Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-12-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634496 4000 NULL Alkaliphilus metalliredigenes
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Alkaliphilus_metalliredigenes
-------------------------------------------------------------------
Alkaliphilus metalliredigenes, species, eubacteria
Clostridiales, order, eubacteria
Clostridia, class, eubacteria
Alkaliphilus, genus, eubacteria
Clostridiaceae, family, eubacteria
Firmicutes (Gram-positive bacteria), phylum, eubacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4635007
# phrap: 4389506
# db:
altered.
4000000
4341504 +/- 261453
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 11747
Number of reads with percent X's >= 20%: 162 = 0.3%
Number of reads with percent X's >= 50%: 90 = 0.2%
Number of reads with percent X's >= 80%: 7 = 0.0%
Total reads in project: 56873
Total bp X'd : 510116
reads >= 20% >= 50% >= 80% screened
Nr with L09136 9266 81 43 1
Nr with LRS 1 1 0 0
Nr with pCC1Fos 2358 9 3 0
Nr with pMCL200_JGI_XZX+XZK 122 71 44 6
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 69
Number of reads with percent X's >= 20%: 4 = 0.9%
Number of reads with percent X's >= 50%: 1 = 0.2%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 466
Total bp X'd : 3822
reads >= 20% >= 50% >= 80% screened
Nr with L09136 30 1 0 0
Nr with pCC1Fos 37 1 0 0
Nr with pMCL200_JGI_XZX+XZK 2 2 1 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 15984941
C = 9842056
G = 9690419
T = 15746038
N = 423986
X = 512067
GC fraction = 0.37
Total = 52199507
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634496_fasta.screen.contigs
-------------------------------------------------------------------
A 1478575
C 868484
G 860032
T 1485182
N 315
fraction GC = 0.37
total bases = 4692588
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 AIBO reads.list > grep.reads.list.AIBO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBO 4 500
-------------------------------------------------------------------
#Found 9982 total values totalling 33797548.0000. <3385.849329 +/- 618.368863>
#Range: [ 902 - 29930 ]
#Most likely bin: [ 3000 - 3500 ] 4142 counts
#Median bin: [ 3000 - 3500 ] 4142 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
| 1000 - 1500 : [ 16 0.00 0.00 ]
| 1500 - 2000 : [ 48 0.00 0.01 ]
|X 2000 - 2500 : [ 58 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2000 0.20 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4142 0.41 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2644 0.26 0.89 ]
|XXXXXXXXXX 4000 - 4500 : [ 1061 0.11 1.00 ]
| 4500 - 5000 : [ 8 0.00 1.00 ]
#...
| 23500 - 24000 : [ 1 0.00 1.00 ]
#...
| 29000 - 29500 : [ 1 0.00 1.00 ]
| 29500 - 30000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBP reads.list > grep.reads.list.AIBP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBP 4 500
-------------------------------------------------------------------
#Found 8890 total values totalling 59108442.0000. <6648.868616 +/- 1389.457241>
#Range: [ 195 - 33838 ]
#Most likely bin: [ 6500 - 7000 ] 2468 counts
#Median bin: [ 6500 - 7000 ] 2468 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
| 500 - 1000 : [ 6 0.00 0.00 ]
|X 1000 - 1500 : [ 67 0.01 0.01 ]
|XX 1500 - 2000 : [ 106 0.01 0.02 ]
|XX 2000 - 2500 : [ 124 0.01 0.03 ]
|XX 2500 - 3000 : [ 119 0.01 0.05 ]
|XX 3000 - 3500 : [ 93 0.01 0.06 ]
|X 3500 - 4000 : [ 77 0.01 0.07 ]
|X 4000 - 4500 : [ 78 0.01 0.08 ]
|X 4500 - 5000 : [ 85 0.01 0.09 ]
|XX 5000 - 5500 : [ 137 0.02 0.10 ]
|XXXX 5500 - 6000 : [ 218 0.02 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1419 0.16 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2468 0.28 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 2033 0.23 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1704 0.19 0.98 ]
|XX 8000 - 8500 : [ 151 0.02 1.00 ]
#...
| 11000 - 11500 : [ 1 0.00 1.00 ]
#...
| 27500 - 28000 : [ 1 0.00 1.00 ]
#...
| 32500 - 33000 : [ 1 0.00 1.00 ]
#...
| 33500 - 34000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBS reads.list > grep.reads.list.AIBS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIBS 4 500
-------------------------------------------------------------------
#Found 298 total values totalling 10537345.0000. <35360.218121 +/- 4821.790089>
#Range: [ 3643 - 45635 ]
#Most likely bin: [ 35000 - 35500 ] 23 counts
#Median bin: [ 35500 - 36000 ] 16 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 3500 - 4000 : [ 1 0.00 0.00 ]
#...
|XX 10000 - 10500 : [ 1 0.00 0.01 ]
#...
|XX 12500 - 13000 : [ 1 0.00 0.01 ]
#...
|XX 14000 - 14500 : [ 1 0.00 0.01 ]
|XX 14500 - 15000 : [ 1 0.00 0.02 ]
|XX 15000 - 15500 : [ 1 0.00 0.02 ]
#...
|XX 21000 - 21500 : [ 1 0.00 0.02 ]
#...
|XX 22000 - 22500 : [ 1 0.00 0.03 ]
#...
|XX 24000 - 24500 : [ 1 0.00 0.03 ]
#...
