Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-13-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3436090 4500 266940 Kineococcus radiotolerans
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Kineococcus_radiotolerans
-------------------------------------------------------------------
Actinobacteria, phylum, actinobacteria
Kineococcus radiotolerans, species, high GC Gram+
Frankineae, suborder, high GC Gram+
Actinobacteridae, subclass, high GC Gram+
Kineosporiaceae, family, high GC Gram+
Kineococcus, genus, high GC Gram+
Actinomycetales, order, high GC Gram+
Actinobacteria (class) (high G+C Gram-positive bacteria), class, high GC Gram+
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4939013
# phrap: 4930673
# db:
altered.
4500000
4789895 +/- 205015
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 51757
Number of reads with percent X's >= 20%: 1407 = 1.6%
Number of reads with percent X's >= 50%: 497 = 0.6%
Number of reads with percent X's >= 80%: 52 = 0.1%
Total reads in project: 87353
Total bp X'd : 3624477
reads >= 20% >= 50% >= 80% screened
Nr with L09136 17562 556 192 19
Nr with pCC1Fos 3057 28 10 0
Nr with pMCL200_JGI_XZX+XZK 31138 823 295 33
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 239
Number of reads with percent X's >= 20%: 10 = 2.0%
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: 498
Total bp X'd : 17201
reads >= 20% >= 50% >= 80% screened
Nr with L09136 13 2 1 0
Nr with pCC1Fos 103 0 0 0
Nr with pMCL200_JGI_XZX+XZK 123 8 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 12948357
C = 30425355
G = 28891076
T = 14677887
N = 309327
X = 3624477
GC fraction = 0.65
Total = 90876479
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436090_fasta.screen.contigs
-------------------------------------------------------------------
A 663433
C 1882130
G 1839478
T 662630
N 165
fraction GC = 0.74
total bases = 5047836
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 ABFI reads.list > grep.reads.list.ABFI
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ABFI 4 500
-------------------------------------------------------------------
#Found 17195 total values totalling 57089592.0000. <3320.127479 +/- 3552.357660>
#Range: [ 364 - 167837 ]
#Most likely bin: [ 2500 - 3000 ] 4392 counts
#Median bin: [ 3000 - 3500 ] 4017 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
|X 500 - 1000 : [ 68 0.00 0.00 ]
|XXXX 1000 - 1500 : [ 462 0.03 0.03 ]
|XXXXXX 1500 - 2000 : [ 682 0.04 0.07 ]
|XXXXXXXXXXXXX 2000 - 2500 : [ 1388 0.08 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 4392 0.26 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4017 0.23 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3041 0.18 0.82 ]
|XXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1904 0.11 0.93 ]
|XXXXXXXXX 4500 - 5000 : [ 1031 0.06 0.99 ]
|XX 5000 - 5500 : [ 184 0.01 1.00 ]
| 5500 - 6000 : [ 8 0.00 1.00 ]
#...
| 17000 - 17500 : [ 1 0.00 1.00 ]
#...
| 44000 - 44500 : [ 1 0.00 1.00 ]
#...
| 51500 - 52000 : [ 1 0.00 1.00 ]
#...
| 57000 - 57500 : [ 1 0.00 1.00 ]
#...
| 59000 - 59500 : [ 3 0.00 1.00 ]
#...
| 60500 - 61000 : [ 2 0.00 1.00 ]
#...
| 106000 - 106500 : [ 1 0.00 1.00 ]
| 106500 - 107000 : [ 1 0.00 1.00 ]
#...
| 165000 - 165500 : [ 1 0.00 1.00 ]
#...
| 166500 - 167000 : [ 2 0.00 1.00 ]
| 167000 - 167500 : [ 1 0.00 1.00 ]
| 167500 - 168000 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ABFK reads.list > grep.reads.list.ABFK
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ABFK 4 500
-------------------------------------------------------------------
#Found 1768 total values totalling 11365136.0000. <6428.244344 +/- 4715.789521>
#Range: [ 1098 - 169448 ]
#Most likely bin: [ 7500 - 8000 ] 269 counts
#Median bin: [ 7000 - 7500 ] 199 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXX 1000 - 1500 : [ 56 0.03 0.03 ]
|XXXXXXXXXXXX 1500 - 2000 : [ 78 0.04 0.08 ]
|XXXXXXXXXX 2000 - 2500 : [ 65 0.04 0.11 ]
|XXXXXXXX 2500 - 3000 : [ 52 0.03 0.14 ]
|XXXXXXX 3000 - 3500 : [ 47 0.03 0.17 ]
|XXXXXX 3500 - 4000 : [ 43 0.02 0.19 ]
|XXXXXXXXXX 4000 - 4500 : [ 67 0.04 0.23 ]
|XXXXXXXX 4500 - 5000 : [ 56 0.03 0.26 ]
|XXXXXXXXX 5000 - 5500 : [ 62 0.04 0.30 ]
|XXXXXXXXXXXXXX 5500 - 6000 : [ 94 0.05 0.35 ]
|XXXXXXXXXXXXXXXX 6000 - 6500 : [ 110 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 138 0.08 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 199 0.11 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 269 0.15 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 211 0.12 0.88 ]
|XXXXXXXXXXXXXXXX 8500 - 9000 : [ 109 0.06 0.94 ]
|XXXXXXXXX 9000 - 9500 : [ 61 0.03 0.97 ]
|XXXX 9500 - 10000 : [ 28 0.02 0.99 ]
|XX 10000 - 10500 : [ 15 0.01 1.00 ]
|X 10500 - 11000 : [ 5 0.00 1.00 ]
| 11000 - 11500 : [ 1 0.00 1.00 ]
#...
