 0.30 = 0.05 +- 0.95
Contig 347 2 reads 1886 bases = 1.10 +- 0.30 = 0.07 +- 0.95
Contig 38 2 reads 1469 bases = 1.10 +- 0.29 = -0.44 +- 0.84
Contig 66 2 reads 1058 bases = 1.11 +- 0.31 = -0.89 +- 0.31
Contig 219 2 reads 1519 bases = 1.12 +- 0.33 = 0.16 +- 0.92
Contig 237 2 reads 1178 bases = 1.12 +- 0.33 = 1.12 +- 0.33
Contig 238 2 reads 949 bases = 1.12 +- 0.32 = 1.12 +- 0.32
Contig 248 2 reads 1563 bases = 1.12 +- 0.32 = -0.15 +- 0.93
Contig 1282 7 reads 1449 bases = 4.52 +- 2.15 = 1.89 +- 1.91
Contig 1862 99 reads 19497 bases = 4.52 +- 2.03 = 0.27 +- 2.83
Contig 1804 24 reads 4231 bases = 4.53 +- 2.38 = 1.02 +- 1.35
Contig 1756 19 reads 3257 bases = 4.55 +- 1.58 = 0.16 +- 3.93
Contig 1866 246 reads 45752 bases = 4.60 +- 1.93 = 0.34 +- 2.22
Contig 1857 65 reads 12320 bases = 4.64 +- 1.92 = 0.21 +- 2.55
Contig 1855 53 reads 9558 bases = 4.67 +- 2.75 = 0.68 +- 2.22
Contig 1845 35 reads 6025 bases = 4.74 +- 2.03 = -0.09 +- 1.66
Contig 1865 160 reads 28135 bases = 4.80 +- 1.98 = 0.05 +- 2.51
Contig 1816 25 reads 4543 bases = 4.88 +- 1.65 = 0.97 +- 1.23
Contig 1864 149 reads 27133 bases = 4.88 +- 1.88 = 0.24 +- 2.40
Contig 1606 12 reads 1935 bases = 4.93 +- 3.02 = 1.05 +- 1.82
Contig 1850 40 reads 6475 bases = 4.98 +- 1.72 = 0.44 +- 2.23
Contig 1806 24 reads 3890 bases = 5.15 +- 2.57 = 0.74 +- 1.86
Contig 1861 92 reads 14058 bases = 5.22 +- 2.17 = 0.06 +- 2.13
Contig 1830 29 reads 4832 bases = 5.32 +- 2.77 = 0.27 +- 1.77
Contig 1609 12 reads 1777 bases = 5.45 +- 2.96 = 0.71 +- 1.00
Contig 1702 16 reads 2602 bases = 5.57 +- 3.06 = 3.51 +- 3.34
Contig 1570 11 reads 1362 bases = 5.73 +- 2.34 = 0.77 +- 1.67
Contig 1859 75 reads 9031 bases = 7.31 +- 4.41 = -0.01 +- 3.20
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 162
HQ Discrepant reads = 513
Chimeric reads = 28
Suspect alignments = 24
-------------------------------------------------------------------
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/microbe2/3634503/edit_dir.01Oct04.QC