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
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Project Size(KB) TaxID GenusSpecies
3634473 2400 115853 Chlorobium vibrioforme
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Chlorobium_vibrioforme
-------------------------------------------------------------------
Chlorobiaceae, family, green sulfur bacteria
Chlorobiales, order, green sulfur bacteria
Chlorobia, class, green sulfur bacteria
Bacteroidetes/Chlorobi group, superphylum, eubacteria
Prosthecochloris, genus, green sulfur bacteria
Prosthecochloris vibrioformis, species, green sulfur bacteria
Chlorobi, phylum, green sulfur bacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
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# contigs: 1971271
# phrap: 1916615
# db:
altered.
2400000
2095962 +/- 216142
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 6317
Number of reads with percent X's >= 20%: 413 = 1.6%
Number of reads with percent X's >= 50%: 227 = 0.9%
Number of reads with percent X's >= 80%: 49 = 0.2%
Total reads in project: 25644
Total bp X'd : 443808
reads >= 20% >= 50% >= 80% screened
Nr with L09136 5104 205 78 3
Nr with pCC1Fos 978 0 0 0
Nr with pMCL200_JGI_XZX+XZK 235 208 149 46
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 2407
Number of reads with percent X's >= 20%: 2297 = 58.7%
Number of reads with percent X's >= 50%: 2182 = 55.7%
Number of reads with percent X's >= 80%: 1930 = 49.3%
Total reads in project: 3915
Total bp X'd : 2069238
reads >= 20% >= 50% >= 80% screened
Nr with L09136 246 196 191 175
Nr with LRS 54 54 54 51
Nr with pCC1Fos 15 1 1 0
Nr with pMCL200_JGI_XZX+XZK 2092 2046 1936 1704
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Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 6335496
C = 7058565
G = 6985365
T = 6285473
N = 179277
X = 2573518
GC fraction = 0.48
Total = 29417694
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634473_fasta.screen.contigs
-------------------------------------------------------------------
A 464937
C 520909
G 528207
T 465967
N 166
fraction GC = 0.53
total bases = 1980186
Libraries and Reads
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Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
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-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXT reads.list > grep.reads.list.AHXT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXT 4 500
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#Found 5829 total values totalling 20514031.0000. <3519.305370 +/- 1771.059509>
#Range: [ 586 - 115359 ]
#Most likely bin: [ 3500 - 4000 ] 1697 counts
#Median bin: [ 3500 - 4000 ] 1697 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 33 0.01 0.01 ]
|XXXX 1000 - 1500 : [ 173 0.03 0.04 ]
|XXXX 1500 - 2000 : [ 188 0.03 0.07 ]
|XXXXXX 2000 - 2500 : [ 266 0.05 0.11 ]
|XXXXXXXXXXX 2500 - 3000 : [ 487 0.08 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1532 0.26 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1697 0.29 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 934 0.16 0.91 ]
|XXXXXXXXX 4500 - 5000 : [ 398 0.07 0.98 ]
|XX 5000 - 5500 : [ 93 0.02 1.00 ]
|X 5500 - 6000 : [ 24 0.00 1.00 ]
| 6000 - 6500 : [ 1 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
#...
| 43500 - 44000 : [ 1 0.00 1.00 ]
#...
