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
3634487 3000 NULL Nitrosospira multiformis
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Nitrosospira_multiformis
-------------------------------------------------------------------
Nitrosomonadaceae, family, b-proteobacteria
Nitrosospira, genus, b-proteobacteria
Nitrosomonadales, order, b-proteobacteria
Betaproteobacteria, class, b-proteobacteria
Nitrosospira multiformis, species, b-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3216472
# phrap: 2964641
# db:
altered.
3000000
3060371 +/- 111319
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 8737
Number of reads with percent X's >= 20%: 188 = 0.5%
Number of reads with percent X's >= 50%: 96 = 0.3%
Number of reads with percent X's >= 80%: 20 = 0.1%
Total reads in project: 37538
Total bp X'd : 396161
reads >= 20% >= 50% >= 80% screened
Nr with L09136 8062 122 62 17
Nr with pCC1Fos 568 1 0 0
Nr with pMCL200_JGI_XZX+XZK 107 65 34 3
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 6
Number of reads with percent X's >= 20%: 2 = 7.4%
Number of reads with percent X's >= 50%: 1 = 3.7%
Number of reads with percent X's >= 80%: 1 = 3.7%
Total reads in project: 27
Total bp X'd : 1324
reads >= 20% >= 50% >= 80% screened
Nr with pCC1Fos 5 1 0 0
Nr with pMCL200_JGI_XZX+XZK 1 1 1 1
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 8322574
C = 9635525
G = 9652042
T = 8241788
N = 137651
X = 396161
GC fraction = 0.53
Total = 36385741
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634487_fasta.screen.contigs
-------------------------------------------------------------------
A 745843
C 872231
G 863059
T 740726
N 17
fraction GC = 0.54
total bases = 3221876
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 AIAA reads.list > grep.reads.list.AIAA
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAA 4 500
-------------------------------------------------------------------
#Found 7984 total values totalling 27321617.0000. <3422.046217 +/- 1622.177181>
#Range: [ 849 - 121684 ]
#Most likely bin: [ 3000 - 3500 ] 4037 counts
#Median bin: [ 3000 - 3500 ] 4037 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 4 0.00 0.00 ]
| 1000 - 1500 : [ 45 0.01 0.01 ]
| 1500 - 2000 : [ 50 0.01 0.01 ]
|X 2000 - 2500 : [ 83 0.01 0.02 ]
|XXXXXX 2500 - 3000 : [ 565 0.07 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4037 0.51 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3005 0.38 0.98 ]
|XX 4000 - 4500 : [ 189 0.02 1.00 ]
#...
| 7000 - 7500 : [ 1 0.00 1.00 ]
| 7500 - 8000 : [ 1 0.00 1.00 ]
#...
| 20500 - 21000 : [ 1 0.00 1.00 ]
#...
| 52000 - 52500 : [ 1 0.00 1.00 ]
#...
| 59500 - 60000 : [ 1 0.00 1.00 ]
#...
| 121500 - 122000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAB reads.list > grep.reads.list.AIAB
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAB 4 500
-------------------------------------------------------------------
#Found 6196 total values totalling 39962524.0000. <6449.729503 +/- 5423.264106>
#Range: [ 869 - 282856 ]
#Most likely bin: [ 5500 - 6000 ] 1456 counts
#Median bin: [ 6000 - 6500 ] 1440 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
|X 1000 - 1500 : [ 27 0.00 0.00 ]
|X 1500 - 2000 : [ 31 0.01 0.01 ]
|X 2000 - 2500 : [ 39 0.01 0.02 ]
|X 2500 - 3000 : [ 33 0.01 0.02 ]
|X 3000 - 3500 : [ 35 0.01 0.03 ]
|XX 3500 - 4000 : [ 57 0.01 0.04 ]
|X 4000 - 4500 : [ 48 0.01 0.04 ]
|XXX 4500 - 5000 : [ 100 0.02 0.06 ]
|XXXXXXXXXX 5000 - 5500 : [ 369 0.06 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1456 0.23 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1440 0.23 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1214 0.20 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 801 0.13 0.91 ]
|XXXXXXXXXXXX 7500 - 8000 : [ 437 0.07 0.98 ]
|XX 8000 - 8500 : [ 82 0.01 1.00 ]
| 8500 - 9000 : [ 5 0.00 1.00 ]
| 9000 - 9500 : [ 2 0.00 1.00 ]
| 9500 - 10000 : [ 3 0.00 1.00 ]
#...
