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
3436091 3100 405 Methylobacillus flagellatus
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Methylobacillus_flagellatus
-------------------------------------------------------------------
Methylophilales, order, b-proteobacteria
Methylophilaceae, family, b-proteobacteria
Betaproteobacteria, class, b-proteobacteria
Methylobacillus flagellatus, species, b-proteobacteria
Methylobacillus, genus, b-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2837564
# phrap: 2755724
# db:
altered.
3100000
2897762 +/- 146854
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 35600
Number of reads with percent X's >= 20%: 1980 = 4.0%
Number of reads with percent X's >= 50%: 1810 = 3.6%
Number of reads with percent X's >= 80%: 876 = 1.8%
Total reads in project: 49600
Total bp X'd : 3675583
reads >= 20% >= 50% >= 80% screened
Nr with L09136 9586 227 96 2
Nr with pCC1Fos 1176 0 0 0
Nr with pMCL200_JGI_XZX+XZK 24838 1753 1714 874
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 285
Number of reads with percent X's >= 20%: 6 = 1.9%
Number of reads with percent X's >= 50%: 6 = 1.9%
Number of reads with percent X's >= 80%: 1 = 0.3%
Total reads in project: 312
Total bp X'd : 23601
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3 1 1 0
Nr with pCC1Fos 3 0 0 0
Nr with pMCL200_JGI_XZX+XZK 279 5 5 1
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 10406687
C = 12735381
G = 12825269
T = 10092955
N = 187856
X = 3675583
GC fraction = 0.51
Total = 49923731
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436091_fasta.screen.contigs
-------------------------------------------------------------------
A 636215
C 811837
G 778557
T 624703
N 18
fraction GC = 0.56
total bases = 2851330
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 ABFG reads.list > grep.reads.list.ABFG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ABFG 4 500
-------------------------------------------------------------------
#Found 8938 total values totalling 60578275.0000. <6777.609644 +/- 3056.262232>
#Range: [ 146 - 214510 ]
#Most likely bin: [ 6000 - 6500 ] 2451 counts
#Median bin: [ 6500 - 7000 ] 2378 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 500 : [ 104 0.01 0.01 ]
| 500 - 1000 : [ 2 0.00 0.01 ]
| 1000 - 1500 : [ 8 0.00 0.01 ]
| 1500 - 2000 : [ 12 0.00 0.01 ]
| 2000 - 2500 : [ 12 0.00 0.02 ]
| 2500 - 3000 : [ 9 0.00 0.02 ]
| 3000 - 3500 : [ 17 0.00 0.02 ]
| 3500 - 4000 : [ 11 0.00 0.02 ]
| 4000 - 4500 : [ 12 0.00 0.02 ]
| 4500 - 5000 : [ 16 0.00 0.02 ]
|X 5000 - 5500 : [ 57 0.01 0.03 ]
|XXXXXXXXX 5500 - 6000 : [ 558 0.06 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2451 0.27 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2378 0.27 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1908 0.21 0.85 ]
|XXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1141 0.13 0.97 ]
|XXXX 8000 - 8500 : [ 228 0.03 1.00 ]
| 8500 - 9000 : [ 1 0.00 1.00 ]
#...
| 10500 - 11000 : [ 1 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
#...
| 16500 - 17000 : [ 1 0.00 1.00 ]
| 17000 - 17500 : [ 1 0.00 1.00 ]
#...
| 21000 - 21500 : [ 1 0.00 1.00 ]
#...
| 27000 - 27500 : [ 1 0.00 1.00 ]
#...
| 46500 - 47000 : [ 1 0.00 1.00 ]
#...
| 58000 - 58500 : [ 1 0.00 1.00 ]
#...
| 68000 - 68500 : [ 1 0.00 1.00 ]
#...
| 80000 - 80500 : [ 1 0.00 1.00 ]
#...
| 83000 - 83500 : [ 1 0.00 1.00 ]
#...
| 111500 - 112000 : [ 1 0.00 1.00 ]
#...
| 214500 - 215000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ABFH reads.list > grep.reads.list.ABFH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ABFH 4 500
-------------------------------------------------------------------
#Found 1216 total values totalling 48525628.0000. <39905.944079 +/- 3138.134173>
#Range: [ 25721 - 51291 ]
#Most likely bin: [ 42500 - 43000 ] 75 counts
#Median bin: [ 40000 - 40500 ] 71 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 25500 - 26000 : [ 1 0.00 0.00 ]
#...