| 64000 - 64500 : [ 1 0.00 1.00 ]
#...
| 169000 - 169500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AGPU reads.list > grep.reads.list.AGPU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AGPU 4 500
-------------------------------------------------------------------
#Found 9820 total values totalling 57453957.0000. <5850.708452 +/- 2466.335020>
#Range: [ 261 - 170204 ]
#Most likely bin: [ 6000 - 6500 ] 3291 counts
#Median bin: [ 6000 - 6500 ] 3291 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
#...
|X 1000 - 1500 : [ 59 0.01 0.01 ]
|X 1500 - 2000 : [ 111 0.01 0.02 ]
|XX 2000 - 2500 : [ 126 0.01 0.03 ]
|X 2500 - 3000 : [ 120 0.01 0.04 ]
|XX 3000 - 3500 : [ 126 0.01 0.06 ]
|XX 3500 - 4000 : [ 128 0.01 0.07 ]
|XXX 4000 - 4500 : [ 214 0.02 0.09 ]
|XXXX 4500 - 5000 : [ 303 0.03 0.12 ]
|XXXXXXXXXXX 5000 - 5500 : [ 866 0.09 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 2622 0.27 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 3291 0.34 0.81 ]
|XXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1539 0.16 0.97 ]
|XXXX 7000 - 7500 : [ 301 0.03 1.00 ]
| 7500 - 8000 : [ 5 0.00 1.00 ]
| 8000 - 8500 : [ 1 0.00 1.00 ]
| 8500 - 9000 : [ 1 0.00 1.00 ]
#...
| 44500 - 45000 : [ 1 0.00 1.00 ]
#...
| 62000 - 62500 : [ 1 0.00 1.00 ]
| 62500 - 63000 : [ 1 0.00 1.00 ]
| 63000 - 63500 : [ 1 0.00 1.00 ]
#...
| 109000 - 109500 : [ 1 0.00 1.00 ]
#...
| 170000 - 170500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ABFN reads.list > grep.reads.list.ABFN
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ABFN 4 500
-------------------------------------------------------------------
#Found 1540 total values totalling 54720267.0000. <35532.640909 +/- 5416.723585>
#Range: [ 1464 - 196092 ]
#Most likely bin: [ 35500 - 36000 ] 130 counts
#Median bin: [ 35500 - 36000 ] 130 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 1 0.00 0.00 ]
|X 1500 - 2000 : [ 2 0.00 0.00 ]
#...
| 13500 - 14000 : [ 1 0.00 0.00 ]
#...
| 18000 - 18500 : [ 1 0.00 0.00 ]
| 18500 - 19000 : [ 1 0.00 0.00 ]
#...
| 19500 - 20000 : [ 1 0.00 0.00 ]
#...
| 23000 - 23500 : [ 1 0.00 0.01 ]
#...
| 24000 - 24500 : [ 1 0.00 0.01 ]
| 24500 - 25000 : [ 1 0.00 0.01 ]
|X 25000 - 25500 : [ 2 0.00 0.01 ]
|X 25500 - 26000 : [ 2 0.00 0.01 ]
|XX 26000 - 26500 : [ 6 0.00 0.01 ]
|X 26500 - 27000 : [ 3 0.00 0.01 ]
|XX 27000 - 27500 : [ 6 0.00 0.02 ]
|XX 27500 - 28000 : [ 7 0.00 0.02 ]
|X 28000 - 28500 : [ 2 0.00 0.02 ]
|XXX 28500 - 29000 : [ 11 0.01 0.03 ]
|XXXX 29000 - 29500 : [ 13 0.01 0.04 ]
|XX 29500 - 30000 : [ 8 0.01 0.05 ]
|XXXXX 30000 - 30500 : [ 16 0.01 0.06 ]
|XXXXXXX 30500 - 31000 : [ 23 0.01 0.07 ]
|XXXXXXXX 31000 - 31500 : [ 27 0.02 0.09 ]
|XXXXXXXXXXXX 31500 - 32000 : [ 38 0.02 0.11 ]
|XXXXXXXXXXXXXX 32000 - 32500 : [ 46 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 64 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 73 0.05 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 87 0.06 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 94 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 93 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 115 0.07 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 130 0.08 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 114 0.07 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 91 0.06 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 83 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 66 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 64 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 60 0.04 0.88 ]
|XXXXXXXXXXXX 39000 - 39500 : [ 38 0.02 0.90 ]
|XXXXXXXXXXX 39500 - 40000 : [ 37 0.02 0.93 ]
|XXXXXXX 40000 - 40500 : [ 23 0.01 0.94 ]
|XXXXXXX 40500 - 41000 : [ 24 0.02 0.96 ]
|XXXXXXX 41000 - 41500 : [ 23 0.01 0.97 ]
|XXXX 41500 - 42000 : [ 14 0.01 0.98 ]
|XXX 42000 - 42500 : [ 9 0.01 0.99 ]
|XX 42500 - 43000 : [ 5 0.00 0.99 ]
|X 43000 - 43500 : [ 2 0.00 0.99 ]
|XX 43500 - 44000 : [ 7 0.00 1.00 ]
| 44000 - 44500 : [ 1 0.00 1.00 ]
| 44500 - 45000 : [ 1 0.00 1.00 ]
| 45000 - 45500 : [ 1 0.00 1.00 ]
#...
| 196000 - 196500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# ABFK 5646 +- 2716 (n=979)
# ABFN 35302 +- 3773 (n=764)
# AGPU 5556 +- 1327 (n=4988)
# ABFI 3063 +- 1025 (n=8958)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436090_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
ABFI 51456 -1 -1 94 569 44191 98 557 100 570
ABFK 7584 -1 -1 94 541 5685 98 527 100 585
ABFN 16512 69 522 81 439 9610 96 571 100 574
AGPU 52992 -1 -1 91 543 27867 97 557 100 605
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
ABFI 21396 97 534 100 552 22795 99 578 100 588
ABFK 2699 98 507 100 573 2986 98 544 100 595
ABFN 4887 96 574 100 576 4723 96 568 100 573
AGPU 13299 98 537 100 593 14568 97 576 100 616
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436090_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 87353 48589 75.45 cumulative total @@
Only indicates plates present in input file.