| 12000 - 12500 : [ 1 0.00 1.00 ]
#...
| 19500 - 20000 : [ 1 0.00 1.00 ]
#...
| 20500 - 21000 : [ 1 0.00 1.00 ]
#...
| 24000 - 24500 : [ 1 0.00 1.00 ]
#...
| 54000 - 54500 : [ 1 0.00 1.00 ]
| 54500 - 55000 : [ 1 0.00 1.00 ]
| 55000 - 55500 : [ 2 0.00 1.00 ]
| 55500 - 56000 : [ 1 0.00 1.00 ]
#...
| 56500 - 57000 : [ 1 0.00 1.00 ]
#...
| 82000 - 82500 : [ 1 0.00 1.00 ]
#...
| 85500 - 86000 : [ 1 0.00 1.00 ]
#...
| 110000 - 110500 : [ 1 0.00 1.00 ]
#...
| 253500 - 254000 : [ 1 0.00 1.00 ]
#...
| 282500 - 283000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAC reads.list > grep.reads.list.AIAC
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIAC 4 500
-------------------------------------------------------------------
#Found 579 total values totalling 21819053.0000. <37684.029361 +/- 5754.777596>
#Range: [ 8793 - 113820 ]
#Most likely bin: [ 36000 - 36500 ] 30 counts
#Median bin: [ 37000 - 37500 ] 30 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 8500 - 9000 : [ 1 0.00 0.00 ]
#...
|X 16500 - 17000 : [ 1 0.00 0.00 ]
#...
|X 18000 - 18500 : [ 1 0.00 0.01 ]
#...
|X 24000 - 24500 : [ 1 0.00 0.01 ]
|X 24500 - 25000 : [ 1 0.00 0.01 ]
#...
|X 26000 - 26500 : [ 1 0.00 0.01 ]
|XXX 26500 - 27000 : [ 2 0.00 0.01 ]
#...
|XXXX 28000 - 28500 : [ 3 0.01 0.02 ]
|X 28500 - 29000 : [ 1 0.00 0.02 ]
|XXXXX 29000 - 29500 : [ 4 0.01 0.03 ]
|XXX 29500 - 30000 : [ 2 0.00 0.03 ]
|XXXXXXXXX 30000 - 30500 : [ 7 0.01 0.04 ]
|XXXXXXXXX 30500 - 31000 : [ 7 0.01 0.06 ]
|XXXXXXXXX 31000 - 31500 : [ 7 0.01 0.07 ]
|XXXXXXXXXXXXXXXXX 31500 - 32000 : [ 13 0.02 0.09 ]
|XXXXXXXXXXXXXXXXX 32000 - 32500 : [ 13 0.02 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 19 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 17 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 27 0.05 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 23 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 23 0.04 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 26 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 23 0.04 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 30 0.05 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 18 0.03 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 30 0.05 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 20 0.03 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 25 0.04 0.60 ]
|XXXXXXXXXXXXXXXXX 38500 - 39000 : [ 13 0.02 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 22 0.04 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 22 0.04 0.70 ]
|XXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 14 0.02 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 18 0.03 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 19 0.03 0.78 ]
|XXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 16 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 16 0.03 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 22 0.04 0.88 ]
|XXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 14 0.02 0.90 ]
|XXXXXXXXXXXX 43500 - 44000 : [ 9 0.02 0.92 ]
|XXXXXXXXXXXXX 44000 - 44500 : [ 10 0.02 0.93 ]
|XXXXXXXXXXXXXXXXX 44500 - 45000 : [ 13 0.02 0.96 ]
|XXXXXXX 45000 - 45500 : [ 5 0.01 0.97 ]
|XXXXXXXXXXXXX 45500 - 46000 : [ 10 0.02 0.98 ]
|XXXX 46000 - 46500 : [ 3 0.01 0.99 ]
|XXXX 46500 - 47000 : [ 3 0.01 0.99 ]
|X 47000 - 47500 : [ 1 0.00 0.99 ]
|X 47500 - 48000 : [ 1 0.00 1.00 ]
#...