|XX 27000 - 27500 : [ 1 0.00 0.03 ]
#...
|XX 28500 - 29000 : [ 1 0.00 0.04 ]
|XXXXX 29000 - 29500 : [ 3 0.01 0.05 ]
|XXX 29500 - 30000 : [ 2 0.01 0.05 ]
|XX 30000 - 30500 : [ 1 0.00 0.06 ]
|XXXXXXXXX 30500 - 31000 : [ 5 0.02 0.07 ]
|XXXXXXX 31000 - 31500 : [ 4 0.01 0.09 ]
|XXXXXXXXX 31500 - 32000 : [ 5 0.02 0.10 ]
|XXXXXXXXXXXXXXXX 32000 - 32500 : [ 9 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 18 0.06 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 16 0.05 0.25 ]
|XXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 12 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 17 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 22 0.07 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 23 0.08 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 16 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 20 0.07 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 14 0.05 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 18 0.06 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 14 0.05 0.77 ]
|XXXXXXXXXXXXXXXXX 38000 - 38500 : [ 10 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 15 0.05 0.86 ]
|XXXXXXXXX 39000 - 39500 : [ 5 0.02 0.87 ]
|XXXXX 39500 - 40000 : [ 3 0.01 0.88 ]
|XXXXXXXXXXXX 40000 - 40500 : [ 7 0.02 0.91 ]
|XXXXXXX 40500 - 41000 : [ 4 0.01 0.92 ]
|XXXXXXXXXXXX 41000 - 41500 : [ 7 0.02 0.94 ]
|XXXXXXX 41500 - 42000 : [ 4 0.01 0.96 ]
|XXXXXXX 42000 - 42500 : [ 4 0.01 0.97 ]
|XXXXX 42500 - 43000 : [ 3 0.01 0.98 ]
|XX 43000 - 43500 : [ 1 0.00 0.98 ]
#...
|XXX 44000 - 44500 : [ 2 0.01 0.99 ]
|XX 44500 - 45000 : [ 1 0.00 0.99 ]
|XX 45000 - 45500 : [ 1 0.00 1.00 ]
|XX 45500 - 46000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep BAOA reads.list > grep.reads.list.BAOA
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BAOA 4 500
-------------------------------------------------------------------
#Found 400 total values totalling 14329948.0000. <35824.870000 +/- 4683.941407>
#Range: [ 2715 - 65024 ]
#Most likely bin: [ 34000 - 34500 ] 30 counts
#Median bin: [ 35500 - 36000 ] 22 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 2500 - 3000 : [ 1 0.00 0.00 ]
#...
|X 12000 - 12500 : [ 1 0.00 0.01 ]
#...
|X 13000 - 13500 : [ 1 0.00 0.01 ]
#...
|X 18500 - 19000 : [ 1 0.00 0.01 ]
#...
|X 21000 - 21500 : [ 1 0.00 0.01 ]
|X 21500 - 22000 : [ 1 0.00 0.01 ]
|X 22000 - 22500 : [ 1 0.00 0.02 ]
#...
|X 24500 - 25000 : [ 1 0.00 0.02 ]
#...
|X 27500 - 28000 : [ 1 0.00 0.02 ]
|X 28000 - 28500 : [ 1 0.00 0.03 ]
|XXX 28500 - 29000 : [ 2 0.01 0.03 ]
|XXX 29000 - 29500 : [ 2 0.01 0.04 ]
#...
|XXXX 30000 - 30500 : [ 3 0.01 0.04 ]
|XXXXXXXX 30500 - 31000 : [ 6 0.01 0.06 ]
|XXXXXXXXXXX 31000 - 31500 : [ 8 0.02 0.08 ]
|XXXXXXXXXXX 31500 - 32000 : [ 8 0.02 0.10 ]
|XXXXXXXXXXXXX 32000 - 32500 : [ 10 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 15 0.04 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 28 0.07 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 27 0.07 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 30 0.07 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 29 0.07 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 20 0.05 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 22 0.06 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 26 0.07 0.61 ]
|XXXXXXXXXXXXXXXXX 36500 - 37000 : [ 13 0.03 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 17 0.04 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 18 0.04 0.73 ]
|XXXXXXXXXXXXXXX 38000 - 38500 : [ 11 0.03 0.76 ]
|XXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 15 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 14 0.04 0.83 ]
|XXXXXXXXXXXXXXXX 39500 - 40000 : [ 12 0.03 0.86 ]
|XXXXXXXXXXX 40000 - 40500 : [ 8 0.02 0.89 ]
|XXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 14 0.04 0.92 ]
|XXXXX 41000 - 41500 : [ 4 0.01 0.93 ]
|XXXXXXXXXXX 41500 - 42000 : [ 8 0.02 0.95 ]
|XXXX 42000 - 42500 : [ 3 0.01 0.96 ]
|XXXX 42500 - 43000 : [ 3 0.01 0.96 ]
|XXXXXXX 43000 - 43500 : [ 5 0.01 0.98 ]
|XXX 43500 - 44000 : [ 2 0.01 0.98 ]
|X 44000 - 44500 : [ 1 0.00 0.98 ]
|XXXX 44500 - 45000 : [ 3 0.01 0.99 ]
|X 45000 - 45500 : [ 1 0.00 0.99 ]
#...
|X 60500 - 61000 : [ 1 0.00 1.00 ]
#...
