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
3436494 1500 1525 Moorella thermoacetica
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Moorella_thermoacetica
-------------------------------------------------------------------
Thermoanaerobacteriaceae, family, eubacteria
Clostridia, class, eubacteria
Thermoanaerobacteriales, order, eubacteria
Moorella, genus, eubacteria
Moorella group, eubacteria
Moorella thermoacetica, species, eubacteria
Firmicutes (Gram-positive bacteria), phylum, eubacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2732159
# phrap: 2566037
# db:
altered.
1500000
2266065 +/- 545918
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 40942
Number of reads with percent X's >= 20%: 522 = 1.0%
Number of reads with percent X's >= 50%: 224 = 0.4%
Number of reads with percent X's >= 80%: 23 = 0.0%
Total reads in project: 54180
Total bp X'd : 2882617
reads >= 20% >= 50% >= 80% screened
Nr with L09136 9235 158 55 4
Nr with pCC1Fos 1451 0 0 0
Nr with pMCL200_JGI_XZX+XZK 30256 364 169 19
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 514
Number of reads with percent X's >= 20%: 4 = 0.7%
Number of reads with percent X's >= 50%: 4 = 0.7%
Number of reads with percent X's >= 80%: 2 = 0.3%
Total reads in project: 592
Total bp X'd : 39444
reads >= 20% >= 50% >= 80% screened
Nr with L09136 8 2 2 2
Nr with pCC1Fos 11 0 0 0
Nr with pMCL200_JGI_XZX+XZK 495 2 2 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 11319778
C = 13782448
G = 13893211
T = 10988287
N = 274922
X = 2882617
GC fraction = 0.52
Total = 53141263
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436494_fasta.screen.contigs
-------------------------------------------------------------------
A 617405
C 761094
G 754022
T 619456
N 1530
fraction GC = 0.55
total bases = 2753507
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 AAOP reads.list > grep.reads.list.AAOP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAOP 4 500
-------------------------------------------------------------------
#Found 8825 total values totalling 30633230.0000. <3471.187535 +/- 1747.209894>
#Range: [ 434 - 35028 ]
#Most likely bin: [ 3000 - 3500 ] 2568 counts
#Median bin: [ 3000 - 3500 ] 2568 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
|X 500 - 1000 : [ 33 0.00 0.00 ]
|XX 1000 - 1500 : [ 136 0.02 0.02 ]
|XX 1500 - 2000 : [ 120 0.01 0.03 ]
|XXXX 2000 - 2500 : [ 255 0.03 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 2159 0.24 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2568 0.29 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1858 0.21 0.81 ]
|XXXXXXXXXXXXXXXX 4000 - 4500 : [ 1050 0.12 0.93 ]
|XXXXXXXX 4500 - 5000 : [ 506 0.06 0.98 ]
|XX 5000 - 5500 : [ 103 0.01 1.00 ]
| 5500 - 6000 : [ 1 0.00 1.00 ]
#...
| 10000 - 10500 : [ 1 0.00 1.00 ]
#...
| 11000 - 11500 : [ 1 0.00 1.00 ]
#...
| 21000 - 21500 : [ 1 0.00 1.00 ]
#...
| 24000 - 24500 : [ 3 0.00 1.00 ]
| 24500 - 25000 : [ 2 0.00 1.00 ]
| 25000 - 25500 : [ 5 0.00 1.00 ]
| 25500 - 26000 : [ 6 0.00 1.00 ]
#...
| 32000 - 32500 : [ 1 0.00 1.00 ]
| 32500 - 33000 : [ 6 0.00 1.00 ]
| 33000 - 33500 : [ 4 0.00 1.00 ]
#...
| 34000 - 34500 : [ 2 0.00 1.00 ]
| 34500 - 35000 : [ 2 0.00 1.00 ]
| 35000 - 35500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAOR reads.list > grep.reads.list.AAOR
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAOR 4 500
-------------------------------------------------------------------
#Found 4524 total values totalling 29624815.0000. <6548.367595 +/- 3151.240186>
#Range: [ 884 - 40420 ]
#Most likely bin: [ 7500 - 8000 ] 479 counts
#Median bin: [ 6500 - 7000 ] 274 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 3 0.00 0.00 ]
|XXXXXXXX 1000 - 1500 : [ 99 0.02 0.02 ]
|XXXXXXXXXXXX 1500 - 2000 : [ 149 0.03 0.06 ]
|XXXXXXXXXXXXX 2000 - 2500 : [ 157 0.03 0.09 ]
|XXXXXXXXXXXXXX 2500 - 3000 : [ 171 0.04 0.13 ]
|XXXXXXXXXXXX 3000 - 3500 : [ 145 0.03 0.16 ]
|XXXXXXXXXXXXXXX 3500 - 4000 : [ 176 0.04 0.20 ]
|XXXXXXXXXXXXXX 4000 - 4500 : [ 173 0.04 0.24 ]
|XXXXXXXXXXXXXXXXXX 4500 - 5000 : [ 210 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXX 5000 - 5500 : [ 218 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 240 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 254 0.06 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 274 0.06 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 396 0.09 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 479 0.11 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 432 0.10 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 355 0.08 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 271 0.06 0.93 ]
|XXXXXXXXXXXXX 9500 - 10000 : [ 151 0.03 0.96 ]
|XXXXXXX 10000 - 10500 : [ 86 0.02 0.98 ]
|XXX 10500 - 11000 : [ 38 0.01 0.99 ]
|X 11000 - 11500 : [ 16 0.00 0.99 ]
|X 11500 - 12000 : [ 7 0.00 0.99 ]
| 12000 - 12500 : [ 1 0.00 0.99 ]
#...
