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 in progress (or initial analysis of completed)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3436094 9000 1172 Anabaena variabilis
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Anabaena_variabilis
-------------------------------------------------------------------
Anabaena variabilis, species, cyanobacteria
Anabaena, genus, cyanobacteria
Nostocaceae, family, cyanobacteria
Nostocales, order, cyanobacteria
Cyanobacteria (blue-green algae), phylum, cyanobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 7114054
# phrap: 6687018
# db:
altered.
9000000
7600357 +/- 1004934
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 82924
Number of reads with percent X's >= 20%: 2811 = 2.1%
Number of reads with percent X's >= 50%: 2076 = 1.5%
Number of reads with percent X's >= 80%: 1488 = 1.1%
Total reads in project: 136662
Total bp X'd : 6778251
reads >= 20% >= 50% >= 80% screened
Nr with L09136 23525 361 205 141
Nr with LRS 146 145 144 139
Nr with pCC1Fos 4007 7 0 0
Nr with pMCL200_JGI_XZX+XZK 55246 2298 1727 1208
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 4111
Number of reads with percent X's >= 20%: 2080 = 13.2%
Number of reads with percent X's >= 50%: 1757 = 11.2%
Number of reads with percent X's >= 80%: 1399 = 8.9%
Total reads in project: 15710
Total bp X'd : 1661593
reads >= 20% >= 50% >= 80% screened
Nr with L09136 327 138 129 116
Nr with LRS 144 143 143 139
Nr with pCC1Fos 156 7 0 0
Nr with pMCL200_JGI_XZX+XZK 3484 1792 1485 1144
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 35744375
C = 26995467
G = 26391445
T = 34861738
N = 983860
X = 6778251
GC fraction = 0.41
Total = 131755136
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436094_fasta.screen.contigs
-------------------------------------------------------------------
A 2105608
C 1490925
G 1493695
T 2094400
N 1830
fraction GC = 0.42
total bases = 7186458
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 AAWX reads.list > grep.reads.list.AAWX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAWX 4 500
-------------------------------------------------------------------
#Found 22247 total values totalling 92132584.0000. <4141.348676 +/- 14739.871384>
#Range: [ 583 - 1057725 ]
#Most likely bin: [ 3500 - 4000 ] 5156 counts
#Median bin: [ 3500 - 4000 ] 5156 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 30 0.00 0.00 ]
|X 1000 - 1500 : [ 155 0.01 0.01 ]
|XX 1500 - 2000 : [ 207 0.01 0.02 ]
|XXX 2000 - 2500 : [ 333 0.01 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2819 0.13 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 5044 0.23 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 5156 0.23 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 4203 0.19 0.81 ]
|XXXXXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 2698 0.12 0.93 ]
|XXXXXXXXXX 5000 - 5500 : [ 1234 0.06 0.98 ]
|XX 5500 - 6000 : [ 313 0.01 1.00 ]
| 6000 - 6500 : [ 31 0.00 1.00 ]
#...
| 12000 - 12500 : [ 1 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
#...
| 42500 - 43000 : [ 1 0.00 1.00 ]
#...
| 43500 - 44000 : [ 1 0.00 1.00 ]
#...
| 55500 - 56000 : [ 1 0.00 1.00 ]
#...
| 57000 - 57500 : [ 1 0.00 1.00 ]
#...
| 75500 - 76000 : [ 1 0.00 1.00 ]
#...
| 122500 - 123000 : [ 1 0.00 1.00 ]
#...
| 131500 - 132000 : [ 1 0.00 1.00 ]
#...
| 144000 - 144500 : [ 1 0.00 1.00 ]
#...
| 196000 - 196500 : [ 1 0.00 1.00 ]
#...
| 228500 - 229000 : [ 1 0.00 1.00 ]
#...
| 279000 - 279500 : [ 1 0.00 1.00 ]
#...
| 341500 - 342000 : [ 1 0.00 1.00 ]
#...
| 362000 - 362500 : [ 1 0.00 1.00 ]
#...
| 474000 - 474500 : [ 1 0.00 1.00 ]
#...
| 494000 - 494500 : [ 1 0.00 1.00 ]
#...
| 513000 - 513500 : [ 1 0.00 1.00 ]
#...
| 566500 - 567000 : [ 1 0.00 1.00 ]
#...
| 620500 - 621000 : [ 1 0.00 1.00 ]
#...
| 701500 - 702000 : [ 1 0.00 1.00 ]
#...
| 748000 - 748500 : [ 1 0.00 1.00 ]
#...
| 886000 - 886500 : [ 1 0.00 1.00 ]
#...
