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
3436109 4000 19 Pelobacter carbinolicus
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Pelobacter_carbinolicus
-------------------------------------------------------------------
Pelobacteraceae, family, d-proteobacteria
Desulfuromonadales, order, d-proteobacteria
delta/epsilon subdivisions, subphylum, proteobacteria
Deltaproteobacteria, class, d-proteobacteria
Pelobacter carbinolicus, species, d-proteobacteria
Pelobacter, genus, d-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3651426
# phrap: 3548535
# db:
altered.
4000000
3733320 +/- 193192
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 0
Number of reads with percent X's >= 20%: 0 = 0.0%
Number of reads with percent X's >= 50%: 0 = 0.0%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 95113
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 0
Number of reads with percent X's >= 20%: 0 = 0.0%
Number of reads with percent X's >= 50%: 0 = 0.0%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 874
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 18472576
C = 22583574
G = 22494869
T = 18505154
N = 446587
X = 811577
GC fraction = 0.54
Total = 83314337
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436109_fasta.screen.contigs
-------------------------------------------------------------------
A 834649
C 1028214
G 993488
T 813959
N 584
fraction GC = 0.55
total bases = 3670894
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 WBJ reads.list > grep.reads.list.WBJ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.WBJ 4 500
-------------------------------------------------------------------
#Found 11855 total values totalling 44496057.0000. <3753.357824 +/- 6742.398473>
#Range: [ 858 - 479680 ]
#Most likely bin: [ 3000 - 3500 ] 4667 counts
#Median bin: [ 3000 - 3500 ] 4667 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 3 0.00 0.00 ]
| 1000 - 1500 : [ 15 0.00 0.00 ]
| 1500 - 2000 : [ 22 0.00 0.00 ]
|X 2000 - 2500 : [ 83 0.01 0.01 ]
|XXXXXXXXXXX 2500 - 3000 : [ 1253 0.11 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4667 0.39 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2997 0.25 0.76 ]
|XXXXXXXXXXXXXXXX 4000 - 4500 : [ 1838 0.16 0.92 ]
|XXXXXX 4500 - 5000 : [ 756 0.06 0.98 ]
|XX 5000 - 5500 : [ 191 0.02 1.00 ]
| 5500 - 6000 : [ 16 0.00 1.00 ]
#...
| 14000 - 14500 : [ 1 0.00 1.00 ]
#...
| 24000 - 24500 : [ 2 0.00 1.00 ]
| 24500 - 25000 : [ 1 0.00 1.00 ]
| 25000 - 25500 : [ 1 0.00 1.00 ]
#...
| 45000 - 45500 : [ 1 0.00 1.00 ]
#...
| 93500 - 94000 : [ 1 0.00 1.00 ]
#...
| 94500 - 95000 : [ 1 0.00 1.00 ]
#...
| 119000 - 119500 : [ 1 0.00 1.00 ]
#...
| 160000 - 160500 : [ 1 0.00 1.00 ]
#...
| 218000 - 218500 : [ 1 0.00 1.00 ]
#...
| 264500 - 265000 : [ 1 0.00 1.00 ]
#...
| 372500 - 373000 : [ 1 0.00 1.00 ]
#...
| 479500 - 480000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep WBT reads.list > grep.reads.list.WBT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.WBT 4 500
-------------------------------------------------------------------
#Found 20320 total values totalling 161708897.0000. <7958.115010 +/- 4123.911900>
#Range: [ 793 - 319531 ]
#Most likely bin: [ 7000 - 7500 ] 3578 counts
#Median bin: [ 7500 - 8000 ] 3195 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 11 0.00 0.00 ]
| 1000 - 1500 : [ 35 0.00 0.00 ]
| 1500 - 2000 : [ 42 0.00 0.00 ]
| 2000 - 2500 : [ 30 0.00 0.01 ]
| 2500 - 3000 : [ 41 0.00 0.01 ]
| 3000 - 3500 : [ 40 0.00 0.01 ]
| 3500 - 4000 : [ 29 0.00 0.01 ]
| 4000 - 4500 : [ 38 0.00 0.01 ]
|X 4500 - 5000 : [ 79 0.00 0.02 ]
|X 5000 - 5500 : [ 84 0.00 0.02 ]
|X 5500 - 6000 : [ 98 0.00 0.03 ]
|XXXXXXXXXXXXX 6000 - 6500 : [ 1131 0.06 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 3183 0.16 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 3578 0.18 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 3195 0.16 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 2769 0.14 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 2199 0.11 0.82 ]
|XXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 1642 0.08 0.90 ]
|XXXXXXXXXXX 9500 - 10000 : [ 1008 0.05 0.95 ]
|XXXXX 10000 - 10500 : [ 489 0.02 0.97 ]
|XXX 10500 - 11000 : [ 291 0.01 0.98 ]
|XX 11000 - 11500 : [ 147 0.01 0.99 ]
|X 11500 - 12000 : [ 90 0.00 1.00 ]
| 12000 - 12500 : [ 37 0.00 1.00 ]
| 12500 - 13000 : [ 16 0.00 1.00 ]
| 13000 - 13500 : [ 6 0.00 1.00 ]
| 13500 - 14000 : [ 1 0.00 1.00 ]
#...