|X 28000 - 28500 : [ 1 0.00 0.00 ]
#...
|X 30500 - 31000 : [ 1 0.00 0.00 ]
|X 31000 - 31500 : [ 1 0.00 0.00 ]
|X 31500 - 32000 : [ 2 0.00 0.00 ]
|XXX 32000 - 32500 : [ 6 0.00 0.01 ]
|X 32500 - 33000 : [ 1 0.00 0.01 ]
|XXXX 33000 - 33500 : [ 8 0.01 0.02 ]
|XXXX 33500 - 34000 : [ 8 0.01 0.02 ]
|XXXXXXXXX 34000 - 34500 : [ 17 0.01 0.04 ]
|XXXXXXXXXXXXXXX 34500 - 35000 : [ 29 0.02 0.06 ]
|XXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 35 0.03 0.09 ]
|XXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 40 0.03 0.12 ]
|XXXXXXXXXXXXXXXX 36000 - 36500 : [ 30 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 56 0.05 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 47 0.04 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 60 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 74 0.06 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 71 0.06 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 52 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 62 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 71 0.06 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 71 0.06 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 68 0.06 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 53 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 59 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 75 0.06 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 52 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 49 0.04 0.90 ]
|XXXXXXXXXXXXXXXXXXXXXXX 44000 - 44500 : [ 43 0.04 0.94 ]
|XXXXXXXXXXXXXXX 44500 - 45000 : [ 29 0.02 0.96 ]
|XXXXXXXXXXX 45000 - 45500 : [ 21 0.02 0.98 ]
|XXXXXX 45500 - 46000 : [ 11 0.01 0.99 ]
|XXXX 46000 - 46500 : [ 7 0.01 1.00 ]
|X 46500 - 47000 : [ 2 0.00 1.00 ]
|X 47000 - 47500 : [ 1 0.00 1.00 ]
#...
|X 48500 - 49000 : [ 1 0.00 1.00 ]
#...
|X 51000 - 51500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ABFF reads.list > grep.reads.list.ABFF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ABFF 4 500
-------------------------------------------------------------------
#Found 9642 total values totalling 37631859.0000. <3902.910081 +/- 2485.390096>
#Range: [ 727 - 173055 ]
#Most likely bin: [ 3500 - 4000 ] 2766 counts
#Median bin: [ 3500 - 4000 ] 2766 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 15 0.00 0.00 ]
|X 1000 - 1500 : [ 88 0.01 0.01 ]
|X 1500 - 2000 : [ 74 0.01 0.02 ]
|X 2000 - 2500 : [ 54 0.01 0.02 ]
|XXXXXXX 2500 - 3000 : [ 491 0.05 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1988 0.21 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2766 0.29 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 2488 0.26 0.83 ]
|XXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 1346 0.14 0.97 ]
|XXXXX 5000 - 5500 : [ 327 0.03 1.00 ]
| 5500 - 6000 : [ 1 0.00 1.00 ]
#...
| 11000 - 11500 : [ 1 0.00 1.00 ]
#...
| 15500 - 16000 : [ 1 0.00 1.00 ]
#...
| 165500 - 166000 : [ 1 0.00 1.00 ]
#...