|X 65000 - 65500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# BAOA 35752 +- 4024 (n=180)
# AIBS 35379 +- 4349 (n=148)
# AIBP 6592 +- 1477 (n=4414)
# AIBO 3229 +- 549 (n=5050)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634496_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
AIBO 34560 74 479 87 483 26694 96 492 100 519
AIBP 32352 71 752 92 675 22407 99 756 100 754
AIBS 5376 55 434 75 311 3477 85 441 100 458
BAOA 5376 74 542 85 463 4295 92 551 100 569
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIBO 13633 97 494 100 518 13061 96 489 100 520
AIBP 11176 99 755 100 753 11231 99 757 100 755
AIBS 1709 84 439 100 454 1768 85 442 100 463
BAOA 2107 91 547 100 560 2188 92 555 100 578
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634496_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
28 4295 2349 83.89 87.39 BAOA @
28 3477 2025 72.32 75.33 AIBS @
168 22407 11433 68.05 70.89 AIBP @
180 26694 15356 85.31 88.87 AIBO @
] 56873 31163 77.14 cumulative total@@
LIBRARY PLATE ID COUNT [ BAOA 28 AIBS 28 AIBP 168 AIBO 180 ] for 404 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 3634496_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 56873 total values totalling 33076042.0000. <581.577233 +/- 223.242628>
#Range: [ 0 - 935 ]
#Most likely bin: [ 750 - 800 ] 8087 counts
#Median bin: [ 600 - 650 ] 4585 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 0 - 50 : [ 593 0.01 0.01 ]
|XXXXXXX 50 - 100 : [ 1417 0.02 0.04 ]
|XXXXXXX 100 - 150 : [ 1507 0.03 0.06 ]
|XXXXXXXX 150 - 200 : [ 1610 0.03 0.09 ]
|XXXXXXXX 200 - 250 : [ 1591 0.03 0.12 ]
|XXXXXXXXX 250 - 300 : [ 1809 0.03 0.15 ]
|XXXXXXXXXX 300 - 350 : [ 1979 0.03 0.18 ]
|XXXXXXXXXX 350 - 400 : [ 2112 0.04 0.22 ]
|XXXXXXXXXXX 400 - 450 : [ 2180 0.04 0.26 ]
|XXXXXXXXXXXXX 450 - 500 : [ 2551 0.04 0.31 ]
|XXXXXXXXXXXXXXX 500 - 550 : [ 3085 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 3828 0.07 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 4585 0.08 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5331 0.09 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6058 0.11 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8087 0.14 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6912 0.12 0.97 ]
|XXXXXXXX 850 - 900 : [ 1589 0.03 1.00 ]
| 900 - 950 : [ 49 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBO 3634496_fasta.screen.trimQ15.SaF > reads.trim15.AIBO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBO.rl 2 50
-------------------------------------------------------------------
#Found 26694 total values totalling 12717472.0000. <476.416873 +/- 191.422040>
#Range: [ 0 - 841 ]
#Most likely bin: [ 600 - 650 ] 3213 counts
#Median bin: [ 500 - 550 ] 2370 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 50 : [ 147 0.01 0.01 ]
|XXXXXXXXXX 50 - 100 : [ 837 0.03 0.04 ]
|XXXXXXXXXXXXXX 100 - 150 : [ 1100 0.04 0.08 ]
|XXXXXXXXXXXXXX 150 - 200 : [ 1109 0.04 0.12 ]
|XXXXXXXXXXXXXX 200 - 250 : [ 1159 0.04 0.16 ]
|XXXXXXXXXXXXXXXX 250 - 300 : [ 1262 0.05 0.21 ]
|XXXXXXXXXXXXXXXXXX 300 - 350 : [ 1445 0.05 0.26 ]
|XXXXXXXXXXXXXXXXXXXXX 350 - 400 : [ 1677 0.06 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXX 400 - 450 : [ 1756 0.07 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 450 - 500 : [ 2047 0.08 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 2370 0.09 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 2846 0.11 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3213 0.12 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3187 0.12 0.90 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2027 0.08 0.98 ]
|XXXXXX 750 - 800 : [ 488 0.02 1.00 ]
| 800 - 850 : [ 24 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBP 3634496_fasta.screen.trimQ15.SaF > reads.trim15.AIBP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBP.rl 2 50
-------------------------------------------------------------------
#Found 22407 total values totalling 16842242.0000. <751.650913 +/- 125.244891>
#Range: [ 20 - 935 ]
#Most likely bin: [ 750 - 800 ] 7248 counts
#Median bin: [ 750 - 800 ] 7248 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 46 0.00 0.00 ]
|X 50 - 100 : [ 93 0.00 0.01 ]
| 100 - 150 : [ 79 0.00 0.01 ]
|X 150 - 200 : [ 139 0.01 0.02 ]
| 200 - 250 : [ 80 0.00 0.02 ]
|X 250 - 300 : [ 96 0.00 0.02 ]
|X 300 - 350 : [ 99 0.00 0.03 ]
|X 350 - 400 : [ 103 0.00 0.03 ]
|X 400 - 450 : [ 159 0.01 0.04 ]
|X 450 - 500 : [ 171 0.01 0.05 ]
|X 500 - 550 : [ 215 0.01 0.06 ]
|XX 550 - 600 : [ 328 0.01 0.07 ]
|XXX 600 - 650 : [ 579 0.03 0.10 ]
|XXXXXXX 650 - 700 : [ 1239 0.06 0.15 ]
|XXXXXXXXXXXXXXXXXX 700 - 750 : [ 3331 0.15 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 7248 0.32 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6778 0.30 0.93 ]
