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
3634486 3000 NULL Nitrosomonas eutropha
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Nitrosomonas_eutropha
-------------------------------------------------------------------
Nitrosomonadaceae, family, b-proteobacteria
Nitrosomonadales, order, b-proteobacteria
Betaproteobacteria, class, b-proteobacteria
Nitrosomonas eutropha, species, b-proteobacteria
Nitrosomonas, genus, b-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2740017
# phrap: 2492555
# db:
altered.
3000000
2744190 +/- 207184
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 5757
Number of reads with percent X's >= 20%: 129 = 0.4%
Number of reads with percent X's >= 50%: 78 = 0.2%
Number of reads with percent X's >= 80%: 14 = 0.0%
Total reads in project: 32806
Total bp X'd : 269378
reads >= 20% >= 50% >= 80% screened
Nr with L09136 5531 92 51 5
Nr with pCC1Fos 184 1 1 0
Nr with pMCL200_JGI_XZX+XZK 42 36 26 9
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 70
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: 431
Total bp X'd : 2698
reads >= 20% >= 50% >= 80% screened
Nr with L09136 68 0 0 0
Nr with pCC1Fos 1 0 0 0
Nr with pMCL200_JGI_XZX+XZK 1 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 8185504
C = 7758715
G = 7796035
T = 7996742
N = 149076
X = 269378
GC fraction = 0.48
Total = 32155450
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634486_fasta.screen.contigs
-------------------------------------------------------------------
A 713751
C 665762
G 666564
T 702717
N 111
fraction GC = 0.48
total bases = 2748905
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 AUSC reads.list > grep.reads.list.AUSC
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AUSC 4 500
-------------------------------------------------------------------
#Found 6299 total values totalling 31250879.0000. <4961.244483 +/- 22460.842679>
#Range: [ 752 - 444922 ]
#Most likely bin: [ 2500 - 3000 ] 2004 counts
#Median bin: [ 3000 - 3500 ] 1943 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 6 0.00 0.00 ]
| 1000 - 1500 : [ 20 0.00 0.00 ]
|X 1500 - 2000 : [ 30 0.00 0.01 ]
|XXXXXXXXXXXXX 2000 - 2500 : [ 631 0.10 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2004 0.32 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1943 0.31 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1358 0.22 0.95 ]
|XXXXX 4000 - 4500 : [ 246 0.04 0.99 ]
| 4500 - 5000 : [ 2 0.00 0.99 ]
| 5000 - 5500 : [ 1 0.00 0.99 ]
#...
| 9000 - 9500 : [ 1 0.00 0.99 ]
#...
| 26000 - 26500 : [ 1 0.00 0.99 ]
#...
| 28000 - 28500 : [ 1 0.00 0.99 ]
#...
| 32000 - 32500 : [ 1 0.00 0.99 ]
#...
| 36500 - 37000 : [ 1 0.00 0.99 ]
#...
| 38000 - 38500 : [ 1 0.00 0.99 ]
#...
| 48000 - 48500 : [ 1 0.00 0.99 ]
#...
| 55500 - 56000 : [ 2 0.00 0.99 ]
#...
| 57000 - 57500 : [ 1 0.00 0.99 ]
#...
| 65500 - 66000 : [ 1 0.00 0.99 ]
#...
| 69000 - 69500 : [ 1 0.00 0.99 ]
#...
| 101000 - 101500 : [ 1 0.00 0.99 ]
| 101500 - 102000 : [ 2 0.00 0.99 ]
#...
| 107500 - 108000 : [ 1 0.00 0.99 ]
#...
| 110500 - 111000 : [ 1 0.00 0.99 ]
| 111000 - 111500 : [ 1 0.00 0.99 ]
#...
| 116500 - 117000 : [ 1 0.00 0.99 ]
#...
| 122000 - 122500 : [ 1 0.00 0.99 ]
#...
| 141000 - 141500 : [ 1 0.00 0.99 ]
#...
| 150500 - 151000 : [ 2 0.00 0.99 ]
#...
| 172500 - 173000 : [ 1 0.00 0.99 ]
#...
| 178000 - 178500 : [ 1 0.00 0.99 ]
#...
| 188500 - 189000 : [ 1 0.00 0.99 ]
#...
| 189500 - 190000 : [ 1 0.00 1.00 ]
| 190000 - 190500 : [ 1 0.00 1.00 ]
| 190500 - 191000 : [ 2 0.00 1.00 ]
| 191000 - 191500 : [ 2 0.00 1.00 ]
#...
| 196500 - 197000 : [ 1 0.00 1.00 ]
#...
| 214000 - 214500 : [ 1 0.00 1.00 ]
#...
| 219500 - 220000 : [ 1 0.00 1.00 ]
#...
| 222000 - 222500 : [ 1 0.00 1.00 ]
#...
| 232500 - 233000 : [ 1 0.00 1.00 ]
#...
| 236000 - 236500 : [ 1 0.00 1.00 ]
#...
| 237000 - 237500 : [ 1 0.00 1.00 ]
#...
| 238000 - 238500 : [ 1 0.00 1.00 ]
#...
| 246500 - 247000 : [ 1 0.00 1.00 ]
#...
| 247500 - 248000 : [ 1 0.00 1.00 ]
#...
| 271500 - 272000 : [ 1 0.00 1.00 ]
#...
| 297500 - 298000 : [ 1 0.00 1.00 ]
#...
| 303000 - 303500 : [ 1 0.00 1.00 ]
#...
| 309500 - 310000 : [ 1 0.00 1.00 ]
#...
| 314000 - 314500 : [ 1 0.00 1.00 ]
#...