| 173000 - 173500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# ABFF 3721 +- 807 (n=4900)
# ABFG 6168 +- 1859 (n=5117)
# ABFH 39906 +- 3092 (n=628)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436091_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
ABFF 23040 -1 -1 95 608 21004 99 558 100 574
ABFG 28800 -1 -1 99 712 25133 99 618 100 710
ABFH 3840 -1 -1 95 596 3463 98 623 100 639
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
ABFF 10442 98 524 100 544 10562 99 592 100 603
ABFG 13417 99 611 100 711 11716 99 626 100 709
ABFH 1776 99 605 100 619 1687 98 641 100 660
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436091_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 49600 23061 88.70 cumulative total @@
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 3436091_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 49600 total values totalling 29154946.0000. <587.801331 +/- 175.414699>
#Range: [ 15 - 923 ]
#Most likely bin: [ 650 - 700 ] 9514 counts
#Median bin: [ 600 - 650 ] 7432 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 96 0.00 0.00 ]
|XX 50 - 100 : [ 399 0.01 0.01 ]
|XXXXXXX 100 - 150 : [ 1567 0.03 0.04 ]
|XXX 150 - 200 : [ 772 0.02 0.06 ]
|XXXXX 200 - 250 : [ 1131 0.02 0.08 ]
|XXXX 250 - 300 : [ 857 0.02 0.10 ]
|XXXX 300 - 350 : [ 1013 0.02 0.12 ]
|XXXXX 350 - 400 : [ 1272 0.03 0.14 ]
|XXXXXX 400 - 450 : [ 1471 0.03 0.17 ]
|XXXXXXXXX 450 - 500 : [ 2176 0.04 0.22 ]
|XXXXXXXXXXXXXX 500 - 550 : [ 3290 0.07 0.28 ]
|XXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 4957 0.10 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 7432 0.15 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 9514 0.19 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 8301 0.17 0.89 ]
|XXXXXXXXXXXXXXXXX 750 - 800 : [ 3950 0.08 0.97 ]
|XXXXX 800 - 850 : [ 1160 0.02 1.00 ]
|X 850 - 900 : [ 220 0.00 1.00 ]
| 900 - 950 : [ 22 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ABFG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ABFG 3436091_fasta.screen.trimQ15.SaF > reads.trim15.ABFG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ABFG.rl 2 50
-------------------------------------------------------------------
#Found 25133 total values totalling 15426465.0000. <613.793220 +/- 180.634252>
#Range: [ 22 - 923 ]
#Most likely bin: [ 650 - 700 ] 5439 counts
#Median bin: [ 650 - 700 ] 5439 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 48 0.00 0.00 ]
|X 50 - 100 : [ 133 0.01 0.01 ]
|XXXXXXXXX 100 - 150 : [ 1167 0.05 0.05 ]
|XX 150 - 200 : [ 316 0.01 0.07 ]
|XXXXX 200 - 250 : [ 621 0.02 0.09 ]
|X 250 - 300 : [ 201 0.01 0.10 ]
|XX 300 - 350 : [ 242 0.01 0.11 ]
|XX 350 - 400 : [ 276 0.01 0.12 ]
|XXX 400 - 450 : [ 365 0.01 0.13 ]
|XXXX 450 - 500 : [ 556 0.02 0.16 ]
|XXXXXXXX 500 - 550 : [ 1073 0.04 0.20 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 2053 0.08 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3814 0.15 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5439 0.22 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5005 0.20 0.85 ]
|XXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2641 0.11 0.95 ]
|XXXXXXX 800 - 850 : [ 948 0.04 0.99 ]
|XX 850 - 900 : [ 213 0.01 1.00 ]
| 900 - 950 : [ 22 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ABFH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ABFH 3436091_fasta.screen.trimQ15.SaF > reads.trim15.ABFH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ABFH.rl 2 50
-------------------------------------------------------------------