| 44500 - 45000 : [ 1 0.00 1.00 ]
#...
| 51000 - 51500 : [ 1 0.00 1.00 ]
#...
| 97000 - 97500 : [ 1 0.00 1.00 ]
#...
| 103000 - 103500 : [ 1 0.00 1.00 ]
#...
| 110000 - 110500 : [ 1 0.00 1.00 ]
#...
| 134500 - 135000 : [ 1 0.00 1.00 ]
#...
| 161000 - 161500 : [ 1 0.00 1.00 ]
#...
| 168000 - 168500 : [ 1 0.00 1.00 ]
#...
| 247500 - 248000 : [ 1 0.00 1.00 ]
#...
| 251000 - 251500 : [ 1 0.00 1.00 ]
#...
| 319500 - 320000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep WBU reads.list > grep.reads.list.WBU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.WBU 4 500
-------------------------------------------------------------------
#Found 5640 total values totalling 212892115.0000. <37746.828901 +/- 9687.095080>
#Range: [ 359 - 504911 ]
#Most likely bin: [ 35000 - 35500 ] 293 counts
#Median bin: [ 37000 - 37500 ] 256 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
#...
| 1000 - 1500 : [ 1 0.00 0.00 ]
#...
| 5000 - 5500 : [ 1 0.00 0.00 ]
| 5500 - 6000 : [ 1 0.00 0.00 ]
#...
| 9500 - 10000 : [ 1 0.00 0.00 ]
#...
| 10500 - 11000 : [ 1 0.00 0.00 ]
#...
| 23500 - 24000 : [ 1 0.00 0.00 ]
| 24000 - 24500 : [ 1 0.00 0.00 ]
| 24500 - 25000 : [ 1 0.00 0.00 ]
| 25000 - 25500 : [ 3 0.00 0.00 ]
| 25500 - 26000 : [ 3 0.00 0.00 ]
| 26000 - 26500 : [ 2 0.00 0.00 ]
|X 26500 - 27000 : [ 4 0.00 0.00 ]
|X 27000 - 27500 : [ 4 0.00 0.00 ]
|X 27500 - 28000 : [ 9 0.00 0.01 ]
|X 28000 - 28500 : [ 10 0.00 0.01 ]
|XX 28500 - 29000 : [ 14 0.00 0.01 ]
|XX 29000 - 29500 : [ 12 0.00 0.01 ]
|XXX 29500 - 30000 : [ 20 0.00 0.02 ]
|XXXXX 30000 - 30500 : [ 36 0.01 0.02 ]
|XXXXX 30500 - 31000 : [ 37 0.01 0.03 ]
|XXXXXXXX 31000 - 31500 : [ 62 0.01 0.04 ]
|XXXXXXXXXXXXXX 31500 - 32000 : [ 100 0.02 0.06 ]
|XXXXXXXXXXXXXXXXX 32000 - 32500 : [ 123 0.02 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 169 0.03 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 205 0.04 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 238 0.04 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 247 0.04 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 263 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 293 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 275 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 289 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 287 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 256 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 284 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 235 0.04 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 246 0.04 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 205 0.04 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 186 0.03 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 199 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 177 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 166 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 152 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 135 0.02 0.88 ]
|XXXXXXXXXXXXXXXX 42500 - 43000 : [ 116 0.02 0.90 ]
|XXXXXXXXXXXXXXXXX 43000 - 43500 : [ 127 0.02 0.92 ]
|XXXXXXXXXXXXXX 43500 - 44000 : [ 102 0.02 0.94 ]
|XXXXXXXXXXXXX 44000 - 44500 : [ 93 0.02 0.96 ]
|XXXXXXXXXXX 44500 - 45000 : [ 79 0.01 0.97 ]
|XXXXXXXX 45000 - 45500 : [ 61 0.01 0.98 ]
|XXXXXXX 45500 - 46000 : [ 54 0.01 0.99 ]
|XXX 46000 - 46500 : [ 24 0.00 0.99 ]
|XX 46500 - 47000 : [ 13 0.00 1.00 ]
|X 47000 - 47500 : [ 7 0.00 1.00 ]
| 47500 - 48000 : [ 2 0.00 1.00 ]
#...
| 53500 - 54000 : [ 1 0.00 1.00 ]
#...
| 122000 - 122500 : [ 1 0.00 1.00 ]
#...
| 183500 - 184000 : [ 1 0.00 1.00 ]
#...
| 237000 - 237500 : [ 1 0.00 1.00 ]
#...
| 278000 - 278500 : [ 1 0.00 1.00 ]
#...
| 346500 - 347000 : [ 1 0.00 1.00 ]
#...