| 13000 - 13500 : [ 1 0.00 1.00 ]
#...
| 24500 - 25000 : [ 1 0.00 1.00 ]
#...
| 29000 - 29500 : [ 2 0.00 1.00 ]
| 29500 - 30000 : [ 1 0.00 1.00 ]
| 30000 - 30500 : [ 1 0.00 1.00 ]
#...
| 31000 - 31500 : [ 1 0.00 1.00 ]
#...
| 32500 - 33000 : [ 1 0.00 1.00 ]
#...
| 36000 - 36500 : [ 2 0.00 1.00 ]
| 36500 - 37000 : [ 1 0.00 1.00 ]
|X 37000 - 37500 : [ 6 0.00 1.00 ]
| 37500 - 38000 : [ 1 0.00 1.00 ]
| 38000 - 38500 : [ 2 0.00 1.00 ]
| 38500 - 39000 : [ 1 0.00 1.00 ]
| 39000 - 39500 : [ 1 0.00 1.00 ]
#...
| 40000 - 40500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAOS reads.list > grep.reads.list.AAOS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAOS 4 500
-------------------------------------------------------------------
#Found 935 total values totalling 35526101.0000. <37995.829947 +/- 5543.374780>
#Range: [ 25864 - 74429 ]
#Most likely bin: [ 35500 - 36000 ] 66 counts
#Median bin: [ 37000 - 37500 ] 53 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 25500 - 26000 : [ 2 0.00 0.00 ]
#...
|X 26500 - 27000 : [ 1 0.00 0.00 ]
|X 27000 - 27500 : [ 1 0.00 0.00 ]
#...
|XX 28000 - 28500 : [ 3 0.00 0.01 ]
|X 28500 - 29000 : [ 2 0.00 0.01 ]
|XXX 29000 - 29500 : [ 5 0.01 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 ]
|XXXX 31000 - 31500 : [ 6 0.01 0.04 ]
|XXXXXX 31500 - 32000 : [ 10 0.01 0.05 ]
|XXXXXXXX 32000 - 32500 : [ 13 0.01 0.06 ]
|XXXXXXXXXX 32500 - 33000 : [ 17 0.02 0.08 ]
|XXXXXXXXXXXXX 33000 - 33500 : [ 22 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 31 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 38 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 36 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 55 0.06 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 66 0.07 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 65 0.07 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 52 0.06 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 53 0.06 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 57 0.06 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 56 0.06 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 54 0.06 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 48 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 42 0.04 0.80 ]
|XXXXXXXXXXXXXXXX 40000 - 40500 : [ 26 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 34 0.04 0.87 ]
|XXXXXXXXXXXXXXXX 41000 - 41500 : [ 27 0.03 0.89 ]
|XXXXXXXXXXXXX 41500 - 42000 : [ 21 0.02 0.92 ]
|XXXXXXXX 42000 - 42500 : [ 13 0.01 0.93 ]
|XXXX 42500 - 43000 : [ 6 0.01 0.94 ]
|XXXX 43000 - 43500 : [ 7 0.01 0.94 ]
|XXXX 43500 - 44000 : [ 6 0.01 0.95 ]
|XX 44000 - 44500 : [ 3 0.00 0.95 ]
|X 44500 - 45000 : [ 1 0.00 0.96 ]
|XX 45000 - 45500 : [ 4 0.00 0.96 ]
#...
|X 51500 - 52000 : [ 1 0.00 0.96 ]
|X 52000 - 52500 : [ 2 0.00 0.96 ]
|X 52500 - 53000 : [ 2 0.00 0.96 ]
|XX 53000 - 53500 : [ 4 0.00 0.97 ]
|X 53500 - 54000 : [ 2 0.00 0.97 ]
|X 54000 - 54500 : [ 2 0.00 0.97 ]
|X 54500 - 55000 : [ 1 0.00 0.97 ]
|X 55000 - 55500 : [ 2 0.00 0.98 ]
|X 55500 - 56000 : [ 1 0.00 0.98 ]
#...
|X 56500 - 57000 : [ 2 0.00 0.98 ]
#...
|X 57500 - 58000 : [ 2 0.00 0.98 ]
|X 58000 - 58500 : [ 2 0.00 0.98 ]
|X 58500 - 59000 : [ 1 0.00 0.99 ]
#...
|X 59500 - 60000 : [ 1 0.00 0.99 ]
#...
|X 61500 - 62000 : [ 1 0.00 0.99 ]
#...
|X 64500 - 65000 : [ 1 0.00 0.99 ]
|X 65000 - 65500 : [ 1 0.00 0.99 ]
|X 65500 - 66000 : [ 1 0.00 0.99 ]
#...
|X 66500 - 67000 : [ 1 0.00 0.99 ]
#...