Make no assumption regarding plates (not) present in project that do not appear above.
-------------------------------------------------------------------
trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3436090_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 87353 total values totalling 47524651.0000. <544.052877 +/- 199.033576>
#Range: [ 16 - 986 ]
#Most likely bin: [ 650 - 700 ] 13038 counts
#Median bin: [ 600 - 650 ] 10240 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 344 0.00 0.00 ]
|XXXXXX 50 - 100 : [ 1916 0.02 0.03 ]
|XXXXXXXX 100 - 150 : [ 2546 0.03 0.06 ]
|XXXXXXXXX 150 - 200 : [ 2806 0.03 0.09 ]
|XXXXXXXXX 200 - 250 : [ 3035 0.03 0.12 ]
|XXXXXXXXXX 250 - 300 : [ 3102 0.04 0.16 ]
|XXXXXXXXXX 300 - 350 : [ 3266 0.04 0.19 ]
|XXXXXXXXXXX 350 - 400 : [ 3522 0.04 0.24 ]
|XXXXXXXXXXXX 400 - 450 : [ 4028 0.05 0.28 ]
|XXXXXXXXXXXXXX 450 - 500 : [ 4613 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXX 500 - 550 : [ 5913 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 7531 0.09 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 10240 0.12 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 13038 0.15 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 12386 0.14 0.90 ]
|XXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6699 0.08 0.97 ]
|XXXXXX 800 - 850 : [ 2014 0.02 1.00 ]
|X 850 - 900 : [ 306 0.00 1.00 ]
| 900 - 950 : [ 37 0.00 1.00 ]
| 950 - 1000 : [ 11 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ABFI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ABFI 3436090_fasta.screen.trimQ15.SaF > reads.trim15.ABFI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ABFI.rl 2 50
-------------------------------------------------------------------
#Found 44191 total values totalling 24107884.0000. <545.538322 +/- 197.660367>
#Range: [ 16 - 986 ]
#Most likely bin: [ 650 - 700 ] 5993 counts
#Median bin: [ 550 - 600 ] 4115 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 136 0.00 0.00 ]
|XXXXXX 50 - 100 : [ 905 0.02 0.02 ]
|XXXXXXXX 100 - 150 : [ 1234 0.03 0.05 ]
|XXXXXXXXX 150 - 200 : [ 1420 0.03 0.08 ]
|XXXXXXXXXX 200 - 250 : [ 1457 0.03 0.12 ]
|XXXXXXXXXX 250 - 300 : [ 1499 0.03 0.15 ]
|XXXXXXXXXXX 300 - 350 : [ 1653 0.04 0.19 ]
|XXXXXXXXXXXXX 350 - 400 : [ 1878 0.04 0.23 ]
|XXXXXXXXXXXXXX 400 - 450 : [ 2081 0.05 0.28 ]
|XXXXXXXXXXXXXXXXX 450 - 500 : [ 2532 0.06 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 3225 0.07 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 4115 0.09 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 5262 0.12 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5993 0.14 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5662 0.13 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3424 0.08 0.96 ]
|XXXXXXXXX 800 - 850 : [ 1398 0.03 0.99 ]
|XX 850 - 900 : [ 270 0.01 1.00 ]
| 900 - 950 : [ 36 0.00 1.00 ]
| 950 - 1000 : [ 11 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ABFK
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ABFK 3436090_fasta.screen.trimQ15.SaF > reads.trim15.ABFK.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ABFK.rl 2 50
-------------------------------------------------------------------
#Found 5685 total values totalling 2943120.0000. <517.699208 +/- 189.535922>
#Range: [ 33 - 799 ]
#Most likely bin: [ 650 - 700 ] 1080 counts
#Median bin: [ 550 - 600 ] 528 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 16 0.00 0.00 ]
|XXX 50 - 100 : [ 94 0.02 0.02 ]
|XXXXXXX 100 - 150 : [ 198 0.03 0.05 ]
|XXXXXXXX 150 - 200 : [ 217 0.04 0.09 ]
|XXXXXXXX 200 - 250 : [ 221 0.04 0.13 ]
|XXXXXXXXXX 250 - 300 : [ 258 0.05 0.18 ]
|XXXXXXXXX 300 - 350 : [ 246 0.04 0.22 ]
|XXXXXXXXXX 350 - 400 : [ 267 0.05 0.27 ]
|XXXXXXXXXXXX 400 - 450 : [ 311 0.05 0.32 ]
|XXXXXXXXXXX 450 - 500 : [ 307 0.05 0.38 ]
|XXXXXXXXXXXXXX 500 - 550 : [ 382 0.07 0.44 ]
|XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 528 0.09 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 745 0.13 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1080 0.19 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 688 0.12 0.98 ]
|XXXXX 750 - 800 : [ 127 0.02 1.00 ]
trimt JAZZ trim 15 readlength histogram for AGPU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AGPU 3436090_fasta.screen.trimQ15.SaF > reads.trim15.AGPU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AGPU.rl 2 50