| 391500 - 392000 : [ 3 0.00 1.00 ]
| 392000 - 392500 : [ 1 0.00 1.00 ]
| 392500 - 393000 : [ 3 0.00 1.00 ]
#...
| 393500 - 394000 : [ 1 0.00 1.00 ]
#...
| 423500 - 424000 : [ 1 0.00 1.00 ]
#...
| 425000 - 425500 : [ 1 0.00 1.00 ]
#...
| 444500 - 445000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AUSF reads.list > grep.reads.list.AUSF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AUSF 4 500
-------------------------------------------------------------------
#Found 6203 total values totalling 55788088.0000. <8993.726906 +/- 25027.139009>
#Range: [ 1302 - 493023 ]
#Most likely bin: [ 6000 - 6500 ] 1764 counts
#Median bin: [ 6500 - 7000 ] 1398 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 4 0.00 0.00 ]
| 1500 - 2000 : [ 8 0.00 0.00 ]
| 2000 - 2500 : [ 14 0.00 0.00 ]
| 2500 - 3000 : [ 16 0.00 0.01 ]
| 3000 - 3500 : [ 16 0.00 0.01 ]
| 3500 - 4000 : [ 17 0.00 0.01 ]
| 4000 - 4500 : [ 13 0.00 0.01 ]
| 4500 - 5000 : [ 12 0.00 0.02 ]
|X 5000 - 5500 : [ 24 0.00 0.02 ]
|XXXXXXXXXXXXXXXXX 5500 - 6000 : [ 731 0.12 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1764 0.28 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1398 0.23 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1110 0.18 0.83 ]
|XXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 859 0.14 0.97 ]
|XXX 8000 - 8500 : [ 139 0.02 0.99 ]
| 8500 - 9000 : [ 1 0.00 0.99 ]
#...
| 9500 - 10000 : [ 1 0.00 0.99 ]
#...
| 13500 - 14000 : [ 1 0.00 0.99 ]
#...
| 15000 - 15500 : [ 1 0.00 0.99 ]
| 15500 - 16000 : [ 1 0.00 0.99 ]
#...
| 21500 - 22000 : [ 1 0.00 0.99 ]
#...
| 32000 - 32500 : [ 1 0.00 0.99 ]
#...
| 34500 - 35000 : [ 1 0.00 0.99 ]
#...
| 37000 - 37500 : [ 1 0.00 0.99 ]
#...
| 45000 - 45500 : [ 1 0.00 0.99 ]
#...
| 49000 - 49500 : [ 1 0.00 0.99 ]
#...
| 53000 - 53500 : [ 1 0.00 0.99 ]
#...
| 57500 - 58000 : [ 1 0.00 0.99 ]
#...
| 59500 - 60000 : [ 1 0.00 0.99 ]
#...
| 67500 - 68000 : [ 1 0.00 0.99 ]
#...
| 81000 - 81500 : [ 1 0.00 0.99 ]
#...
| 112500 - 113000 : [ 1 0.00 0.99 ]
#...
| 113500 - 114000 : [ 1 0.00 0.99 ]
| 114000 - 114500 : [ 8 0.00 0.99 ]
| 114500 - 115000 : [ 5 0.00 0.99 ]
| 115000 - 115500 : [ 3 0.00 0.99 ]
| 115500 - 116000 : [ 1 0.00 0.99 ]
| 116000 - 116500 : [ 1 0.00 0.99 ]
#...
| 161500 - 162000 : [ 1 0.00 0.99 ]
#...
| 176500 - 177000 : [ 1 0.00 0.99 ]
| 177000 - 177500 : [ 1 0.00 0.99 ]
#...
| 182500 - 183000 : [ 1 0.00 0.99 ]
#...
| 186000 - 186500 : [ 1 0.00 0.99 ]
#...
| 193000 - 193500 : [ 2 0.00 0.99 ]
| 193500 - 194000 : [ 7 0.00 1.00 ]
| 194000 - 194500 : [ 2 0.00 1.00 ]
| 194500 - 195000 : [ 6 0.00 1.00 ]
#...
| 232000 - 232500 : [ 1 0.00 1.00 ]
#...
| 318000 - 318500 : [ 1 0.00 1.00 ]
#...
| 333500 - 334000 : [ 1 0.00 1.00 ]
#...
| 394500 - 395000 : [ 1 0.00 1.00 ]
| 395000 - 395500 : [ 3 0.00 1.00 ]
| 395500 - 396000 : [ 6 0.00 1.00 ]
| 396000 - 396500 : [ 1 0.00 1.00 ]
| 396500 - 397000 : [ 3 0.00 1.00 ]
| 397000 - 397500 : [ 2 0.00 1.00 ]
#...
| 493000 - 493500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AUSG reads.list > grep.reads.list.AUSG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AUSG 4 500
-------------------------------------------------------------------
#Found 720 total values totalling 42335086.0000. <58798.730556 +/- 65089.095847>
#Range: [ 24805 - 434344 ]
#Most likely bin: [ 42000 - 42500 ] 49 counts
#Median bin: [ 40500 - 41000 ] 47 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 24500 - 25000 : [ 1 0.00 0.00 ]
#...
|XX 26000 - 26500 : [ 2 0.00 0.00 ]
#...
|X 27000 - 27500 : [ 1 0.00 0.01 ]
|X 27500 - 28000 : [ 1 0.00 0.01 ]
#...