| 1057500 - 1058000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAWY reads.list > grep.reads.list.AAWY
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAWY 4 500
-------------------------------------------------------------------
#Found 21175 total values totalling 202600702.0000. <9567.919811 +/- 6863.060203>
#Range: [ 748 - 739676 ]
#Most likely bin: [ 9500 - 10000 ] 3180 counts
#Median bin: [ 9500 - 10000 ] 3180 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 5 0.00 0.00 ]
|X 1000 - 1500 : [ 44 0.00 0.00 ]
|X 1500 - 2000 : [ 80 0.00 0.01 ]
|X 2000 - 2500 : [ 106 0.01 0.01 ]
|XX 2500 - 3000 : [ 147 0.01 0.02 ]
|XX 3000 - 3500 : [ 129 0.01 0.02 ]
|XX 3500 - 4000 : [ 142 0.01 0.03 ]
|XX 4000 - 4500 : [ 139 0.01 0.04 ]
|XX 4500 - 5000 : [ 152 0.01 0.04 ]
|XX 5000 - 5500 : [ 139 0.01 0.05 ]
|XX 5500 - 6000 : [ 141 0.01 0.06 ]
|XX 6000 - 6500 : [ 152 0.01 0.06 ]
|XX 6500 - 7000 : [ 197 0.01 0.07 ]
|XXXXX 7000 - 7500 : [ 372 0.02 0.09 ]
|XXXXXXXXX 7500 - 8000 : [ 715 0.03 0.13 ]
|XXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1373 0.06 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 2289 0.11 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 3109 0.15 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 3180 0.15 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 2838 0.13 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 10500 - 11000 : [ 2189 0.10 0.83 ]
|XXXXXXXXXXXXXXXXXXX 11000 - 11500 : [ 1516 0.07 0.90 ]
|XXXXXXXXXXXXX 11500 - 12000 : [ 1029 0.05 0.95 ]
|XXXXXXX 12000 - 12500 : [ 559 0.03 0.98 ]
|XXXX 12500 - 13000 : [ 291 0.01 0.99 ]
|X 13000 - 13500 : [ 102 0.00 1.00 ]
| 13500 - 14000 : [ 20 0.00 1.00 ]
| 14000 - 14500 : [ 7 0.00 1.00 ]
| 14500 - 15000 : [ 4 0.00 1.00 ]
#...
| 41000 - 41500 : [ 1 0.00 1.00 ]
#...
| 84500 - 85000 : [ 1 0.00 1.00 ]
#...
| 89500 - 90000 : [ 1 0.00 1.00 ]
#...
| 99500 - 100000 : [ 1 0.00 1.00 ]
#...
| 193500 - 194000 : [ 1 0.00 1.00 ]
#...
| 219000 - 219500 : [ 1 0.00 1.00 ]
#...
| 229500 - 230000 : [ 1 0.00 1.00 ]
#...
| 499000 - 499500 : [ 1 0.00 1.00 ]
#...
| 739500 - 740000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAWZ reads.list > grep.reads.list.AAWZ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAWZ 4 500
-------------------------------------------------------------------
#Found 2552 total values totalling 87102723.0000. <34131.161050 +/- 3642.610323>
#Range: [ 18802 - 44921 ]
#Most likely bin: [ 34000 - 34500 ] 168 counts
#Median bin: [ 34000 - 34500 ] 168 counts
#Histogram Bins Count Fraction Cum_Fraction
| 18500 - 19000 : [ 1 0.00 0.00 ]
#...
| 19500 - 20000 : [ 1 0.00 0.00 ]
| 20000 - 20500 : [ 1 0.00 0.00 ]
#...
| 21000 - 21500 : [ 1 0.00 0.00 ]
#...
| 22000 - 22500 : [ 1 0.00 0.00 ]
| 22500 - 23000 : [ 2 0.00 0.00 ]
#...
|X 23500 - 24000 : [ 4 0.00 0.00 ]
|X 24000 - 24500 : [ 5 0.00 0.01 ]
|XX 24500 - 25000 : [ 8 0.00 0.01 ]
|XXX 25000 - 25500 : [ 13 0.01 0.01 ]
|XXXX 25500 - 26000 : [ 15 0.01 0.02 ]
|XXXXX 26000 - 26500 : [ 22 0.01 0.03 ]
|XXXXXXX 26500 - 27000 : [ 30 0.01 0.04 ]
|XXXXX 27000 - 27500 : [ 21 0.01 0.05 ]
|XXXXXX 27500 - 28000 : [ 25 0.01 0.06 ]
|XXXXXXXXX 28000 - 28500 : [ 36 0.01 0.07 ]
|XXXXXXXXXX 28500 - 29000 : [ 40 0.02 0.09 ]
|XXXXXXXXXXX 29000 - 29500 : [ 46 0.02 0.11 ]
|XXXXXXXXXXXXXX 29500 - 30000 : [ 58 0.02 0.13 ]
|XXXXXXXXXXXXXX 30000 - 30500 : [ 60 0.02 0.15 ]
|XXXXXXXXXXXXXXXXX 30500 - 31000 : [ 71 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXX 31000 - 31500 : [ 87 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXX 31500 - 32000 : [ 88 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 113 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 121 0.05 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 144 0.06 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 160 0.06 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 168 0.07 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 150 0.06 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 158 0.06 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 143 0.06 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 134 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 119 0.05 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 93 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 78 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 79 0.03 0.90 ]