| 504500 - 505000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# WBJ 3489 +- 769 (n=6161)
# WBU 37330 +- 3909 (n=2933)
# WBT 7819 +- 1385 (n=10158)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436109_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
WBJ 31104 -1 -1 90 599 27445 98 608 100 614
WBT 53760 -1 -1 95 624 46796 99 649 100 647
WBU 29376 -1 -1 85 417 20872 90 547 100 535
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
WBJ 13424 98 605 100 612 14021 99 611 100 616
WBT 23134 99 649 100 648 23662 99 650 100 647
WBU 10329 87 530 100 512 10543 92 562 100 557
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436109_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 95113 48333 86.62 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 3436109_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 95113 total values totalling 56934294.0000. <598.596343 +/- 173.477534>
#Range: [ 12 - 872 ]
#Most likely bin: [ 700 - 750 ] 22848 counts
#Median bin: [ 650 - 700 ] 21182 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 50 : [ 1214 0.01 0.01 ]
|XXX 50 - 100 : [ 1788 0.02 0.03 ]
|XX 100 - 150 : [ 1398 0.01 0.05 ]
|XX 150 - 200 : [ 1272 0.01 0.06 ]
|XX 200 - 250 : [ 1366 0.01 0.07 ]
|XXX 250 - 300 : [ 1472 0.02 0.09 ]
|XXX 300 - 350 : [ 1638 0.02 0.11 ]
|XXX 350 - 400 : [ 1935 0.02 0.13 ]
|XXXX 400 - 450 : [ 2447 0.03 0.15 ]
|XXXXXX 450 - 500 : [ 3503 0.04 0.19 ]
|XXXXXXXXX 500 - 550 : [ 5109 0.05 0.24 ]
|XXXXXXXXXXXXXX 550 - 600 : [ 7732 0.08 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 12850 0.14 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 21182 0.22 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 22848 0.24 0.92 ]
|XXXXXXXXXXXX 750 - 800 : [ 7082 0.07 1.00 ]
| 800 - 850 : [ 271 0.00 1.00 ]
| 850 - 900 : [ 6 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for WBJ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep WBJ 3436109_fasta.screen.trimQ15.SaF > reads.trim15.WBJ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.WBJ.rl 2 50
-------------------------------------------------------------------
#Found 27445 total values totalling 16444050.0000. <599.163782 +/- 159.034373>
#Range: [ 20 - 823 ]
#Most likely bin: [ 700 - 750 ] 7159 counts
#Median bin: [ 650 - 700 ] 6608 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 109 0.00 0.00 ]
|XX 50 - 100 : [ 335 0.01 0.02 ]
|XX 100 - 150 : [ 363 0.01 0.03 ]
|XX 150 - 200 : [ 362 0.01 0.04 ]
|XX 200 - 250 : [ 424 0.02 0.06 ]
|XXX 250 - 300 : [ 484 0.02 0.08 ]
|XXX 300 - 350 : [ 553 0.02 0.10 ]
|XXXX 350 - 400 : [ 676 0.02 0.12 ]
|XXXXX 400 - 450 : [ 836 0.03 0.15 ]
|XXXXXXX 450 - 500 : [ 1190 0.04 0.19 ]
|XXXXXXXXX 500 - 550 : [ 1662 0.06 0.25 ]
|XXXXXXXXXXXXX 550 - 600 : [ 2298 0.08 0.34 ]
|XXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3382 0.12 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 6608 0.24 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7159 0.26 0.96 ]
|XXXXXX 750 - 800 : [ 985 0.04 1.00 ]
| 800 - 850 : [ 19 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for WBT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep WBT 3436109_fasta.screen.trimQ15.SaF > reads.trim15.WBT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.WBT.rl 2 50
-------------------------------------------------------------------
#Found 46796 total values totalling 30141340.0000. <644.100778 +/- 134.383594>
#Range: [ 16 - 841 ]
#Most likely bin: [ 700 - 750 ] 13493 counts
#Median bin: [ 650 - 700 ] 11467 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 82 0.00 0.00 ]
|X 50 - 100 : [ 325 0.01 0.01 ]
|X 100 - 150 : [ 365 0.01 0.02 ]
|X 150 - 200 : [ 365 0.01 0.02 ]