|XXXXXXXXX 850 - 900 : [ 1575 0.07 1.00 ]
| 900 - 950 : [ 49 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIBS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIBS 3634496_fasta.screen.trimQ15.SaF > reads.trim15.AIBS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIBS.rl 2 50
-------------------------------------------------------------------
#Found 3477 total values totalling 1325483.0000. <381.214553 +/- 222.293154>
#Range: [ 0 - 834 ]
#Most likely bin: [ 550 - 600 ] 328 counts
#Median bin: [ 350 - 400 ] 160 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 270 0.08 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 50 - 100 : [ 259 0.07 0.15 ]
|XXXXXXXXXXXXXXXXXXX 100 - 150 : [ 155 0.04 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 150 - 200 : [ 211 0.06 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 200 - 250 : [ 200 0.06 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 326 0.09 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 300 - 350 : [ 264 0.08 0.48 ]
|XXXXXXXXXXXXXXXXXXXX 350 - 400 : [ 160 0.05 0.53 ]
|XXXXXXXXXXXXXXX 400 - 450 : [ 123 0.04 0.57 ]
|XXXXXXXXXXXXXXXXXXXXX 450 - 500 : [ 175 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 261 0.08 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 328 0.09 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 281 0.08 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 258 0.07 0.94 ]
|XXXXXXXXXXXXXXXXXX 700 - 750 : [ 144 0.04 0.98 ]
|XXXXXX 750 - 800 : [ 50 0.01 1.00 ]
|X 800 - 850 : [ 12 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for BAOA
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep BAOA 3634496_fasta.screen.trimQ15.SaF > reads.trim15.BAOA.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.BAOA.rl 2 50
-------------------------------------------------------------------
#Found 4295 total values totalling 2190845.0000. <510.091967 +/- 230.457065>
#Range: [ 15 - 887 ]
#Most likely bin: [ 650 - 700 ] 647 counts
#Median bin: [ 550 - 600 ] 326 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXX 0 - 50 : [ 130 0.03 0.03 ]
|XXXXXXXXXXXXXX 50 - 100 : [ 228 0.05 0.08 ]
|XXXXXXXXXXX 100 - 150 : [ 173 0.04 0.12 ]
|XXXXXXXXX 150 - 200 : [ 151 0.04 0.16 ]
|XXXXXXXXX 200 - 250 : [ 152 0.04 0.19 ]
|XXXXXXXX 250 - 300 : [ 125 0.03 0.22 ]
|XXXXXXXXXXX 300 - 350 : [ 171 0.04 0.26 ]
|XXXXXXXXXXX 350 - 400 : [ 172 0.04 0.30 ]
|XXXXXXXXX 400 - 450 : [ 142 0.03 0.34 ]
|XXXXXXXXXX 450 - 500 : [ 158 0.04 0.37 ]
|XXXXXXXXXXXXXXX 500 - 550 : [ 239 0.06 0.43 ]
|XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 326 0.08 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 512 0.12 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 647 0.15 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 556 0.13 0.90 ]
|XXXXXXXXXXXXXXXXXXX 750 - 800 : [ 301 0.07 0.97 ]
|XXXXXX 800 - 850 : [ 98 0.02 1.00 ]
|X 850 - 900 : [ 14 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for BAOB
trimt JAZZ trim 15 readlength histogram for BAOC
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634496
-------------------------------------------------------------------
AIBO.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIBO.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIBP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIBP.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AIBP.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
AIBS.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
BAOA.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AIBO.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIBO.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIBP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIBP.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AIBP.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
AIBS.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
BAOA.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634496_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634496_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 56366 total values totalling 20662.6897. <0.366581 +/- 0.051926>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.36 - 0.365 ] 2556 counts
#Median bin: [ 0.36 - 0.365 ] 2556 counts
#Entropy = 5.3530 bits
| 0 - 0.005 : [ 1 1.77e-05 1.77e-05 1 ]
#...
| 0.06 - 0.065 : [ 1 1.77e-05 3.55e-05 2 ]
#...
| 0.085 - 0.09 : [ 2 3.55e-05 7.10e-05 4 ]
| 0.09 - 0.095 : [ 2 3.55e-05 1.06e-04 6 ]
#...
| 0.1 - 0.105 : [ 1 1.77e-05 1.24e-04 7 ]
| 0.105 - 0.11 : [ 1 1.77e-05 1.42e-04 8 ]
#...
| 0.115 - 0.12 : [ 3 5.32e-05 1.95e-04 11 ]
#...