| 115000 - 115500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXU reads.list > grep.reads.list.AHXU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXU 4 500
-------------------------------------------------------------------
#Found 4688 total values totalling 40534753.0000. <8646.491681 +/- 8673.056868>
#Range: [ 985 - 246339 ]
#Most likely bin: [ 8500 - 9000 ] 777 counts
#Median bin: [ 8500 - 9000 ] 777 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 4 0.00 0.00 ]
|XX 1000 - 1500 : [ 36 0.01 0.01 ]
|XX 1500 - 2000 : [ 40 0.01 0.02 ]
|XX 2000 - 2500 : [ 35 0.01 0.02 ]
|XX 2500 - 3000 : [ 32 0.01 0.03 ]
|XX 3000 - 3500 : [ 31 0.01 0.04 ]
|X 3500 - 4000 : [ 27 0.01 0.04 ]
|X 4000 - 4500 : [ 19 0.00 0.05 ]
|X 4500 - 5000 : [ 29 0.01 0.05 ]
|XX 5000 - 5500 : [ 31 0.01 0.06 ]
|XXX 5500 - 6000 : [ 51 0.01 0.07 ]
|XXXX 6000 - 6500 : [ 72 0.02 0.09 ]
|XXXXXXX 6500 - 7000 : [ 132 0.03 0.11 ]
|XXXXXXXXXXXXXXXXX 7000 - 7500 : [ 324 0.07 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 635 0.14 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 763 0.16 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 777 0.17 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 698 0.15 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 468 0.10 0.90 ]
|XXXXXXXXXXXXX 10000 - 10500 : [ 254 0.05 0.95 ]
|XXXXXX 10500 - 11000 : [ 120 0.03 0.98 ]
|XXX 11000 - 11500 : [ 51 0.01 0.99 ]
|XX 11500 - 12000 : [ 36 0.01 1.00 ]
| 12000 - 12500 : [ 9 0.00 1.00 ]
| 12500 - 13000 : [ 3 0.00 1.00 ]
| 13000 - 13500 : [ 2 0.00 1.00 ]
| 13500 - 14000 : [ 1 0.00 1.00 ]
#...
| 42000 - 42500 : [ 1 0.00 1.00 ]
#...
| 58500 - 59000 : [ 1 0.00 1.00 ]
#...
| 242000 - 242500 : [ 1 0.00 1.00 ]
#...
| 244000 - 244500 : [ 1 0.00 1.00 ]
| 244500 - 245000 : [ 1 0.00 1.00 ]
| 245000 - 245500 : [ 2 0.00 1.00 ]
#...
| 246000 - 246500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXW reads.list > grep.reads.list.AHXW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHXW 4 500
-------------------------------------------------------------------
#Found 820 total values totalling 30077930.0000. <36680.402439 +/- 3935.525765>
#Range: [ 24423 - 46894 ]
#Most likely bin: [ 34500 - 35000 ] 45 counts
#Median bin: [ 36000 - 36500 ] 41 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 24000 - 24500 : [ 2 0.00 0.00 ]
#...
|X 25000 - 25500 : [ 1 0.00 0.00 ]
#...
|X 26000 - 26500 : [ 1 0.00 0.00 ]
|X 26500 - 27000 : [ 1 0.00 0.01 ]
|XXX 27000 - 27500 : [ 3 0.00 0.01 ]
#...
|XX 28000 - 28500 : [ 2 0.00 0.01 ]
|XX 28500 - 29000 : [ 2 0.00 0.01 ]
|XXXXX 29000 - 29500 : [ 6 0.01 0.02 ]
|XXXXXXXX 29500 - 30000 : [ 9 0.01 0.03 ]
|XXXXXXXXX 30000 - 30500 : [ 10 0.01 0.05 ]
|XXXXXX 30500 - 31000 : [ 7 0.01 0.05 ]
|XXXXXXXXXXXXXXXX 31000 - 31500 : [ 18 0.02 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 31500 - 32000 : [ 30 0.04 0.11 ]
|XXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 23 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 29 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 35 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 43 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 31 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 45 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 44 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 35 0.04 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 41 0.05 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 30 0.04 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 38 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 30 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 44 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 26 0.03 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 35 0.04 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 33 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 23 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 24 0.03 0.85 ]
|XXXXXXXXXXXX 41000 - 41500 : [ 14 0.02 0.87 ]
|XXXXXXX 41500 - 42000 : [ 8 0.01 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 25 0.03 0.91 ]
|XXXXXXXXXXX 42500 - 43000 : [ 12 0.01 0.93 ]
|XXXXXXXXXXXXX 43000 - 43500 : [ 15 0.02 0.95 ]
|XXXXXXXXXXXX 43500 - 44000 : [ 13 0.02 0.96 ]
|XXXXXXXXXXXX 44000 - 44500 : [ 14 0.02 0.98 ]
|XXXXXXXX 44500 - 45000 : [ 9 0.01 0.99 ]
|XX 45000 - 45500 : [ 2 0.00 0.99 ]
|XXXX 45500 - 46000 : [ 5 0.01 1.00 ]
|X 46000 - 46500 : [ 1 0.00 1.00 ]
|X 46500 - 47000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHXT 3309 +- 959 (n=3002)
# AHXW 36697 +- 3942 (n=423)
# AHXU 8061 +- 2304 (n=2380)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634473_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
AHXT 13920 93 714 97 711 13892 91 649 95 658
AHXU 13056 79 751 95 703 13056 79 751 95 740
AHXW 3072 79 581 87 523 3072 79 591 88 596
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHXT 6897 89 634 94 649 6995 92 663 95 666
AHXU 6528 79 751 97 740 6528 79 752 93 740
AHXW 1536 78 585 87 595 1536 80 596 88 597
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634473_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
72 13892 6909 95.96 99.96 AHXT @
68 13056 6528 96.00 100.00 AHXU @
16 3072 1536 96.00 100.00 AHXW @
] 30020 14973 95.98 cumulative total@@
LIBRARY PLATE ID COUNT [ AHXT 72 AHXU 68 AHXW 16 ] for 156 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.