|X 200 - 250 : [ 403 0.01 0.03 ]
|X 250 - 300 : [ 457 0.01 0.04 ]
|XX 300 - 350 : [ 528 0.01 0.05 ]
|XX 350 - 400 : [ 648 0.01 0.07 ]
|XX 400 - 450 : [ 763 0.02 0.08 ]
|XXX 450 - 500 : [ 1097 0.02 0.11 ]
|XXXXX 500 - 550 : [ 1673 0.04 0.14 ]
|XXXXXXXXX 550 - 600 : [ 3089 0.07 0.21 ]
|XXXXXXXXXXXXXXXXXXX 600 - 650 : [ 6455 0.14 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 11467 0.25 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 13493 0.29 0.88 ]
|XXXXXXXXXXXXXXXX 750 - 800 : [ 5434 0.12 1.00 ]
| 800 - 850 : [ 152 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for WBU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep WBU 3436109_fasta.screen.trimQ15.SaF > reads.trim15.WBU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.WBU.rl 2 50
-------------------------------------------------------------------
#Found 20872 total values totalling 10348904.0000. <495.827137 +/- 219.520189>
#Range: [ 12 - 872 ]
#Most likely bin: [ 650 - 700 ] 3107 counts
#Median bin: [ 550 - 600 ] 2345 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXX 0 - 50 : [ 1023 0.05 0.05 ]
|XXXXXXXXXXXXXXX 50 - 100 : [ 1128 0.05 0.10 ]
|XXXXXXXXX 100 - 150 : [ 670 0.03 0.14 ]
|XXXXXXX 150 - 200 : [ 545 0.03 0.16 ]
|XXXXXXX 200 - 250 : [ 539 0.03 0.19 ]
|XXXXXXX 250 - 300 : [ 531 0.03 0.21 ]
|XXXXXXX 300 - 350 : [ 557 0.03 0.24 ]
|XXXXXXXX 350 - 400 : [ 611 0.03 0.27 ]
|XXXXXXXXXXX 400 - 450 : [ 848 0.04 0.31 ]
|XXXXXXXXXXXXXXXX 450 - 500 : [ 1216 0.06 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 1774 0.08 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 2345 0.11 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3013 0.14 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3107 0.15 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2196 0.11 0.96 ]
|XXXXXXXXX 750 - 800 : [ 663 0.03 0.99 ]
|X 800 - 850 : [ 100 0.00 1.00 ]
| 850 - 900 : [ 6 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AKBK
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436109
-------------------------------------------------------------------
WBJ.000001.000100 pCC1Fos.fa.4 LRS.fasta
WBJ.000101.000200 pCC1Fos.fa.4 LRS.fasta
WBT.000001.000100 pCUGIblu21.fa.2 LRS.fasta
WBT.000101.000200 pCUGIblu21.fa.2 LRS.fasta
WBT.000201.000300 pCUGIblu21.fa.2 LRS.fasta
WBT.000301.000400 pCUGIblu21.fa.2 LRS.fasta
WBU.000001.000100 pCC1FOS.fasta LRS.fasta
WBU.000101.000200 pCC1FOS.fasta ../SCREENME_TOO.fasta LRS.fasta
WBJ.000001.000100 pCC1Fos.fa.4 LRS.fasta
WBJ.000101.000200 pCC1Fos.fa.4 LRS.fasta
WBT.000001.000100 pCUGIblu21.fa.2 LRS.fasta
WBT.000101.000200 pCUGIblu21.fa.2 LRS.fasta
WBT.000201.000300 pCUGIblu21.fa.2 LRS.fasta
WBT.000301.000400 pCUGIblu21.fa.2 LRS.fasta
WBU.000001.000100 pCC1FOS.fasta LRS.fasta
WBU.000101.000200 pCC1FOS.fasta ../SCREENME_TOO.fasta LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436109_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436109_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 94145 total values totalling 51579.9902. <0.547878 +/- 0.062901>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.57 - 0.575 ] 3785 counts
#Median bin: [ 0.55 - 0.555 ] 3620 counts
| 0 - 0.005 : [ 4 0.00 0.00 ]
| 0.005 - 0.01 : [ 1 0.00 0.00 ]
#...
| 0.08 - 0.085 : [ 1 0.00 0.00 ]
#...
| 0.09 - 0.095 : [ 1 0.00 0.00 ]
#...
| 0.1 - 0.105 : [ 1 0.00 0.00 ]
#...
| 0.115 - 0.12 : [ 1 0.00 0.00 ]
| 0.12 - 0.125 : [ 1 0.00 0.00 ]
| 0.125 - 0.13 : [ 1 0.00 0.00 ]
| 0.13 - 0.135 : [ 1 0.00 0.00 ]
| 0.135 - 0.14 : [ 1 0.00 0.00 ]
#...
| 0.15 - 0.155 : [ 3 0.00 0.00 ]
| 0.155 - 0.16 : [ 2 0.00 0.00 ]
#...
| 0.17 - 0.175 : [ 2 0.00 0.00 ]
| 0.175 - 0.18 : [ 1 0.00 0.00 ]
#...
| 0.2 - 0.205 : [ 1 0.00 0.00 ]
#...