| 0.125 - 0.13 : [ 1 1.77e-05 2.13e-04 12 ]
| 0.13 - 0.135 : [ 4 7.10e-05 2.84e-04 16 ]
| 0.135 - 0.14 : [ 3 5.32e-05 3.37e-04 19 ]
| 0.14 - 0.145 : [ 1 1.77e-05 3.55e-04 20 ]
| 0.145 - 0.15 : [ 4 7.10e-05 4.26e-04 24 ]
| 0.15 - 0.155 : [ 2 3.55e-05 4.61e-04 26 ]
| 0.155 - 0.16 : [ 1 1.77e-05 4.79e-04 27 ]
| 0.16 - 0.165 : [ 5 8.87e-05 5.68e-04 32 ]
| 0.165 - 0.17 : [ 4 7.10e-05 6.39e-04 36 ]
| 0.17 - 0.175 : [ 8 1.42e-04 7.81e-04 44 ]
| 0.175 - 0.18 : [ 7 1.24e-04 9.05e-04 51 ]
| 0.18 - 0.185 : [ 8 1.42e-04 1.05e-03 59 ]
| 0.185 - 0.19 : [ 11 1.95e-04 1.24e-03 70 ]
| 0.19 - 0.195 : [ 10 1.77e-04 1.42e-03 80 ]
| 0.195 - 0.2 : [ 10 1.77e-04 1.60e-03 90 ]
| 0.2 - 0.205 : [ 25 4.44e-04 2.04e-03 115 ]
| 0.205 - 0.21 : [ 16 2.84e-04 2.32e-03 131 ]
| 0.21 - 0.215 : [ 26 4.61e-04 2.79e-03 157 ]
| 0.215 - 0.22 : [ 29 5.14e-04 3.30e-03 186 ]
|X 0.22 - 0.225 : [ 35 6.21e-04 3.92e-03 221 ]
|X 0.225 - 0.23 : [ 38 6.74e-04 4.59e-03 259 ]
|X 0.23 - 0.235 : [ 42 7.45e-04 5.34e-03 301 ]
|X 0.235 - 0.24 : [ 53 9.40e-04 6.28e-03 354 ]
|X 0.24 - 0.245 : [ 83 1.47e-03 7.75e-03 437 ]
|X 0.245 - 0.25 : [ 76 1.35e-03 9.10e-03 513 ]
|XX 0.25 - 0.255 : [ 150 2.66e-03 1.18e-02 663 ]
|XX 0.255 - 0.26 : [ 153 2.71e-03 1.45e-02 816 ]
|XXX 0.26 - 0.265 : [ 178 3.16e-03 1.76e-02 994 ]
|XXX 0.265 - 0.27 : [ 214 3.80e-03 2.14e-02 1208 ]
|XXXXX 0.27 - 0.275 : [ 311 5.52e-03 2.69e-02 1519 ]
|XXXXXX 0.275 - 0.28 : [ 361 6.40e-03 3.34e-02 1880 ]
|XXXXXXXX 0.28 - 0.285 : [ 495 8.78e-03 4.21e-02 2375 ]
|XXXXXXXXX 0.285 - 0.29 : [ 594 1.05e-02 5.27e-02 2969 ]
|XXXXXXXXXXX 0.29 - 0.295 : [ 671 1.19e-02 6.46e-02 3640 ]
|XXXXXXXXXXXX 0.295 - 0.3 : [ 798 1.42e-02 7.87e-02 4438 ]
|XXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 1009 1.79e-02 9.66e-02 5447 ]
|XXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 1092 1.94e-02 1.16e-01 6539 ]
|XXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 1256 2.23e-02 1.38e-01 7795 ]
|XXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 1348 2.39e-02 1.62e-01 9143 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 1591 2.82e-02 1.90e-01 10734 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 1697 3.01e-02 2.21e-01 12431 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 1866 3.31e-02 2.54e-01 14297 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 1995 3.54e-02 2.89e-01 16292 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 2246 3.98e-02 3.29e-01 18538 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 2409 4.27e-02 3.72e-01 20947 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 2316 4.11e-02 4.13e-01 23263 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 2464 4.37e-02 4.56e-01 25727 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 2556 4.53e-02 5.02e-01 28283 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 2520 4.47e-02 5.46e-01 30803 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 2415 4.28e-02 5.89e-01 33218 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 2442 4.33e-02 6.33e-01 35660 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 2360 4.19e-02 6.75e-01 38020 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 2067 3.67e-02 7.11e-01 40087 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 2060 3.65e-02 7.48e-01 42147 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 1733 3.07e-02 7.78e-01 43880 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 1797 3.19e-02 8.10e-01 45677 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 1475 2.62e-02 8.37e-01 47152 ]
|XXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 1278 2.27e-02 8.59e-01 48430 ]
|XXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 1130 2.00e-02 8.79e-01 49560 ]
|XXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 1001 1.78e-02 8.97e-01 50561 ]
|XXXXXXXXXXXXXXX 0.425 - 0.43 : [ 934 1.66e-02 9.14e-01 51495 ]
|XXXXXXXXXXX 0.43 - 0.435 : [ 697 1.24e-02 9.26e-01 52192 ]
|XXXXXXXXX 0.435 - 0.44 : [ 555 9.85e-03 9.36e-01 52747 ]
|XXXXXXX 0.44 - 0.445 : [ 478 8.48e-03 9.44e-01 53225 ]
|XXXXXX 0.445 - 0.45 : [ 388 6.88e-03 9.51e-01 53613 ]
|XXXXXX 0.45 - 0.455 : [ 359 6.37e-03 9.58e-01 53972 ]
|XXXXX 0.455 - 0.46 : [ 299 5.30e-03 9.63e-01 54271 ]
|XXXX 0.46 - 0.465 : [ 233 4.13e-03 9.67e-01 54504 ]
|XX 0.465 - 0.47 : [ 142 2.52e-03 9.69e-01 54646 ]
|XX 0.47 - 0.475 : [ 131 2.32e-03 9.72e-01 54777 ]
|XX 0.475 - 0.48 : [ 108 1.92e-03 9.74e-01 54885 ]
|XX 0.48 - 0.485 : [ 110 1.95e-03 9.76e-01 54995 ]
|XX 0.485 - 0.49 : [ 98 1.74e-03 9.77e-01 55093 ]
|XX 0.49 - 0.495 : [ 127 2.25e-03 9.80e-01 55220 ]
|XX 0.495 - 0.5 : [ 120 2.13e-03 9.82e-01 55340 ]
|XX 0.5 - 0.505 : [ 156 2.77e-03 9.85e-01 55496 ]
|X 0.505 - 0.51 : [ 89 1.58e-03 9.86e-01 55585 ]
|X 0.51 - 0.515 : [ 64 1.14e-03 9.87e-01 55649 ]
|X 0.515 - 0.52 : [ 57 1.01e-03 9.88e-01 55706 ]
|X 0.52 - 0.525 : [ 64 1.14e-03 9.89e-01 55770 ]
|X 0.525 - 0.53 : [ 36 6.39e-04 9.90e-01 55806 ]
|X 0.53 - 0.535 : [ 50 8.87e-04 9.91e-01 55856 ]
|X 0.535 - 0.54 : [ 78 1.38e-03 9.92e-01 55934 ]
|X 0.54 - 0.545 : [ 66 1.17e-03 9.94e-01 56000 ]
|X 0.545 - 0.55 : [ 82 1.45e-03 9.95e-01 56082 ]
|X 0.55 - 0.555 : [ 70 1.24e-03 9.96e-01 56152 ]
|X 0.555 - 0.56 : [ 34 6.03e-04 9.97e-01 56186 ]
| 0.56 - 0.565 : [ 31 5.50e-04 9.97e-01 56217 ]
| 0.565 - 0.57 : [ 15 2.66e-04 9.98e-01 56232 ]
| 0.57 - 0.575 : [ 10 1.77e-04 9.98e-01 56242 ]
| 0.575 - 0.58 : [ 12 2.13e-04 9.98e-01 56254 ]
| 0.58 - 0.585 : [ 11 1.95e-04 9.98e-01 56265 ]
| 0.585 - 0.59 : [ 4 7.10e-05 9.98e-01 56269 ]
| 0.59 - 0.595 : [ 10 1.77e-04 9.98e-01 56279 ]
| 0.595 - 0.6 : [ 5 8.87e-05 9.99e-01 56284 ]
| 0.6 - 0.605 : [ 4 7.10e-05 9.99e-01 56288 ]
| 0.605 - 0.61 : [ 2 3.55e-05 9.99e-01 56290 ]
| 0.61 - 0.615 : [ 5 8.87e-05 9.99e-01 56295 ]
| 0.615 - 0.62 : [ 8 1.42e-04 9.99e-01 56303 ]
| 0.62 - 0.625 : [ 5 8.87e-05 9.99e-01 56308 ]
| 0.625 - 0.63 : [ 7 1.24e-04 9.99e-01 56315 ]
| 0.63 - 0.635 : [ 7 1.24e-04 9.99e-01 56322 ]
| 0.635 - 0.64 : [ 9 1.60e-04 9.99e-01 56331 ]
| 0.64 - 0.645 : [ 4 7.10e-05 9.99e-01 56335 ]
#...
| 0.65 - 0.655 : [ 2 3.55e-05 9.99e-01 56337 ]
| 0.655 - 0.66 : [ 3 5.32e-05 1.00e+00 56340 ]
| 0.66 - 0.665 : [ 1 1.77e-05 1.00e+00 56341 ]
| 0.665 - 0.67 : [ 3 5.32e-05 1.00e+00 56344 ]
| 0.67 - 0.675 : [ 4 7.10e-05 1.00e+00 56348 ]
| 0.675 - 0.68 : [ 4 7.10e-05 1.00e+00 56352 ]
#...
| 0.69 - 0.695 : [ 2 3.55e-05 1.00e+00 56354 ]
| 0.695 - 0.7 : [ 1 1.77e-05 1.00e+00 56355 ]
#...
| 0.72 - 0.725 : [ 1 1.77e-05 1.00e+00 56356 ]
| 0.725 - 0.73 : [ 1 1.77e-05 1.00e+00 56357 ]
#...
| 0.735 - 0.74 : [ 1 1.77e-05 1.00e+00 56358 ]
#...
| 0.75 - 0.755 : [ 1 1.77e-05 1.00e+00 56359 ]
#...
| 0.765 - 0.77 : [ 1 1.77e-05 1.00e+00 56360 ]
| 0.77 - 0.775 : [ 1 1.77e-05 1.00e+00 56361 ]
#...
| 0.78 - 0.785 : [ 1 1.77e-05 1.00e+00 56362 ]
#...
| 0.79 - 0.795 : [ 1 1.77e-05 1.00e+00 56363 ]
#...
| 0.8 - 0.805 : [ 1 1.77e-05 1.00e+00 56364 ]
#...
| 1 - 1.005 : [ 2 3.55e-05 1.00e+00 56366 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 308. 533 reads; 37651 bp (untrimmed), 37625 (trimmed).
Contig 309. 553 reads; 38995 bp (untrimmed), 38969 (trimmed).
Contig 310. 564 reads; 43420 bp (untrimmed), 43007 (trimmed).
Contig 311. 576 reads; 50997 bp (untrimmed), 50848 (trimmed).