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trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3634473_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 30020 total values totalling 17431896.0000. <580.676083 +/- 288.006457>
#Range: [ 0 - 923 ]
#Most likely bin: [ 750 - 800 ] 6879 counts
#Median bin: [ 700 - 750 ] 4381 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 4224 0.14 0.14 ]
|XX 50 - 100 : [ 423 0.01 0.15 ]
|XX 100 - 150 : [ 324 0.01 0.17 ]
|XX 150 - 200 : [ 315 0.01 0.18 ]
|XX 200 - 250 : [ 350 0.01 0.19 ]
|XXX 250 - 300 : [ 453 0.02 0.20 ]
|XXX 300 - 350 : [ 449 0.01 0.22 ]
|XXX 350 - 400 : [ 470 0.02 0.23 ]
|XXX 400 - 450 : [ 485 0.02 0.25 ]
|XXX 450 - 500 : [ 548 0.02 0.27 ]
|XXXX 500 - 550 : [ 700 0.02 0.29 ]
|XXXXX 550 - 600 : [ 941 0.03 0.32 ]
|XXXXXXXX 600 - 650 : [ 1407 0.05 0.37 ]
|XXXXXXXXXXXXXX 650 - 700 : [ 2399 0.08 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4381 0.15 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6879 0.23 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4521 0.15 0.97 ]
|XXXX 850 - 900 : [ 727 0.02 1.00 ]
| 900 - 950 : [ 24 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXT 3634473_fasta.screen.trimQ15.SaF > reads.trim15.AHXT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXT.rl 2 50
-------------------------------------------------------------------
#Found 13892 total values totalling 8198928.0000. <590.190613 +/- 249.544638>
#Range: [ 0 - 923 ]
#Most likely bin: [ 750 - 800 ] 2366 counts
#Median bin: [ 650 - 700 ] 1488 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXX 0 - 50 : [ 1047 0.08 0.08 ]
|XXXX 50 - 100 : [ 245 0.02 0.09 ]
|XXX 100 - 150 : [ 192 0.01 0.11 ]
|XXX 150 - 200 : [ 206 0.01 0.12 ]
|XXXX 200 - 250 : [ 218 0.02 0.14 ]
|XXXXX 250 - 300 : [ 291 0.02 0.16 ]
|XXXXX 300 - 350 : [ 287 0.02 0.18 ]
|XXXXX 350 - 400 : [ 313 0.02 0.20 ]
|XXXXXX 400 - 450 : [ 381 0.03 0.23 ]
|XXXXXXX 450 - 500 : [ 418 0.03 0.26 ]
|XXXXXXXXX 500 - 550 : [ 560 0.04 0.30 ]
|XXXXXXXXXXXX 550 - 600 : [ 738 0.05 0.35 ]
|XXXXXXXXXXXXXXXXX 600 - 650 : [ 1032 0.07 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1488 0.11 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1952 0.14 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2366 0.17 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1776 0.13 0.97 ]
|XXXXXX 850 - 900 : [ 369 0.03 1.00 ]
| 900 - 950 : [ 13 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXU 3634473_fasta.screen.trimQ15.SaF > reads.trim15.AHXU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXU.rl 2 50
-------------------------------------------------------------------
#Found 13056 total values totalling 7779429.0000. <595.850873 +/- 317.860992>
#Range: [ 0 - 921 ]
#Most likely bin: [ 750 - 800 ] 4107 counts