#Found 3463 total values totalling 2123543.0000. <613.209067 +/- 176.424278>
#Range: [ 15 - 884 ]
#Most likely bin: [ 700 - 750 ] 767 counts
#Median bin: [ 650 - 700 ] 615 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 18 0.01 0.01 ]
|XX 50 - 100 : [ 40 0.01 0.02 ]
|XX 100 - 150 : [ 34 0.01 0.03 ]
|XXX 150 - 200 : [ 54 0.02 0.04 ]
|XXXX 200 - 250 : [ 74 0.02 0.06 ]
|XXXX 250 - 300 : [ 73 0.02 0.08 ]
|XXXXX 300 - 350 : [ 101 0.03 0.11 ]
|XXXXXXXX 350 - 400 : [ 155 0.04 0.16 ]
|XXX 400 - 450 : [ 51 0.01 0.17 ]
|XXXX 450 - 500 : [ 70 0.02 0.19 ]
|XXXXXXX 500 - 550 : [ 137 0.04 0.23 ]
|XXXXXXXXXXXXX 550 - 600 : [ 246 0.07 0.30 ]
|XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 401 0.12 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 615 0.18 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 767 0.22 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 524 0.15 0.97 ]
|XXXXX 800 - 850 : [ 99 0.03 1.00 ]
| 850 - 900 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIZP
trimt JAZZ trim 15 readlength histogram for ABFF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ABFF 3436091_fasta.screen.trimQ15.SaF > reads.trim15.ABFF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ABFF.rl 2 50
-------------------------------------------------------------------
#Found 21004 total values totalling 11604938.0000. <552.510855 +/- 162.258339>
#Range: [ 27 - 861 ]
#Most likely bin: [ 650 - 700 ] 3460 counts
#Median bin: [ 550 - 600 ] 2658 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 30 0.00 0.00 ]
|XXX 50 - 100 : [ 226 0.01 0.01 ]
|XXXX 100 - 150 : [ 366 0.02 0.03 ]
|XXXXX 150 - 200 : [ 402 0.02 0.05 ]
|XXXXX 200 - 250 : [ 436 0.02 0.07 ]
|XXXXXXX 250 - 300 : [ 583 0.03 0.10 ]
|XXXXXXXX 300 - 350 : [ 670 0.03 0.13 ]
|XXXXXXXXXX 350 - 400 : [ 841 0.04 0.17 ]
|XXXXXXXXXXXX 400 - 450 : [ 1055 0.05 0.22 ]
|XXXXXXXXXXXXXXXXXX 450 - 500 : [ 1550 0.07 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 2080 0.10 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 2658 0.13 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3217 0.15 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3460 0.16 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2529 0.12 0.96 ]
|XXXXXXXXX 750 - 800 : [ 785 0.04 0.99 ]
|X 800 - 850 : [ 113 0.01 1.00 ]
| 850 - 900 : [ 3 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436091
-------------------------------------------------------------------
ABFF.000001.000100 pUC18.fa.4 pEpiFos5.fa.4 LRS.fasta
ABFF.000101.000200 pUC18.fa.4 pEpiFos5.fa.4 LRS.fasta
ABFG.000001.000100 pMCL200.fa.4 LRS.fasta
ABFG.000101.000200 pMCL200.fa.4 LRS.fasta
ABFH.000001.000100 pCC1Fos.fa.4 LRS.fasta
ABFF.000001.000100 pUC18.fa.4 pEpiFos5.fa.4 LRS.fasta
ABFF.000101.000200 pUC18.fa.4 pEpiFos5.fa.4 LRS.fasta
ABFG.000001.000100 pMCL200.fa.4 LRS.fasta
ABFG.000101.000200 pMCL200.fa.4 LRS.fasta
ABFH.000001.000100 pCC1Fos.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436091_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436091_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 49496 total values totalling 27579.3698. <0.557204 +/- 0.052869>
#Range: [ 0.147 - 0.875 ]
#Most likely bin: [ 0.585 - 0.59 ] 2579 counts
#Median bin: [ 0.56 - 0.565 ] 2229 counts
| 0.145 - 0.15 : [ 1 0.00 0.00 ]
#...
| 0.2 - 0.205 : [ 1 0.00 0.00 ]
#...
| 0.24 - 0.245 : [ 1 0.00 0.00 ]
#...
| 0.25 - 0.255 : [ 1 0.00 0.00 ]
| 0.255 - 0.26 : [ 2 0.00 0.00 ]
| 0.26 - 0.265 : [ 1 0.00 0.00 ]
| 0.265 - 0.27 : [ 2 0.00 0.00 ]
| 0.27 - 0.275 : [ 5 0.00 0.00 ]
#...