-------------------------------------------------------------------
#Found 27867 total values totalling 15182254.0000. <544.811210 +/- 196.185820>
#Range: [ 16 - 873 ]
#Most likely bin: [ 650 - 700 ] 4661 counts
#Median bin: [ 600 - 650 ] 3371 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 109 0.00 0.00 ]
|XXXXX 50 - 100 : [ 608 0.02 0.03 ]
|XXXXXXX 100 - 150 : [ 838 0.03 0.06 ]
|XXXXXXXX 150 - 200 : [ 889 0.03 0.09 ]
|XXXXXXXXX 200 - 250 : [ 1031 0.04 0.12 ]
|XXXXXXXX 250 - 300 : [ 887 0.03 0.16 ]
|XXXXXXXXX 300 - 350 : [ 1020 0.04 0.19 ]
|XXXXXXXX 350 - 400 : [ 962 0.03 0.23 ]
|XXXXXXXXXXX 400 - 450 : [ 1252 0.04 0.27 ]
|XXXXXXXXXXXX 450 - 500 : [ 1407 0.05 0.32 ]
|XXXXXXXXXXXXXXXX 500 - 550 : [ 1840 0.07 0.39 ]
|XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 2272 0.08 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3371 0.12 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4661 0.17 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4545 0.16 0.92 ]
|XXXXXXXXXXXXXXXXX 750 - 800 : [ 1943 0.07 0.99 ]
|XX 800 - 850 : [ 220 0.01 1.00 ]
| 850 - 900 : [ 12 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ABFN
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ABFN 3436090_fasta.screen.trimQ15.SaF > reads.trim15.ABFN.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ABFN.rl 2 50
-------------------------------------------------------------------
#Found 9610 total values totalling 5291393.0000. <550.613215 +/- 217.026499>
#Range: [ 21 - 907 ]
#Most likely bin: [ 700 - 750 ] 1491 counts
#Median bin: [ 600 - 650 ] 862 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 50 : [ 83 0.01 0.01 ]
|XXXXXXXX 50 - 100 : [ 309 0.03 0.04 ]
|XXXXXXX 100 - 150 : [ 276 0.03 0.07 ]
|XXXXXXXX 150 - 200 : [ 280 0.03 0.10 ]
|XXXXXXXXX 200 - 250 : [ 326 0.03 0.13 ]
|XXXXXXXXXXXX 250 - 300 : [ 458 0.05 0.18 ]
|XXXXXXXXX 300 - 350 : [ 347 0.04 0.22 ]
|XXXXXXXXXXX 350 - 400 : [ 415 0.04 0.26 ]
|XXXXXXXXXX 400 - 450 : [ 384 0.04 0.30 ]
|XXXXXXXXXX 450 - 500 : [ 367 0.04 0.34 ]
|XXXXXXXXXXXXX 500 - 550 : [ 466 0.05 0.39 ]
|XXXXXXXXXXXXXXXXX 550 - 600 : [ 616 0.06 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 862 0.09 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1304 0.14 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1491 0.16 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1205 0.13 0.96 ]
|XXXXXXXXXXX 800 - 850 : [ 396 0.04 1.00 ]
|X 850 - 900 : [ 24 0.00 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AUOC
trimt JAZZ trim 15 readlength histogram for AUOF
trimt JAZZ trim 15 readlength histogram for AUOG
trimt JAZZ trim 15 readlength histogram for AZPT
trimt JAZZ trim 15 readlength histogram for AZPU
trimt JAZZ trim 15 readlength histogram for AZPW
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436090
-------------------------------------------------------------------
ABFI.000001.000100 pUC.fasta pUC.fasta LRS.fasta
ABFI.000101.000200 pUC.fasta LRS.fasta
ABFI.000201.000300 pUC18.fa.4 LRS.fasta
ABFI.000301.000400 pUC18.fa.4 LRS.fasta
ABFK.000001.000100 pMCL200.fa.4 LRS.fasta
ABFN.000001.000100 pCC1Fos.fa LRS.fasta
AGPU.000001.000100 pMCL200.fa.4 LRS.fasta
AGPU.000101.000200 pMCL200.fa.4 LRS.fasta
AGPU.000201.000300 pMCL200.fa.4 LRS.fasta
AGPU.000301.000400 pMCL200.fa.4 LRS.fasta
ABFI.000001.000100 pUC.fasta pUC.fasta LRS.fasta
ABFI.000101.000200 pUC.fasta LRS.fasta
ABFI.000201.000300 pUC18.fa.4 LRS.fasta
ABFI.000301.000400 pUC18.fa.4 LRS.fasta
ABFK.000001.000100 pMCL200.fa.4 LRS.fasta
ABFN.000001.000100 pCC1Fos.fa LRS.fasta
AGPU.000001.000100 pMCL200.fa.4 LRS.fasta
AGPU.000101.000200 pMCL200.fa.4 LRS.fasta
AGPU.000201.000300 pMCL200.fa.4 LRS.fasta
AGPU.000301.000400 pMCL200.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436090_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436090_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 86903 total values totalling 63364.8275. <0.729144 +/- 0.047830>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.75 - 0.755 ] 3999 counts
#Median bin: [ 0.73 - 0.735 ] 3726 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.205 - 0.21 : [ 1 0.00 0.00 ]
#...
| 0.215 - 0.22 : [ 1 0.00 0.00 ]
| 0.22 - 0.225 : [ 1 0.00 0.00 ]
#...
| 0.23 - 0.235 : [ 1 0.00 0.00 ]
| 0.235 - 0.24 : [ 1 0.00 0.00 ]
| 0.24 - 0.245 : [ 1 0.00 0.00 ]
#...
