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
3635544 2500 1129 Synechococcus sp.
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Synechococcus_sp.
-------------------------------------------------------------------
Synechococcus sp., species, cyanobacteria
Synechococcus, genus, cyanobacteria
Chroococcales, order, cyanobacteria
Cyanobacteria (blue-green algae), phylum, cyanobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2510981
# phrap: 2419717
# db:
altered.
2500000
2476899 +/- 40681
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 10716
Number of reads with percent X's >= 20%: 367 = 0.8%
Number of reads with percent X's >= 50%: 141 = 0.3%
Number of reads with percent X's >= 80%: 17 = 0.0%
Total reads in project: 43218
Total bp X'd : 562681
reads >= 20% >= 50% >= 80% screened
Nr with L09136 9761 150 53 9
Nr with pCC1Fos 568 1 0 0
Nr with pMCL200_JGI_XZX+XZK 387 216 88 8
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 2
Number of reads with percent X's >= 20%: 1 = 6.7%
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: 15
Total bp X'd : 234
reads >= 20% >= 50% >= 80% screened
Nr with L09136 1 0 0 0
Nr with pCC1Fos 1 1 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 8472004
C = 12133743
G = 12195570
T = 8283407
N = 219169
X = 562681
GC fraction = 0.58
Total = 41866574
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3635544_fasta.screen.contigs
-------------------------------------------------------------------
A 502978
C 738479
G 749159
T 521344
N 4
fraction GC = 0.59
total bases = 2511964
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 AOZP reads.list > grep.reads.list.AOZP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOZP 4 500
-------------------------------------------------------------------
#Found 10310 total values totalling 35988086.0000. <3490.600000 +/- 15703.108383>
#Range: [ 675 - 691813 ]
#Most likely bin: [ 3000 - 3500 ] 7155 counts
#Median bin: [ 3000 - 3500 ] 7155 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 9 0.00 0.00 ]
|X 1000 - 1500 : [ 99 0.01 0.01 ]
|X 1500 - 2000 : [ 145 0.01 0.02 ]
|X 2000 - 2500 : [ 249 0.02 0.05 ]
|XXXXXXXXXXXXXX 2500 - 3000 : [ 2525 0.24 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 7155 0.69 0.99 ]
|X 3500 - 4000 : [ 118 0.01 1.00 ]
#...
| 108000 - 108500 : [ 1 0.00 1.00 ]
#...
| 116000 - 116500 : [ 1 0.00 1.00 ]
#...
| 202000 - 202500 : [ 1 0.00 1.00 ]
#...
| 329500 - 330000 : [ 1 0.00 1.00 ]
#...
| 404000 - 404500 : [ 1 0.00 1.00 ]
#...
| 632000 - 632500 : [ 1 0.00 1.00 ]
#...
| 671500 - 672000 : [ 2 0.00 1.00 ]
| 672000 - 672500 : [ 1 0.00 1.00 ]
#...
| 691500 - 692000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOZS reads.list > grep.reads.list.AOZS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOZS 4 500
-------------------------------------------------------------------
#Found 7467 total values totalling 79264698.0000. <10615.333869 +/- 43565.332258>
#Range: [ 956 - 1439401 ]
#Most likely bin: [ 8500 - 9000 ] 1203 counts
#Median bin: [ 8000 - 8500 ] 982 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 3 0.00 0.00 ]
|XXXX 1000 - 1500 : [ 113 0.02 0.02 ]
|XXXXX 1500 - 2000 : [ 155 0.02 0.04 ]
|XXXX 2000 - 2500 : [ 129 0.02 0.05 ]
|XXXXX 2500 - 3000 : [ 149 0.02 0.07 ]
|XXXXX 3000 - 3500 : [ 146 0.02 0.09 ]
|XXXXX 3500 - 4000 : [ 155 0.02 0.11 ]
|XXXXXX 4000 - 4500 : [ 172 0.02 0.14 ]
|XXXXXX 4500 - 5000 : [ 173 0.02 0.16 ]
|XXXXXXXX 5000 - 5500 : [ 232 0.03 0.19 ]
|XXXXXXXXX 5500 - 6000 : [ 284 0.04 0.23 ]
|XXXXXXXXXXX 6000 - 6500 : [ 329 0.04 0.27 ]
|XXXXXXXXXXXX 6500 - 7000 : [ 347 0.05 0.32 ]
|XXXXXXXXXXXXX 7000 - 7500 : [ 393 0.05 0.37 ]
|XXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 627 0.08 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 982 0.13 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 1203 0.16 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 922 0.12 0.87 ]
|XXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 565 0.08 0.95 ]
|XXXXXXXXX 10000 - 10500 : [ 274 0.04 0.98 ]
|XX 10500 - 11000 : [ 54 0.01 0.99 ]
#...