Contig 312. 584 reads; 46819 bp (untrimmed), 46753 (trimmed).
Contig 313. 669 reads; 50421 bp (untrimmed), 50399 (trimmed).
Contig 314. 682 reads; 58949 bp (untrimmed), 58882 (trimmed).
Contig 315. 693 reads; 43753 bp (untrimmed), 43704 (trimmed).
Contig 316. 700 reads; 62266 bp (untrimmed), 62236 (trimmed).
Contig 317. 708 reads; 59661 bp (untrimmed), 59592 (trimmed).
Contig 318. 710 reads; 51544 bp (untrimmed), 51519 (trimmed).
Contig 319. 722 reads; 60226 bp (untrimmed), 59987 (trimmed).
Contig 320. 742 reads; 47481 bp (untrimmed), 47451 (trimmed).
Contig 321. 770 reads; 45153 bp (untrimmed), 45100 (trimmed).
Contig 322. 770 reads; 65887 bp (untrimmed), 65862 (trimmed).
Contig 323. 824 reads; 65927 bp (untrimmed), 65890 (trimmed).
Contig 324. 830 reads; 57977 bp (untrimmed), 57944 (trimmed).
Contig 325. 855 reads; 39242 bp (untrimmed), 39222 (trimmed).
Contig 326. 878 reads; 55875 bp (untrimmed), 55853 (trimmed).
Contig 327. 881 reads; 56021 bp (untrimmed), 55551 (trimmed).
Contig 328. 930 reads; 49901 bp (untrimmed), 49803 (trimmed).
Contig 329. 1199 reads; 75527 bp (untrimmed), 75294 (trimmed).
Contig 330. 1208 reads; 88670 bp (untrimmed), 88556 (trimmed).
Contig 331. 1426 reads; 98162 bp (untrimmed), 97829 (trimmed).
Contig 332. 1784 reads; 114655 bp (untrimmed), 114136 (trimmed).
Contig 333. 2046 reads; 95313 bp (untrimmed), 94701 (trimmed).
Contig 334. 3825 reads; 198703 bp (untrimmed), 198553 (trimmed).
--------------------------------------------------------------
Totals 56407 reads; 4692588 bp (untrimmed), 4635007 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4691320 bases = 9.89 +- 6.92 = 0.93 +- 4.48
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 332 total values totalling 2159.3900. <6.504187 +/- 3.829772>
#Range: [ 1.00 - 26.48 ]
#Most likely bin: [ 2 - 2.5 ] 32 counts
#Median bin: [ 5.5 - 6 ] 13 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 1 - 1.5 : [ 3 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 14 0.04 0.05 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 32 0.10 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 25 0.08 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 20 0.06 0.28 ]
|XXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 16 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 21 0.06 0.39 ]
|XXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 14 0.04 0.44 ]
|XXXXXXXXXXX 5 - 5.5 : [ 9 0.03 0.46 ]
|XXXXXXXXXXXXXXXX 5.5 - 6 : [ 13 0.04 0.50 ]
|XXXXXXXXXXXXXXX 6 - 6.5 : [ 12 0.04 0.54 ]
|XXXXXXXXXXXX 6.5 - 7 : [ 10 0.03 0.57 ]
|XXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 17 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 16 0.05 0.67 ]
|XXXXXXXXXXXX 8 - 8.5 : [ 10 0.03 0.70 ]
|XXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 14 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 16 0.05 0.79 ]
|XXXXXXXXXXXX 9.5 - 10 : [ 10 0.03 0.82 ]
|XXXXXXXXXXXXXXX 10 - 10.5 : [ 12 0.04 0.86 ]
|XXXXXXXXXX 10.5 - 11 : [ 8 0.02 0.88 ]
|XXXXXXXXX 11 - 11.5 : [ 7 0.02 0.90 ]
|XXXXXXXXX 11.5 - 12 : [ 7 0.02 0.92 ]
|XXXXX 12 - 12.5 : [ 4 0.01 0.93 ]
|XXXXXXXX 12.5 - 13 : [ 6 0.02 0.95 ]
|XXXXX 13 - 13.5 : [ 4 0.01 0.96 ]
|XX 13.5 - 14 : [ 2 0.01 0.97 ]
|XX 14 - 14.5 : [ 2 0.01 0.98 ]
|X 14.5 - 15 : [ 1 0.00 0.98 ]
|X 15 - 15.5 : [ 1 0.00 0.98 ]
|X 15.5 - 16 : [ 1 0.00 0.98 ]
#...
|XXXX 17.5 - 18 : [ 3 0.01 0.99 ]
#...
|X 19.5 - 20 : [ 1 0.00 1.00 ]
#...