|X 29500 - 30000 : [ 1 0.00 0.01 ]
|XX 30000 - 30500 : [ 3 0.00 0.01 ]
|XX 30500 - 31000 : [ 2 0.00 0.02 ]
|X 31000 - 31500 : [ 1 0.00 0.02 ]
|XXXXX 31500 - 32000 : [ 6 0.01 0.03 ]
|XXXXXX 32000 - 32500 : [ 7 0.01 0.03 ]
|XXXXXXXX 32500 - 33000 : [ 10 0.01 0.05 ]
|XXXXXXXXX 33000 - 33500 : [ 11 0.02 0.06 ]
|XXXXXXXXX 33500 - 34000 : [ 11 0.02 0.08 ]
|XXXXXXXXXXXXXXX 34000 - 34500 : [ 18 0.03 0.10 ]
|XXXXXXXXX 34500 - 35000 : [ 11 0.02 0.12 ]
|XXXXXXX 35000 - 35500 : [ 9 0.01 0.13 ]
|XXXXXXXXXXX 35500 - 36000 : [ 14 0.02 0.15 ]
|XXXXXXXXXX 36000 - 36500 : [ 12 0.02 0.17 ]
|XXXXXXXXXXXXXXXXX 36500 - 37000 : [ 21 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 24 0.03 0.23 ]
|XXXXXXXXXXXXX 37500 - 38000 : [ 16 0.02 0.25 ]
|XXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 24 0.03 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 31 0.04 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 31 0.04 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 34 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 35 0.05 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 47 0.07 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 37 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 35 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 49 0.07 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 32 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 31 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 35 0.05 0.84 ]
|XXXXXXXXXXXXXXX 44000 - 44500 : [ 18 0.03 0.86 ]
|XXXXXXXXXXX 44500 - 45000 : [ 14 0.02 0.88 ]
|XXXXXXX 45000 - 45500 : [ 9 0.01 0.89 ]
|XX 45500 - 46000 : [ 3 0.00 0.90 ]
|X 46000 - 46500 : [ 1 0.00 0.90 ]
#...
|X 138000 - 138500 : [ 1 0.00 0.90 ]
#...
|X 141000 - 141500 : [ 1 0.00 0.90 ]
|X 141500 - 142000 : [ 1 0.00 0.90 ]
#...
|X 142500 - 143000 : [ 1 0.00 0.91 ]
#...
|X 144500 - 145000 : [ 1 0.00 0.91 ]
|X 145000 - 145500 : [ 1 0.00 0.91 ]
#...
|X 147000 - 147500 : [ 1 0.00 0.91 ]
#...
|X 148000 - 148500 : [ 1 0.00 0.91 ]
#...
|XX 149000 - 149500 : [ 2 0.00 0.91 ]
|XX 149500 - 150000 : [ 3 0.00 0.92 ]
|XX 150000 - 150500 : [ 3 0.00 0.92 ]
|XX 150500 - 151000 : [ 2 0.00 0.93 ]
|XX 151000 - 151500 : [ 2 0.00 0.93 ]
|XX 151500 - 152000 : [ 3 0.00 0.93 ]
|XX 152000 - 152500 : [ 2 0.00 0.93 ]
|X 152500 - 153000 : [ 1 0.00 0.94 ]
#...
|X 153500 - 154000 : [ 1 0.00 0.94 ]
#...
|X 220000 - 220500 : [ 1 0.00 0.94 ]
#...
|XX 221500 - 222000 : [ 2 0.00 0.94 ]
|XX 222000 - 222500 : [ 2 0.00 0.94 ]
|XX 222500 - 223000 : [ 2 0.00 0.95 ]
#...
|X 223500 - 224000 : [ 1 0.00 0.95 ]
#...
|XX 226000 - 226500 : [ 2 0.00 0.95 ]
|XX 226500 - 227000 : [ 2 0.00 0.95 ]
|XX 227000 - 227500 : [ 2 0.00 0.96 ]
|X 227500 - 228000 : [ 1 0.00 0.96 ]
|XX 228000 - 228500 : [ 2 0.00 0.96 ]
|XX 228500 - 229000 : [ 3 0.00 0.97 ]
|XX 229000 - 229500 : [ 3 0.00 0.97 ]
|XXX 229500 - 230000 : [ 4 0.01 0.97 ]
|XX 230000 - 230500 : [ 2 0.00 0.98 ]
|X 230500 - 231000 : [ 1 0.00 0.98 ]
|XX 231000 - 231500 : [ 2 0.00 0.98 ]
|X 231500 - 232000 : [ 1 0.00 0.98 ]
#...
|XX 425000 - 425500 : [ 2 0.00 0.99 ]
#...
|X 426000 - 426500 : [ 1 0.00 0.99 ]
|XX 426500 - 427000 : [ 2 0.00 0.99 ]
#...
|X 428000 - 428500 : [ 1 0.00 0.99 ]
#...
|X 430000 - 430500 : [ 1 0.00 0.99 ]
#...
|XX 431500 - 432000 : [ 2 0.00 1.00 ]
|XX 432000 - 432500 : [ 2 0.00 1.00 ]
#...
|X 434000 - 434500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AUSG 39637 +- 3577 (n=321)
# AUSC 3002 +- 846 (n=3103)
# AUSF 6633 +- 944 (n=3091)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634486_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
AHZX 7680 -1 -1 96 727 7680 92 752 96 754
AHZY 7680 -1 -1 88 531 7630 72 472 86 541
AUSC 16128 91 705 96 735 16076 91 697 94 706
AUSF 16128 90 791 97 758 16128 90 791 97 785
AUSG 3840 91 705 96 677 3840 90 716 96 705
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHZX 3840 92 738 96 749 3840 92 766 96 759
AHZY 3822 63 430 79 507 3808 81 505 92 569
AUSC 8030 90 689 94 700 8046 91 704 95 711
AUSF 8064 90 791 97 784 8064 90 791 96 785
AUSG 1920 90 708 95 690 1920 91 724 97 719
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634486_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
80 14469 6973 87.16 90.79 AUSF @
20 3544 1868 93.40 97.29 AUSG @
80 14793 7384 92.30 96.15 AUSC @
] 32806 16225 90.14 cumulative total@@
LIBRARY PLATE ID COUNT [ AUSF 80 AUSG 20 AUSC 80 ] for 180 total 96 well plate ids.