| 19500 - 20000 : [ 1 0.00 0.99 ]
#...
| 24000 - 24500 : [ 1 0.00 0.99 ]
#...
| 32500 - 33000 : [ 1 0.00 0.99 ]
#...
| 37500 - 38000 : [ 1 0.00 0.99 ]
| 38000 - 38500 : [ 1 0.00 0.99 ]
#...
| 89000 - 89500 : [ 1 0.00 0.99 ]
#...
| 90500 - 91000 : [ 1 0.00 0.99 ]
#...
| 109500 - 110000 : [ 1 0.00 0.99 ]
#...
| 114500 - 115000 : [ 1 0.00 0.99 ]
#...
| 133500 - 134000 : [ 1 0.00 0.99 ]
#...
| 143500 - 144000 : [ 1 0.00 0.99 ]
#...
| 154500 - 155000 : [ 1 0.00 0.99 ]
#...
| 166000 - 166500 : [ 1 0.00 0.99 ]
#...
| 173000 - 173500 : [ 1 0.00 0.99 ]
#...
| 176500 - 177000 : [ 1 0.00 0.99 ]
#...
| 202000 - 202500 : [ 1 0.00 0.99 ]
#...
| 212000 - 212500 : [ 1 0.00 0.99 ]
#...
| 231500 - 232000 : [ 1 0.00 0.99 ]
#...
| 254500 - 255000 : [ 1 0.00 0.99 ]
#...
| 275500 - 276000 : [ 1 0.00 0.99 ]
#...
| 296000 - 296500 : [ 1 0.00 0.99 ]
#...
| 301000 - 301500 : [ 1 0.00 0.99 ]
#...
| 305500 - 306000 : [ 1 0.00 1.00 ]
#...
| 309000 - 309500 : [ 1 0.00 1.00 ]
| 309500 - 310000 : [ 1 0.00 1.00 ]
#...
| 320000 - 320500 : [ 1 0.00 1.00 ]
#...
| 326000 - 326500 : [ 1 0.00 1.00 ]
#...
| 331500 - 332000 : [ 1 0.00 1.00 ]
#...
| 338000 - 338500 : [ 1 0.00 1.00 ]
| 338500 - 339000 : [ 1 0.00 1.00 ]
#...
| 363000 - 363500 : [ 1 0.00 1.00 ]
#...
| 366500 - 367000 : [ 1 0.00 1.00 ]
#...
| 383500 - 384000 : [ 1 0.00 1.00 ]
#...
| 392500 - 393000 : [ 1 0.00 1.00 ]
| 393000 - 393500 : [ 1 0.00 1.00 ]
#...
| 460500 - 461000 : [ 1 0.00 1.00 ]
#...
| 468000 - 468500 : [ 1 0.00 1.00 ]
#...
| 471500 - 472000 : [ 1 0.00 1.00 ]
#...
| 473000 - 473500 : [ 1 0.00 1.00 ]
#...
| 474000 - 474500 : [ 1 0.00 1.00 ]
#...
| 497000 - 497500 : [ 1 0.00 1.00 ]
#...
| 502000 - 502500 : [ 1 0.00 1.00 ]
#...
| 503500 - 504000 : [ 1 0.00 1.00 ]
#...
| 566000 - 566500 : [ 1 0.00 1.00 ]
#...
| 567500 - 568000 : [ 1 0.00 1.00 ]
| 568000 - 568500 : [ 1 0.00 1.00 ]
#...
| 572500 - 573000 : [ 1 0.00 1.00 ]
#...
| 662500 - 663000 : [ 1 0.00 1.00 ]
#...
| 677000 - 677500 : [ 1 0.00 1.00 ]
| 677500 - 678000 : [ 1 0.00 1.00 ]
#...
| 734000 - 734500 : [ 1 0.00 1.00 ]
#...
| 742000 - 742500 : [ 1 0.00 1.00 ]
#...
| 755000 - 755500 : [ 1 0.00 1.00 ]
#...