|X 71000 - 71500 : [ 1 0.00 1.00 ]
#...
|X 113500 - 114000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIAA 3309 +- 518 (n=3956)
# AIAB 6147 +- 1150 (n=3300)
# AIAC 37636 +- 4400 (n=295)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634487_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
AIAA 19200 -1 -1 97 777 19200 94 794 97 797
AIAB 22656 -1 -1 89 651 22091 76 645 82 651
AIAC 3072 -1 -1 80 435 3072 75 519 80 545
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIAA 9600 94 786 98 799 9600 94 803 97 795
AIAB 9817 72 646 79 644 12274 80 644 85 655
AIAC 1536 75 521 80 556 1536 74 518 80 534
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634487_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
96 18104 8725 90.89 94.67 AIAA @
92 17072 8006 87.02 90.65 AIAB @
16 2362 1290 80.62 83.98 AIAC @
] 37538 18021 88.34 cumulative total@@
LIBRARY PLATE ID COUNT [ AIAA 96 AIAB 92 AIAC 16 ] for 204 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 3634487_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 44363 total values totalling 26494380.0000. <597.217952 +/- 298.901018>
#Range: [ 0 - 934 ]
#Most likely bin: [ 800 - 850 ] 10380 counts
#Median bin: [ 700 - 750 ] 4035 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 6647 0.15 0.15 ]
|XX 50 - 100 : [ 471 0.01 0.16 ]
|X 100 - 150 : [ 380 0.01 0.17 ]
|X 150 - 200 : [ 382 0.01 0.18 ]
|XX 200 - 250 : [ 394 0.01 0.19 ]
|XXX 250 - 300 : [ 664 0.01 0.20 ]
|XX 300 - 350 : [ 570 0.01 0.21 ]
|XX 350 - 400 : [ 523 0.01 0.23 ]
|XX 400 - 450 : [ 549 0.01 0.24 ]
|XXX 450 - 500 : [ 783 0.02 0.26 ]
|XXXX 500 - 550 : [ 994 0.02 0.28 ]
|XXXXXX 550 - 600 : [ 1469 0.03 0.31 ]
|XXXXXXXX 600 - 650 : [ 2097 0.05 0.36 ]
|XXXXXXXXXX 650 - 700 : [ 2649 0.06 0.42 ]
|XXXXXXXXXXXXXXXX 700 - 750 : [ 4035 0.09 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8283 0.19 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 10380 0.23 0.93 ]
|XXXXXXXXXXXX 850 - 900 : [ 3010 0.07 1.00 ]
| 900 - 950 : [ 83 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ASKW
trimt JAZZ trim 15 readlength histogram for ASKY
trimt JAZZ trim 15 readlength histogram for ASKZ
trimt JAZZ trim 15 readlength histogram for ASNP
trimt JAZZ trim 15 readlength histogram for ASNS
trimt JAZZ trim 15 readlength histogram for ASNT
trimt JAZZ trim 15 readlength histogram for AIAA
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAA 3634487_fasta.screen.trimQ15.SaF > reads.trim15.AIAA.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAA.rl 2 50
-------------------------------------------------------------------
#Found 19200 total values totalling 14379890.0000. <748.952604 +/- 200.084098>
#Range: [ 0 - 934 ]
#Most likely bin: [ 800 - 850 ] 7870 counts
#Median bin: [ 800 - 850 ] 7870 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 0 - 50 : [ 1067 0.06 0.06 ]
| 50 - 100 : [ 37 0.00 0.06 ]
| 100 - 150 : [ 31 0.00 0.06 ]
| 150 - 200 : [ 32 0.00 0.06 ]
| 200 - 250 : [ 24 0.00 0.06 ]
| 250 - 300 : [ 37 0.00 0.06 ]
| 300 - 350 : [ 40 0.00 0.07 ]
| 350 - 400 : [ 48 0.00 0.07 ]
| 400 - 450 : [ 34 0.00 0.07 ]
| 450 - 500 : [ 49 0.00 0.07 ]
| 500 - 550 : [ 86 0.00 0.08 ]
|X 550 - 600 : [ 116 0.01 0.08 ]
|X 600 - 650 : [ 161 0.01 0.09 ]
|XX 650 - 700 : [ 346 0.02 0.11 ]
|XXXXXXX 700 - 750 : [ 1449 0.08 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5064 0.26 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 7870 0.41 0.86 ]
|XXXXXXXXXXXXX 850 - 900 : [ 2630 0.14 1.00 ]