| 0.28 - 0.285 : [ 1 0.00 0.00 ]
| 0.285 - 0.29 : [ 4 0.00 0.00 ]
| 0.29 - 0.295 : [ 6 0.00 0.00 ]
| 0.295 - 0.3 : [ 6 0.00 0.00 ]
| 0.3 - 0.305 : [ 13 0.00 0.00 ]
| 0.305 - 0.31 : [ 2 0.00 0.00 ]
| 0.31 - 0.315 : [ 13 0.00 0.00 ]
| 0.315 - 0.32 : [ 17 0.00 0.00 ]
| 0.32 - 0.325 : [ 13 0.00 0.00 ]
| 0.325 - 0.33 : [ 9 0.00 0.00 ]
| 0.33 - 0.335 : [ 18 0.00 0.00 ]
| 0.335 - 0.34 : [ 27 0.00 0.00 ]
| 0.34 - 0.345 : [ 24 0.00 0.00 ]
| 0.345 - 0.35 : [ 29 0.00 0.00 ]
| 0.35 - 0.355 : [ 32 0.00 0.00 ]
| 0.355 - 0.36 : [ 31 0.00 0.01 ]
|X 0.36 - 0.365 : [ 36 0.00 0.01 ]
|X 0.365 - 0.37 : [ 56 0.00 0.01 ]
|X 0.37 - 0.375 : [ 53 0.00 0.01 ]
|X 0.375 - 0.38 : [ 44 0.00 0.01 ]
|X 0.38 - 0.385 : [ 57 0.00 0.01 ]
|X 0.385 - 0.39 : [ 52 0.00 0.01 ]
|X 0.39 - 0.395 : [ 54 0.00 0.01 ]
|X 0.395 - 0.4 : [ 55 0.00 0.01 ]
|X 0.4 - 0.405 : [ 89 0.00 0.02 ]
|X 0.405 - 0.41 : [ 87 0.00 0.02 ]
|X 0.41 - 0.415 : [ 77 0.00 0.02 ]
|XX 0.415 - 0.42 : [ 100 0.00 0.02 ]
|XX 0.42 - 0.425 : [ 106 0.00 0.02 ]
|XX 0.425 - 0.43 : [ 138 0.00 0.03 ]
|XX 0.43 - 0.435 : [ 110 0.00 0.03 ]
|XXX 0.435 - 0.44 : [ 209 0.00 0.03 ]
|XXX 0.44 - 0.445 : [ 172 0.00 0.04 ]
|XX 0.445 - 0.45 : [ 160 0.00 0.04 ]
|XXXX 0.45 - 0.455 : [ 226 0.00 0.04 ]
|XXX 0.455 - 0.46 : [ 225 0.00 0.05 ]
|XXXX 0.46 - 0.465 : [ 244 0.00 0.05 ]
|XXXX 0.465 - 0.47 : [ 269 0.01 0.06 ]
|XXXXX 0.47 - 0.475 : [ 320 0.01 0.06 ]
|XXXXXX 0.475 - 0.48 : [ 374 0.01 0.07 ]
|XXXXXXX 0.48 - 0.485 : [ 423 0.01 0.08 ]
|XXXXXXX 0.485 - 0.49 : [ 481 0.01 0.09 ]
|XXXXXXXX 0.49 - 0.495 : [ 520 0.01 0.10 ]
|XXXXXXXX 0.495 - 0.5 : [ 518 0.01 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1656 0.03 0.14 ]
|XXXXXXXXXXX 0.505 - 0.51 : [ 726 0.01 0.16 ]
|XXXXXXXXXXXXXX 0.51 - 0.515 : [ 892 0.02 0.18 ]
|XXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1046 0.02 0.20 ]
|XXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1141 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1293 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1389 0.03 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1591 0.03 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1680 0.03 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1832 0.04 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1872 0.04 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 2086 0.04 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 2229 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 2242 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 2346 0.05 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 2407 0.05 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 2328 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 2579 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 1914 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 1779 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1695 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1423 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1168 0.02 0.91 ]
|XXXXXXXXXXXXXX 0.615 - 0.62 : [ 903 0.02 0.92 ]