|XXXXXXXXXXXXXXX 38500 - 39000 : [ 64 0.03 0.92 ]
|XXXXXXXXXXX 39000 - 39500 : [ 45 0.02 0.94 ]
|XXXXXXXX 39500 - 40000 : [ 34 0.01 0.96 ]
|XXX 40000 - 40500 : [ 14 0.01 0.96 ]
|XXXXX 40500 - 41000 : [ 21 0.01 0.97 ]
|XXXX 41000 - 41500 : [ 16 0.01 0.98 ]
|XXXX 41500 - 42000 : [ 17 0.01 0.98 ]
|XXXX 42000 - 42500 : [ 17 0.01 0.99 ]
|X 42500 - 43000 : [ 5 0.00 0.99 ]
|XX 43000 - 43500 : [ 9 0.00 0.99 ]
|XX 43500 - 44000 : [ 7 0.00 1.00 ]
|X 44000 - 44500 : [ 5 0.00 1.00 ]
| 44500 - 45000 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AAWZ 34131 +- 3647 (n=1282)
# AAWX 3681 +- 996 (n=11332)
# AAWY 9205 +- 2027 (n=10682)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436094_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
AAWX 62592 -1 -1 96 668 62493 90 662 92 666
AAWY 65280 -1 -1 92 589 64953 79 519 86 558
AAWZ 9984 -1 -1 90 584 9216 86 644 90 639
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AAWX 30656 84 669 86 681 31837 95 656 97 654
AAWY 32426 77 518 85 556 32527 81 521 88 560
AAWZ 4608 86 655 90 640 4608 86 632 90 638
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436094_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 136662 66788 95.96 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 3436094_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 136662 total values totalling 69296740.0000. <507.066632 +/- 258.398707>
#Range: [ 0 - 936 ]
#Most likely bin: [ 650 - 700 ] 21469 counts
#Median bin: [ 600 - 650 ] 17507 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 18505 0.14 0.14 ]
|XXXXX 50 - 100 : [ 2729 0.02 0.16 ]
|XXXX 100 - 150 : [ 2238 0.02 0.17 ]
|XXXX 150 - 200 : [ 2285 0.02 0.19 ]
|XXXX 200 - 250 : [ 2304 0.02 0.21 ]
|XXXXX 250 - 300 : [ 2505 0.02 0.22 ]
|XXXXX 300 - 350 : [ 2734 0.02 0.24 ]
|XXXXXX 350 - 400 : [ 3354 0.02 0.27 ]
|XXXXXXX 400 - 450 : [ 3882 0.03 0.30 ]
|XXXXXXXXX 450 - 500 : [ 4994 0.04 0.33 ]
|XXXXXXXXXXXXX 500 - 550 : [ 7097 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 11632 0.09 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 17507 0.13 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 21469 0.16 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 20327 0.15 0.90 ]
|XXXXXXXXXXXXXXXXX 750 - 800 : [ 9288 0.07 0.97 ]
|XXXXXX 800 - 850 : [ 3160 0.02 1.00 ]
|X 850 - 900 : [ 642 0.00 1.00 ]
| 900 - 950 : [ 10 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHST
trimt JAZZ trim 15 readlength histogram for AAWX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAWX 3436094_fasta.screen.trimQ15.SaF > reads.trim15.AAWX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAWX.rl 2 50
-------------------------------------------------------------------
#Found 62493 total values totalling 37253928.0000. <596.129615 +/- 230.433913>
#Range: [ 0 - 915 ]
#Most likely bin: [ 700 - 750 ] 16205 counts
#Median bin: [ 650 - 700 ] 12847 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 0 - 50 : [ 5893 0.09 0.09 ]
|X 50 - 100 : [ 474 0.01 0.10 ]
|X 100 - 150 : [ 404 0.01 0.11 ]
|X 150 - 200 : [ 450 0.01 0.12 ]
|X 200 - 250 : [ 455 0.01 0.12 ]
|X 250 - 300 : [ 496 0.01 0.13 ]
|X 300 - 350 : [ 562 0.01 0.14 ]
|XX 350 - 400 : [ 747 0.01 0.15 ]
|XX 400 - 450 : [ 919 0.01 0.17 ]
|XXX 450 - 500 : [ 1171 0.02 0.19 ]
|XXXX 500 - 550 : [ 1653 0.03 0.21 ]
|XXXXXXXX 550 - 600 : [ 3257 0.05 0.26 ]
|XXXXXXXXXXXXXXXXX 600 - 650 : [ 6939 0.11 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 12847 0.21 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 16205 0.26 0.84 ]
|XXXXXXXXXXXXXXXXXX 750 - 800 : [ 7233 0.12 0.96 ]
|XXXXXX 800 - 850 : [ 2304 0.04 0.99 ]
|X 850 - 900 : [ 478 0.01 1.00 ]
| 900 - 950 : [ 6 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAWY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAWY 3436094_fasta.screen.trimQ15.SaF > reads.trim15.AAWY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAWY.rl 2 50