| 900 - 950 : [ 79 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAB
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAB 3634487_fasta.screen.trimQ15.SaF > reads.trim15.AIAB.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAB.rl 2 50
-------------------------------------------------------------------
#Found 22091 total values totalling 10912604.0000. <493.984156 +/- 312.047014>
#Range: [ 0 - 926 ]
#Most likely bin: [ 0 - 50 ] 4904 counts
#Median bin: [ 600 - 650 ] 1712 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 4904 0.22 0.22 ]
|XXX 50 - 100 : [ 332 0.02 0.24 ]
|XX 100 - 150 : [ 285 0.01 0.25 ]
|XX 150 - 200 : [ 284 0.01 0.26 ]
|XX 200 - 250 : [ 297 0.01 0.28 ]
|XXX 250 - 300 : [ 354 0.02 0.29 ]
|XXX 300 - 350 : [ 353 0.02 0.31 ]
|XXX 350 - 400 : [ 369 0.02 0.32 ]
|XXX 400 - 450 : [ 427 0.02 0.34 ]
|XXXXX 450 - 500 : [ 625 0.03 0.37 ]
|XXXXXX 500 - 550 : [ 774 0.04 0.41 ]
|XXXXXXXXX 550 - 600 : [ 1160 0.05 0.46 ]
|XXXXXXXXXXXXXX 600 - 650 : [ 1712 0.08 0.54 ]
|XXXXXXXXXXXXXXXXX 650 - 700 : [ 2037 0.09 0.63 ]
|XXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2284 0.10 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3049 0.14 0.87 ]
|XXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2462 0.11 0.98 ]
|XXX 850 - 900 : [ 379 0.02 1.00 ]
| 900 - 950 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIAC
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIAC 3634487_fasta.screen.trimQ15.SaF > reads.trim15.AIAC.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIAC.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 1201886.0000. <391.238932 +/- 277.131816>
#Range: [ 0 - 856 ]
#Most likely bin: [ 0 - 50 ] 676 counts
#Median bin: [ 350 - 400 ] 106 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 676 0.22 0.22 ]
|XXXXXX 50 - 100 : [ 102 0.03 0.25 ]
|XXXX 100 - 150 : [ 64 0.02 0.27 ]
|XXXX 150 - 200 : [ 66 0.02 0.30 ]
|XXXX 200 - 250 : [ 73 0.02 0.32 ]
|XXXXXXXXXXXXXXXX 250 - 300 : [ 273 0.09 0.41 ]
|XXXXXXXXXX 300 - 350 : [ 177 0.06 0.47 ]
|XXXXXX 350 - 400 : [ 106 0.03 0.50 ]
|XXXXX 400 - 450 : [ 88 0.03 0.53 ]
|XXXXXX 450 - 500 : [ 109 0.04 0.56 ]
|XXXXXXXX 500 - 550 : [ 134 0.04 0.61 ]
|XXXXXXXXXXX 550 - 600 : [ 193 0.06 0.67 ]
|XXXXXXXXXXXXX 600 - 650 : [ 224 0.07 0.74 ]
|XXXXXXXXXXXXXXXX 650 - 700 : [ 266 0.09 0.83 ]
|XXXXXXXXXXXXXXXXXX 700 - 750 : [ 302 0.10 0.93 ]
|XXXXXXXXXX 750 - 800 : [ 170 0.06 0.98 ]
|XXX 800 - 850 : [ 48 0.02 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APYZ
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634487
-------------------------------------------------------------------
AIAA.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIAA.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIAB.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIAB.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AIAC.000001.000100 pCC1Fos.fa LRS.fasta
AIAA.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIAA.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIAB.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIAB.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AIAC.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634487_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634487_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 37443 total values totalling 20147.2256. <0.538077 +/- 0.041759>
#Range: [ 0.2273 - 0.8181 ]
#Most likely bin: [ 0.54 - 0.545 ] 2132 counts
#Median bin: [ 0.54 - 0.545 ] 2132 counts
| 0.225 - 0.23 : [ 1 0.00 0.00 ]
#...