#Median bin: [ 750 - 800 ] 4107 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2654 0.20 0.20 ]
|X 50 - 100 : [ 64 0.00 0.21 ]
|X 100 - 150 : [ 53 0.00 0.21 ]
|X 150 - 200 : [ 53 0.00 0.22 ]
| 200 - 250 : [ 37 0.00 0.22 ]
| 250 - 300 : [ 36 0.00 0.22 ]
| 300 - 350 : [ 42 0.00 0.23 ]
|X 350 - 400 : [ 54 0.00 0.23 ]
| 400 - 450 : [ 48 0.00 0.23 ]
|X 450 - 500 : [ 63 0.00 0.24 ]
|X 500 - 550 : [ 69 0.01 0.24 ]
|X 550 - 600 : [ 86 0.01 0.25 ]
|XX 600 - 650 : [ 180 0.01 0.26 ]
|XXXXXX 650 - 700 : [ 583 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2019 0.15 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4107 0.31 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2564 0.20 0.97 ]
|XXX 850 - 900 : [ 335 0.03 1.00 ]
| 900 - 950 : [ 9 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHXW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHXW 3634473_fasta.screen.trimQ15.SaF > reads.trim15.AHXW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHXW.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 1453539.0000. <473.157227 +/- 294.315919>
#Range: [ 0 - 914 ]
#Most likely bin: [ 0 - 50 ] 523 counts
#Median bin: [ 600 - 650 ] 195 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 523 0.17 0.17 ]
|XXXXXXXXX 50 - 100 : [ 114 0.04 0.21 ]
|XXXXXX 100 - 150 : [ 79 0.03 0.23 ]
|XXXX 150 - 200 : [ 56 0.02 0.25 ]
|XXXXXXX 200 - 250 : [ 95 0.03 0.28 ]
|XXXXXXXXXX 250 - 300 : [ 126 0.04 0.32 ]
|XXXXXXXXX 300 - 350 : [ 120 0.04 0.36 ]
|XXXXXXXX 350 - 400 : [ 103 0.03 0.40 ]
|XXXX 400 - 450 : [ 56 0.02 0.41 ]
|XXXXX 450 - 500 : [ 67 0.02 0.44 ]
|XXXXX 500 - 550 : [ 71 0.02 0.46 ]
|XXXXXXXXX 550 - 600 : [ 117 0.04 0.50 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 195 0.06 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 328 0.11 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 410 0.13 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 406 0.13 0.93 ]
|XXXXXXXXXXXXXX 800 - 850 : [ 181 0.06 0.99 ]
|XX 850 - 900 : [ 23 0.01 1.00 ]
| 900 - 950 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634473
-------------------------------------------------------------------
AHXT.000001.000100 pUC18.fa LRS.fasta
AHXU.000001.000100 pMCL200.fa LRS.fasta
AHXW.000001.000100 pCC1Fos.fa LRS.fasta
AHXT.000001.000100 pUC18.fa LRS.fasta
AHXU.000001.000100 pMCL200.fa LRS.fasta
AHXW.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634473_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634473_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 25851 total values totalling 13704.7239. <0.530143 +/- 0.039876>
#Range: [ 0.16 - 1 ]
#Most likely bin: [ 0.535 - 0.54 ] 1572 counts
#Median bin: [ 0.53 - 0.535 ] 1552 counts
| 0.16 - 0.165 : [ 1 0.00 0.00 ]
#...
| 0.18 - 0.185 : [ 1 0.00 0.00 ]
#...
| 0.205 - 0.21 : [ 1 0.00 0.00 ]
#...