|X 68500 - 69000 : [ 2 0.00 0.99 ]
|X 69000 - 69500 : [ 2 0.00 1.00 ]
#...
|X 71000 - 71500 : [ 2 0.00 1.00 ]
|X 71500 - 72000 : [ 1 0.00 1.00 ]
#...
|X 74000 - 74500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACOB reads.list > grep.reads.list.ACOB
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACOB 4 500
-------------------------------------------------------------------
#Found 8512 total values totalling 62325106.0000. <7322.028430 +/- 2425.771883>
#Range: [ 476 - 51734 ]
#Most likely bin: [ 6500 - 7000 ] 1562 counts
#Median bin: [ 7000 - 7500 ] 1466 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 2 0.00 0.00 ]
| 500 - 1000 : [ 7 0.00 0.00 ]
|X 1000 - 1500 : [ 39 0.00 0.01 ]
|X 1500 - 2000 : [ 38 0.00 0.01 ]
|X 2000 - 2500 : [ 36 0.00 0.01 ]
|X 2500 - 3000 : [ 37 0.00 0.02 ]
|X 3000 - 3500 : [ 52 0.01 0.02 ]
|X 3500 - 4000 : [ 29 0.00 0.03 ]
|X 4000 - 4500 : [ 45 0.01 0.03 ]
|XX 4500 - 5000 : [ 87 0.01 0.04 ]
|XXXXX 5000 - 5500 : [ 197 0.02 0.07 ]
|XXXXXXXXXXXXX 5500 - 6000 : [ 512 0.06 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1035 0.12 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1562 0.18 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1466 0.17 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1227 0.14 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 902 0.11 0.85 ]
|XXXXXXXXXXXXXXX 8500 - 9000 : [ 593 0.07 0.92 ]
|XXXXXXXXX 9000 - 9500 : [ 361 0.04 0.97 ]
|XXXX 9500 - 10000 : [ 171 0.02 0.99 ]
|X 10000 - 10500 : [ 48 0.01 0.99 ]
| 10500 - 11000 : [ 5 0.00 0.99 ]
#...
| 23000 - 23500 : [ 1 0.00 0.99 ]
| 23500 - 24000 : [ 3 0.00 0.99 ]
| 24000 - 24500 : [ 6 0.00 0.99 ]
| 24500 - 25000 : [ 5 0.00 0.99 ]
| 25000 - 25500 : [ 12 0.00 1.00 ]
| 25500 - 26000 : [ 3 0.00 1.00 ]
| 26000 - 26500 : [ 6 0.00 1.00 ]
#...
| 35500 - 36000 : [ 4 0.00 1.00 ]
| 36000 - 36500 : [ 5 0.00 1.00 ]
| 36500 - 37000 : [ 4 0.00 1.00 ]
| 37000 - 37500 : [ 2 0.00 1.00 ]
| 37500 - 38000 : [ 4 0.00 1.00 ]
| 38000 - 38500 : [ 3 0.00 1.00 ]
| 38500 - 39000 : [ 1 0.00 1.00 ]
| 39000 - 39500 : [ 1 0.00 1.00 ]
#...
| 51500 - 52000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AAOS 37183 +- 3095 (n=445)
# ACOB 7092 +- 2594 (n=4184)
# AAOP 3326 +- 1474 (n=4537)
# AAOR 6146 +- 3153 (n=2274)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436494_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
AAOP 20640 -1 -1 99 669 20901 96 670 97 673
AAOR 13056 -1 -1 96 670 13055 78 564 95 627
AAOS 3072 -1 -1 99 749 3072 97 751 99 760
ACOB 25344 -1 -1 97 700 25358 80 572 94 623
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AAOP 10633 96 666 98 677 10268 96 675 97 669
AAOR 6562 78 555 95 625 6493 78 574 95 628
AAOS 1536 96 747 98 734 1536 99 755 99 787
ACOB 12728 78 565 93 614 12630 83 579 96 633
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436494_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
68 10245 5282 77.68 80.91 AAOR @
16 2990 1517 94.81 98.76 AAOS @
124 20818 10355 83.51 86.99 ACOB @
108 20127 10176 94.22 98.15 AAOP @
] 54180 27330 86.49 cumulative total@@
LIBRARY PLATE ID COUNT [ AAOR 68 AAOS 16 ACOB 124 AAOP 108 ] for 316 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 3436494_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 62386 total values totalling 33207054.0000. <532.283750 +/- 254.117767>
#Range: [ 0 - 954 ]
#Most likely bin: [ 700 - 750 ] 11663 counts
#Median bin: [ 600 - 650 ] 7923 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 7783 0.12 0.12 ]
|XXX 50 - 100 : [ 990 0.02 0.14 ]
|XXX 100 - 150 : [ 858 0.01 0.15 ]
|XXX 150 - 200 : [ 908 0.01 0.17 ]
|XXX 200 - 250 : [ 863 0.01 0.18 ]
|XXX 250 - 300 : [ 986 0.02 0.20 ]
|XXXX 300 - 350 : [ 1022 0.02 0.21 ]
|XXXX 350 - 400 : [ 1196 0.02 0.23 ]
|XXXXX 400 - 450 : [ 1458 0.02 0.26 ]
|XXXXXX 450 - 500 : [ 1813 0.03 0.29 ]