| 0.26 - 0.265 : [ 1 0.00 0.00 ]
#...
| 0.29 - 0.295 : [ 1 0.00 0.00 ]
| 0.295 - 0.3 : [ 1 0.00 0.00 ]
| 0.3 - 0.305 : [ 2 0.00 0.00 ]
| 0.305 - 0.31 : [ 1 0.00 0.00 ]
| 0.31 - 0.315 : [ 1 0.00 0.00 ]
#...
| 0.32 - 0.325 : [ 2 0.00 0.00 ]
#...
| 0.33 - 0.335 : [ 5 0.00 0.00 ]
| 0.335 - 0.34 : [ 3 0.00 0.00 ]
| 0.34 - 0.345 : [ 6 0.00 0.00 ]
| 0.345 - 0.35 : [ 2 0.00 0.00 ]
| 0.35 - 0.355 : [ 4 0.00 0.00 ]
| 0.355 - 0.36 : [ 10 0.00 0.00 ]
| 0.36 - 0.365 : [ 9 0.00 0.00 ]
| 0.365 - 0.37 : [ 9 0.00 0.00 ]
| 0.37 - 0.375 : [ 8 0.00 0.00 ]
| 0.375 - 0.38 : [ 19 0.00 0.00 ]
| 0.38 - 0.385 : [ 14 0.00 0.00 ]
| 0.385 - 0.39 : [ 19 0.00 0.00 ]
| 0.39 - 0.395 : [ 25 0.00 0.00 ]
|X 0.395 - 0.4 : [ 33 0.00 0.00 ]
|X 0.4 - 0.405 : [ 40 0.00 0.01 ]
|X 0.405 - 0.41 : [ 57 0.00 0.01 ]
|X 0.41 - 0.415 : [ 66 0.00 0.01 ]
|X 0.415 - 0.42 : [ 63 0.00 0.01 ]
|X 0.42 - 0.425 : [ 72 0.00 0.01 ]
|XX 0.425 - 0.43 : [ 102 0.00 0.02 ]
|XX 0.43 - 0.435 : [ 131 0.00 0.02 ]
|XXX 0.435 - 0.44 : [ 138 0.00 0.02 ]
|XXXX 0.44 - 0.445 : [ 193 0.01 0.03 ]
|XXX 0.445 - 0.45 : [ 171 0.00 0.03 ]
|XXXX 0.45 - 0.455 : [ 205 0.01 0.04 ]
|XXXX 0.455 - 0.46 : [ 224 0.01 0.04 ]
|XXXXXX 0.46 - 0.465 : [ 301 0.01 0.05 ]
|XXXXXX 0.465 - 0.47 : [ 334 0.01 0.06 ]
|XXXXXXXX 0.47 - 0.475 : [ 423 0.01 0.07 ]
|XXXXXXXXX 0.475 - 0.48 : [ 496 0.01 0.09 ]
|XXXXXXXXXX 0.48 - 0.485 : [ 549 0.01 0.10 ]
|XXXXXXXXXXXX 0.485 - 0.49 : [ 637 0.02 0.12 ]
|XXXXXXXXXXXXX 0.49 - 0.495 : [ 707 0.02 0.14 ]
|XXXXXXXXXXXXXX 0.495 - 0.5 : [ 727 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1143 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1102 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1300 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1434 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1556 0.04 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1703 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1856 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1939 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 2132 0.06 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 2100 0.06 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 2123 0.06 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1994 0.05 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1862 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1727 0.05 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1489 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1288 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1043 0.03 0.90 ]
|XXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 853 0.02 0.92 ]
|XXXXXXXXXXXXXX 0.59 - 0.595 : [ 722 0.02 0.94 ]
|XXXXXXXXXX 0.595 - 0.6 : [ 524 0.01 0.95 ]
|XXXXXXXXX 0.6 - 0.605 : [ 455 0.01 0.97 ]
|XXXXXX 0.605 - 0.61 : [ 317 0.01 0.97 ]
|XXXX 0.61 - 0.615 : [ 220 0.01 0.98 ]
|XXX 0.615 - 0.62 : [ 176 0.00 0.98 ]
|XX 0.62 - 0.625 : [ 100 0.00 0.99 ]
|XX 0.625 - 0.63 : [ 91 0.00 0.99 ]
|X 0.63 - 0.635 : [ 77 0.00 0.99 ]
|X 0.635 - 0.64 : [ 68 0.00 0.99 ]
|X 0.64 - 0.645 : [ 49 0.00 0.99 ]
|X 0.645 - 0.65 : [ 53 0.00 1.00 ]
|X 0.65 - 0.655 : [ 27 0.00 1.00 ]
| 0.655 - 0.66 : [ 20 0.00 1.00 ]
|X 0.66 - 0.665 : [ 28 0.00 1.00 ]
| 0.665 - 0.67 : [ 21 0.00 1.00 ]
| 0.67 - 0.675 : [ 8 0.00 1.00 ]
| 0.675 - 0.68 : [ 8 0.00 1.00 ]
| 0.68 - 0.685 : [ 6 0.00 1.00 ]
| 0.685 - 0.69 : [ 2 0.00 1.00 ]
| 0.69 - 0.695 : [ 2 0.00 1.00 ]
| 0.695 - 0.7 : [ 3 0.00 1.00 ]
| 0.7 - 0.705 : [ 3 0.00 1.00 ]
#...
| 0.71 - 0.715 : [ 1 0.00 1.00 ]
#...
| 0.72 - 0.725 : [ 1 0.00 1.00 ]
| 0.725 - 0.73 : [ 1 0.00 1.00 ]
| 0.73 - 0.735 : [ 1 0.00 1.00 ]
| 0.735 - 0.74 : [ 1 0.00 1.00 ]
| 0.74 - 0.745 : [ 1 0.00 1.00 ]
#...
| 0.815 - 0.82 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 26. 241 reads; 21530 bp (untrimmed), 21457 (trimmed).
Contig 27. 245 reads; 21435 bp (untrimmed), 21292 (trimmed).
Contig 28. 246 reads; 20819 bp (untrimmed), 20794 (trimmed).
Contig 29. 272 reads; 33550 bp (untrimmed), 33420 (trimmed).
Contig 30. 426 reads; 38372 bp (untrimmed), 38362 (trimmed).
Contig 31. 443 reads; 46223 bp (untrimmed), 45994 (trimmed).
Contig 32. 480 reads; 47707 bp (untrimmed), 47674 (trimmed).
Contig 33. 623 reads; 55064 bp (untrimmed), 55045 (trimmed).
Contig 34. 661 reads; 58731 bp (untrimmed), 58555 (trimmed).
Contig 35. 670 reads; 60022 bp (untrimmed), 59993 (trimmed).
Contig 36. 754 reads; 54452 bp (untrimmed), 54221 (trimmed).
Contig 37. 948 reads; 81479 bp (untrimmed), 81356 (trimmed).
Contig 38. 953 reads; 89650 bp (untrimmed), 89379 (trimmed).
Contig 39. 1003 reads; 84916 bp (untrimmed), 84916 (trimmed).
Contig 40. 1030 reads; 83087 bp (untrimmed), 82992 (trimmed).
Contig 41. 1068 reads; 92985 bp (untrimmed), 92637 (trimmed).
Contig 42. 1094 reads; 87992 bp (untrimmed), 87757 (trimmed).
Contig 43. 1208 reads; 113603 bp (untrimmed), 113571 (trimmed).