| 757500 - 758000 : [ 1 0.00 1.00 ]
#...
| 766000 - 766500 : [ 1 0.00 1.00 ]
#...
| 784000 - 784500 : [ 1 0.00 1.00 ]
#...
| 833000 - 833500 : [ 1 0.00 1.00 ]
#...
| 865500 - 866000 : [ 1 0.00 1.00 ]
#...
| 948500 - 949000 : [ 1 0.00 1.00 ]
#...
| 1439000 - 1439500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOZT reads.list > grep.reads.list.AOZT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOZT 4 500
-------------------------------------------------------------------
#Found 828 total values totalling 30244124.0000. <36526.719807 +/- 3447.927078>
#Range: [ 26774 - 46475 ]
#Most likely bin: [ 34000 - 34500 ] 59 counts
#Median bin: [ 36000 - 36500 ] 57 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 26500 - 27000 : [ 2 0.00 0.00 ]
|X 27000 - 27500 : [ 1 0.00 0.00 ]
#...
|X 28000 - 28500 : [ 2 0.00 0.01 ]
|XXX 28500 - 29000 : [ 4 0.00 0.01 ]
|X 29000 - 29500 : [ 2 0.00 0.01 ]
|XX 29500 - 30000 : [ 3 0.00 0.02 ]
|XXX 30000 - 30500 : [ 5 0.01 0.02 ]
|XXXX 30500 - 31000 : [ 6 0.01 0.03 ]
|XXXXXXXX 31000 - 31500 : [ 12 0.01 0.04 ]
|XXXXXXXXXXXXX 31500 - 32000 : [ 19 0.02 0.07 ]
|XXXXXXXXXXXXXXXXX 32000 - 32500 : [ 25 0.03 0.10 ]
|XXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 31 0.04 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 34 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 48 0.06 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 59 0.07 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 50 0.06 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 47 0.06 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 51 0.06 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 57 0.07 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 48 0.06 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 37 0.04 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 38 0.05 0.70 ]
|XXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 29 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 30 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 31 0.04 0.81 ]
|XXXXXXXXXXX 39500 - 40000 : [ 16 0.02 0.83 ]
|XXXXXXXXXXXXXXXX 40000 - 40500 : [ 24 0.03 0.86 ]
|XXXXXXXXXX 40500 - 41000 : [ 15 0.02 0.88 ]
|XXXXXXXXX 41000 - 41500 : [ 14 0.02 0.89 ]
|XXXXXXXXXXXX 41500 - 42000 : [ 17 0.02 0.91 ]
|XXXXXXXXXXXXXX 42000 - 42500 : [ 20 0.02 0.94 ]
|XXXXXXXXX 42500 - 43000 : [ 14 0.02 0.96 ]
|XXXXXX 43000 - 43500 : [ 9 0.01 0.97 ]
|XXXXX 43500 - 44000 : [ 7 0.01 0.97 ]
|XXXX 44000 - 44500 : [ 6 0.01 0.98 ]
|XXX 44500 - 45000 : [ 5 0.01 0.99 ]
|XXX 45000 - 45500 : [ 5 0.01 0.99 ]
|XX 45500 - 46000 : [ 3 0.00 1.00 ]
|X 46000 - 46500 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AOZT 36284 +- 3302 (n=397)
# AOZS 7181 +- 2517 (n=3744)
# AOZP 2925 +- 392 (n=5472)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3635544_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
AOZP 26880 -1 -1 96 695 26758 90 635 95 652
AOZS 18432 -1 -1 97 710 18417 92 713 97 707
AOZT 3072 92 591 88 525 2303 80 541 86 556
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AOZP 13398 90 626 95 651 13360 90 644 94 653
AOZS 9213 91 710 96 703 9204 93 716 97 711
AOZT 1151 79 545 84 554 1152 81 538 87 558
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3635544_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
96 17028 8710 90.73 94.51 AOZS @
12 1909 1014 84.50 88.02 AOZT @
124 24281 11024 88.90 92.61 AOZP @
] 43218 20748 89.43 cumulative total@@
LIBRARY PLATE ID COUNT [ AOZS 96 AOZT 12 AOZP 124 ] for 232 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.