|XXXXXXXXX 500 - 550 : [ 2623 0.04 0.33 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 4320 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 7923 0.13 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 11442 0.18 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 11663 0.19 0.90 ]
|XXXXXXXXXXXXXXXXXX 750 - 800 : [ 5272 0.08 0.98 ]
|XXXX 800 - 850 : [ 1064 0.02 1.00 ]
|X 850 - 900 : [ 176 0.00 1.00 ]
| 900 - 950 : [ 25 0.00 1.00 ]
| 950 - 1000 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAOP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAOP 3436494_fasta.screen.trimQ15.SaF > reads.trim15.AAOP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAOP.rl 2 50
-------------------------------------------------------------------
#Found 20901 total values totalling 13445622.0000. <643.300416 +/- 158.066218>
#Range: [ 0 - 954 ]
#Most likely bin: [ 650 - 700 ] 6348 counts
#Median bin: [ 650 - 700 ] 6348 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 0 - 50 : [ 773 0.04 0.04 ]
|X 50 - 100 : [ 88 0.00 0.04 ]
| 100 - 150 : [ 63 0.00 0.04 ]
| 150 - 200 : [ 71 0.00 0.05 ]
| 200 - 250 : [ 65 0.00 0.05 ]
| 250 - 300 : [ 79 0.00 0.05 ]
|X 300 - 350 : [ 106 0.01 0.06 ]
|X 350 - 400 : [ 140 0.01 0.07 ]
|X 400 - 450 : [ 156 0.01 0.07 ]
|X 450 - 500 : [ 163 0.01 0.08 ]
|XX 500 - 550 : [ 324 0.02 0.10 ]
|XXXXXXX 550 - 600 : [ 1060 0.05 0.15 ]
|XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3313 0.16 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 6348 0.30 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6245 0.30 0.91 ]
|XXXXXXXXXXX 750 - 800 : [ 1682 0.08 0.99 ]
|X 800 - 850 : [ 140 0.01 1.00 ]
| 850 - 900 : [ 70 0.00 1.00 ]
| 900 - 950 : [ 14 0.00 1.00 ]
| 950 - 1000 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAOR
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAOR 3436494_fasta.screen.trimQ15.SaF > reads.trim15.AAOR.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAOR.rl 2 50
-------------------------------------------------------------------
#Found 13055 total values totalling 5760592.0000. <441.255611 +/- 261.959007>
#Range: [ 0 - 944 ]
#Most likely bin: [ 0 - 50 ] 2752 counts
#Median bin: [ 550 - 600 ] 1557 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2752 0.21 0.21 ]
|XX 50 - 100 : [ 121 0.01 0.22 ]
|XX 100 - 150 : [ 116 0.01 0.23 ]
|XX 150 - 200 : [ 161 0.01 0.24 ]
|XXX 200 - 250 : [ 187 0.01 0.26 ]
|XXXX 250 - 300 : [ 254 0.02 0.28 ]
|XXXX 300 - 350 : [ 282 0.02 0.30 ]
|XXXXX 350 - 400 : [ 352 0.03 0.32 ]
|XXXXXX 400 - 450 : [ 445 0.03 0.36 ]
|XXXXXXXXX 450 - 500 : [ 634 0.05 0.41 ]
|XXXXXXXXXXXXXX 500 - 550 : [ 959 0.07 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1557 0.12 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2262 0.17 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1977 0.15 0.92 ]
|XXXXXXXXXXXX 700 - 750 : [ 800 0.06 0.98 ]
|XX 750 - 800 : [ 159 0.01 1.00 ]
| 800 - 850 : [ 25 0.00 1.00 ]
| 850 - 900 : [ 10 0.00 1.00 ]
| 900 - 950 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAOS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAOS 3436494_fasta.screen.trimQ15.SaF > reads.trim15.AAOS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAOS.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 2245708.0000. <731.024740 +/- 150.840708>
#Range: [ 0 - 901 ]
#Most likely bin: [ 750 - 800 ] 1251 counts
#Median bin: [ 750 - 800 ] 1251 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 0 - 50 : [ 79 0.03 0.03 ]
| 50 - 100 : [ 6 0.00 0.03 ]
| 100 - 150 : [ 2 0.00 0.03 ]
| 150 - 200 : [ 4 0.00 0.03 ]
| 200 - 250 : [ 12 0.00 0.03 ]
| 250 - 300 : [ 15 0.00 0.04 ]
| 300 - 350 : [ 15 0.00 0.04 ]
| 350 - 400 : [ 11 0.00 0.05 ]
|X 400 - 450 : [ 20 0.01 0.05 ]
| 450 - 500 : [ 12 0.00 0.06 ]
| 500 - 550 : [ 13 0.00 0.06 ]
|X 550 - 600 : [ 31 0.01 0.07 ]
|XX 600 - 650 : [ 67 0.02 0.09 ]
|XXXXX 650 - 700 : [ 168 0.05 0.15 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 643 0.21 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1251 0.41 0.76 ]
|XXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 665 0.22 0.98 ]
|XX 850 - 900 : [ 57 0.02 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AGXN
trimt JAZZ trim 15 readlength histogram for ACOB
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACOB 3436494_fasta.screen.trimQ15.SaF > reads.trim15.ACOB.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACOB.rl 2 50
-------------------------------------------------------------------
#Found 25358 total values totalling 11755132.0000. <463.567001 +/- 276.152225>
#Range: [ 0 - 928 ]
#Most likely bin: [ 0 - 50 ] 4179 counts
#Median bin: [ 550 - 600 ] 1672 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 4179 0.16 0.16 ]
|XXXXXXX 50 - 100 : [ 775 0.03 0.20 ]
|XXXXXX 100 - 150 : [ 677 0.03 0.22 ]
|XXXXXX 150 - 200 : [ 672 0.03 0.25 ]
|XXXXXX 200 - 250 : [ 599 0.02 0.27 ]
|XXXXXX 250 - 300 : [ 638 0.03 0.30 ]
|XXXXXX 300 - 350 : [ 619 0.02 0.32 ]
|XXXXXXX 350 - 400 : [ 693 0.03 0.35 ]
|XXXXXXXX 400 - 450 : [ 837 0.03 0.38 ]
|XXXXXXXXXX 450 - 500 : [ 1004 0.04 0.42 ]
|XXXXXXXXXXXXX 500 - 550 : [ 1327 0.05 0.47 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 1672 0.07 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2281 0.09 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2949 0.12 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3975 0.16 0.90 ]
|XXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2180 0.09 0.99 ]
|XX 800 - 850 : [ 234 0.01 1.00 ]
| 850 - 900 : [ 39 0.00 1.00 ]
| 900 - 950 : [ 8 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436494
-------------------------------------------------------------------
AAOP.000001.000100 pUC18.fa.4 LRS.fasta
AAOP.000101.000200 pUC18.fa.4 LRS.fasta
AAOR.000001.000100 pMCL200.fa.4 LRS.fasta
AAOS.000001.000100 pCC1Fos.fa.4 LRS.fasta
ACOB.000001.000100 pMCL200.fa.4 LRS.fasta
ACOB.000101.000200 pMCL200.fa.4 LRS.fasta
AAOP.000001.000100 pUC18.fa.4 LRS.fasta
AAOP.000101.000200 pUC18.fa.4 LRS.fasta
AAOR.000001.000100 pMCL200.fa.4 LRS.fasta
AAOS.000001.000100 pCC1Fos.fa.4 LRS.fasta
ACOB.000001.000100 pMCL200.fa.4 LRS.fasta
ACOB.000101.000200 pMCL200.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436494_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436494_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 54009 total values totalling 29895.5387. <0.553529 +/- 0.071250>
#Range: [ 0 - 0.9656 ]
#Most likely bin: [ 0.58 - 0.585 ] 1900 counts
#Median bin: [ 0.56 - 0.565 ] 1702 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.2 - 0.205 : [ 1 0.00 0.00 ]
| 0.205 - 0.21 : [ 2 0.00 0.00 ]
| 0.21 - 0.215 : [ 1 0.00 0.00 ]
| 0.215 - 0.22 : [ 4 0.00 0.00 ]
| 0.22 - 0.225 : [ 3 0.00 0.00 ]
| 0.225 - 0.23 : [ 3 0.00 0.00 ]
| 0.23 - 0.235 : [ 2 0.00 0.00 ]
| 0.235 - 0.24 : [ 3 0.00 0.00 ]
| 0.24 - 0.245 : [ 5 0.00 0.00 ]
| 0.245 - 0.25 : [ 2 0.00 0.00 ]
| 0.25 - 0.255 : [ 9 0.00 0.00 ]
| 0.255 - 0.26 : [ 6 0.00 0.00 ]
| 0.26 - 0.265 : [ 3 0.00 0.00 ]
| 0.265 - 0.27 : [ 14 0.00 0.00 ]
| 0.27 - 0.275 : [ 12 0.00 0.00 ]
| 0.275 - 0.28 : [ 11 0.00 0.00 ]
| 0.28 - 0.285 : [ 11 0.00 0.00 ]
| 0.285 - 0.29 : [ 15 0.00 0.00 ]
|X 0.29 - 0.295 : [ 26 0.00 0.00 ]
| 0.295 - 0.3 : [ 22 0.00 0.00 ]
| 0.3 - 0.305 : [ 19 0.00 0.00 ]
|X 0.305 - 0.31 : [ 43 0.00 0.00 ]
|X 0.31 - 0.315 : [ 40 0.00 0.00 ]
|X 0.315 - 0.32 : [ 38 0.00 0.01 ]
|X 0.32 - 0.325 : [ 63 0.00 0.01 ]
|X 0.325 - 0.33 : [ 70 0.00 0.01 ]
|X 0.33 - 0.335 : [ 56 0.00 0.01 ]
|XX 0.335 - 0.34 : [ 87 0.00 0.01 ]
|XX 0.34 - 0.345 : [ 103 0.00 0.01 ]
|XX 0.345 - 0.35 : [ 104 0.00 0.01 ]
|XX 0.35 - 0.355 : [ 97 0.00 0.02 ]
|XX 0.355 - 0.36 : [ 101 0.00 0.02 ]
|XX 0.36 - 0.365 : [ 103 0.00 0.02 ]
|XX 0.365 - 0.37 : [ 107 0.00 0.02 ]
|XX 0.37 - 0.375 : [ 98 0.00 0.02 ]
|XX 0.375 - 0.38 : [ 107 0.00 0.03 ]
|XX 0.38 - 0.385 : [ 118 0.00 0.03 ]