| 0.25 - 0.255 : [ 1 0.00 0.00 ]
#...
| 0.26 - 0.265 : [ 1 0.00 0.00 ]
| 0.265 - 0.27 : [ 2 0.00 0.00 ]
#...
| 0.28 - 0.285 : [ 1 0.00 0.00 ]
| 0.285 - 0.29 : [ 1 0.00 0.00 ]
| 0.29 - 0.295 : [ 1 0.00 0.00 ]
#...
| 0.3 - 0.305 : [ 2 0.00 0.00 ]
| 0.305 - 0.31 : [ 2 0.00 0.00 ]
#...
| 0.315 - 0.32 : [ 2 0.00 0.00 ]
#...
| 0.325 - 0.33 : [ 5 0.00 0.00 ]
| 0.33 - 0.335 : [ 1 0.00 0.00 ]
| 0.335 - 0.34 : [ 1 0.00 0.00 ]
| 0.34 - 0.345 : [ 3 0.00 0.00 ]
| 0.345 - 0.35 : [ 2 0.00 0.00 ]
| 0.35 - 0.355 : [ 3 0.00 0.00 ]
| 0.355 - 0.36 : [ 5 0.00 0.00 ]
| 0.36 - 0.365 : [ 1 0.00 0.00 ]
| 0.365 - 0.37 : [ 5 0.00 0.00 ]
| 0.37 - 0.375 : [ 1 0.00 0.00 ]
| 0.375 - 0.38 : [ 1 0.00 0.00 ]
| 0.38 - 0.385 : [ 2 0.00 0.00 ]
| 0.385 - 0.39 : [ 2 0.00 0.00 ]
| 0.39 - 0.395 : [ 3 0.00 0.00 ]
| 0.395 - 0.4 : [ 1 0.00 0.00 ]
| 0.4 - 0.405 : [ 3 0.00 0.00 ]
| 0.405 - 0.41 : [ 2 0.00 0.00 ]
| 0.41 - 0.415 : [ 4 0.00 0.00 ]
| 0.415 - 0.42 : [ 3 0.00 0.00 ]
| 0.42 - 0.425 : [ 6 0.00 0.00 ]
| 0.425 - 0.43 : [ 3 0.00 0.00 ]
| 0.43 - 0.435 : [ 4 0.00 0.00 ]
| 0.435 - 0.44 : [ 1 0.00 0.00 ]
| 0.44 - 0.445 : [ 5 0.00 0.00 ]
| 0.445 - 0.45 : [ 1 0.00 0.00 ]
| 0.45 - 0.455 : [ 2 0.00 0.00 ]
| 0.455 - 0.46 : [ 3 0.00 0.00 ]
| 0.46 - 0.465 : [ 5 0.00 0.00 ]
| 0.465 - 0.47 : [ 2 0.00 0.00 ]
| 0.47 - 0.475 : [ 3 0.00 0.00 ]
| 0.475 - 0.48 : [ 5 0.00 0.00 ]
| 0.48 - 0.485 : [ 6 0.00 0.00 ]
| 0.485 - 0.49 : [ 6 0.00 0.00 ]
| 0.49 - 0.495 : [ 2 0.00 0.00 ]
| 0.495 - 0.5 : [ 1 0.00 0.00 ]
| 0.5 - 0.505 : [ 13 0.00 0.00 ]
| 0.505 - 0.51 : [ 8 0.00 0.00 ]
| 0.51 - 0.515 : [ 5 0.00 0.00 ]
| 0.515 - 0.52 : [ 9 0.00 0.00 ]
| 0.52 - 0.525 : [ 13 0.00 0.00 ]
| 0.525 - 0.53 : [ 44 0.00 0.00 ]
| 0.53 - 0.535 : [ 30 0.00 0.00 ]
| 0.535 - 0.54 : [ 28 0.00 0.00 ]
| 0.54 - 0.545 : [ 25 0.00 0.00 ]
| 0.545 - 0.55 : [ 28 0.00 0.00 ]
| 0.55 - 0.555 : [ 46 0.00 0.00 ]
|X 0.555 - 0.56 : [ 65 0.00 0.01 ]
|X 0.56 - 0.565 : [ 77 0.00 0.01 ]
|X 0.565 - 0.57 : [ 74 0.00 0.01 ]
|X 0.57 - 0.575 : [ 85 0.00 0.01 ]
|X 0.575 - 0.58 : [ 84 0.00 0.01 ]
|X 0.58 - 0.585 : [ 97 0.00 0.01 ]
|X 0.585 - 0.59 : [ 100 0.00 0.01 ]
|X 0.59 - 0.595 : [ 96 0.00 0.01 ]
|X 0.595 - 0.6 : [ 71 0.00 0.01 ]
|X 0.6 - 0.605 : [ 102 0.00 0.01 ]
|X 0.605 - 0.61 : [ 111 0.00 0.02 ]
|X 0.61 - 0.615 : [ 110 0.00 0.02 ]
|X 0.615 - 0.62 : [ 137 0.00 0.02 ]
|XX 0.62 - 0.625 : [ 157 0.00 0.02 ]
|XX 0.625 - 0.63 : [ 234 0.00 0.02 ]
|XXX 0.63 - 0.635 : [ 288 0.00 0.03 ]
|XXXX 0.635 - 0.64 : [ 377 0.00 0.03 ]
|XXXXX 0.64 - 0.645 : [ 453 0.01 0.04 ]
|XXXXXX 0.645 - 0.65 : [ 551 0.01 0.04 ]
|XXXXXX 0.65 - 0.655 : [ 633 0.01 0.05 ]
|XXXXXXXX 0.655 - 0.66 : [ 840 0.01 0.06 ]
|XXXXXXXXXX 0.66 - 0.665 : [ 1020 0.01 0.07 ]
|XXXXXXXXXXXXXX 0.665 - 0.67 : [ 1363 0.02 0.09 ]
|XXXXXXXXXXXXXXX 0.67 - 0.675 : [ 1461 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 1859 0.02 0.12 ]
|XXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 2070 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 2411 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 2707 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 3107 0.04 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 3280 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 3414 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 3542 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 3582 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 3746 0.04 