Contig 44. 1283 reads; 105192 bp (untrimmed), 105160 (trimmed).
Contig 45. 1324 reads; 121378 bp (untrimmed), 121351 (trimmed).
Contig 46. 1410 reads; 110596 bp (untrimmed), 110439 (trimmed).
Contig 47. 1635 reads; 142646 bp (untrimmed), 142596 (trimmed).
Contig 48. 2024 reads; 162482 bp (untrimmed), 162271 (trimmed).
Contig 49. 2839 reads; 252086 bp (untrimmed), 252022 (trimmed).
Contig 50. 3070 reads; 263549 bp (untrimmed), 263501 (trimmed).
Contig 51. 3165 reads; 255897 bp (untrimmed), 255877 (trimmed).
Contig 52. 6714 reads; 586224 bp (untrimmed), 586186 (trimmed).
--------------------------------------------------------------
Totals 36785 reads; 3221876 bp (untrimmed), 3216472 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3220706 bases = 10.30 +- 3.89 = 0.19 +- 3.84
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 50 total values totalling 396.9600. <7.939200 +/- 3.060014>
#Range: [ 1.68 - 12.54 ]
#Most likely bin: [ 10 - 10.5 ] 9 counts
#Median bin: [ 9 - 9.5 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 1.5 - 2 : [ 2 0.04 0.04 ]
|XXXXXXXXX 2 - 2.5 : [ 2 0.04 0.08 ]
|XXXXXXXXXXXXX 2.5 - 3 : [ 3 0.06 0.14 ]
#...
|XXXX 3.5 - 4 : [ 1 0.02 0.16 ]
#...
|XXXXXXXXXXXXX 5 - 5.5 : [ 3 0.06 0.22 ]
|XXXXXXXXXXXXX 5.5 - 6 : [ 3 0.06 0.28 ]
|XXXX 6 - 6.5 : [ 1 0.02 0.30 ]
|XXXXXXXXXXXXX 6.5 - 7 : [ 3 0.06 0.36 ]
|XXXXXXXXXXXXX 7 - 7.5 : [ 3 0.06 0.42 ]
|XXXX 7.5 - 8 : [ 1 0.02 0.44 ]
#...
|XXXXXXXXX 8.5 - 9 : [ 2 0.04 0.48 ]
|XXXXXXXXX 9 - 9.5 : [ 2 0.04 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 5 0.10 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 9 0.18 0.80 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 3 0.06 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 6 0.12 0.98 ]
#...
|XXXX 12.5 - 13 : [ 1 0.02 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 39 total values totalling 359.8100. <9.225897 +/- 1.921816>
#Range: [ 5.13 - 12.54 ]
#Most likely bin: [ 10 - 10.5 ] 9 counts
#Median bin: [ 9.5 - 10 ] 5 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 5 - 5.5 : [ 2 0.05 0.05 ]
|XXXXXXXXX 5.5 - 6 : [ 2 0.05 0.10 ]
|XXXX 6 - 6.5 : [ 1 0.03 0.13 ]
|XXXXXXXXX 6.5 - 7 : [ 2 0.05 0.18 ]
|XXXXXXXXXXXXX 7 - 7.5 : [ 3 0.08 0.26 ]
|XXXX 7.5 - 8 : [ 1 0.03 0.28 ]
#...
|XXXXXXXXX 8.5 - 9 : [ 2 0.05 0.33 ]
|XXXXXXXXX 9 - 9.5 : [ 2 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 5 0.13 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 9 0.23 0.74 ]
|XXXXXXXXXXXXX 10.5 - 11 : [ 3 0.08 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 6 0.15 0.97 ]
#...