|XXX 0.385 - 0.39 : [ 132 0.00 0.03 ]
|XXX 0.39 - 0.395 : [ 135 0.00 0.03 ]
|XXX 0.395 - 0.4 : [ 152 0.00 0.04 ]
|XXXX 0.4 - 0.405 : [ 185 0.00 0.04 ]
|XXXX 0.405 - 0.41 : [ 202 0.00 0.04 ]
|XXXXX 0.41 - 0.415 : [ 214 0.00 0.05 ]
|XXXXX 0.415 - 0.42 : [ 237 0.00 0.05 ]
|XXXXXX 0.42 - 0.425 : [ 265 0.00 0.06 ]
|XXXXXX 0.425 - 0.43 : [ 275 0.01 0.06 ]
|XXXXXX 0.43 - 0.435 : [ 300 0.01 0.07 ]
|XXXXXX 0.435 - 0.44 : [ 288 0.01 0.07 ]
|XXXXXXX 0.44 - 0.445 : [ 339 0.01 0.08 ]
|XXXXXXXX 0.445 - 0.45 : [ 388 0.01 0.09 ]
|XXXXXXX 0.45 - 0.455 : [ 351 0.01 0.09 ]
|XXXXXXXXX 0.455 - 0.46 : [ 419 0.01 0.10 ]
|XXXXXXXXXXX 0.46 - 0.465 : [ 517 0.01 0.11 ]
|XXXXXXXXXXX 0.465 - 0.47 : [ 526 0.01 0.12 ]
|XXXXXXXXXXXX 0.47 - 0.475 : [ 580 0.01 0.13 ]
|XXXXXXXXXXXXX 0.475 - 0.48 : [ 631 0.01 0.14 ]
|XXXXXXXXXXXXXXX 0.48 - 0.485 : [ 690 0.01 0.15 ]
|XXXXXXXXXXXXXXX 0.485 - 0.49 : [ 707 0.01 0.17 ]
|XXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 814 0.02 0.18 ]
|XXXXXXXXXXXXXXX 0.495 - 0.5 : [ 713 0.01 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 1053 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 866 0.02 0.23 ]
|XXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 941 0.02 0.25 ]
|XXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 1010 0.02 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 1153 0.02 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 1181 0.02 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 1316 0.02 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 1353 0.03 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1372 0.03 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1397 0.03 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1509 0.03 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1663 0.03 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1702 0.03 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1801 0.03 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1861 0.03 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1828 0.03 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1900 0.04 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1840 0.03 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 1763 0.03 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 1683 0.03 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1736 0.03 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1527 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1427 0.03 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1301 0.02 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 1192 0.02 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 1145 0.02 0.89 ]
|XXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 958 0.02 0.91 ]
|XXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 866 0.02 0.92 ]
|XXXXXXXXXXXXXXX 0.64 - 0.645 : [ 731 0.01 0.94 ]
|XXXXXXXXXXXXX 0.645 - 0.65 : [ 616 0.01 0.95 ]
|XXXXXXXXXXX 0.65 - 0.655 : [ 520 0.01 0.96 ]
|XXXXXXXXX 0.655 - 0.66 : [ 424 0.01 0.97 ]
|XXXXXXXX 0.66 - 0.665 : [ 357 0.01 0.97 ]
|XXXXXXX 0.665 - 0.67 : [ 330 0.01 0.98 ]
|XXXXX 0.67 - 0.675 : [ 228 0.00 0.98 ]
|XXXX 0.675 - 0.68 : [ 206 0.00 0.99 ]
|XXX 0.68 - 0.685 : [ 136 0.00 0.99 ]
|XX 0.685 - 0.69 : [ 113 0.00 0.99 ]
|XX 0.69 - 0.695 : [ 94 0.00 0.99 ]
|XX 0.695 - 0.7 : [ 75 0.00 1.00 ]
|X 0.7 - 0.705 : [ 70 0.00 1.00 ]
|X 0.705 - 0.71 : [ 45 0.00 1.00 ]
|X 0.71 - 0.715 : [ 35 0.00 1.00 ]
| 0.715 - 0.72 : [ 19 0.00 1.00 ]
| 0.72 - 0.725 : [ 20 0.00 1.00 ]
| 0.725 - 0.73 : [ 14 0.00 1.00 ]
| 0.73 - 0.735 : [ 12 0.00 1.00 ]
| 0.735 - 0.74 : [ 6 0.00 1.00 ]
| 0.74 - 0.745 : [ 5 0.00 1.00 ]
| 0.745 - 0.75 : [ 4 0.00 1.00 ]
| 0.75 - 0.755 : [ 9 0.00 1.00 ]
| 0.755 - 0.76 : [ 2 0.00 1.00 ]
| 0.76 - 0.765 : [ 3 0.00 1.00 ]
| 0.765 - 0.77 : [ 5 0.00 1.00 ]
| 0.77 - 0.775 : [ 3 0.00 1.00 ]
| 0.775 - 0.78 : [ 2 0.00 1.00 ]
| 0.78 - 0.785 : [ 2 0.00 1.00 ]
#...