-------------------------------------------------------------------
#Found 64953 total values totalling 26926025.0000. <414.546287 +/- 249.926240>
#Range: [ 0 - 854 ]
#Most likely bin: [ 0 - 50 ] 11462 counts
#Median bin: [ 500 - 550 ] 5249 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 11462 0.18 0.18 ]
|XXXXXXX 50 - 100 : [ 2100 0.03 0.21 ]
|XXXXXX 100 - 150 : [ 1708 0.03 0.24 ]
|XXXXXX 150 - 200 : [ 1680 0.03 0.26 ]
|XXXXXX 200 - 250 : [ 1678 0.03 0.29 ]
|XXXXXX 250 - 300 : [ 1840 0.03 0.32 ]
|XXXXXXX 300 - 350 : [ 1972 0.03 0.35 ]
|XXXXXXXX 350 - 400 : [ 2394 0.04 0.38 ]
|XXXXXXXXXX 400 - 450 : [ 2786 0.04 0.43 ]
|XXXXXXXXXXXXX 450 - 500 : [ 3695 0.06 0.48 ]
|XXXXXXXXXXXXXXXXXX 500 - 550 : [ 5249 0.08 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 8070 0.12 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 9788 0.15 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 7128 0.11 0.95 ]
|XXXXXXXXX 700 - 750 : [ 2459 0.04 0.99 ]
|XXX 750 - 800 : [ 808 0.01 1.00 ]
| 800 - 850 : [ 135 0.00 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAWZ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAWZ 3436094_fasta.screen.trimQ15.SaF > reads.trim15.AAWZ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAWZ.rl 2 50
-------------------------------------------------------------------
#Found 9216 total values totalling 5116787.0000. <555.206923 +/- 270.895432>
#Range: [ 0 - 936 ]
#Most likely bin: [ 700 - 750 ] 1663 counts
#Median bin: [ 650 - 700 ] 1494 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1150 0.12 0.12 ]
|XXXX 50 - 100 : [ 155 0.02 0.14 ]
|XXX 100 - 150 : [ 126 0.01 0.16 ]
|XXXX 150 - 200 : [ 155 0.02 0.17 ]
|XXXX 200 - 250 : [ 171 0.02 0.19 ]
|XXXX 250 - 300 : [ 169 0.02 0.21 ]
|XXXXX 300 - 350 : [ 200 0.02 0.23 ]
|XXXXX 350 - 400 : [ 213 0.02 0.25 ]
|XXXX 400 - 450 : [ 177 0.02 0.27 ]
|XXX 450 - 500 : [ 128 0.01 0.29 ]
|XXXXX 500 - 550 : [ 195 0.02 0.31 ]
|XXXXXXX 550 - 600 : [ 305 0.03 0.34 ]
|XXXXXXXXXXXXXXXXXXX 600 - 650 : [ 780 0.08 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1494 0.16 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1663 0.18 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1247 0.14 0.90 ]
|XXXXXXXXXXXXXXXXX 800 - 850 : [ 721 0.08 0.98 ]
|XXXX 850 - 900 : [ 163 0.02 1.00 ]
| 900 - 950 : [ 4 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436094
-------------------------------------------------------------------
AAWX.000001.000100 pUC18.fa.4 LRS.fasta
AAWX.000101.000200 pUC18.fa.4 LRS.fasta
AAWX.000201.000300 pUC18.fa.4 LRS.fasta
AAWX.000301.000400 pUC18.fa.4 LRS.fasta
AAWY.000001.000100 pMCL200.fa.4 LRS.fasta
AAWY.000101.000200 pMCL200.fa LRS.fasta
AAWY.000201.000300 pMCL200.fa.4 LRS.fasta
AAWY.000301.000400 pMCL200.fa.4 LRS.fasta
AAWZ.000001.000100 pCC1Fos.fa.4 LRS.fasta
AAWX.000001.000100 pUC18.fa.4 LRS.fasta
AAWX.000101.000200 pUC18.fa.4 LRS.fasta
AAWX.000201.000300 pUC18.fa.4 LRS.fasta
AAWX.000301.000400 pUC18.fa.4 LRS.fasta
AAWY.000001.000100 pMCL200.fa.4 LRS.fasta
AAWY.000101.000200 pMCL200.fa LRS.fasta
AAWY.000201.000300 pMCL200.fa.4 LRS.fasta
AAWY.000301.000400 pMCL200.fa.4 LRS.fasta
AAWZ.000001.000100 pCC1Fos.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436094_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436094_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 118454 total values totalling 49066.4758. <0.414224 +/- 0.053245>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.435 - 0.44 ] 5160 counts
#Median bin: [ 0.415 - 0.42 ] 4730 counts
| 0 - 0.005 : [ 7 0.00 0.00 ]
#...
| 0.04 - 0.045 : [ 1 0.00 0.00 ]
#...
| 0.08 - 0.085 : [ 1 0.00 0.00 ]
| 0.085 - 0.09 : [ 1 0.00 0.00 ]
| 0.09 - 0.095 : [ 2 0.00 0.00 ]
#...
| 0.1 - 0.105 : [ 1 0.00 0.00 ]
| 0.105 - 0.11 : [ 2 0.00 0.00 ]
| 0.11 - 0.115 : [ 1 0.00 0.00 ]
#...
| 0.12 - 0.125 : [ 1 0.00 0.00 ]
#...
| 0.13 - 0.135 : [ 2 0.00 0.00 ]
#...
| 0.14 - 0.145 : [ 2 0.00 0.00 ]
| 0.145 - 0.15 : [ 2 0.00 0.00 ]
| 0.15 - 0.155 : [ 2 0.00 0.00 ]
#...