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trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3635544_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 47478 total values totalling 28405770.0000. <598.293315 +/- 250.910151>
#Range: [ 0 - 991 ]
#Most likely bin: [ 750 - 800 ] 9512 counts
#Median bin: [ 650 - 700 ] 5068 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXX 0 - 50 : [ 4083 0.09 0.09 ]
|XX 50 - 100 : [ 580 0.01 0.10 ]
|XX 100 - 150 : [ 579 0.01 0.11 ]
|XX 150 - 200 : [ 558 0.01 0.12 ]
|XXX 200 - 250 : [ 665 0.01 0.14 ]
|XXX 250 - 300 : [ 811 0.02 0.15 ]
|XXX 300 - 350 : [ 813 0.02 0.17 ]
|XXXX 350 - 400 : [ 915 0.02 0.19 ]
|XXXX 400 - 450 : [ 1054 0.02 0.21 ]
|XXXXX 450 - 500 : [ 1304 0.03 0.24 ]
|XXXXXXX 500 - 550 : [ 1721 0.04 0.28 ]
|XXXXXXXXXX 550 - 600 : [ 2261 0.05 0.32 ]
|XXXXXXXXXXXXXX 600 - 650 : [ 3360 0.07 0.39 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5068 0.11 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7292 0.15 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 9512 0.20 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5761 0.12 0.98 ]
|XXXX 850 - 900 : [ 1000 0.02 1.00 ]
|X 900 - 950 : [ 128 0.00 1.00 ]
| 950 - 1000 : [ 13 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOZP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOZP 3635544_fasta.screen.trimQ15.SaF > reads.trim15.AOZP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOZP.rl 2 50
-------------------------------------------------------------------
#Found 26758 total values totalling 15312941.0000. <572.275245 +/- 251.427786>
#Range: [ 0 - 991 ]
#Most likely bin: [ 750 - 800 ] 4054 counts
#Median bin: [ 650 - 700 ] 3165 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2355 0.09 0.09 ]
|XXX 50 - 100 : [ 354 0.01 0.10 ]
|XXXX 100 - 150 : [ 393 0.01 0.12 ]
|XXXX 150 - 200 : [ 399 0.01 0.13 ]
|XXXXX 200 - 250 : [ 470 0.02 0.15 ]
|XXXXX 250 - 300 : [ 485 0.02 0.17 ]
|XXXXXX 300 - 350 : [ 578 0.02 0.19 ]
|XXXXXX 350 - 400 : [ 639 0.02 0.21 ]
|XXXXXXXX 400 - 450 : [ 783 0.03 0.24 ]
|XXXXXXXXX 450 - 500 : [ 926 0.03 0.28 ]
|XXXXXXXXXXXX 500 - 550 : [ 1246 0.05 0.32 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 1629 0.06 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2322 0.09 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3165 0.12 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3815 0.14 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4054 0.15 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2374 0.09 0.97 ]
|XXXXXX 850 - 900 : [ 632 0.02 0.99 ]
|X 900 - 950 : [ 126 0.00 1.00 ]
| 950 - 1000 : [ 13 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOZS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOZS 3635544_fasta.screen.trimQ15.SaF > reads.trim15.AOZS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOZS.rl 2 50
-------------------------------------------------------------------
#Found 18417 total values totalling 12090386.0000. <656.479666 +/- 231.348483>
#Range: [ 0 - 919 ]
#Most likely bin: [ 750 - 800 ] 5296 counts