|XXXXXXXXXXXXX 0.62 - 0.625 : [ 819 0.02 0.94 ]
|XXXXXXXXXXX 0.625 - 0.63 : [ 723 0.01 0.96 ]
|XXXXXXXXX 0.63 - 0.635 : [ 556 0.01 0.97 ]
|XXXXXX 0.635 - 0.64 : [ 368 0.01 0.97 ]
|XXXX 0.64 - 0.645 : [ 290 0.01 0.98 ]
|XXX 0.645 - 0.65 : [ 218 0.00 0.98 ]
|XXX 0.65 - 0.655 : [ 164 0.00 0.99 ]
|XX 0.655 - 0.66 : [ 124 0.00 0.99 ]
|X 0.66 - 0.665 : [ 88 0.00 0.99 ]
|X 0.665 - 0.67 : [ 60 0.00 0.99 ]
|X 0.67 - 0.675 : [ 56 0.00 0.99 ]
|X 0.675 - 0.68 : [ 41 0.00 0.99 ]
| 0.68 - 0.685 : [ 31 0.00 1.00 ]
| 0.685 - 0.69 : [ 29 0.00 1.00 ]
| 0.69 - 0.695 : [ 30 0.00 1.00 ]
| 0.695 - 0.7 : [ 18 0.00 1.00 ]
| 0.7 - 0.705 : [ 25 0.00 1.00 ]
| 0.705 - 0.71 : [ 21 0.00 1.00 ]
| 0.71 - 0.715 : [ 7 0.00 1.00 ]
| 0.715 - 0.72 : [ 8 0.00 1.00 ]
| 0.72 - 0.725 : [ 7 0.00 1.00 ]
| 0.725 - 0.73 : [ 14 0.00 1.00 ]
| 0.73 - 0.735 : [ 8 0.00 1.00 ]
| 0.735 - 0.74 : [ 9 0.00 1.00 ]
| 0.74 - 0.745 : [ 10 0.00 1.00 ]
| 0.745 - 0.75 : [ 1 0.00 1.00 ]
| 0.75 - 0.755 : [ 5 0.00 1.00 ]
| 0.755 - 0.76 : [ 3 0.00 1.00 ]
| 0.76 - 0.765 : [ 9 0.00 1.00 ]
| 0.765 - 0.77 : [ 6 0.00 1.00 ]
| 0.77 - 0.775 : [ 2 0.00 1.00 ]
| 0.775 - 0.78 : [ 4 0.00 1.00 ]
| 0.78 - 0.785 : [ 1 0.00 1.00 ]
| 0.785 - 0.79 : [ 1 0.00 1.00 ]
| 0.79 - 0.795 : [ 2 0.00 1.00 ]
#...
| 0.805 - 0.81 : [ 5 0.00 1.00 ]
#...
| 0.86 - 0.865 : [ 1 0.00 1.00 ]
#...
| 0.875 - 0.88 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 105. 87 reads; 154 bp (untrimmed), 154 (trimmed).
Contig 106. 90 reads; 9927 bp (untrimmed), 9501 (trimmed).
Contig 107. 165 reads; 19787 bp (untrimmed), 19444 (trimmed).
Contig 108. 322 reads; 22460 bp (untrimmed), 22440 (trimmed).
Contig 109. 324 reads; 21539 bp (untrimmed), 21222 (trimmed).
Contig 110. 343 reads; 28146 bp (untrimmed), 27272 (trimmed).
Contig 111. 442 reads; 21684 bp (untrimmed), 21675 (trimmed).
Contig 112. 476 reads; 727 bp (untrimmed), 570 (trimmed).
Contig 113. 503 reads; 46672 bp (untrimmed), 46590 (trimmed).
Contig 114. 657 reads; 52968 bp (untrimmed), 52440 (trimmed).
Contig 115. 750 reads; 38496 bp (untrimmed), 38496 (trimmed).
Contig 116. 1013 reads; 70469 bp (untrimmed), 70469 (trimmed).
Contig 117. 1218 reads; 73606 bp (untrimmed), 73606 (trimmed).
Contig 118. 1318 reads; 91644 bp (untrimmed), 91140 (trimmed).
Contig 119. 1333 reads; 91983 bp (untrimmed), 91983 (trimmed).
Contig 120. 1501 reads; 92307 bp (untrimmed), 92307 (trimmed).
Contig 121. 1856 reads; 98853 bp (untrimmed), 98827 (trimmed).
Contig 122. 1884 reads; 109448 bp (untrimmed), 109381 (trimmed).
Contig 123. 2012 reads; 136350 bp (untrimmed), 136299 (trimmed).
Contig 124. 2041 reads; 144920 bp (untrimmed), 144457 (trimmed).
Contig 125. 2487 reads; 156881 bp (untrimmed), 156881 (trimmed).
Contig 126. 2617 reads; 159560 bp (untrimmed), 159543 (trimmed).
Contig 127. 3325 reads; 198938 bp (untrimmed), 198751 (trimmed).
Contig 128. 3595 reads; 223767 bp (untrimmed), 223572 (trimmed).
Contig 129. 4227 reads; 173522 bp (untrimmed), 173491 (trimmed).
Contig 130. 6318 reads; 307340 bp (untrimmed), 307340 (trimmed).
Contig 131. 7748 reads; 353720 bp (untrimmed), 353711 (trimmed).