| 0.16 - 0.165 : [ 3 0.00 0.00 ]
| 0.165 - 0.17 : [ 5 0.00 0.00 ]
| 0.17 - 0.175 : [ 9 0.00 0.00 ]
| 0.175 - 0.18 : [ 1 0.00 0.00 ]
| 0.18 - 0.185 : [ 5 0.00 0.00 ]
| 0.185 - 0.19 : [ 10 0.00 0.00 ]
| 0.19 - 0.195 : [ 10 0.00 0.00 ]
| 0.195 - 0.2 : [ 3 0.00 0.00 ]
| 0.2 - 0.205 : [ 9 0.00 0.00 ]
| 0.205 - 0.21 : [ 15 0.00 0.00 ]
| 0.21 - 0.215 : [ 23 0.00 0.00 ]
| 0.215 - 0.22 : [ 17 0.00 0.00 ]
| 0.22 - 0.225 : [ 13 0.00 0.00 ]
| 0.225 - 0.23 : [ 36 0.00 0.00 ]
| 0.23 - 0.235 : [ 31 0.00 0.00 ]
| 0.235 - 0.24 : [ 23 0.00 0.00 ]
| 0.24 - 0.245 : [ 36 0.00 0.00 ]
| 0.245 - 0.25 : [ 19 0.00 0.00 ]
| 0.25 - 0.255 : [ 59 0.00 0.00 ]
|X 0.255 - 0.26 : [ 69 0.00 0.00 ]
|X 0.26 - 0.265 : [ 83 0.00 0.00 ]
|X 0.265 - 0.27 : [ 112 0.00 0.01 ]
|X 0.27 - 0.275 : [ 146 0.00 0.01 ]
|X 0.275 - 0.28 : [ 188 0.00 0.01 ]
|XX 0.28 - 0.285 : [ 249 0.00 0.01 ]
|XX 0.285 - 0.29 : [ 247 0.00 0.01 ]
|XX 0.29 - 0.295 : [ 296 0.00 0.01 ]
|XXX 0.295 - 0.3 : [ 391 0.00 0.02 ]
|XXXX 0.3 - 0.305 : [ 497 0.00 0.02 ]
|XXXXX 0.305 - 0.31 : [ 584 0.00 0.03 ]
|XXXXX 0.31 - 0.315 : [ 696 0.01 0.03 ]
|XXXXXX 0.315 - 0.32 : [ 795 0.01 0.04 ]
|XXXXXXXX 0.32 - 0.325 : [ 997 0.01 0.05 ]
|XXXXXXXXX 0.325 - 0.33 : [ 1146 0.01 0.06 ]
|XXXXXXXXXX 0.33 - 0.335 : [ 1307 0.01 0.07 ]
|XXXXXXXXXXX 0.335 - 0.34 : [ 1446 0.01 0.08 ]
|XXXXXXXXXXXXXX 0.34 - 0.345 : [ 1747 0.01 0.10 ]
|XXXXXXXXXXXXXX 0.345 - 0.35 : [ 1864 0.02 0.11 ]
|XXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 2055 0.02 0.13 ]
|XXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 2175 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 2519 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 2756 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 2814 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 3183 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 3445 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 3644 0.03 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 3696 0.03 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 3704 0.03 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 4213 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 4335 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 4529 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 4730 0.04 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 4869 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 5078 0.04 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 5001 0.04 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 5160 0.04 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 4881 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 4440 0.04 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 4314 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 3826 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 3519 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 2952 0.02 0.89 ]
|XXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 2514 0.02 0.91 ]
|XXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 2124 0.02 0.93 ]
|XXXXXXXXXXXXX 0.48 - 0.485 : [ 1740 0.01 0.94 ]
|XXXXXXXXXXX 0.485 - 0.49 : [ 1364 0.01 0.95 ]
|XXXXXXXXX 0.49 - 0.495 : [ 1097 0.01 0.96 ]
|XXXXX 0.495 - 0.5 : [ 687 0.01 0.97 ]
|XXXXXXX 0.5 - 0.505 : [ 865 0.01 0.97 ]
|XXXX 0.505 - 0.51 : [ 457 0.00 0.98 ]
|XXX 0.51 - 0.515 : [ 407 0.00 0.98 ]
|XXX 0.515 - 0.52 : [ 338 0.00 0.98 ]