| 0.215 - 0.22 : [ 1 0.00 0.00 ]
#...
| 0.225 - 0.23 : [ 1 0.00 0.00 ]
#...
| 0.245 - 0.25 : [ 1 0.00 0.00 ]
| 0.25 - 0.255 : [ 2 0.00 0.00 ]
| 0.255 - 0.26 : [ 1 0.00 0.00 ]
| 0.26 - 0.265 : [ 1 0.00 0.00 ]
| 0.265 - 0.27 : [ 1 0.00 0.00 ]
#...
| 0.275 - 0.28 : [ 1 0.00 0.00 ]
| 0.28 - 0.285 : [ 1 0.00 0.00 ]
| 0.285 - 0.29 : [ 1 0.00 0.00 ]
#...
| 0.295 - 0.3 : [ 1 0.00 0.00 ]
| 0.3 - 0.305 : [ 3 0.00 0.00 ]
| 0.305 - 0.31 : [ 2 0.00 0.00 ]
| 0.31 - 0.315 : [ 7 0.00 0.00 ]
| 0.315 - 0.32 : [ 6 0.00 0.00 ]
| 0.32 - 0.325 : [ 4 0.00 0.00 ]
| 0.325 - 0.33 : [ 4 0.00 0.00 ]
| 0.33 - 0.335 : [ 4 0.00 0.00 ]
| 0.335 - 0.34 : [ 3 0.00 0.00 ]
| 0.34 - 0.345 : [ 11 0.00 0.00 ]
| 0.345 - 0.35 : [ 7 0.00 0.00 ]
|X 0.35 - 0.355 : [ 21 0.00 0.00 ]
| 0.355 - 0.36 : [ 12 0.00 0.00 ]
| 0.36 - 0.365 : [ 13 0.00 0.00 ]
| 0.365 - 0.37 : [ 4 0.00 0.00 ]
| 0.37 - 0.375 : [ 9 0.00 0.00 ]
|X 0.375 - 0.38 : [ 21 0.00 0.01 ]
| 0.38 - 0.385 : [ 13 0.00 0.01 ]
| 0.385 - 0.39 : [ 14 0.00 0.01 ]
| 0.39 - 0.395 : [ 18 0.00 0.01 ]
|X 0.395 - 0.4 : [ 20 0.00 0.01 ]
|X 0.4 - 0.405 : [ 31 0.00 0.01 ]
|X 0.405 - 0.41 : [ 23 0.00 0.01 ]
|X 0.41 - 0.415 : [ 33 0.00 0.01 ]
|X 0.415 - 0.42 : [ 31 0.00 0.01 ]
|X 0.42 - 0.425 : [ 40 0.00 0.01 ]
|X 0.425 - 0.43 : [ 29 0.00 0.02 ]
|X 0.43 - 0.435 : [ 54 0.00 0.02 ]
|XX 0.435 - 0.44 : [ 77 0.00 0.02 ]
|XX 0.44 - 0.445 : [ 81 0.00 0.02 ]
|XXX 0.445 - 0.45 : [ 109 0.00 0.03 ]
|XXX 0.45 - 0.455 : [ 129 0.00 0.03 ]
|XXXXX 0.455 - 0.46 : [ 198 0.01 0.04 ]
|XXXXXX 0.46 - 0.465 : [ 217 0.01 0.05 ]
|XXXXXX 0.465 - 0.47 : [ 246 0.01 0.06 ]
|XXXXXXX 0.47 - 0.475 : [ 280 0.01 0.07 ]
|XXXXXXXXXX 0.475 - 0.48 : [ 385 0.01 0.08 ]
|XXXXXXXXXXXXX 0.48 - 0.485 : [ 495 0.02 0.10 ]
|XXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 621 0.02 0.13 ]
|XXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 661 0.03 0.15 ]
|XXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 678 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1013 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 998 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1171 0.05 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1365 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1427 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1531 0.06 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1552 0.06 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1572 0.06 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1565 0.06 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1392 0.05 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1380 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1183 0.05 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 917 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 841 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 739 0.03 0.90 ]