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.725 - 0.73 : [ 3798 0.04 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.73 - 0.735 : [ 3726 0.04 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.735 - 0.74 : [ 3723 0.04 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.74 - 0.745 : [ 3772 0.04 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.745 - 0.75 : [ 3584 0.04 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.75 - 0.755 : [ 3999 0.05 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.755 - 0.76 : [ 3490 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.76 - 0.765 : [ 3323 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.765 - 0.77 : [ 3046 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.77 - 0.775 : [ 2757 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.775 - 0.78 : [ 2432 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXXX 0.78 - 0.785 : [ 2124 0.02 0.90 ]
|XXXXXXXXXXXXXXXXX 0.785 - 0.79 : [ 1704 0.02 0.92 ]
|XXXXXXXXXXXXXX 0.79 - 0.795 : [ 1447 0.02 0.94 ]
|XXXXXXXXXXX 0.795 - 0.8 : [ 1089 0.01 0.95 ]
|XXXXXXXXXX 0.8 - 0.805 : [ 1002 0.01 0.96 ]
|XXXXXXX 0.805 - 0.81 : [ 749 0.01 0.97 ]
|XXXXX 0.81 - 0.815 : [ 543 0.01 0.98 ]
|XXXX 0.815 - 0.82 : [ 445 0.01 0.98 ]
|XXX 0.82 - 0.825 : [ 325 0.00 0.99 ]
|XXX 0.825 - 0.83 : [ 266 0.00 0.99 ]
|XX 0.83 - 0.835 : [ 193 0.00 0.99 ]
|X 0.835 - 0.84 : [ 145 0.00 0.99 ]
|X 0.84 - 0.845 : [ 109 0.00 0.99 ]
|X 0.845 - 0.85 : [ 72 0.00 1.00 ]
|X 0.85 - 0.855 : [ 66 0.00 1.00 ]
| 0.855 - 0.86 : [ 47 0.00 1.00 ]
|X 0.86 - 0.865 : [ 59 0.00 1.00 ]
| 0.865 - 0.87 : [ 39 0.00 1.00 ]
| 0.87 - 0.875 : [ 19 0.00 1.00 ]
| 0.875 - 0.88 : [ 32 0.00 1.00 ]
| 0.88 - 0.885 : [ 22 0.00 1.00 ]
| 0.885 - 0.89 : [ 8 0.00 1.00 ]
| 0.89 - 0.895 : [ 21 0.00 1.00 ]
| 0.895 - 0.9 : [ 5 0.00 1.00 ]
| 0.9 - 0.905 : [ 8 0.00 1.00 ]
| 0.905 - 0.91 : [ 3 0.00 1.00 ]
| 0.91 - 0.915 : [ 3 0.00 1.00 ]
| 0.915 - 0.92 : [ 6 0.00 1.00 ]
| 0.92 - 0.925 : [ 4 0.00 1.00 ]
| 0.925 - 0.93 : [ 4 0.00 1.00 ]
| 0.93 - 0.935 : [ 3 0.00 1.00 ]
| 0.935 - 0.94 : [ 4 0.00 1.00 ]
#...
| 0.945 - 0.95 : [ 1 0.00 1.00 ]
| 0.95 - 0.955 : [ 2 0.00 1.00 ]
| 0.955 - 0.96 : [ 2 0.00 1.00 ]
| 0.96 - 0.965 : [ 3 0.00 1.00 ]
| 0.965 - 0.97 : [ 2 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 205. 743 reads; 48985 bp (untrimmed), 48589 (trimmed).
Contig 206. 786 reads; 44296 bp (untrimmed), 44293 (trimmed).
Contig 207. 796 reads; 50609 bp (untrimmed), 49067 (trimmed).
Contig 208. 822 reads; 55259 bp (untrimmed), 54531 (trimmed).
Contig 209. 829 reads; 59486 bp (untrimmed), 59468 (trimmed).
Contig 210. 830 reads; 52951 bp (untrimmed), 51979 (trimmed).
Contig 211. 838 reads; 55009 bp (untrimmed), 54312 (trimmed).
Contig 212. 841 reads; 57646 bp (untrimmed), 57519 (trimmed).
Contig 213. 850 reads; 55857 bp (untrimmed), 54754 (trimmed).
Contig 214. 851 reads; 57111 bp (untrimmed), 55982 (trimmed).
Contig 215. 889 reads; 59128 bp (untrimmed), 59128 (trimmed).
Contig 216. 906 reads; 61046 bp (untrimmed), 59527 (trimmed).
Contig 217. 954 reads; 57039 bp (untrimmed), 55581 (trimmed).
Contig 218. 970 reads; 58804 bp (untrimmed), 58111 (trimmed).
Contig 219. 1049 reads; 55765 bp (untrimmed), 55228 (trimmed).
Contig 220. 1239 reads; 60076 bp (untrimmed), 59065 (trimmed).
Contig 221. 1250 reads; 80292 bp (untrimmed), 80153 (trimmed).
Contig 222. 1269 reads; 82292 bp (untrimmed), 82275 (trimmed).