Only indicates plates present in input file.
Make no assumption regarding plates (not) present in project that do not appear above.
-------------------------------------------------------------------
trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3634486_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 51354 total values totalling 32133951.0000. <625.734140 +/- 282.235865>
#Range: [ 0 - 989 ]
#Most likely bin: [ 800 - 850 ] 11008 counts
#Median bin: [ 750 - 800 ] 8806 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXX 0 - 50 : [ 5269 0.10 0.10 ]
|XXXX 50 - 100 : [ 988 0.02 0.12 ]
|XX 100 - 150 : [ 623 0.01 0.13 ]
|XX 150 - 200 : [ 632 0.01 0.15 ]
|XX 200 - 250 : [ 677 0.01 0.16 ]
|XXX 250 - 300 : [ 780 0.02 0.17 ]
|XX 300 - 350 : [ 553 0.01 0.19 ]
|XXX 350 - 400 : [ 706 0.01 0.20 ]
|XXX 400 - 450 : [ 823 0.02 0.22 ]
|XXXX 450 - 500 : [ 974 0.02 0.23 ]
|XXXX 500 - 550 : [ 1228 0.02 0.26 ]
|XXXXXX 550 - 600 : [ 1636 0.03 0.29 ]
|XXXXXXXX 600 - 650 : [ 2247 0.04 0.33 ]
|XXXXXXXXXXX 650 - 700 : [ 3119 0.06 0.39 ]
|XXXXXXXXXXXXXXXXX 700 - 750 : [ 4773 0.09 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8806 0.17 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 11008 0.21 0.87 ]
|XXXXXXXXXXXXXXXXXXX 850 - 900 : [ 5258 0.10 0.98 ]
|XXXX 900 - 950 : [ 1173 0.02 1.00 ]
| 950 - 1000 : [ 81 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZX 3634486_fasta.screen.trimQ15.SaF > reads.trim15.AHZX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZX.rl 2 50
-------------------------------------------------------------------
#Found 7680 total values totalling 5324315.0000. <693.270182 +/- 218.729377>
#Range: [ 0 - 911 ]
#Most likely bin: [ 750 - 800 ] 2604 counts
#Median bin: [ 750 - 800 ] 2604 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 0 - 50 : [ 588 0.08 0.08 ]
| 50 - 100 : [ 18 0.00 0.08 ]
| 100 - 150 : [ 15 0.00 0.08 ]
| 150 - 200 : [ 12 0.00 0.08 ]
| 200 - 250 : [ 16 0.00 0.08 ]
| 250 - 300 : [ 22 0.00 0.09 ]
| 300 - 350 : [ 15 0.00 0.09 ]
| 350 - 400 : [ 27 0.00 0.09 ]
|X 400 - 450 : [ 33 0.00 0.10 ]
|X 450 - 500 : [ 36 0.00 0.10 ]
| 500 - 550 : [ 32 0.00 0.11 ]
|X 550 - 600 : [ 53 0.01 0.11 ]
|XXX 600 - 650 : [ 195 0.03 0.14 ]
|XXXXXXXXX 650 - 700 : [ 592 0.08 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1574 0.20 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2604 0.34 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1618 0.21 0.97 ]
|XXXX 850 - 900 : [ 229 0.03 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZY 3634486_fasta.screen.trimQ15.SaF > reads.trim15.AHZY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZY.rl 2 50
-------------------------------------------------------------------
#Found 7630 total values totalling 2629509.0000. <344.627654 +/- 254.989093>
#Range: [ 0 - 805 ]
#Most likely bin: [ 0 - 50 ] 1701 counts
#Median bin: [ 350 - 400 ] 246 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1701 0.22 0.22 ]
|XXXXXXXXXXX 50 - 100 : [ 468 0.06 0.28 ]
|XXXXXXX 100 - 150 : [ 279 0.04 0.32 ]
|XXXXXXXX 150 - 200 : [ 329 0.04 0.36 ]
|XXXXXXXX 200 - 250 : [ 342 0.04 0.41 ]
|XXXXXXXXXX 250 - 300 : [ 414 0.05 0.46 ]
|XXXXX 300 - 350 : [ 202 0.03 0.49 ]
|XXXXXX 350 - 400 : [ 246 0.03 0.52 ]
|XXXXXXX 400 - 450 : [ 308 0.04 0.56 ]
|XXXXXXXXXX 450 - 500 : [ 409 0.05 0.62 ]
|XXXXXXXXXXXX 500 - 550 : [ 528 0.07 0.68 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 677 0.09 0.77 ]
|XXXXXXXXXXXXXXXXXX 600 - 650 : [ 748 0.10 0.87 ]
|XXXXXXXXXXXXXXX 650 - 700 : [ 629 0.08 0.95 ]
|XXXXXXX 700 - 750 : [ 304 0.04 0.99 ]
|X 750 - 800 : [ 44 0.01 1.00 ]
| 800 - 850 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZZ
trimt JAZZ trim 15 readlength histogram for AUSC
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AUSC 3634486_fasta.screen.trimQ15.SaF > reads.trim15.AUSC.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AUSC.rl 2 50
-------------------------------------------------------------------
#Found 16076 total values totalling 10180585.0000. <633.278490 +/- 271.447541>
#Range: [ 0 - 989 ]
#Most likely bin: [ 850 - 900 ] 2576 counts
#Median bin: [ 700 - 750 ] 1502 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1193 0.07 0.07 ]
|XXXXX 50 - 100 : [ 317 0.02 0.09 ]
|XXXX 100 - 150 : [ 226 0.01 0.11 ]
|XXX 150 - 200 : [ 218 0.01 0.12 ]
|XXXX 200 - 250 : [ 227 0.01 0.14 ]
|XXXX 250 - 300 : [ 256 0.02 0.15 ]
|XXXX 300 - 350 : [ 258 0.02 0.17 ]
|XXXXX 350 - 400 : [ 319 0.02 0.19 ]
|XXXXXX 400 - 450 : [ 368 0.02 0.21 ]
|XXXXXX 450 - 500 : [ 410 0.03 0.24 ]
|XXXXXXXX 500 - 550 : [ 522 0.03 0.27 ]