--------------------------------------------------------------
Totals 49288 reads; 2851330 bp (untrimmed), 2837564 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2842146 bases = 14.17 +- 7.85 = 0.19 +- 5.72
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 82 total values totalling 632.6600. <7.715366 +/- 14.642126>
#Range: [ 1.25 - 131.60 ]
#Most likely bin: [ 2.5 - 3 ] 30 counts
#Median bin: [ 2.5 - 3 ] 30 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1 - 1.5 : [ 1 0.01 0.01 ]
|X 1.5 - 2 : [ 1 0.01 0.02 ]
|XXXXXXXXXXXXX 2 - 2.5 : [ 10 0.12 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 30 0.37 0.51 ]
|XXXX 3 - 3.5 : [ 3 0.04 0.55 ]
|XXXXXXX 3.5 - 4 : [ 5 0.06 0.61 ]
|X 4 - 4.5 : [ 1 0.01 0.62 ]
|X 4.5 - 5 : [ 1 0.01 0.63 ]
|X 5 - 5.5 : [ 1 0.01 0.65 ]
#...
|X 6 - 6.5 : [ 1 0.01 0.66 ]
|X 6.5 - 7 : [ 1 0.01 0.67 ]
#...
|XXX 7.5 - 8 : [ 2 0.02 0.70 ]
#...
|X 8.5 - 9 : [ 1 0.01 0.71 ]
|X 9 - 9.5 : [ 1 0.01 0.72 ]
#...
|X 10 - 10.5 : [ 1 0.01 0.73 ]
|X 10.5 - 11 : [ 1 0.01 0.74 ]
#...
|XXXXXXXX 12 - 12.5 : [ 6 0.07 0.82 ]
|X 12.5 - 13 : [ 1 0.01 0.83 ]
|X 13 - 13.5 : [ 1 0.01 0.84 ]
|XXXXX 13.5 - 14 : [ 4 0.05 0.89 ]
|X 14 - 14.5 : [ 1 0.01 0.90 ]
|X 14.5 - 15 : [ 1 0.01 0.91 ]
#...
|XXXX 16 - 16.5 : [ 3 0.04 0.95 ]
#...
|XXX 17 - 17.5 : [ 2 0.02 0.98 ]
#...
|X 18 - 18.5 : [ 1 0.01 0.99 ]
#...
|X 131.5 - 132 : [ 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 35 total values totalling 374.7900. <10.708286 +/- 4.655386>
#Range: [ 2.86 - 18.45 ]
#Most likely bin: [ 12 - 12.5 ] 6 counts
#Median bin: [ 12 - 12.5 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 2.5 - 3 : [ 1 0.03 0.03 ]
|XXXXXXX 3 - 3.5 : [ 1 0.03 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 5 0.14 0.20 ]
#...
|XXXXXXX 5 - 5.5 : [ 1 0.03 0.23 ]
#...
|XXXXXXX 6.5 - 7 : [ 1 0.03 0.26 ]
#...
|XXXXXXXXXXXXX 7.5 - 8 : [ 2 0.06 0.31 ]
#...
|XXXXXXX 8.5 - 9 : [ 1 0.03 0.34 ]
|XXXXXXX 9 - 9.5 : [ 1 0.03 0.37 ]
#...
|XXXXXXX 10 - 10.5 : [ 1 0.03 0.40 ]
|XXXXXXX 10.5 - 11 : [ 1 0.03 0.43 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 6 0.17 0.60 ]
|XXXXXXX 12.5 - 13 : [ 1 0.03 0.63 ]
|XXXXXXX 13 - 13.5 : [ 1 0.03 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 4 0.11 0.77 ]
|XXXXXXX 14 - 14.5 : [ 1 0.03 0.80 ]
|XXXXXXX 14.5 - 15 : [ 1 0.03 0.83 ]
#...
|XXXXXXXXXXXXXXXXXXXX 16 - 16.5 : [ 3 0.09 0.91 ]
#...
|XXXXXXXXXXXXX 17 - 17.5 : [ 2 0.06 0.97 ]
#...