|XXXX 12.5 - 13 : [ 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 2 3 reads 1526 bases = 1.68 +- 0.72 = 1.68 +- 0.72
Contig 8 3 reads 1611 bases = 1.73 +- 0.67 = 1.73 +- 0.67
Contig 5 3 reads 881 bases = 2.03 +- 0.86 = 0.75 +- 0.43
Contig 4 3 reads 875 bases = 2.10 +- 0.34 = 1.87 +- 0.33
Contig 9 5 reads 1656 bases = 2.56 +- 1.29 = 1.37 +- 0.96
Contig 7 3 reads 914 bases = 2.77 +- 0.53 = 2.77 +- 0.53
Contig 6 3 reads 908 bases = 2.81 +- 0.50 = 2.81 +- 0.50
Contig 10 7 reads 1603 bases = 3.74 +- 1.86 = 3.74 +- 1.86
Contig 18 46 reads 8027 bases = 5.13 +- 1.57 = 2.59 +- 3.93
Contig 12 8 reads 1384 bases = 5.22 +- 2.60 = 5.22 +- 2.60
Contig 15 28 reads 4606 bases = 5.42 +- 2.99 = 0.25 +- 1.56
Contig 20 56 reads 8904 bases = 5.51 +- 2.53 = 1.06 +- 3.01
Contig 14 19 reads 2980 bases = 5.68 +- 3.29 = 2.62 +- 2.65
Contig 11 8 reads 1064 bases = 5.97 +- 2.32 = 5.97 +- 2.32
Contig 19 49 reads 7263 bases = 6.11 +- 2.87 = 2.33 +- 3.45
Contig 13 11 reads 1513 bases = 6.54 +- 3.23 = 6.54 +- 3.23
Contig 24 137 reads 18832 bases = 6.77 +- 2.77 = 0.09 +- 3.27
Contig 21 77 reads 10100 bases = 6.97 +- 3.97 = 0.05 +- 5.24
Contig 17 42 reads 5306 bases = 7.17 +- 2.76 = 3.33 +- 3.87
Contig 22 98 reads 12066 bases = 7.31 +- 3.60 = 1.03 +- 3.60
Contig 26 241 reads 21530 bases = 9.98 +- 3.96 = -0.00 +- 3.42
Contig 33 623 reads 55064 bases = 10.04 +- 3.79 = 0.22 +- 4.07
Contig 27 245 reads 21435 bases = 10.10 +- 3.69 = 0.78 +- 4.49
Contig 34 661 reads 58731 bases = 10.11 +- 3.74 = 0.37 +- 3.46
Contig 35 670 reads 60022 bases = 10.15 +- 2.96 = 0.16 +- 4.02
Contig 49 2839 reads 252086 bases = 10.18 +- 3.45 = 0.08 +- 3.74
Contig 52 6714 reads 586224 bases = 10.30 +- 3.72 = 0.03 +- 3.67
Contig 41 1068 reads 92985 bases = 10.36 +- 4.05 = 0.24 +- 4.23
Contig 47 1635 reads 142646 bases = 10.37 +- 3.74 = 0.06 +- 3.87
Contig 50 3070 reads 263549 bases = 10.47 +- 4.11 = 0.02 +- 3.66
Contig 37 948 reads 81479 bases = 10.54 +- 3.60 = -0.01 +- 3.45
Contig 28 246 reads 20819 bases = 10.68 +- 3.18 = 1.53 +- 4.35
Contig 39 1003 reads 84916 bases = 10.80 +- 3.79 = 0.38 +- 3.61
Contig 44 1283 reads 105192 bases = 11.03 +- 3.57 = 0.12 +- 4.13
Contig 40 1030 reads 83087 bases = 11.13 +- 3.45 = 0.43 +- 3.98
Contig 42 1094 reads 87992 bases = 11.15 +- 3.91 = -0.06 +- 3.61
Contig 51 3165 reads 255897 bases = 11.20 +- 3.73 = 0.11 +- 3.82
Contig 48 2024 reads 162482 bases = 11.26 +- 3.54 = 0.05 +- 4.16
Contig 46 1410 reads 110596 bases = 11.47 +- 5.11 = 0.16 +- 4.47
Contig 36 754 reads 54452 bases = 12.54 +- 4.12 = 0.39 +- 4.23
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 836
HQ Discrepant reads = 22
Chimeric reads = 26
Suspect alignments = 174
-------------------------------------------------------------------
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/finished2/microbe/3634487/edit_dir.06Jul04.QD