|XXXXXXXXXXX 550 - 600 : [ 728 0.05 0.31 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 1036 0.06 0.38 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1350 0.08 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1502 0.09 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1426 0.09 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2005 0.12 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 850 - 900 : [ 2576 0.16 0.93 ]
|XXXXXXXXXXXXXXXX 900 - 950 : [ 1059 0.07 1.00 ]
|X 950 - 1000 : [ 80 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AUSH
trimt JAZZ trim 15 readlength histogram for AUSI
trimt JAZZ trim 15 readlength histogram for AUSF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AUSF 3634486_fasta.screen.trimQ15.SaF > reads.trim15.AUSF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AUSF.rl 2 50
-------------------------------------------------------------------
#Found 16128 total values totalling 11501962.0000. <713.167287 +/- 251.096921>
#Range: [ 0 - 942 ]
#Most likely bin: [ 800 - 850 ] 6523 counts
#Median bin: [ 800 - 850 ] 6523 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 0 - 50 : [ 1502 0.09 0.09 ]
|X 50 - 100 : [ 104 0.01 0.10 ]
| 100 - 150 : [ 51 0.00 0.10 ]
| 150 - 200 : [ 35 0.00 0.10 ]
| 200 - 250 : [ 49 0.00 0.11 ]
| 250 - 300 : [ 44 0.00 0.11 ]
| 300 - 350 : [ 34 0.00 0.11 ]
| 350 - 400 : [ 44 0.00 0.12 ]
| 400 - 450 : [ 37 0.00 0.12 ]
| 450 - 500 : [ 63 0.00 0.12 ]
| 500 - 550 : [ 66 0.00 0.13 ]
| 550 - 600 : [ 80 0.00 0.13 ]
|X 600 - 650 : [ 116 0.01 0.14 ]
|XX 650 - 700 : [ 260 0.02 0.15 ]
|XXXXXX 700 - 750 : [ 984 0.06 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4118 0.26 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6523 0.40 0.87 ]
|XXXXXXXXXXXX 850 - 900 : [ 1956 0.12 1.00 ]
| 900 - 950 : [ 62 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AUSN
trimt JAZZ trim 15 readlength histogram for AUSO
trimt JAZZ trim 15 readlength histogram for AUSG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AUSG 3634486_fasta.screen.trimQ15.SaF > reads.trim15.AUSG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AUSG.rl 2 50
-------------------------------------------------------------------
#Found 3840 total values totalling 2497580.0000. <650.411458 +/- 260.844123>
#Range: [ 0 - 959 ]
#Most likely bin: [ 800 - 850 ] 860 counts
#Median bin: [ 750 - 800 ] 614 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXX 0 - 50 : [ 285 0.07 0.07 ]
|XXXX 50 - 100 : [ 81 0.02 0.10 ]
|XX 100 - 150 : [ 52 0.01 0.11 ]
|XX 150 - 200 : [ 38 0.01 0.12 ]
|XX 200 - 250 : [ 43 0.01 0.13 ]
|XX 250 - 300 : [ 44 0.01 0.14 ]
|XX 300 - 350 : [ 44 0.01 0.15 ]
|XXX 350 - 400 : [ 70 0.02 0.17 ]
|XXXX 400 - 450 : [ 77 0.02 0.19 ]
|XXX 450 - 500 : [ 56 0.01 0.21 ]
|XXXX 500 - 550 : [ 80 0.02 0.23 ]
|XXXXX 550 - 600 : [ 98 0.03 0.25 ]
|XXXXXXX 600 - 650 : [ 152 0.04 0.29 ]
|XXXXXXXXXXXXX 650 - 700 : [ 288 0.07 0.37 ]
|XXXXXXXXXXXXXXXXXXX 700 - 750 : [ 409 0.11 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 614 0.16 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 860 0.22 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXX 850 - 900 : [ 497 0.13 0.99 ]
|XX 900 - 950 : [ 51 0.01 1.00 ]
| 950 - 1000 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AUSP
trimt JAZZ trim 15 readlength histogram for AUSS
trimt JAZZ trim 15 readlength histogram for AZXN
trimt JAZZ trim 15 readlength histogram for AZXO
trimt JAZZ trim 15 readlength histogram for AZXP
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634486
-------------------------------------------------------------------
AHZX.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHZY.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AUSC.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AUSF.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AUSG.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AHZX.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHZY.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AUSC.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AUSF.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AUSG.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634486_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634486_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 32705 total values totalling 15991.9714. <0.488976 +/- 0.053540>
#Range: [ 0.1352 - 1 ]
#Most likely bin: [ 0.485 - 0.49 ] 1599 counts
#Median bin: [ 0.485 - 0.49 ] 1599 counts
#Entropy = 5.3961 bits
| 0.135 - 0.14 : [ 1 0.00 0.00 ]
#...