#Median bin: [ 700 - 750 ] 3201 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 0 - 50 : [ 1342 0.07 0.07 ]
|X 50 - 100 : [ 143 0.01 0.08 ]
|X 100 - 150 : [ 119 0.01 0.09 ]
|X 150 - 200 : [ 115 0.01 0.09 ]
|X 200 - 250 : [ 126 0.01 0.10 ]
|X 250 - 300 : [ 139 0.01 0.11 ]
|X 300 - 350 : [ 166 0.01 0.12 ]
|XX 350 - 400 : [ 219 0.01 0.13 ]
|XX 400 - 450 : [ 211 0.01 0.14 ]
|XX 450 - 500 : [ 294 0.02 0.16 ]
|XXX 500 - 550 : [ 367 0.02 0.18 ]
|XXXX 550 - 600 : [ 471 0.03 0.20 ]
|XXXXXX 600 - 650 : [ 827 0.04 0.25 ]
|XXXXXXXXXXXX 650 - 700 : [ 1646 0.09 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3201 0.17 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5296 0.29 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3366 0.18 0.98 ]
|XXX 850 - 900 : [ 367 0.02 1.00 ]
| 900 - 950 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOZT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOZT 3635544_fasta.screen.trimQ15.SaF > reads.trim15.AOZT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOZT.rl 2 50
-------------------------------------------------------------------
#Found 2303 total values totalling 1002443.0000. <435.277030 +/- 271.775390>
#Range: [ 0 - 850 ]
#Most likely bin: [ 0 - 50 ] 386 counts
#Median bin: [ 500 - 550 ] 108 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 386 0.17 0.17 ]
|XXXXXXXXX 50 - 100 : [ 83 0.04 0.20 ]
|XXXXXXX 100 - 150 : [ 67 0.03 0.23 ]
|XXXXX 150 - 200 : [ 44 0.02 0.25 ]
|XXXXXXX 200 - 250 : [ 69 0.03 0.28 ]
|XXXXXXXXXXXXXXXXXXX 250 - 300 : [ 187 0.08 0.36 ]
|XXXXXXX 300 - 350 : [ 69 0.03 0.39 ]
|XXXXXX 350 - 400 : [ 57 0.02 0.42 ]
|XXXXXX 400 - 450 : [ 60 0.03 0.44 ]
|XXXXXXXXX 450 - 500 : [ 84 0.04 0.48 ]
|XXXXXXXXXXX 500 - 550 : [ 108 0.05 0.53 ]
|XXXXXXXXXXXXXXXXX 550 - 600 : [ 161 0.07 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 211 0.09 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 257 0.11 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 276 0.12 0.92 ]
|XXXXXXXXXXXXXXXXX 750 - 800 : [ 162 0.07 0.99 ]
|XX 800 - 850 : [ 21 0.01 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ASYI
trimt JAZZ trim 15 readlength histogram for ASWZ
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3635544
-------------------------------------------------------------------
AOZP.000001.000100 pUC18.fa LRS.fasta
AOZP.000101.000200 pUC18.fa pTARBAC2.1.fa LRS.fasta
AOZS.000001.000100 pMCL200.fa LRS.fasta
AOZS.000101.000200 pMCL200.fa LRS.fasta
AOZT.000001.000100 pCC1Fos.fa LRS.fasta
AOZP.000001.000100 pUC18.fa LRS.fasta
AOZP.000101.000200 pUC18.fa pTARBAC2.1.fa LRS.fasta
AOZS.000001.000100 pMCL200.fa LRS.fasta
AOZS.000101.000200 pMCL200.fa LRS.fasta
AOZT.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3635544_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3635544_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 43140 total values totalling 25689.6069. <0.595494 +/- 0.062617>
#Range: [ 0.2264 - 0.8148 ]
#Most likely bin: [ 0.62 - 0.625 ] 2253 counts
#Median bin: [ 0.61 - 0.615 ] 2106 counts
| 0.225 - 0.23 : [ 1 0.00 0.00 ]
#...
| 0.255 - 0.26 : [ 1 0.00 0.00 ]
#...
| 0.27 - 0.275 : [ 1 0.00 0.00 ]
#...