| 0.21 - 0.215 : [ 2 0.00 0.00 ]
| 0.215 - 0.22 : [ 2 0.00 0.00 ]
| 0.22 - 0.225 : [ 5 0.00 0.00 ]
| 0.225 - 0.23 : [ 6 0.00 0.00 ]
| 0.23 - 0.235 : [ 3 0.00 0.00 ]
| 0.235 - 0.24 : [ 2 0.00 0.00 ]
| 0.24 - 0.245 : [ 3 0.00 0.00 ]
| 0.245 - 0.25 : [ 2 0.00 0.00 ]
| 0.25 - 0.255 : [ 2 0.00 0.00 ]
| 0.255 - 0.26 : [ 5 0.00 0.00 ]
| 0.26 - 0.265 : [ 3 0.00 0.00 ]
| 0.265 - 0.27 : [ 3 0.00 0.00 ]
| 0.27 - 0.275 : [ 10 0.00 0.00 ]
| 0.275 - 0.28 : [ 9 0.00 0.00 ]
| 0.28 - 0.285 : [ 18 0.00 0.00 ]
| 0.285 - 0.29 : [ 15 0.00 0.00 ]
| 0.29 - 0.295 : [ 20 0.00 0.00 ]
| 0.295 - 0.3 : [ 17 0.00 0.00 ]
| 0.3 - 0.305 : [ 19 0.00 0.00 ]
| 0.305 - 0.31 : [ 38 0.00 0.00 ]
| 0.31 - 0.315 : [ 41 0.00 0.00 ]
| 0.315 - 0.32 : [ 32 0.00 0.00 ]
|X 0.32 - 0.325 : [ 57 0.00 0.00 ]
|X 0.325 - 0.33 : [ 69 0.00 0.00 ]
|X 0.33 - 0.335 : [ 80 0.00 0.01 ]
|X 0.335 - 0.34 : [ 75 0.00 0.01 ]
|X 0.34 - 0.345 : [ 92 0.00 0.01 ]
|XX 0.345 - 0.35 : [ 175 0.00 0.01 ]
|X 0.35 - 0.355 : [ 84 0.00 0.01 ]
|X 0.355 - 0.36 : [ 88 0.00 0.01 ]
|X 0.36 - 0.365 : [ 140 0.00 0.01 ]
|X 0.365 - 0.37 : [ 105 0.00 0.01 ]
|X 0.37 - 0.375 : [ 105 0.00 0.01 ]
|XX 0.375 - 0.38 : [ 159 0.00 0.02 ]
|X 0.38 - 0.385 : [ 129 0.00 0.02 ]
|XX 0.385 - 0.39 : [ 178 0.00 0.02 ]
|XX 0.39 - 0.395 : [ 188 0.00 0.02 ]
|XX 0.395 - 0.4 : [ 175 0.00 0.02 ]
|XXX 0.4 - 0.405 : [ 256 0.00 0.03 ]
|XX 0.405 - 0.41 : [ 221 0.00 0.03 ]
|XXX 0.41 - 0.415 : [ 276 0.00 0.03 ]
|XXX 0.415 - 0.42 : [ 298 0.00 0.03 ]
|XXX 0.42 - 0.425 : [ 326 0.00 0.04 ]
|XXXX 0.425 - 0.43 : [ 365 0.00 0.04 ]
|XXXX 0.43 - 0.435 : [ 406 0.00 0.05 ]
|XXXXX 0.435 - 0.44 : [ 452 0.00 0.05 ]
|XXXXX 0.44 - 0.445 : [ 519 0.01 0.06 ]
|XXXXXX 0.445 - 0.45 : [ 597 0.01 0.06 ]
|XXXXXXX 0.45 - 0.455 : [ 669 0.01 0.07 ]
|XXXXXXXX 0.455 - 0.46 : [ 763 0.01 0.08 ]
|XXXXXXXXX 0.46 - 0.465 : [ 865 0.01 0.09 ]
|XXXXXXXXXX 0.465 - 0.47 : [ 922 0.01 0.10 ]
|XXXXXXXXXX 0.47 - 0.475 : [ 991 0.01 0.11 ]
|XXXXXXXXXXXX 0.475 - 0.48 : [ 1131 0.01 0.12 ]
|XXXXXXXXXXXXX 0.48 - 0.485 : [ 1272 0.01 0.13 ]
|XXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1414 0.02 0.15 ]
|XXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1489 0.02 0.16 ]
|XXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1489 0.02 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 2211 0.02 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 2100 0.02 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 2148 0.02 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 2373 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 2512 0.03 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 2758 0.03 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 2950 0.03 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 3097 0.03 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 3360 0.04 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 3398 0.04 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 3620 0.04 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 3672 0.04 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 3634 0.04 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 3717 0.04 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 3785 0.04 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 3507 0.04 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 3464 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 3183 0.03 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 3024 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 2581 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 2664 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 2183 0.02 0.88 ]
|XXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 2010 0.02 0.90 ]
|XXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1700 0.02 0.92 ]
|XXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1475 0.02 0.93 ]
|XXXXXXXXXXXXX 0.625 - 0.63 : [ 1276 0.01 0.95 ]
|XXXXXXXXXXX 0.63 - 0.635 : [ 1011 0.01 0.96 ]
|XXXXXXXX 0.635 - 0.64 : [ 787 0.01 0.97 ]
|XXXXXXX 0.64 - 0.645 : [ 688 0.01 0.97 ]
|XXXXX 0.645 - 0.65 : [ 493 0.01 0.98 ]
|XXXX 0.65 - 0.655 : [ 353 0.00 0.98 ]
|XXX 0.655 - 0.66 : [ 290 0.00 0.99 ]
|XX 0.66 - 0.665 : [ 203 0.00 0.99 ]
|XX 0.665 - 0.67 : [ 210 0.00 0.99 ]
|X 0.67 - 0.675 : [ 120 0.00 0.99 ]
|X 0.675 - 0.68 : [ 108 0.00 0.99 ]
|X 0.68 - 0.685 : [ 67 0.00 0.99 ]
|X 0.685 - 0.69 : [ 51 0.00 1.00 ]
| 0.69 - 0.695 : [ 45 0.00 1.00 ]
| 0.695 - 0.7 : [ 38 0.00 1.00 ]
| 0.7 - 0.705 : [ 34 0.00 1.00 ]
| 0.705 - 0.71 : [ 30 0.00 1.00 ]
| 0.71 - 0.715 : [ 24 0.00 1.00 ]
| 0.715 - 0.72 : [ 9 0.00 1.00 ]
| 0.72 - 0.725 : [ 14 0.00 1.00 ]
| 0.725 - 0.73 : [ 8 0.00 1.00 ]
| 0.73 - 0.735 : [ 11 0.00 1.00 ]
| 0.735 - 0.74 : [ 11 0.00 1.00 ]
| 0.74 - 0.745 : [ 12 0.00 1.00 ]
| 0.745 - 0.75 : [ 1 0.00 1.00 ]
| 0.75 - 0.755 : [ 9 0.00 1.00 ]
| 0.755 - 0.76 : [ 3 0.00 1.00 ]
| 0.76 - 0.765 : [ 4 0.00 1.00 ]
| 0.765 - 0.77 : [ 3 0.00 1.00 ]
| 0.77 - 0.775 : [ 2 0.00 1.00 ]
| 0.775 - 0.78 : [ 5 0.00 1.00 ]
| 0.78 - 0.785 : [ 9 0.00 1.00 ]
| 0.785 - 0.79 : [ 3 0.00 1.00 ]
| 0.79 - 0.795 : [ 7 0.00 1.00 ]
#...