| 0.21 - 0.215 : [ 1 0.00 0.00 ]
#...
| 0.24 - 0.245 : [ 1 0.00 0.00 ]
| 0.245 - 0.25 : [ 1 0.00 0.00 ]
| 0.25 - 0.255 : [ 1 0.00 0.00 ]
#...
| 0.265 - 0.27 : [ 1 0.00 0.00 ]
| 0.27 - 0.275 : [ 3 0.00 0.00 ]
| 0.275 - 0.28 : [ 4 0.00 0.00 ]
| 0.28 - 0.285 : [ 5 0.00 0.00 ]
| 0.285 - 0.29 : [ 3 0.00 0.00 ]
| 0.29 - 0.295 : [ 2 0.00 0.00 ]
| 0.295 - 0.3 : [ 5 0.00 0.00 ]
| 0.3 - 0.305 : [ 7 0.00 0.00 ]
| 0.305 - 0.31 : [ 4 0.00 0.00 ]
| 0.31 - 0.315 : [ 4 0.00 0.00 ]
| 0.315 - 0.32 : [ 13 0.00 0.00 ]
| 0.32 - 0.325 : [ 13 0.00 0.00 ]
| 0.325 - 0.33 : [ 16 0.00 0.00 ]
|X 0.33 - 0.335 : [ 25 0.00 0.00 ]
| 0.335 - 0.34 : [ 17 0.00 0.00 ]
|X 0.34 - 0.345 : [ 25 0.00 0.00 ]
|X 0.345 - 0.35 : [ 40 0.00 0.01 ]
|X 0.35 - 0.355 : [ 32 0.00 0.01 ]
|X 0.355 - 0.36 : [ 50 0.00 0.01 ]
|XX 0.36 - 0.365 : [ 60 0.00 0.01 ]
|XX 0.365 - 0.37 : [ 75 0.00 0.01 ]
|XX 0.37 - 0.375 : [ 83 0.00 0.02 ]
|XX 0.375 - 0.38 : [ 94 0.00 0.02 ]
|XXX 0.38 - 0.385 : [ 119 0.00 0.02 ]
|XXXX 0.385 - 0.39 : [ 149 0.00 0.03 ]
|XXXXX 0.39 - 0.395 : [ 184 0.01 0.03 ]
|XXXXX 0.395 - 0.4 : [ 194 0.01 0.04 ]
|XXXXXX 0.4 - 0.405 : [ 249 0.01 0.05 ]
|XXXXXXX 0.405 - 0.41 : [ 284 0.01 0.05 ]
|XXXXXXXXX 0.41 - 0.415 : [ 377 0.01 0.07 ]
|XXXXXXXXXX 0.415 - 0.42 : [ 404 0.01 0.08 ]
|XXXXXXXXXXXX 0.42 - 0.425 : [ 465 0.01 0.09 ]
|XXXXXXXXXXXXX 0.425 - 0.43 : [ 518 0.02 0.11 ]
|XXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 624 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 708 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 825 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 946 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 1003 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 1165 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 1242 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 1316 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 1430 0.04 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 1478 0.05 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 1518 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 1599 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 1550 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 1380 0.04 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1543 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 1260 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 1211 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 986 0.03 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 923 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 897 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 701 0.02 0.85 ]
|XXXXXXXXXXXXXXX 0.535 - 0.54 : [ 593 0.02 0.87 ]
|XXXXXXXXXXXXX 0.54 - 0.545 : [ 516 0.02 0.88 ]
|XXXXXXXXXX 0.545 - 0.55 : [ 412 0.01 0.90 ]
|XXXXXXXXX 0.55 - 0.555 : [ 356 0.01 0.91 ]
|XXXXXXX 0.555 - 0.56 : [ 287 0.01 0.92 ]
|XXXXXXX 0.56 - 0.565 : [ 269 0.01 0.93 ]
|XXXXXX 0.565 - 0.57 : [ 232 0.01 0.93 ]
|XXXXX 0.57 - 0.575 : [ 215 0.01 0.94 ]
|XXXXXX 0.575 - 0.58 : [ 234 0.01 0.95 ]
|XXXXX 0.58 - 0.585 : [ 185 0.01 0.95 ]
|XXX 0.585 - 0.59 : [ 136 0.00 0.96 ]
|XXX 0.59 - 0.595 : [ 135 0.00 0.96 ]
|XXX 0.595 - 0.6 : [ 135 0.00 0.96 ]
|XXX 0.6 - 0.605 : [ 127 0.00 0.97 ]
|XXX 0.605 - 0.61 : [ 117 0.00 0.97 ]
|XXX 0.61 - 0.615 : [ 122 0.00 0.98 ]
|XXX 0.615 - 0.62 : [ 121 0.00 0.98 ]
|XX 0.62 - 0.625 : [ 92 0.00 0.98 ]
|XX 0.625 - 0.63 : [ 70 0.00 0.98 ]
|XX 0.63 - 0.635 : [ 66 0.00 0.99 ]
|X 0.635 - 0.64 : [ 42 0.00 0.99 ]
|X 0.64 - 0.645 : [ 36 0.00 0.99 ]
|X 0.645 - 0.65 : [ 37 0.00 0.99 ]
|X 0.65 - 0.655 : [ 43 0.00 0.99 ]
|X 0.655 - 0.66 : [ 22 0.00 0.99 ]
|X 0.66 - 0.665 : [ 26 0.00 0.99 ]
|X 0.665 - 0.67 : [ 25 0.00 0.99 ]
|X 0.67 - 0.675 : [ 25 0.00 0.99 ]
|X 0.675 - 0.68 : [ 28 0.00 0.99 ]
|X 0.68 - 0.685 : [ 31 0.00 1.00 ]
|X 0.685 - 0.69 : [ 24 0.00 1.00 ]
|X 0.69 - 0.695 : [ 22 0.00 1.00 ]
| 0.695 - 0.7 : [ 16 0.00 1.00 ]
| 0.7 - 0.705 : [ 13 0.00 1.00 ]
| 0.705 - 0.71 : [ 12 0.00 1.00 ]
| 0.71 - 0.715 : [ 16 0.00 1.00 ]
| 0.715 - 0.72 : [ 6 0.00 1.00 ]
| 0.72 - 0.725 : [ 2 0.00 1.00 ]
| 0.725 - 0.73 : [ 7 0.00 1.00 ]
| 0.73 - 0.735 : [ 2 0.00 1.00 ]
| 0.735 - 0.74 : [ 4 0.00 1.00 ]
| 0.74 - 0.745 : [ 2 0.00 1.00 ]
| 0.745 - 0.75 : [ 3 0.00 1.00 ]
| 0.75 - 0.755 : [ 2 0.00 1.00 ]
#...