|XX 0.52 - 0.525 : [ 244 0.00 0.99 ]
|XX 0.525 - 0.53 : [ 194 0.00 0.99 ]
|X 0.53 - 0.535 : [ 161 0.00 0.99 ]
|X 0.535 - 0.54 : [ 136 0.00 0.99 ]
|X 0.54 - 0.545 : [ 95 0.00 0.99 ]
|X 0.545 - 0.55 : [ 86 0.00 0.99 ]
|X 0.55 - 0.555 : [ 74 0.00 0.99 ]
| 0.555 - 0.56 : [ 59 0.00 0.99 ]
|X 0.56 - 0.565 : [ 65 0.00 0.99 ]
| 0.565 - 0.57 : [ 40 0.00 0.99 ]
| 0.57 - 0.575 : [ 40 0.00 0.99 ]
| 0.575 - 0.58 : [ 28 0.00 1.00 ]
| 0.58 - 0.585 : [ 41 0.00 1.00 ]
| 0.585 - 0.59 : [ 22 0.00 1.00 ]
| 0.59 - 0.595 : [ 27 0.00 1.00 ]
| 0.595 - 0.6 : [ 22 0.00 1.00 ]
| 0.6 - 0.605 : [ 27 0.00 1.00 ]
| 0.605 - 0.61 : [ 24 0.00 1.00 ]
| 0.61 - 0.615 : [ 20 0.00 1.00 ]
| 0.615 - 0.62 : [ 21 0.00 1.00 ]
| 0.62 - 0.625 : [ 12 0.00 1.00 ]
| 0.625 - 0.63 : [ 14 0.00 1.00 ]
| 0.63 - 0.635 : [ 13 0.00 1.00 ]
| 0.635 - 0.64 : [ 18 0.00 1.00 ]
| 0.64 - 0.645 : [ 16 0.00 1.00 ]
| 0.645 - 0.65 : [ 14 0.00 1.00 ]
| 0.65 - 0.655 : [ 15 0.00 1.00 ]
| 0.655 - 0.66 : [ 15 0.00 1.00 ]
| 0.66 - 0.665 : [ 19 0.00 1.00 ]
| 0.665 - 0.67 : [ 12 0.00 1.00 ]
| 0.67 - 0.675 : [ 11 0.00 1.00 ]
| 0.675 - 0.68 : [ 12 0.00 1.00 ]
| 0.68 - 0.685 : [ 17 0.00 1.00 ]
| 0.685 - 0.69 : [ 9 0.00 1.00 ]
| 0.69 - 0.695 : [ 12 0.00 1.00 ]
| 0.695 - 0.7 : [ 8 0.00 1.00 ]
| 0.7 - 0.705 : [ 10 0.00 1.00 ]
| 0.705 - 0.71 : [ 11 0.00 1.00 ]
| 0.71 - 0.715 : [ 22 0.00 1.00 ]
| 0.715 - 0.72 : [ 19 0.00 1.00 ]
| 0.72 - 0.725 : [ 12 0.00 1.00 ]
| 0.725 - 0.73 : [ 10 0.00 1.00 ]
| 0.73 - 0.735 : [ 7 0.00 1.00 ]
| 0.735 - 0.74 : [ 7 0.00 1.00 ]
| 0.74 - 0.745 : [ 5 0.00 1.00 ]
| 0.745 - 0.75 : [ 4 0.00 1.00 ]
| 0.75 - 0.755 : [ 7 0.00 1.00 ]
| 0.755 - 0.76 : [ 8 0.00 1.00 ]
| 0.76 - 0.765 : [ 7 0.00 1.00 ]
| 0.765 - 0.77 : [ 6 0.00 1.00 ]
| 0.77 - 0.775 : [ 6 0.00 1.00 ]
| 0.775 - 0.78 : [ 6 0.00 1.00 ]
#...
| 0.785 - 0.79 : [ 1 0.00 1.00 ]
| 0.79 - 0.795 : [ 3 0.00 1.00 ]
#...
| 0.8 - 0.805 : [ 1 0.00 1.00 ]
| 0.805 - 0.81 : [ 2 0.00 1.00 ]
| 0.81 - 0.815 : [ 2 0.00 1.00 ]
#...
| 0.825 - 0.83 : [ 1 0.00 1.00 ]
| 0.83 - 0.835 : [ 1 0.00 1.00 ]
| 0.835 - 0.84 : [ 1 0.00 1.00 ]
| 0.84 - 0.845 : [ 1 0.00 1.00 ]
#...
| 0.855 - 0.86 : [ 2 0.00 1.00 ]
#...
| 1 - 1.005 : [ 6 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 231. 1308 reads; 75697 bp (untrimmed), 75672 (trimmed).
Contig 232. 1350 reads; 81334 bp (untrimmed), 80802 (trimmed).
Contig 233. 1358 reads; 84427 bp (untrimmed), 84402 (trimmed).
Contig 234. 1426 reads; 88725 bp (untrimmed), 88626 (trimmed).
Contig 235. 1428 reads; 96685 bp (untrimmed), 96609 (trimmed).
Contig 236. 1522 reads; 82065 bp (untrimmed), 82065 (trimmed).
Contig 237. 1563 reads; 101340 bp (untrimmed), 101175 (trimmed).
Contig 238. 1597 reads; 94976 bp (untrimmed), 94976 (trimmed).
Contig 239. 1776 reads; 101596 bp (untrimmed), 101291 (trimmed).
Contig 240. 1791 reads; 99994 bp (untrimmed), 99817 (trimmed).
Contig 241. 2089 reads; 128424 bp (untrimmed), 128060 (trimmed).
Contig 242. 2491 reads; 135712 bp (untrimmed), 135431 (trimmed).
Contig 243. 2882 reads; 160640 bp (untrimmed), 160603 (trimmed).
Contig 244. 3209 reads; 174661 bp (untrimmed), 174661 (trimmed).
Contig 245. 3320 reads; 204596 bp (untrimmed), 204492 (trimmed).
Contig 246. 3493 reads; 217987 bp (untrimmed), 217710 (trimmed).
Contig 247. 3544 reads; 191334 bp (untrimmed), 191334 (trimmed).
Contig 248. 3658 reads; 208797 bp (untrimmed), 208600 (trimmed).
Contig 249. 4482 reads; 277937 bp (untrimmed), 277685 (trimmed).