| 0.8 - 0.805 : [ 3 0.00 1.00 ]
| 0.805 - 0.81 : [ 3 0.00 1.00 ]
| 0.81 - 0.815 : [ 1 0.00 1.00 ]
| 0.815 - 0.82 : [ 5 0.00 1.00 ]
| 0.82 - 0.825 : [ 3 0.00 1.00 ]
| 0.825 - 0.83 : [ 5 0.00 1.00 ]
| 0.83 - 0.835 : [ 3 0.00 1.00 ]
#...
| 0.845 - 0.85 : [ 1 0.00 1.00 ]
#...
| 0.865 - 0.87 : [ 1 0.00 1.00 ]
#...
| 0.905 - 0.91 : [ 1 0.00 1.00 ]
#...
| 0.92 - 0.925 : [ 1 0.00 1.00 ]
#...
| 0.945 - 0.95 : [ 1 0.00 1.00 ]
#...
| 0.96 - 0.965 : [ 3 0.00 1.00 ]
| 0.965 - 0.97 : [ 1 0.00 1.00 ]
| 0.97 - 0.975 : [ 1 0.00 1.00 ]
#...
| 0.98 - 0.985 : [ 2 0.00 1.00 ]
| 0.985 - 0.99 : [ 1 0.00 1.00 ]
| 0.99 - 0.995 : [ 1 0.00 1.00 ]
#...
|XX 1 - 1.005 : [ 144 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 94. 582 reads; 33617 bp (untrimmed), 33408 (trimmed).
Contig 95. 602 reads; 30055 bp (untrimmed), 29878 (trimmed).
Contig 96. 659 reads; 40846 bp (untrimmed), 40497 (trimmed).
Contig 97. 671 reads; 24225 bp (untrimmed), 24189 (trimmed).
Contig 98. 784 reads; 33086 bp (untrimmed), 32951 (trimmed).
Contig 99. 835 reads; 34288 bp (untrimmed), 34048 (trimmed).
Contig 100. 1085 reads; 62540 bp (untrimmed), 62106 (trimmed).
Contig 101. 1120 reads; 37284 bp (untrimmed), 37223 (trimmed).
Contig 102. 1202 reads; 50710 bp (untrimmed), 50059 (trimmed).
Contig 103. 1215 reads; 58083 bp (untrimmed), 57995 (trimmed).
Contig 104. 1360 reads; 65435 bp (untrimmed), 65403 (trimmed).
Contig 105. 1477 reads; 63461 bp (untrimmed), 63460 (trimmed).
Contig 106. 1623 reads; 74250 bp (untrimmed), 74190 (trimmed).
Contig 107. 1878 reads; 74450 bp (untrimmed), 74320 (trimmed).
Contig 108. 1989 reads; 76722 bp (untrimmed), 76695 (trimmed).
Contig 109. 2106 reads; 88335 bp (untrimmed), 88253 (trimmed).
Contig 110. 2176 reads; 94035 bp (untrimmed), 93985 (trimmed).
Contig 111. 3090 reads; 118336 bp (untrimmed), 118294 (trimmed).
Contig 112. 3182 reads; 111112 bp (untrimmed), 110772 (trimmed).
Contig 113. 3606 reads; 123119 bp (untrimmed), 123043 (trimmed).
Contig 114. 3793 reads; 126883 bp (untrimmed), 126860 (trimmed).
Contig 115. 4033 reads; 124336 bp (untrimmed), 124253 (trimmed).
Contig 116. 5876 reads; 204480 bp (untrimmed), 204453 (trimmed).
Contig 117. 7710 reads; 316305 bp (untrimmed), 316086 (trimmed).
Contig 118. 8071 reads; 246267 bp (untrimmed), 246232 (trimmed).
Contig 119. 9901 reads; 324000 bp (untrimmed), 323608 (trimmed).
Contig 120. 17157 reads; 581595 bp (untrimmed), 581589 (trimmed).