| 0.28 - 0.285 : [ 1 0.00 0.00 ]
| 0.285 - 0.29 : [ 2 0.00 0.00 ]
| 0.29 - 0.295 : [ 4 0.00 0.00 ]
| 0.295 - 0.3 : [ 3 0.00 0.00 ]
| 0.3 - 0.305 : [ 8 0.00 0.00 ]
| 0.305 - 0.31 : [ 3 0.00 0.00 ]
| 0.31 - 0.315 : [ 5 0.00 0.00 ]
| 0.315 - 0.32 : [ 3 0.00 0.00 ]
| 0.32 - 0.325 : [ 10 0.00 0.00 ]
| 0.325 - 0.33 : [ 19 0.00 0.00 ]
|X 0.33 - 0.335 : [ 30 0.00 0.00 ]
| 0.335 - 0.34 : [ 27 0.00 0.00 ]
| 0.34 - 0.345 : [ 28 0.00 0.00 ]
| 0.345 - 0.35 : [ 24 0.00 0.00 ]
| 0.35 - 0.355 : [ 27 0.00 0.00 ]
| 0.355 - 0.36 : [ 19 0.00 0.01 ]
|X 0.36 - 0.365 : [ 29 0.00 0.01 ]
|X 0.365 - 0.37 : [ 36 0.00 0.01 ]
|X 0.37 - 0.375 : [ 42 0.00 0.01 ]
|X 0.375 - 0.38 : [ 52 0.00 0.01 ]
|X 0.38 - 0.385 : [ 67 0.00 0.01 ]
|X 0.385 - 0.39 : [ 81 0.00 0.01 ]
|X 0.39 - 0.395 : [ 80 0.00 0.01 ]
|X 0.395 - 0.4 : [ 79 0.00 0.02 ]
|XX 0.4 - 0.405 : [ 96 0.00 0.02 ]
|XX 0.405 - 0.41 : [ 103 0.00 0.02 ]
|XX 0.41 - 0.415 : [ 119 0.00 0.02 ]
|XX 0.415 - 0.42 : [ 135 0.00 0.03 ]
|XX 0.42 - 0.425 : [ 109 0.00 0.03 ]
|XXX 0.425 - 0.43 : [ 152 0.00 0.03 ]
|XXX 0.43 - 0.435 : [ 144 0.00 0.04 ]
|XX 0.435 - 0.44 : [ 133 0.00 0.04 ]
|XXX 0.44 - 0.445 : [ 159 0.00 0.04 ]
|XXX 0.445 - 0.45 : [ 141 0.00 0.05 ]
|XXX 0.45 - 0.455 : [ 165 0.00 0.05 ]
|XXX 0.455 - 0.46 : [ 165 0.00 0.05 ]
|XXX 0.46 - 0.465 : [ 153 0.00 0.06 ]
|XX 0.465 - 0.47 : [ 115 0.00 0.06 ]
|XXX 0.47 - 0.475 : [ 144 0.00 0.06 ]
|XXX 0.475 - 0.48 : [ 150 0.00 0.07 ]
|XXXX 0.48 - 0.485 : [ 202 0.00 0.07 ]
|XXX 0.485 - 0.49 : [ 196 0.00 0.08 ]
|XXXX 0.49 - 0.495 : [ 224 0.01 0.08 ]
|XXXX 0.495 - 0.5 : [ 205 0.00 0.09 ]
|XXXXX 0.5 - 0.505 : [ 291 0.01 0.09 ]
|XXXX 0.505 - 0.51 : [ 253 0.01 0.10 ]
|XXXXX 0.51 - 0.515 : [ 265 0.01 0.10 ]
|XXXXX 0.515 - 0.52 : [ 306 0.01 0.11 ]
|XXXXXX 0.52 - 0.525 : [ 324 0.01 0.12 ]
|XXXXXX 0.525 - 0.53 : [ 361 0.01 0.13 ]
|XXXXXXX 0.53 - 0.535 : [ 410 0.01 0.14 ]
|XXXXXXXX 0.535 - 0.54 : [ 438 0.01 0.15 ]
|XXXXXXXXX 0.54 - 0.545 : [ 519 0.01 0.16 ]
|XXXXXXXXX 0.545 - 0.55 : [ 517 0.01 0.17 ]
|XXXXXXXXXXX 0.55 - 0.555 : [ 642 0.01 0.19 ]
|XXXXXXXXXXXX 0.555 - 0.56 : [ 664 0.02 0.20 ]
|XXXXXXXXXXXX 0.56 - 0.565 : [ 674 0.02 0.22 ]
|XXXXXXXXXXXXX 0.565 - 0.57 : [ 733 0.02 0.23 ]
|XXXXXXXXXXXXXXX 0.57 - 0.575 : [ 820 0.02 0.25 ]
|XXXXXXXXXXXXXXX 0.575 - 0.58 : [ 865 0.02 0.27 ]
|XXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1105 0.03 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1309 0.03 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 1501 0.03 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 1626 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1937 0.04 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1979 0.05 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 2106 0.05 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 2194 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 2253 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 2245 0.05 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 2102 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 1934 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 1759 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 1581 0.04 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 1346 0.03 0.90 ]
|XXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 1103 0.03 0.92 ]
|XXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 899 0.02 0.94 ]
|XXXXXXXXXXXXX 0.665 - 0.67 : [ 705 0.02 0.96 ]
|XXXXXXXXX 0.67 - 0.675 : [ 500 0.01 0.97 ]
|XXXXXXX 0.675 - 0.68 : [ 383 0.01 0.98 ]
|XXXX 0.68 - 0.685 : [ 232 0.01 0.99 ]
|XXX 0.685 - 0.69 : [ 170 0.00 0.99 ]
|XXX 0.69 - 0.695 : [ 150 0.00 0.99 ]
|XX 0.695 - 0.7 : [ 89 0.00 1.00 ]
|X 0.7 - 0.705 : [ 47 0.00 1.00 ]
|X 0.705 - 0.71 : [ 35 0.00 1.00 ]
| 0.71 - 0.715 : [ 25 0.00 1.00 ]
| 0.715 - 0.72 : [ 13 0.00 1.00 ]
| 0.72 - 0.725 : [ 7 0.00 1.00 ]
| 0.725 - 0.73 : [ 10 0.00 1.00 ]
| 0.73 - 0.735 : [ 6 0.00 1.00 ]
#...