| 0.76 - 0.765 : [ 1 0.00 1.00 ]
| 0.765 - 0.77 : [ 1 0.00 1.00 ]
| 0.77 - 0.775 : [ 1 0.00 1.00 ]
#...
| 0.785 - 0.79 : [ 1 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 48. 255 reads; 23544 bp (untrimmed), 23518 (trimmed).
Contig 49. 256 reads; 24730 bp (untrimmed), 24243 (trimmed).
Contig 50. 268 reads; 25641 bp (untrimmed), 25583 (trimmed).
Contig 51. 286 reads; 32383 bp (untrimmed), 32380 (trimmed).
Contig 52. 328 reads; 30189 bp (untrimmed), 29898 (trimmed).
Contig 53. 349 reads; 34466 bp (untrimmed), 34444 (trimmed).
Contig 54. 367 reads; 31374 bp (untrimmed), 31322 (trimmed).
Contig 55. 476 reads; 38385 bp (untrimmed), 38359 (trimmed).
Contig 56. 478 reads; 43605 bp (untrimmed), 43531 (trimmed).
Contig 57. 489 reads; 43580 bp (untrimmed), 43560 (trimmed).
Contig 58. 518 reads; 44577 bp (untrimmed), 44448 (trimmed).
Contig 59. 539 reads; 41914 bp (untrimmed), 41897 (trimmed).
Contig 60. 609 reads; 56220 bp (untrimmed), 56217 (trimmed).
Contig 61. 639 reads; 62808 bp (untrimmed), 62625 (trimmed).
Contig 62. 648 reads; 55613 bp (untrimmed), 55523 (trimmed).
Contig 63. 702 reads; 53207 bp (untrimmed), 53184 (trimmed).
Contig 64. 713 reads; 67480 bp (untrimmed), 67403 (trimmed).
Contig 65. 752 reads; 50078 bp (untrimmed), 50038 (trimmed).
Contig 66. 858 reads; 65114 bp (untrimmed), 64734 (trimmed).
Contig 67. 864 reads; 79838 bp (untrimmed), 79186 (trimmed).
Contig 68. 889 reads; 74888 bp (untrimmed), 74740 (trimmed).
Contig 69. 1094 reads; 95131 bp (untrimmed), 94992 (trimmed).
Contig 70. 1263 reads; 100524 bp (untrimmed), 100363 (trimmed).
Contig 71. 1455 reads; 120362 bp (untrimmed), 120304 (trimmed).
Contig 72. 1775 reads; 135482 bp (untrimmed), 135321 (trimmed).
Contig 73. 5279 reads; 429571 bp (untrimmed), 429530 (trimmed).
Contig 74. 8322 reads; 628056 bp (untrimmed), 627978 (trimmed).
--------------------------------------------------------------
Totals 32375 reads; 2748905 bp (untrimmed), 2740017 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2746292 bases = 10.93 +- 4.47 = 0.26 +- 3.81
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 68 total values totalling 498.1700. <7.326029 +/- 3.956317>
#Range: [ 1.52 - 17.61 ]
#Most likely bin: [ 10 - 10.5 ] 8 counts
#Median bin: [ 8 - 8.5 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 7 0.10 0.10 ]
|XXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 4 0.06 0.16 ]
|XXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 4 0.06 0.22 ]
|XXXXXXXXXXXXXXX 3 - 3.5 : [ 3 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 5 0.07 0.34 ]
|XXXXXXXXXX 4 - 4.5 : [ 2 0.03 0.37 ]
|XXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 4 0.06 0.43 ]
#...
|XXXXX 7 - 7.5 : [ 1 0.01 0.44 ]
|XXXXXXXXXX 7.5 - 8 : [ 2 0.03 0.47 ]
|XXXXXXXXXX 8 - 8.5 : [ 2 0.03 0.50 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 7 0.10 0.60 ]
|XXXXXXXXXXXXXXX 9.5 - 10 : [ 3 0.04 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 8 0.12 0.76 ]
|XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 4 0.06 0.82 ]
|XXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.06 0.88 ]
|XXXXX 11.5 - 12 : [ 1 0.01 0.90 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 5 0.07 0.97 ]
#...
|XXXXX 13.5 - 14 : [ 1 0.01 0.99 ]
#...