--------------------------------------------------------------
Totals 94239 reads; 3670894 bp (untrimmed), 3651426 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3658390 bases = 20.23 +- 10.12 = 0.84 +- 8.80
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 92 total values totalling 999.9200. <10.868696 +/- 8.764834>
#Range: [ 1.07 - 38.40 ]
#Most likely bin: [ 1 - 1.5 ] 7 counts
#Median bin: [ 8 - 8.5 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 7 0.08 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 5 0.05 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 5 0.05 0.18 ]
|XXXXXXXXXXXXXXXXX 2.5 - 3 : [ 3 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 6 0.07 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 5 0.05 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 5 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 4 0.04 0.43 ]
|XXXXXXXXXXX 5 - 5.5 : [ 2 0.02 0.46 ]
#...
|XXXXXX 6 - 6.5 : [ 1 0.01 0.47 ]
#...
|XXXXXXXXXXX 7 - 7.5 : [ 2 0.02 0.49 ]
#...
|XXXXXXXXXXX 8 - 8.5 : [ 2 0.02 0.51 ]
#...
|XXXXXXXXXXX 9.5 - 10 : [ 2 0.02 0.53 ]
|XXXXXX 10 - 10.5 : [ 1 0.01 0.54 ]
#...
|XXXXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.03 0.58 ]
|XXXXXX 12 - 12.5 : [ 1 0.01 0.59 ]
|XXXXXX 12.5 - 13 : [ 1 0.01 0.60 ]
#...
|XXXXXXXXXXXXXXXXX 13.5 - 14 : [ 3 0.03 0.63 ]
|XXXXXXXXXXXXXXXXX 14 - 14.5 : [ 3 0.03 0.66 ]
#...
|XXXXXX 15 - 15.5 : [ 1 0.01 0.67 ]
|XXXXXX 15.5 - 16 : [ 1 0.01 0.68 ]
|XXXXXXXXXXX 16 - 16.5 : [ 2 0.02 0.71 ]
|XXXXXX 16.5 - 17 : [ 1 0.01 0.72 ]
|XXXXXXXXXXX 17 - 17.5 : [ 2 0.02 0.74 ]
|XXXXXX 17.5 - 18 : [ 1 0.01 0.75 ]
|XXXXXXXXXXX 18 - 18.5 : [ 2 0.02 0.77 ]
|XXXXXXXXXXXXXXXXX 18.5 - 19 : [ 3 0.03 0.80 ]
|XXXXXXXXXXX 19 - 19.5 : [ 2 0.02 0.83 ]
|XXXXXX 19.5 - 20 : [ 1 0.01 0.84 ]
|XXXXXXXXXXX 20 - 20.5 : [ 2 0.02 0.86 ]
#...
|XXXXXX 21.5 - 22 : [ 1 0.01 0.87 ]
#...
|XXXXXXXXXXX 22.5 - 23 : [ 2 0.02 0.89 ]
|XXXXXXXXXXXXXXXXX 23 - 23.5 : [ 3 0.03 0.92 ]
|XXXXXX 23.5 - 24 : [ 1 0.01 0.93 ]
|XXXXXX 24 - 24.5 : [ 1 0.01 0.95 ]
#...
|XXXXXX 25 - 25.5 : [ 1 0.01 0.96 ]
|XXXXXX 25.5 - 26 : [ 1 0.01 0.97 ]
#...
|XXXXXX 28.5 - 29 : [ 1 0.01 0.98 ]
#...
|XXXXXX 35.5 - 36 : [ 1 0.01 0.99 ]
#...
|XXXXXX 38 - 38.5 : [ 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 60 total values totalling 884.5600. <14.742667 +/- 7.497511>
#Range: [ 3.19 - 38.40 ]
#Most likely bin: [ 13.5 - 14 ] 3 counts
#Median bin: [ 14 - 14.5 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 2 0.03 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 2 0.03 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 3 0.05 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 3 0.05 0.17 ]
|XXXXXXXXXXXXX 5 - 5.5 : [ 1 0.02 0.18 ]
#...
|XXXXXXXXXXXXX 6 - 6.5 : [ 1 0.02 0.20 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 2 0.03 0.23 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 2 0.03 0.27 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 2 0.03 0.30 ]
|XXXXXXXXXXXXX 10 - 10.5 : [ 1 0.02 0.32 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.05 0.37 ]
|XXXXXXXXXXXXX 12 - 12.5 : [ 1 0.02 0.38 ]
|XXXXXXXXXXXXX 12.5 - 13 : [ 1 0.02 0.40 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 3 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 3 0.05 0.50 ]
#...
|XXXXXXXXXXXXX 15 - 15.5 : [ 1 0.02 0.52 ]
|XXXXXXXXXXXXX 15.5 - 16 : [ 1 0.02 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 16 - 16.5 : [ 2 0.03 0.57 ]
|XXXXXXXXXXXXX 16.5 - 17 : [ 1 0.02 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 17 - 17.5 : [ 2 0.03 0.62 ]
|XXXXXXXXXXXXX 17.5 - 18 : [ 1 0.02 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 18 - 18.5 : [ 2 0.03 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 18.5 - 19 : [ 3 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 19 - 19.5 : [ 2 0.03 0.75 ]
|XXXXXXXXXXXXX 19.5 - 20 : [ 1 0.02 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 20 - 20.5 : [ 2 0.03 0.80 ]
#...