|XXXXXXXXXXXXXXX 0.575 - 0.58 : [ 571 0.02 0.92 ]
|XXXXXXXXXXXX 0.58 - 0.585 : [ 472 0.02 0.94 ]
|XXXXXXXXX 0.585 - 0.59 : [ 353 0.01 0.95 ]
|XXXXXXXX 0.59 - 0.595 : [ 311 0.01 0.97 ]
|XXXXX 0.595 - 0.6 : [ 196 0.01 0.97 ]
|XXXX 0.6 - 0.605 : [ 156 0.01 0.98 ]
|XXX 0.605 - 0.61 : [ 112 0.00 0.98 ]
|XX 0.61 - 0.615 : [ 75 0.00 0.99 ]
|XX 0.615 - 0.62 : [ 63 0.00 0.99 ]
|X 0.62 - 0.625 : [ 52 0.00 0.99 ]
|X 0.625 - 0.63 : [ 50 0.00 0.99 ]
|X 0.63 - 0.635 : [ 42 0.00 1.00 ]
|X 0.635 - 0.64 : [ 38 0.00 1.00 ]
| 0.64 - 0.645 : [ 13 0.00 1.00 ]
|X 0.645 - 0.65 : [ 23 0.00 1.00 ]
| 0.65 - 0.655 : [ 10 0.00 1.00 ]
| 0.655 - 0.66 : [ 6 0.00 1.00 ]
| 0.66 - 0.665 : [ 2 0.00 1.00 ]
| 0.665 - 0.67 : [ 7 0.00 1.00 ]
| 0.67 - 0.675 : [ 2 0.00 1.00 ]
| 0.675 - 0.68 : [ 3 0.00 1.00 ]
| 0.68 - 0.685 : [ 3 0.00 1.00 ]
| 0.685 - 0.69 : [ 4 0.00 1.00 ]
| 0.69 - 0.695 : [ 1 0.00 1.00 ]
| 0.695 - 0.7 : [ 2 0.00 1.00 ]
| 0.7 - 0.705 : [ 3 0.00 1.00 ]
| 0.705 - 0.71 : [ 1 0.00 1.00 ]
| 0.71 - 0.715 : [ 2 0.00 1.00 ]
#...
| 0.74 - 0.745 : [ 1 0.00 1.00 ]
#...
| 0.775 - 0.78 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 31. 16 reads; 1953 bp (untrimmed), 1950 (trimmed).
Contig 32. 31 reads; 8524 bp (untrimmed), 8100 (trimmed).
Contig 33. 38 reads; 6428 bp (untrimmed), 6303 (trimmed).
Contig 34. 41 reads; 7855 bp (untrimmed), 6973 (trimmed).
Contig 35. 48 reads; 1565 bp (untrimmed), 1486 (trimmed).
Contig 36. 56 reads; 8266 bp (untrimmed), 8225 (trimmed).
Contig 37. 115 reads; 13825 bp (untrimmed), 13758 (trimmed).
Contig 38. 170 reads; 21317 bp (untrimmed), 21286 (trimmed).
Contig 39. 211 reads; 19196 bp (untrimmed), 18138 (trimmed).
Contig 40. 215 reads; 26337 bp (untrimmed), 26267 (trimmed).
Contig 41. 283 reads; 16701 bp (untrimmed), 16640 (trimmed).
Contig 42. 352 reads; 33534 bp (untrimmed), 33497 (trimmed).
Contig 43. 384 reads; 30308 bp (untrimmed), 29603 (trimmed).
Contig 44. 392 reads; 31970 bp (untrimmed), 31888 (trimmed).
Contig 45. 473 reads; 36998 bp (untrimmed), 36978 (trimmed).
Contig 46. 736 reads; 62939 bp (untrimmed), 62834 (trimmed).
Contig 47. 867 reads; 67931 bp (untrimmed), 67717 (trimmed).
Contig 48. 935 reads; 85362 bp (untrimmed), 85334 (trimmed).
Contig 49. 1128 reads; 78559 bp (untrimmed), 78484 (trimmed).