|X 26 - 26.5 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Histogram of Major Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000
-------------------------------------------------------------------
#Found 235 total values totalling 1858.9200. <7.910298 +/- 3.563675>
#Range: [ 2.00 - 26.48 ]
#Most likely bin: [ 7 - 7.5 ] 16 counts
#Median bin: [ 7.5 - 8 ] 15 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXX 2 - 2.5 : [ 3 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 9 0.04 0.05 ]
|XXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 7 0.03 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 12 0.05 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 14 0.06 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 12 0.05 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 9 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 12 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 11 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 8 0.03 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 16 0.07 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 15 0.06 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 10 0.04 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 14 0.06 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 15 0.06 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 10 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 10 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 8 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 7 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.03 0.89 ]
|XXXXXXXXXX 12 - 12.5 : [ 4 0.02 0.91 ]
|XXXXXXXXXXXXXXX 12.5 - 13 : [ 6 0.03 0.93 ]
|XXXXXXXXXX 13 - 13.5 : [ 4 0.02 0.95 ]
|XXXXX 13.5 - 14 : [ 2 0.01 0.96 ]
|XXXXX 14 - 14.5 : [ 2 0.01 0.97 ]
|XX 14.5 - 15 : [ 1 0.00 0.97 ]
|XX 15 - 15.5 : [ 1 0.00 0.97 ]
|XX 15.5 - 16 : [ 1 0.00 0.98 ]
#...
|XXXXXXXX 17.5 - 18 : [ 3 0.01 0.99 ]
#...
|XX 19.5 - 20 : [ 1 0.00 1.00 ]
#...
|XX 26 - 26.5 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 2 2 reads 693 bases = 1.00 +- 0.04 = -1.00 +- 0.04
Contig 3 2 reads 1113 bases = 1.49 +- 0.50 = 1.49 +- 0.50
Contig 30 4 reads 2007 bases = 1.49 +- 0.61 = 1.49 +- 0.61
Contig 10 3 reads 1392 bases = 1.57 +- 0.60 = 0.59 +- 0.53
Contig 29 4 reads 2265 bases = 1.63 +- 0.48 = 0.04 +- 1.51
Contig 5 3 reads 1203 bases = 1.69 +- 0.64 = 0.29 +- 1.09
Contig 20 3 reads 1564 bases = 1.70 +- 0.65 = 0.73 +- 1.20
Contig 27 4 reads 2012 bases = 1.72 +- 0.85 = 1.72 +- 0.85
Contig 39 4 reads 1734 bases = 1.76 +- 0.67 = 1.76 +- 0.67
Contig 17 3 reads 1413 bases = 1.77 +- 0.53 = 1.11 +- 0.81
Contig 31 4 reads 1841 bases = 1.77 +- 0.85 = 1.77 +- 0.85
Contig 6 3 reads 1267 bases = 1.83 +- 0.72 = 0.31 +- 0.66
Contig 22 4 reads 1557 bases = 1.91 +- 0.87 = 0.66 +- 0.97
Contig 40 4 reads 1110 bases = 1.92 +- 0.74 = 1.92 +- 0.74
Contig 38 4 reads 1736 bases = 1.93 +- 0.93 = 0.91 +- 1.56
Contig 8 3 reads 1106 bases = 1.94 +- 0.75 = 0.56 +- 0.50
Contig 59 7 reads 2643 bases = 1.98 +- 1.07 = 1.98 +- 1.07
Contig 90 10 reads 4028 bases = 2.00 +- 1.01 = 0.42 +- 2.13
Contig 11 3 reads 1095 bases = 2.01 +- 0.69 = 2.01 +- 0.69
Contig 25 4 reads 1938 bases = 2.01 +- 0.57 = -0.02 +- 1.74
Contig 301 480 reads 31102 bases = 12.93 +- 4.68 = 0.11 +- 4.09
Contig 332 1784 reads 114655 bases = 12.93 +- 5.11 = 0.17 +- 4.61
Contig 326 878 reads 55875 bases = 12.96 +- 4.65 = 1.05 +- 4.55
Contig 320 742 reads 47481 bases = 12.98 +- 5.45 = 1.12 +- 4.35
Contig 327 881 reads 56021 bases = 13.07 +- 5.33 = 0.95 +- 5.00
Contig 262 239 reads 15332 bases = 13.15 +- 4.57 = 0.24 +- 2.85
Contig 329 1199 reads 75527 bases = 13.26 +- 4.79 = 0.35 +- 4.33
Contig 304 495 reads 30495 bases = 13.38 +- 3.80 = 0.12 +- 3.93
Contig 189 66 reads 4222 bases = 13.51 +- 6.99 = 4.47 +- 7.36
Contig 321 770 reads 45153 bases = 13.94 +- 4.53 = 1.02 +- 5.17
Contig 191 71 reads 4073 bases = 14.34 +- 6.00 = 5.82 +- 5.29
Contig 228 129 reads 7426 bases = 14.49 +- 5.82 = 2.08 +- 3.13
Contig 181 58 reads 3086 bases = 14.65 +- 8.96 = 2.97 +- 4.82
Contig 328 930 reads 49901 bases = 15.31 +- 5.63 = 0.46 +- 4.83
Contig 334 3825 reads 198703 bases = 15.96 +- 11.87 = 0.00 +- 6.69
Contig 333 2046 reads 95313 bases = 17.57 +- 18.25 = 0.32 +- 7.04
Contig 267 258 reads 11998 bases = 17.69 +- 28.36 = 0.97 +- 5.36
Contig 325 855 reads 39242 bases = 17.87 +- 22.72 = 1.57 +- 4.39
Contig 230 137 reads 5818 bases = 19.52 +- 14.23 = 1.66 +- 6.26
Contig 276 305 reads 9508 bases = 26.48 +- 29.49 = 1.59 +- 10.24
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 2890
HQ Discrepant reads = 164
Chimeric reads = 128
Suspect alignments = 349
-------------------------------------------------------------------
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
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confirm_score: 30
node_seg: 8
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forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/microbe2/3634496/edit_dir.11Oct05.QD