Contig 223. 1323 reads; 85430 bp (untrimmed), 85378 (trimmed).
Contig 224. 1513 reads; 86707 bp (untrimmed), 86037 (trimmed).
Contig 225. 1513 reads; 93653 bp (untrimmed), 92695 (trimmed).
Contig 226. 2018 reads; 53458 bp (untrimmed), 53403 (trimmed).
Contig 227. 2475 reads; 113618 bp (untrimmed), 113604 (trimmed).
Contig 228. 4011 reads; 180097 bp (untrimmed), 179980 (trimmed).
Contig 229. 5581 reads; 128424 bp (untrimmed), 128380 (trimmed).
Contig 230. 6968 reads; 306786 bp (untrimmed), 305540 (trimmed).
Contig 231. 7459 reads; 359214 bp (untrimmed), 359214 (trimmed).
--------------------------------------------------------------
Totals 86855 reads; 5047836 bp (untrimmed), 4939013 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 5044178 bases = 13.69 +- 7.73 = 0.47 +- 4.10
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 222 total values totalling 2212.1800. <9.964775 +/- 4.737867>
#Range: [ 1.36 - 40.27 ]
#Most likely bin: [ 11 - 11.5 ] 27 counts
#Median bin: [ 10.5 - 11 ] 21 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1 - 1.5 : [ 1 0.00 0.00 ]
|XXXX 1.5 - 2 : [ 3 0.01 0.02 ]
|XXXXXX 2 - 2.5 : [ 4 0.02 0.04 ]
|XXXXXXXXXX 2.5 - 3 : [ 7 0.03 0.07 ]
|XXXXXXXXX 3 - 3.5 : [ 6 0.03 0.09 ]
|XXXXXXXXX 3.5 - 4 : [ 6 0.03 0.12 ]
|XXXX 4 - 4.5 : [ 3 0.01 0.14 ]
|XXXXXXX 4.5 - 5 : [ 5 0.02 0.16 ]
|XXX 5 - 5.5 : [ 2 0.01 0.17 ]
|XXXXXXX 5.5 - 6 : [ 5 0.02 0.19 ]
|XXXXXXX 6 - 6.5 : [ 5 0.02 0.21 ]
|XXXX 6.5 - 7 : [ 3 0.01 0.23 ]
|XXX 7 - 7.5 : [ 2 0.01 0.23 ]
|XXXX 7.5 - 8 : [ 3 0.01 0.25 ]
|XXXXXXX 8 - 8.5 : [ 5 0.02 0.27 ]
|XXXXXXXXXXXX 8.5 - 9 : [ 8 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 13 0.06 0.36 ]
|XXXXXXXXXXXXX 9.5 - 10 : [ 9 0.04 0.41 ]
|XXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 14 0.06 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 21 0.09 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 27 0.12 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 25 0.11 0.80 ]
|XXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 13 0.06 0.86 ]
|XXXXXXXXXXXX 12.5 - 13 : [ 8 0.04 0.89 ]
|XXXXXXX 13 - 13.5 : [ 5 0.02 0.91 ]
|XXXXXXXXX 13.5 - 14 : [ 6 0.03 0.94 ]
|XXXX 14 - 14.5 : [ 3 0.01 0.95 ]
#...
|X 15 - 15.5 : [ 1 0.00 0.96 ]
|X 15.5 - 16 : [ 1 0.00 0.96 ]
#...
|XXX 17.5 - 18 : [ 2 0.01 0.97 ]
#...
|XXX 18.5 - 19 : [ 2 0.01 0.98 ]
|X 19 - 19.5 : [ 1 0.00 0.99 ]
#...
|X 32 - 32.5 : [ 1 0.00 0.99 ]
#...
|X 37 - 37.5 : [ 1 0.00 1.00 ]
#...
|X 40 - 40.5 : [ 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 190 total values totalling 2052.5700. <10.803000 +/- 3.742346>
#Range: [ 2.58 - 37.46 ]
#Most likely bin: [ 11 - 11.5 ] 27 counts
#Median bin: [ 11 - 11.5 ] 27 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 2.5 - 3 : [ 1 0.01 0.01 ]
|XXXXXX 3 - 3.5 : [ 4 0.02 0.03 ]
|XXXX 3.5 - 4 : [ 3 0.02 0.04 ]
#...
|XXXX 4.5 - 5 : [ 3 0.02 0.06 ]
|X 5 - 5.5 : [ 1 0.01 0.06 ]
|XXXXXX 5.5 - 6 : [ 4 0.02 0.08 ]
|XXXX 6 - 6.5 : [ 3 0.02 0.10 ]
|XXX 6.5 - 7 : [ 2 0.01 0.11 ]
|XXX 7 - 7.5 : [ 2 0.01 0.12 ]
|XXXX 7.5 - 8 : [ 3 0.02 0.14 ]
|XXXXXX 8 - 8.5 : [ 4 0.02 0.16 ]
|XXXXXXXXXXXX 8.5 - 9 : [ 8 0.04 0.20 ]
|XXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 12 0.06 0.26 ]
|XXXXXXXXXXXXX 9.5 - 10 : [ 9 0.05 0.31 ]
|XXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 14 0.07 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 21 0.11 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 27 0.14 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 25 0.13 0.77 ]
|XXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 13 0.07 0.84 ]
|XXXXXXXXXXXX 12.5 - 13 : [ 8 0.04 0.88 ]
|XXXXXXX 13 - 13.5 : [ 5 0.03 0.91 ]
|XXXXXXXXX 13.5 - 14 : [ 6 0.03 0.94 ]
|XXXX 14 - 14.5 : [ 3 0.02 0.95 ]
#...