| 0.795 - 0.8 : [ 1 0.00 1.00 ]
| 0.8 - 0.805 : [ 2 0.00 1.00 ]
#...
| 0.815 - 0.82 : [ 1 0.00 1.00 ]
| 0.82 - 0.825 : [ 1 0.00 1.00 ]
#...
| 0.83 - 0.835 : [ 2 0.00 1.00 ]
#...
| 0.845 - 0.85 : [ 1 0.00 1.00 ]
#...
| 0.965 - 0.97 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 92. 271 reads; 9933 bp (untrimmed), 9859 (trimmed).
Contig 93. 282 reads; 19965 bp (untrimmed), 19963 (trimmed).
Contig 94. 358 reads; 16829 bp (untrimmed), 16829 (trimmed).
Contig 95. 515 reads; 31712 bp (untrimmed), 31712 (trimmed).
Contig 96. 581 reads; 36050 bp (untrimmed), 36050 (trimmed).
Contig 97. 745 reads; 42060 bp (untrimmed), 41026 (trimmed).
Contig 98. 747 reads; 34307 bp (untrimmed), 34307 (trimmed).
Contig 99. 868 reads; 41450 bp (untrimmed), 41450 (trimmed).
Contig 100. 943 reads; 41956 bp (untrimmed), 41956 (trimmed).
Contig 101. 1127 reads; 65478 bp (untrimmed), 65478 (trimmed).
Contig 102. 1301 reads; 66343 bp (untrimmed), 66037 (trimmed).
Contig 103. 1398 reads; 71512 bp (untrimmed), 71512 (trimmed).
Contig 104. 1499 reads; 68398 bp (untrimmed), 68393 (trimmed).
Contig 105. 1749 reads; 89267 bp (untrimmed), 89267 (trimmed).
Contig 106. 1806 reads; 88008 bp (untrimmed), 88004 (trimmed).
Contig 107. 1890 reads; 91256 bp (untrimmed), 91237 (trimmed).
Contig 108. 2041 reads; 96149 bp (untrimmed), 95874 (trimmed).
Contig 109. 2119 reads; 95780 bp (untrimmed), 95779 (trimmed).
Contig 110. 2505 reads; 110124 bp (untrimmed), 110124 (trimmed).
Contig 111. 2601 reads; 149568 bp (untrimmed), 149103 (trimmed).
Contig 112. 2894 reads; 133726 bp (untrimmed), 133726 (trimmed).
Contig 113. 3249 reads; 168298 bp (untrimmed), 168232 (trimmed).
Contig 114. 3485 reads; 149988 bp (untrimmed), 149649 (trimmed).
Contig 115. 3504 reads; 146641 bp (untrimmed), 146632 (trimmed).
Contig 116. 3764 reads; 166343 bp (untrimmed), 166343 (trimmed).
Contig 117. 4810 reads; 232403 bp (untrimmed), 232323 (trimmed).
Contig 118. 5167 reads; 280156 bp (untrimmed), 280156 (trimmed).
--------------------------------------------------------------
Totals 53588 reads; 2753507 bp (untrimmed), 2732159 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2904341 bases = 15.54 +- 9.01 = 0.39 +- 6.93
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 240 total values totalling 959.0600. <3.996083 +/- 5.101181>
#Range: [ 1.04 - 22.38 ]
#Most likely bin: [ 1.5 - 2 ] 74 counts
#Median bin: [ 1.5 - 2 ] 74 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 69 0.29 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 74 0.31 0.60 ]
|XXXXXXXXXXXX 2 - 2.5 : [ 22 0.09 0.69 ]
|XXXXXXXXXXXX 2.5 - 3 : [ 22 0.09 0.78 ]
|XXX 3 - 3.5 : [ 6 0.03 0.80 ]
|X 3.5 - 4 : [ 2 0.01 0.81 ]
|X 4 - 4.5 : [ 1 0.00 0.82 ]
|X 4.5 - 5 : [ 1 0.00 0.82 ]
|X 5 - 5.5 : [ 2 0.01 0.83 ]
#...
|XX 6.5 - 7 : [ 3 0.01 0.84 ]
|X 7 - 7.5 : [ 2 0.01 0.85 ]
|XX 7.5 - 8 : [ 3 0.01 0.86 ]
#...
|X 9 - 9.5 : [ 1 0.00 0.87 ]
#...
|X 11 - 11.5 : [ 1 0.00 0.87 ]
|XX 11.5 - 12 : [ 3 0.01 0.88 ]
#...
|XX 13 - 13.5 : [ 3 0.01 0.90 ]
#...
|XX 14.5 - 15 : [ 3 0.01 0.91 ]
|X 15 - 15.5 : [ 2 0.01 0.92 ]
#...