| 0.74 - 0.745 : [ 4 0.00 1.00 ]
| 0.745 - 0.75 : [ 3 0.00 1.00 ]
| 0.75 - 0.755 : [ 1 0.00 1.00 ]
| 0.755 - 0.76 : [ 1 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 ]
| 0.775 - 0.78 : [ 1 0.00 1.00 ]
| 0.78 - 0.785 : [ 1 0.00 1.00 ]
#...
| 0.81 - 0.815 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
--------------------------------------------------------------
Contig 1. 3 reads; 1652 bp (untrimmed), 1490 (trimmed).
Contig 2. 5 reads; 1332 bp (untrimmed), 1089 (trimmed).
Contig 3. 6 reads; 932 bp (untrimmed), 932 (trimmed).
Contig 4. 7 reads; 1196 bp (untrimmed), 1129 (trimmed).
Contig 5. 709 reads; 48916 bp (untrimmed), 48852 (trimmed).
Contig 6. 1992 reads; 116255 bp (untrimmed), 116066 (trimmed).
Contig 7. 14995 reads; 849704 bp (untrimmed), 849522 (trimmed).
Contig 8. 25486 reads; 1491977 bp (untrimmed), 1491901 (trimmed).
--------------------------------------------------------------
Totals 43203 reads; 2511964 bp (untrimmed), 2510981 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2511964 bases = 15.23 +- 4.57 = 0.03 +- 4.24
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 8 total values totalling 75.5100. <9.438750 +/- 5.443639>
#Range: [ 1.59 - 15.60 ]
#Most likely bin: [ 5.5 - 6 ] 2 counts
#Median bin: [ 5.5 - 6 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 1 0.12 0.12 ]
#...
|XXXXXXXXXXXXXXXXXXXX 3.5 - 4 : [ 1 0.12 0.25 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 2 0.25 0.50 ]
#...
|XXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 1 0.12 0.62 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15 - 15.5 : [ 2 0.25 0.88 ]
|XXXXXXXXXXXXXXXXXXXX 15.5 - 16 : [ 1 0.12 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 4 total values totalling 58.7800. <14.695000 +/- 1.053221>
#Range: [ 12.90 - 15.60 ]
#Most likely bin: [ 15 - 15.5 ] 2 counts
#Median bin: [ 15 - 15.5 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 1 0.25 0.25 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 15 - 15.5 : [ 2 0.50 0.75 ]
|XXXXXXXXXXXXXXXXXXXX 15.5 - 16 : [ 1 0.25 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 1 3 reads 1652 bases = 1.59 +- 0.68 = 1.59 +- 0.68
Contig 2 5 reads 1332 bases = 3.72 +- 1.55 = 3.72 +- 1.55
Contig 4 7 reads 1196 bases = 5.68 +- 1.86 = 0.84 +- 1.12
Contig 3 6 reads 932 bases = 5.74 +- 0.75 = 5.74 +- 0.75
Contig 5 709 reads 48916 bases = 12.90 +- 4.57 = 0.39 +- 3.79
Contig 6 1992 reads 116255 bases = 15.14 +- 4.31 = 0.02 +- 4.50
Contig 8 25486 reads 1491977 bases = 15.14 +- 4.42 = 0.04 +- 4.17
Contig 7 14995 reads 849704 bases = 15.60 +- 4.73 = -0.01 +- 4.34
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 982
HQ Discrepant reads = 21
Chimeric reads = 210
Suspect alignments = 232
-------------------------------------------------------------------
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/finished2/microbe/3635544/edit_dir.11Aug04.QD