|X 15 - 15.5 : [ 1 0.01 0.96 ]
|X 15.5 - 16 : [ 1 0.01 0.96 ]
#...
|XXX 17.5 - 18 : [ 2 0.01 0.97 ]
#...
|XXX 18.5 - 19 : [ 2 0.01 0.98 ]
|X 19 - 19.5 : [ 1 0.01 0.99 ]
#...
|X 32 - 32.5 : [ 1 0.01 0.99 ]
#...
|X 37 - 37.5 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 13 4 reads 2258 bases = 1.36 +- 0.86 = 0.35 +- 1.01
Contig 5 3 reads 1252 bases = 1.67 +- 0.79 = 1.67 +- 0.79
Contig 9 3 reads 1464 bases = 1.72 +- 0.70 = 0.54 +- 1.39
Contig 3 2 reads 968 bases = 1.79 +- 0.40 = 1.79 +- 0.40
Contig 11 4 reads 1449 bases = 2.11 +- 1.30 = 0.39 +- 0.94
Contig 8 3 reads 762 bases = 2.11 +- 0.79 = 0.43 +- 0.67
Contig 16 5 reads 1272 bases = 2.24 +- 1.27 = 2.24 +- 1.27
Contig 25 9 reads 1495 bases = 2.45 +- 2.12 = 1.25 +- 2.48
Contig 14 4 reads 560 bases = 2.54 +- 1.02 = 0.54 +- 1.02
Contig 33 13 reads 2785 bases = 2.58 +- 1.76 = 0.31 +- 1.34
Contig 27 9 reads 3356 bases = 2.66 +- 1.17 = 2.66 +- 1.17
Contig 26 9 reads 1961 bases = 2.89 +- 1.47 = 0.78 +- 1.22
Contig 24 8 reads 1684 bases = 2.90 +- 2.20 = 1.06 +- 0.59
Contig 12 4 reads 924 bases = 2.98 +- 1.35 = 1.74 +- 0.49
Contig 7 3 reads 800 bases = 2.99 +- 0.09 = 0.99 +- 0.09
Contig 31 12 reads 2234 bases = 3.00 +- 1.93 = -0.43 +- 0.87
Contig 39 15 reads 3014 bases = 3.10 +- 2.31 = 1.43 +- 2.42
Contig 19 6 reads 1413 bases = 3.14 +- 2.08 = 2.23 +- 1.21
Contig 50 25 reads 4964 bases = 3.32 +- 2.60 = 0.40 +- 1.66
Contig 40 15 reads 2947 bases = 3.43 +- 2.68 = 0.35 +- 2.33
Contig 156 320 reads 18728 bases = 13.45 +- 3.92 = 0.50 +- 4.14
Contig 141 236 reads 12545 bases = 13.57 +- 5.19 = 0.09 +- 4.08
Contig 224 1513 reads 86707 bases = 13.57 +- 4.63 = 0.23 +- 4.04
Contig 206 786 reads 44296 bases = 13.58 +- 4.31 = 0.86 +- 4.00
Contig 217 954 reads 57039 bases = 13.60 +- 5.36 = 0.28 +- 4.36
Contig 152 291 reads 17227 bases = 13.89 +- 5.27 = 0.27 +- 3.88
Contig 107 124 reads 6524 bases = 13.91 +- 5.41 = 0.36 +- 4.70
Contig 184 493 reads 28579 bases = 14.01 +- 5.95 = 0.22 +- 3.16
Contig 164 343 reads 19704 bases = 14.20 +- 4.83 = 1.70 +- 4.36
Contig 121 162 reads 9238 bases = 14.21 +- 4.70 = 0.76 +- 3.30
Contig 192 552 reads 29696 bases = 15.41 +- 5.81 = 0.27 +- 4.12
Contig 219 1049 reads 55765 bases = 15.75 +- 5.79 = 0.24 +- 4.33
Contig 231 7459 reads 359214 bases = 17.55 +- 8.38 = 0.07 +- 4.41
Contig 220 1239 reads 60076 bases = 17.75 +- 5.18 = 0.31 +- 4.54
Contig 228 4011 reads 180097 bases = 18.60 +- 6.29 = 0.85 +- 4.77
Contig 227 2475 reads 113618 bases = 18.82 +- 5.35 = 0.30 +- 4.85
Contig 230 6968 reads 306786 bases = 19.39 +- 7.65 = 0.40 +- 4.95
Contig 226 2018 reads 53458 bases = 32.48 +- 9.83 = 2.24 +- 7.54
Contig 229 5581 reads 128424 bases = 37.46 +- 8.11 = 0.90 +- 7.22
Contig 72 57 reads 1274 bases = 40.27 +- 19.27 = 40.27 +- 19.27
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 11213
HQ Discrepant reads = 276
Chimeric reads = 257
Suspect alignments = 269
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 3.57 SUN/Ultra-2/3
Equivalent to Phil Green's version 0.990329
Score matrix (set by value of penalty: -2)
A C G T N X
A 1 -2 -2 -2 0 -3
C -2 1 -2 -2 0 -3
G -2 -2 1 -2 0 -3
T -2 -2 -2 1 0 -3
N 0 0 0 0 0 0
X -3 -3 -3 -3 0 -3
gap_init: -4
gap_ext: -3
ins_gap_ext: -3
del_gap_ext: -3
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 30
maxmatch: 55
max_group_size: 20
minscore: 55
bandwidth: 14
indexwordsize: 10
vector_bound: 20
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 13
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -5
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/microbe2/3436090/edit_dir.09Mar04.QD