|XXXXX 17.5 - 18 : [ 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 50 total values totalling 427.6900. <8.553800 +/- 3.209889>
#Range: [ 2.42 - 13.95 ]
#Most likely bin: [ 10 - 10.5 ] 8 counts
#Median bin: [ 9 - 9.5 ] 7 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 2 - 2.5 : [ 2 0.04 0.04 ]
|XXXXXXXXXX 2.5 - 3 : [ 2 0.04 0.08 ]
|XXXXXXXXXX 3 - 3.5 : [ 2 0.04 0.12 ]
|XXXXXXXXXXXXXXX 3.5 - 4 : [ 3 0.06 0.18 ]
|XXXXX 4 - 4.5 : [ 1 0.02 0.20 ]
|XXXXXXXXXXXXXXX 4.5 - 5 : [ 3 0.06 0.26 ]
#...
|XXXXX 7 - 7.5 : [ 1 0.02 0.28 ]
|XXXXXXXXXX 7.5 - 8 : [ 2 0.04 0.32 ]
|XXXXXXXXXX 8 - 8.5 : [ 2 0.04 0.36 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 7 0.14 0.50 ]
|XXXXXXXXXX 9.5 - 10 : [ 2 0.04 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 8 0.16 0.70 ]
|XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 4 0.08 0.78 ]
|XXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.08 0.86 ]
|XXXXX 11.5 - 12 : [ 1 0.02 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 5 0.10 0.98 ]
#...
|XXXXX 13.5 - 14 : [ 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 5 2 reads 962 bases = 1.52 +- 0.50 = 1.52 +- 0.50
Contig 4 2 reads 963 bases = 1.72 +- 0.45 = 1.72 +- 0.45
Contig 13 5 reads 1548 bases = 1.73 +- 1.42 = 0.23 +- 1.19
Contig 7 2 reads 1012 bases = 1.83 +- 0.38 = 1.83 +- 0.38
Contig 12 4 reads 1990 bases = 1.84 +- 0.74 = 0.80 +- 0.62
Contig 16 5 reads 2484 bases = 1.93 +- 1.02 = 0.36 +- 1.03
Contig 8 3 reads 1573 bases = 1.98 +- 0.79 = 1.98 +- 0.79
Contig 14 5 reads 2016 bases = 2.08 +- 0.82 = 0.28 +- 0.77
Contig 15 5 reads 2265 bases = 2.33 +- 0.57 = 0.40 +- 0.52
Contig 23 10 reads 3423 bases = 2.42 +- 0.91 = 0.61 +- 1.04
Contig 31 22 reads 8246 bases = 2.49 +- 1.23 = 0.54 +- 1.63
Contig 22 7 reads 2322 bases = 2.76 +- 1.48 = 1.92 +- 0.79
Contig 11 4 reads 1210 bases = 2.90 +- 1.15 = 0.29 +- 0.62
Contig 26 13 reads 4348 bases = 2.91 +- 1.15 = 0.73 +- 0.55
Contig 27 15 reads 5072 bases = 2.97 +- 1.15 = 0.18 +- 0.98
Contig 25 12 reads 3500 bases = 3.11 +- 1.69 = 0.43 +- 1.97
Contig 19 6 reads 1689 bases = 3.21 +- 1.54 = -0.23 +- 0.74
Contig 35 29 reads 8203 bases = 3.25 +- 1.81 = 0.63 +- 1.25
Contig 34 28 reads 7115 bases = 3.68 +- 1.76 = 0.16 +- 1.88
Contig 32 23 reads 5207 bases = 3.89 +- 1.78 = 1.11 +- 3.79
Contig 48 255 reads 23544 bases = 10.21 +- 4.29 = 0.86 +- 3.83
Contig 42 157 reads 14404 bases = 10.22 +- 3.89 = 0.10 +- 3.11
Contig 57 489 reads 43580 bases = 10.29 +- 3.75 = 0.16 +- 3.98
Contig 45 178 reads 15645 bases = 10.30 +- 3.58 = 0.19 +- 3.40
Contig 54 367 reads 31374 bases = 10.61 +- 3.98 = -0.02 +- 4.07
Contig 69 1094 reads 95131 bases = 10.61 +- 3.98 = 0.04 +- 4.48
Contig 62 648 reads 55613 bases = 10.80 +- 3.63 = 0.29 +- 3.35
Contig 58 518 reads 44577 bases = 10.94 +- 3.40 = 0.30 +- 3.46
Contig 68 889 reads 74888 bases = 11.13 +- 4.14 = 0.47 +- 4.00
Contig 71 1455 reads 120362 bases = 11.27 +- 3.92 = 0.22 +- 3.92
Contig 73 5279 reads 429571 bases = 11.39 +- 4.13 = 0.13 +- 4.04
Contig 55 476 reads 38385 bases = 11.40 +- 4.15 = 0.59 +- 3.99
Contig 70 1263 reads 100524 bases = 11.73 +- 3.60 = 0.07 +- 3.60
Contig 59 539 reads 41914 bases = 12.06 +- 5.24 = 0.15 +- 3.92
Contig 72 1775 reads 135482 bases = 12.16 +- 5.87 = 0.44 +- 4.39
Contig 66 858 reads 65114 bases = 12.26 +- 4.18 = 0.10 +- 3.47
Contig 63 702 reads 53207 bases = 12.32 +- 3.98 = 0.84 +- 4.10
Contig 74 8322 reads 628056 bases = 12.32 +- 3.87 = 0.03 +- 3.64
Contig 65 752 reads 50078 bases = 13.95 +- 4.13 = 0.32 +- 4.04
Contig 33 26 reads 1273 bases = 17.61 +- 9.04 = 2.97 +- 1.29
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 893
HQ Discrepant reads = 18
Chimeric reads = 131
Suspect alignments = 224
-------------------------------------------------------------------
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/microbe4/3634486/edit_dir.20Dec04.QD