|XXXXXXX 18 - 18.5 : [ 1 0.03 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 1 2 reads 1348 bases = 1.25 +- 0.43 = -0.19 +- 0.85
Contig 2 2 reads 760 bases = 1.67 +- 0.47 = -0.03 +- 0.57
Contig 93 10 reads 1127 bases = 2.02 +- 2.46 = 0.90 +- 0.33
Contig 69 4 reads 1200 bases = 2.05 +- 1.03 = 0.89 +- 1.90
Contig 64 4 reads 1346 bases = 2.10 +- 1.05 = 1.19 +- 1.75
Contig 88 6 reads 2137 bases = 2.15 +- 0.93 = 1.33 +- 0.73
Contig 82 5 reads 907 bases = 2.19 +- 0.62 = 1.93 +- 0.25
Contig 56 4 reads 592 bases = 2.24 +- 0.65 = 0.00 +- 0.00
Contig 18 3 reads 937 bases = 2.28 +- 0.68 = 2.28 +- 0.68
Contig 71 4 reads 665 bases = 2.37 +- 0.78 = 0.00 +- 0.00
Contig 91 7 reads 1855 bases = 2.41 +- 0.81 = 2.41 +- 0.81
Contig 89 7 reads 2124 bases = 2.47 +- 0.63 = 2.11 +- 0.84
Contig 35 3 reads 983 bases = 2.53 +- 0.66 = 2.53 +- 0.66
Contig 26 3 reads 937 bases = 2.54 +- 0.81 = 2.54 +- 0.81
Contig 27 3 reads 965 bases = 2.55 +- 0.64 = 2.55 +- 0.64
Contig 17 3 reads 976 bases = 2.59 +- 0.80 = 2.59 +- 0.80
Contig 10 3 reads 983 bases = 2.61 +- 0.75 = 2.61 +- 0.75
Contig 33 3 reads 1062 bases = 2.62 +- 0.69 = 2.62 +- 0.69
Contig 37 3 reads 1008 bases = 2.63 +- 0.77 = 2.63 +- 0.77
Contig 23 3 reads 979 bases = 2.68 +- 0.68 = 2.68 +- 0.68
Contig 124 2041 reads 144920 bases = 12.01 +- 5.26 = 0.19 +- 4.86
Contig 118 1318 reads 91644 bases = 12.05 +- 5.35 = 0.30 +- 6.08
Contig 116 1013 reads 70469 bases = 12.17 +- 4.70 = 0.25 +- 4.57
Contig 119 1333 reads 91983 bases = 12.20 +- 5.05 = -0.03 +- 4.24
Contig 123 2012 reads 136350 bases = 12.45 +- 5.24 = 0.15 +- 5.62
Contig 109 324 reads 21539 bases = 12.79 +- 5.76 = 0.67 +- 6.00
Contig 125 2487 reads 156881 bases = 13.26 +- 5.29 = -0.01 +- 6.37
Contig 128 3595 reads 223767 bases = 13.58 +- 5.08 = 0.15 +- 5.24
Contig 120 1501 reads 92307 bases = 13.73 +- 4.79 = 0.61 +- 4.61
Contig 126 2617 reads 159560 bases = 13.78 +- 5.37 = -0.09 +- 5.77
Contig 117 1218 reads 73606 bases = 13.89 +- 5.24 = 0.27 +- 4.84
Contig 127 3325 reads 198938 bases = 14.03 +- 5.08 = 0.02 +- 5.50
Contig 122 1884 reads 109448 bases = 14.57 +- 6.36 = 0.17 +- 5.94
Contig 121 1856 reads 98853 bases = 16.08 +- 7.24 = 0.40 +- 6.16
Contig 129 4227 reads 173522 bases = 16.13 +- 7.94 = -0.21 +- 5.52
Contig 115 750 reads 38496 bases = 16.28 +- 6.47 = 0.43 +- 5.82
Contig 111 442 reads 21684 bases = 17.29 +- 6.59 = 0.05 +- 7.11
Contig 130 6318 reads 307340 bases = 17.43 +- 6.02 = 0.04 +- 6.14
Contig 131 7748 reads 353720 bases = 18.45 +- 8.55 = 0.11 +- 7.19
Contig 112 476 reads 727 bases = 131.60 +- 211.98 = 2.96 +- 3.22
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 3968
HQ Discrepant reads = 58
Chimeric reads = 75
Suspect alignments = 232
-------------------------------------------------------------------
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/microbe2/3436091/edit_dir.19Nov03.QD