|XXXXXXXXXXXXX 21.5 - 22 : [ 1 0.02 0.82 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 22.5 - 23 : [ 2 0.03 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 23 - 23.5 : [ 3 0.05 0.90 ]
|XXXXXXXXXXXXX 23.5 - 24 : [ 1 0.02 0.92 ]
|XXXXXXXXXXXXX 24 - 24.5 : [ 1 0.02 0.93 ]
#...
|XXXXXXXXXXXXX 25 - 25.5 : [ 1 0.02 0.95 ]
|XXXXXXXXXXXXX 25.5 - 26 : [ 1 0.02 0.97 ]
#...
|XXXXXXXXXXXXX 28.5 - 29 : [ 1 0.02 0.98 ]
#...
|XXXXXXXXXXXXX 38 - 38.5 : [ 1 0.02 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 12 2 reads 892 bases = 1.07 +- 0.25 = 1.07 +- 0.25
Contig 22 2 reads 904 bases = 1.11 +- 0.31 = 1.11 +- 0.31
Contig 27 3 reads 871 bases = 1.12 +- 0.47 = 1.00 +- 0.00
Contig 25 3 reads 888 bases = 1.14 +- 0.50 = 1.14 +- 0.50
Contig 34 3 reads 844 bases = 1.16 +- 0.53 = 1.16 +- 0.53
Contig 30 3 reads 1815 bases = 1.39 +- 0.49 = 0.42 +- 1.24
Contig 13 2 reads 1011 bases = 1.46 +- 0.50 = 0.00 +- 0.73
Contig 14 2 reads 857 bases = 1.50 +- 0.50 = 1.50 +- 0.50
Contig 26 3 reads 1067 bases = 1.63 +- 0.59 = 0.49 +- 0.50
Contig 15 2 reads 779 bases = 1.88 +- 0.33 = 1.88 +- 0.33
Contig 31 3 reads 1126 bases = 1.90 +- 0.67 = 1.90 +- 0.67
Contig 20 2 reads 562 bases = 1.96 +- 0.19 = -0.04 +- 0.19
Contig 40 4 reads 1084 bases = 2.13 +- 0.79 = 2.13 +- 0.79
Contig 35 4 reads 1194 bases = 2.31 +- 1.10 = 2.31 +- 1.10
Contig 44 5 reads 1770 bases = 2.35 +- 1.08 = 2.35 +- 1.08
Contig 39 4 reads 771 bases = 2.36 +- 0.80 = 0.01 +- 0.21
Contig 36 4 reads 577 bases = 2.41 +- 0.82 = -0.01 +- 0.31
Contig 42 4 reads 1118 bases = 2.57 +- 0.97 = -0.01 +- 0.33
Contig 33 3 reads 821 bases = 2.71 +- 0.67 = 0.71 +- 0.67
Contig 41 4 reads 883 bases = 2.95 +- 1.06 = 0.00 +- 0.35
Contig 109 2106 reads 88335 bases = 18.65 +- 7.26 = 1.41 +- 8.61
Contig 98 784 reads 33086 bases = 18.86 +- 6.64 = 5.44 +- 8.49
Contig 99 835 reads 34288 bases = 19.12 +- 9.58 = 0.36 +- 9.08
Contig 117 7710 reads 316305 bases = 19.20 +- 8.45 = 0.05 +- 9.39
Contig 107 1878 reads 74450 bases = 19.78 +- 9.11 = 1.35 +- 7.54
Contig 108 1989 reads 76722 bases = 20.47 +- 8.70 = 1.00 +- 8.51
Contig 111 3090 reads 118336 bases = 20.49 +- 8.64 = 0.61 +- 8.96
Contig 97 671 reads 24225 bases = 21.97 +- 9.64 = 2.49 +- 10.30
Contig 112 3182 reads 111112 bases = 22.61 +- 9.25 = 0.21 +- 9.01
Contig 116 5876 reads 204480 bases = 22.69 +- 8.45 = 0.73 +- 9.64
Contig 114 3793 reads 126883 bases = 23.09 +- 10.10 = 1.23 +- 8.91
Contig 120 17157 reads 581595 bases = 23.15 +- 9.51 = 0.28 +- 8.74
Contig 113 3606 reads 123119 bases = 23.18 +- 10.53 = 1.86 +- 9.52
Contig 101 1120 reads 37284 bases = 23.79 +- 9.37 = 0.34 +- 9.37
Contig 119 9901 reads 324000 bases = 24.05 +- 10.19 = 0.30 +- 8.43
Contig 115 4033 reads 124336 bases = 25.40 +- 10.24 = -0.06 +- 7.91
Contig 118 8071 reads 246267 bases = 25.87 +- 8.79 = 0.14 +- 9.33
Contig 91 486 reads 13405 bases = 28.55 +- 6.96 = 1.98 +- 5.14
Contig 72 44 reads 562 bases = 35.73 +- 13.06 = 35.73 +- 13.06
Contig 88 330 reads 6432 bases = 38.40 +- 14.58 = 1.73 +- 16.72
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 44
Chimeric reads = 1778
Suspect alignments = 1854
-------------------------------------------------------------------
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/microbe1/3436109/edit_dir.12Nov03.QD