Contig 50. 1199 reads; 103947 bp (untrimmed), 103839 (trimmed).
Contig 51. 1216 reads; 93860 bp (untrimmed), 93358 (trimmed).
Contig 52. 1329 reads; 84591 bp (untrimmed), 83884 (trimmed).
Contig 53. 1460 reads; 100143 bp (untrimmed), 99959 (trimmed).
Contig 54. 2506 reads; 172236 bp (untrimmed), 172236 (trimmed).
Contig 55. 2951 reads; 216408 bp (untrimmed), 216368 (trimmed).
Contig 56. 3426 reads; 261817 bp (untrimmed), 261788 (trimmed).
Contig 57. 5439 reads; 369427 bp (untrimmed), 369154 (trimmed).
--------------------------------------------------------------
Totals 26105 reads; 1980186 bp (untrimmed), 1971271 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 1974519 bases = 11.66 +- 4.54 = 0.24 +- 4.02
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 38 total values totalling 312.8800. <8.233684 +/- 5.096931>
#Range: [ 1.13 - 25.65 ]
#Most likely bin: [ 1 - 1.5 ] 3 counts
#Median bin: [ 9 - 9.5 ] 1 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 3 0.08 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 3 0.08 0.16 ]
|XXXXXXXXXXXXX 2 - 2.5 : [ 1 0.03 0.18 ]
|XXXXXXXXXXXXX 2.5 - 3 : [ 1 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 2 0.05 0.26 ]
#...
|XXXXXXXXXXXXX 4 - 4.5 : [ 1 0.03 0.29 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 3 0.08 0.37 ]
#...
|XXXXXXXXXXXXX 6 - 6.5 : [ 1 0.03 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 2 0.05 0.45 ]
|XXXXXXXXXXXXX 7 - 7.5 : [ 1 0.03 0.47 ]
#...
|XXXXXXXXXXXXX 9 - 9.5 : [ 1 0.03 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 3 0.08 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 2 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 2 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 2 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 2 0.05 0.79 ]
|XXXXXXXXXXXXX 12 - 12.5 : [ 1 0.03 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 3 0.08 0.89 ]
|XXXXXXXXXXXXX 13 - 13.5 : [ 1 0.03 0.92 ]
#...
|XXXXXXXXXXXXX 14 - 14.5 : [ 1 0.03 0.95 ]
|XXXXXXXXXXXXX 14.5 - 15 : [ 1 0.03 0.97 ]
#...
|XXXXXXXXXXXXX 25.5 - 26 : [ 1 0.03 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 26 total values totalling 253.9500. <9.767308 +/- 3.130619>
#Range: [ 3.27 - 14.95 ]
#Most likely bin: [ 12.5 - 13 ] 3 counts
#Median bin: [ 10 - 10.5 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXX 3 - 3.5 : [ 1 0.04 0.04 ]
#...
|XXXXXXXXXXXXX 4 - 4.5 : [ 1 0.04 0.08 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 3 0.12 0.19 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 2 0.08 0.27 ]
|XXXXXXXXXXXXX 7 - 7.5 : [ 1 0.04 0.31 ]
#...
|XXXXXXXXXXXXX 9 - 9.5 : [ 1 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 2 0.08 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 2 0.08 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 2 0.08 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 2 0.08 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 2 0.08 0.73 ]
|XXXXXXXXXXXXX 12 - 12.5 : [ 1 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 3 0.12 0.88 ]
|XXXXXXXXXXXXX 13 - 13.5 : [ 1 0.04 0.92 ]
#...