Contig 250. 4548 reads; 273420 bp (untrimmed), 273195 (trimmed).
Contig 251. 4559 reads; 243370 bp (untrimmed), 243347 (trimmed).
Contig 252. 4749 reads; 270786 bp (untrimmed), 270777 (trimmed).
Contig 253. 5410 reads; 327335 bp (untrimmed), 326941 (trimmed).
Contig 254. 5511 reads; 311414 bp (untrimmed), 311294 (trimmed).
Contig 255. 5703 reads; 308304 bp (untrimmed), 307986 (trimmed).
Contig 256. 7440 reads; 422632 bp (untrimmed), 422617 (trimmed).
Contig 257. 21945 reads; 1231758 bp (untrimmed), 1231758 (trimmed).
--------------------------------------------------------------
Totals 120952 reads; 7186458 bp (untrimmed), 7114054 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 7152061 bases = 13.26 +- 5.66 = 0.22 +- 4.35
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 132 total values totalling 919.2200. <6.963788 +/- 5.374402>
#Range: [ 1.04 - 21.84 ]
#Most likely bin: [ 1 - 1.5 ] 31 counts
#Median bin: [ 5.5 - 6 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 31 0.23 0.23 ]
|XXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 14 0.11 0.34 ]
|XXXXXXXX 2 - 2.5 : [ 6 0.05 0.39 ]
|XXXXXX 2.5 - 3 : [ 5 0.04 0.42 ]
#...
|XXXXX 3.5 - 4 : [ 4 0.03 0.45 ]
|X 4 - 4.5 : [ 1 0.01 0.46 ]
|X 4.5 - 5 : [ 1 0.01 0.47 ]
|XXX 5 - 5.5 : [ 2 0.02 0.48 ]
|XXX 5.5 - 6 : [ 2 0.02 0.50 ]
|XXX 6 - 6.5 : [ 2 0.02 0.52 ]
|XXX 6.5 - 7 : [ 2 0.02 0.53 ]
|X 7 - 7.5 : [ 1 0.01 0.54 ]
|XXXX 7.5 - 8 : [ 3 0.02 0.56 ]
#...
|XXXXX 8.5 - 9 : [ 4 0.03 0.59 ]
|X 9 - 9.5 : [ 1 0.01 0.60 ]
|XXX 9.5 - 10 : [ 2 0.02 0.61 ]
|XXX 10 - 10.5 : [ 2 0.02 0.63 ]
|XXXXX 10.5 - 11 : [ 4 0.03 0.66 ]
|XXXX 11 - 11.5 : [ 3 0.02 0.68 ]
|XXXX 11.5 - 12 : [ 3 0.02 0.70 ]
|XXX 12 - 12.5 : [ 2 0.02 0.72 ]
|XXXXXXXXXXXXXX 12.5 - 13 : [ 11 0.08 0.80 ]
|XXXXXXXX 13 - 13.5 : [ 6 0.05 0.85 ]
|XXXXXXXXXXXXX 13.5 - 14 : [ 10 0.08 0.92 ]
|XXXXX 14 - 14.5 : [ 4 0.03 0.95 ]
|XXXXX 14.5 - 15 : [ 4 0.03 0.98 ]
|X 15 - 15.5 : [ 1 0.01 0.99 ]
#...
|X 21.5 - 22 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Histogram of Major Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000
-------------------------------------------------------------------
#Found 67 total values totalling 779.2200. <11.630149 +/- 3.131588>
#Range: [ 2.86 - 21.84 ]
#Most likely bin: [ 12.5 - 13 ] 11 counts
#Median bin: [ 12.5 - 13 ] 11 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 2.5 - 3 : [ 1 0.01 0.01 ]
#...
|XXXX 4 - 4.5 : [ 1 0.01 0.03 ]
|XXXX 4.5 - 5 : [ 1 0.01 0.04 ]
|XXXX 5 - 5.5 : [ 1 0.01 0.06 ]
|XXXX 5.5 - 6 : [ 1 0.01 0.07 ]
|XXXX 6 - 6.5 : [ 1 0.01 0.09 ]
|XXXXXXX 6.5 - 7 : [ 2 0.03 0.12 ]
#...
|XXXXXXXXXXX 7.5 - 8 : [ 3 0.04 0.16 ]
#...
|XXXXXXX 8.5 - 9 : [ 2 0.03 0.19 ]
|XXXX 9 - 9.5 : [ 1 0.01 0.21 ]
|XXXXXXX 9.5 - 10 : [ 2 0.03 0.24 ]
|XXXXXXX 10 - 10.5 : [ 2 0.03 0.27 ]
|XXXXXXXXXXXXXXX 10.5 - 11 : [ 4 0.06 0.33 ]
|XXXXXXXXXXX 11 - 11.5 : [ 3 0.04 0.37 ]
|XXXXXXXXXXX 11.5 - 12 : [ 3 0.04 0.42 ]
|XXXXXXX 12 - 12.5 : [ 2 0.03 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 11 0.16 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 6 0.09 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 10 0.15 0.85 ]
|XXXXXXXXXXXXXXX 14 - 14.5 : [ 4 0.06 0.91 ]
|XXXXXXXXXXXXXXX 14.5 - 15 : [ 4 0.06 0.97 ]
|XXXX 15 - 15.5 : [ 1 0.01 0.99 ]
#...