|XXXXXXXXXXXXX 14 - 14.5 : [ 1 0.04 0.96 ]
|XXXXXXXXXXXXX 14.5 - 15 : [ 1 0.04 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 24 3 reads 999 bases = 1.13 +- 0.48 = 1.13 +- 0.48
Contig 23 3 reads 1293 bases = 1.47 +- 0.50 = 0.71 +- 1.03
Contig 5 2 reads 1323 bases = 1.47 +- 0.50 = 0.02 +- 0.73
Contig 18 2 reads 575 bases = 1.65 +- 0.48 = -0.35 +- 0.48
Contig 21 2 reads 957 bases = 1.80 +- 0.40 = 0.20 +- 0.40
Contig 4 2 reads 1050 bases = 1.86 +- 0.35 = 1.86 +- 0.35
Contig 26 3 reads 976 bases = 2.17 +- 0.80 = 2.17 +- 0.80
Contig 27 4 reads 1217 bases = 2.61 +- 1.07 = 0.40 +- 0.63
Contig 28 6 reads 1260 bases = 3.24 +- 1.45 = 1.45 +- 0.64
Contig 32 31 reads 8524 bases = 3.27 +- 1.64 = 0.16 +- 2.37
Contig 34 41 reads 7855 bases = 4.46 +- 2.26 = 2.21 +- 3.60
Contig 33 38 reads 6428 bases = 5.28 +- 2.37 = 0.56 +- 1.93
Contig 30 15 reads 2237 bases = 5.46 +- 2.20 = 2.94 +- 3.28
Contig 36 56 reads 8266 bases = 5.49 +- 3.40 = 2.32 +- 3.25
Contig 31 16 reads 1953 bases = 6.06 +- 3.43 = 4.53 +- 2.72
Contig 38 170 reads 21317 bases = 6.74 +- 2.75 = 0.11 +- 4.29
Contig 40 215 reads 26337 bases = 6.99 +- 3.52 = 0.70 +- 3.89
Contig 37 115 reads 13825 bases = 7.22 +- 2.54 = 1.43 +- 3.31
Contig 42 352 reads 33534 bases = 9.27 +- 3.87 = 0.79 +- 4.51
Contig 48 935 reads 85362 bases = 9.50 +- 3.79 = 0.12 +- 4.17
Contig 42 352 reads 33534 bases = 9.27 +- 3.87 = 0.79 +- 4.51
Contig 48 935 reads 85362 bases = 9.50 +- 3.79 = 0.12 +- 4.17
Contig 39 211 reads 19196 bases = 9.55 +- 4.27 = 1.48 +- 3.72
Contig 29 10 reads 635 bases = 9.82 +- 0.72 = 0.11 +- 0.47
Contig 50 1199 reads 103947 bases = 10.27 +- 4.03 = 0.32 +- 3.75
Contig 46 736 reads 62939 bases = 10.38 +- 3.47 = 0.28 +- 3.51
Contig 44 392 reads 31970 bases = 10.88 +- 4.01 = 1.13 +- 3.70
Contig 43 384 reads 30308 bases = 10.96 +- 4.08 = 0.24 +- 4.11
Contig 47 867 reads 67931 bases = 11.07 +- 4.03 = 0.20 +- 3.85
Contig 45 473 reads 36998 bases = 11.34 +- 4.11 = 1.19 +- 3.28
Contig 56 3426 reads 261817 bases = 11.56 +- 4.35 = 0.07 +- 3.96
Contig 51 1216 reads 93860 bases = 11.64 +- 4.90 = 0.28 +- 4.41
Contig 55 2951 reads 216408 bases = 12.01 +- 4.09 = 0.02 +- 4.00
Contig 49 1128 reads 78559 bases = 12.84 +- 4.17 = 0.12 +- 3.96
Contig 54 2506 reads 172236 bases = 12.87 +- 3.95 = 0.17 +- 3.98
Contig 53 1460 reads 100143 bases = 12.91 +- 4.40 = 0.23 +- 4.23
Contig 57 5439 reads 369427 bases = 13.00 +- 4.16 = 0.04 +- 4.09
Contig 52 1329 reads 84591 bases = 14.04 +- 4.28 = 0.12 +- 4.33
Contig 41 283 reads 16701 bases = 14.95 +- 4.52 = 0.43 +- 4.74
Contig 35 48 reads 1565 bases = 25.65 +- 14.48 = 4.71 +- 3.24
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1239
HQ Discrepant reads = 55
Chimeric reads = 84
Suspect alignments = 218
-------------------------------------------------------------------
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/microbe4/3634473/edit_dir.12Oct04.QD