|XXXX 21.5 - 22 : [ 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 48 2 reads 2655 bases = 1.04 +- 0.19 = 1.04 +- 0.19
Contig 57 2 reads 1856 bases = 1.04 +- 0.21 = 1.04 +- 0.21
Contig 146 2 reads 1575 bases = 1.05 +- 0.22 = 1.05 +- 0.22
Contig 148 2 reads 2272 bases = 1.05 +- 0.22 = 1.05 +- 0.22
Contig 19 2 reads 1580 bases = 1.05 +- 0.22 = 1.05 +- 0.22
Contig 49 2 reads 1607 bases = 1.05 +- 0.22 = 1.05 +- 0.22
Contig 155 2 reads 1605 bases = 1.06 +- 0.25 = 0.94 +- 0.25
Contig 22 2 reads 1727 bases = 1.06 +- 0.24 = 1.06 +- 0.24
Contig 79 2 reads 1242 bases = 1.08 +- 0.27 = 1.08 +- 0.27
Contig 27 2 reads 1987 bases = 1.09 +- 0.29 = 0.68 +- 0.67
Contig 172 3 reads 2104 bases = 1.10 +- 0.42 = 1.10 +- 0.42
Contig 68 2 reads 1675 bases = 1.10 +- 0.29 = 1.10 +- 0.29
Contig 59 2 reads 2315 bases = 1.12 +- 0.33 = 1.12 +- 0.33
Contig 179 3 reads 1432 bases = 1.15 +- 0.51 = 1.15 +- 0.51
Contig 25 2 reads 1460 bases = 1.15 +- 0.36 = 0.85 +- 0.36
Contig 41 2 reads 1892 bases = 1.16 +- 0.37 = 0.78 +- 0.48
Contig 53 2 reads 1656 bases = 1.16 +- 0.36 = 0.83 +- 0.38
Contig 168 2 reads 1560 bases = 1.18 +- 0.39 = 1.18 +- 0.39
Contig 24 2 reads 1234 bases = 1.19 +- 0.39 = 1.19 +- 0.39
Contig 136 2 reads 1850 bases = 1.22 +- 0.41 = 1.22 +- 0.41
Contig 231 1308 reads 75697 bases = 13.56 +- 4.34 = 0.26 +- 4.74
Contig 226 933 reads 54108 bases = 13.58 +- 4.60 = 0.60 +- 3.92
Contig 215 583 reads 33448 bases = 13.62 +- 3.94 = 0.46 +- 3.15
Contig 239 1776 reads 101596 bases = 13.64 +- 4.37 = 0.57 +- 4.25
Contig 213 442 reads 26111 bases = 13.65 +- 4.45 = 1.69 +- 3.98
Contig 252 4749 reads 270786 bases = 13.75 +- 4.66 = 0.16 +- 4.75
Contig 248 3658 reads 208797 bases = 13.80 +- 4.34 = 0.07 +- 4.14
Contig 256 7440 reads 422632 bases = 13.83 +- 9.94 = 0.03 +- 4.32
Contig 254 5511 reads 311414 bases = 13.85 +- 4.54 = 0.31 +- 4.15
Contig 257 21945 reads 1231758 bases = 13.99 +- 5.20 = -0.00 +- 4.25
Contig 240 1791 reads 99994 bases = 14.02 +- 4.47 = 0.33 +- 4.11
Contig 243 2882 reads 160640 bases = 14.17 +- 11.10 = 0.48 +- 4.98
Contig 244 3209 reads 174661 bases = 14.31 +- 4.49 = 0.22 +- 4.36
Contig 242 2491 reads 135712 bases = 14.46 +- 4.85 = 0.07 +- 4.24
Contig 247 3544 reads 191334 bases = 14.54 +- 4.23 = 0.09 +- 4.10
Contig 236 1522 reads 82065 bases = 14.57 +- 4.69 = 0.58 +- 3.84
Contig 255 5703 reads 308304 bases = 14.61 +- 4.61 = -0.04 +- 4.71
Contig 251 4559 reads 243370 bases = 14.76 +- 5.20 = -0.02 +- 4.15
Contig 227 957 reads 50365 bases = 15.02 +- 4.70 = 0.68 +- 4.46
Contig 229 1013 reads 36735 bases = 21.84 +- 5.34 = 0.30 +- 4.48
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1029
HQ Discrepant reads = 92
Chimeric reads = 203
Suspect alignments = 752
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 3.01 SUN/Ultra-2
Equivalent to Phil Green's version 0.990329
Score matrix (set by value of penalty: -2)
A C G T N X
A 1 -2 -2 -2 0 -3
C -2 1 -2 -2 0 -3
G -2 -2 1 -2 0 -3
T -2 -2 -2 1 0 -3
N 0 0 0 0 0 0
X -3 -3 -3 -3 0 -3
gap_init: -4
gap_ext: -3
ins_gap_ext: -3
del_gap_ext: -3
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 30
maxmatch: 55
max_group_size: 20
minscore: 55
bandwidth: 14
indexwordsize: 10
vector_bound: 20
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 13
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -5
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/microbe4/3436094/edit_dir