|XX 16 - 16.5 : [ 3 0.01 0.93 ]
|X 16.5 - 17 : [ 1 0.00 0.93 ]
|XXX 17 - 17.5 : [ 5 0.02 0.95 ]
|X 17.5 - 18 : [ 1 0.00 0.96 ]
|XX 18 - 18.5 : [ 3 0.01 0.97 ]
|XX 18.5 - 19 : [ 3 0.01 0.98 ]
|X 19 - 19.5 : [ 2 0.01 0.99 ]
#...
|X 20 - 20.5 : [ 1 0.00 1.00 ]
#...
|X 22 - 22.5 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Histogram of Major Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000
-------------------------------------------------------------------
#Found 36 total values totalling 539.7500. <14.993056 +/- 4.377870>
#Range: [ 5.13 - 22.38 ]
#Most likely bin: [ 17 - 17.5 ] 5 counts
#Median bin: [ 16 - 16.5 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXX 5 - 5.5 : [ 2 0.06 0.06 ]
#...
|XXXXXXXX 6.5 - 7 : [ 1 0.03 0.08 ]
|XXXXXXXX 7 - 7.5 : [ 1 0.03 0.11 ]
|XXXXXXXXXXXXXXXX 7.5 - 8 : [ 2 0.06 0.17 ]
#...
|XXXXXXXX 11 - 11.5 : [ 1 0.03 0.19 ]
|XXXXXXXX 11.5 - 12 : [ 1 0.03 0.22 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 3 0.08 0.31 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXX 14.5 - 15 : [ 3 0.08 0.39 ]
|XXXXXXXXXXXXXXXX 15 - 15.5 : [ 2 0.06 0.44 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXX 16 - 16.5 : [ 3 0.08 0.53 ]
|XXXXXXXX 16.5 - 17 : [ 1 0.03 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 17 - 17.5 : [ 5 0.14 0.69 ]
|XXXXXXXX 17.5 - 18 : [ 1 0.03 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 18 - 18.5 : [ 3 0.08 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 18.5 - 19 : [ 3 0.08 0.89 ]
|XXXXXXXXXXXXXXXX 19 - 19.5 : [ 2 0.06 0.94 ]
#...
|XXXXXXXX 20 - 20.5 : [ 1 0.03 0.97 ]
#...
|XXXXXXXX 22 - 22.5 : [ 1 0.03 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 72 2 reads 1834 bases = 1.04 +- 0.20 = 1.04 +- 0.20
Contig 125 2 reads 1771 bases = 1.06 +- 0.23 = 0.19 +- 0.95
Contig 129 2 reads 1543 bases = 1.06 +- 0.23 = 1.06 +- 0.23
Contig 99 2 reads 2226 bases = 1.11 +- 0.32 = 0.17 +- 0.93
Contig 164 2 reads 1840 bases = 1.12 +- 0.32 = 0.01 +- 0.94
Contig 117 2 reads 1492 bases = 1.14 +- 0.35 = 1.14 +- 0.35
Contig 123 2 reads 1500 bases = 1.16 +- 0.36 = 0.03 +- 0.92
Contig 135 2 reads 1770 bases = 1.16 +- 0.37 = 1.16 +- 0.37
Contig 18 2 reads 1439 bases = 1.18 +- 0.39 = 1.18 +- 0.39
Contig 66 2 reads 1298 bases = 1.18 +- 0.38 = -0.43 +- 0.80
Contig 85 2 reads 1785 bases = 1.19 +- 0.39 = 1.19 +- 0.39
Contig 201 3 reads 744 bases = 1.20 +- 0.61 = 1.00 +- 0.00
Contig 53 2 reads 1533 bases = 1.20 +- 0.40 = 1.20 +- 0.40
Contig 146 2 reads 1539 bases = 1.21 +- 0.41 = -0.20 +- 0.86
Contig 90 2 reads 1218 bases = 1.21 +- 0.40 = -0.45 +- 0.77
Contig 161 2 reads 1289 bases = 1.22 +- 0.41 = 1.22 +- 0.41
Contig 26 2 reads 900 bases = 1.22 +- 0.41 = 1.22 +- 0.41
Contig 121 2 reads 1577 bases = 1.23 +- 0.42 = 1.23 +- 0.42
Contig 152 2 reads 1574 bases = 1.23 +- 0.42 = 1.23 +- 0.42
Contig 174 2 reads 1696 bases = 1.23 +- 0.42 = -0.03 +- 0.88
Contig 282 1420 reads 71512 bases = 16.00 +- 6.92 = 0.24 +- 8.04
Contig 292 3299 reads 168298 bases = 16.25 +- 7.56 = 0.42 +- 7.45
Contig 284 1774 reads 89267 bases = 16.35 +- 8.08 = 0.09 +- 7.76
Contig 281 1320 reads 66343 bases = 16.54 +- 8.24 = 0.18 +- 7.08
Contig 285 1827 reads 88008 bases = 17.18 +- 7.35 = 0.70 +- 7.72
Contig 286 1905 reads 91256 bases = 17.43 +- 7.40 = 0.69 +- 8.17
Contig 278 880 reads 41450 bases = 17.46 +- 7.89 = 0.19 +- 8.20
Contig 296 4884 reads 232406 bases = 17.47 +- 8.70 = -0.11 +- 6.42
Contig 273 366 reads 16829 bases = 17.48 +- 6.46 = 3.47 +- 5.86
Contig 287 2082 reads 96149 bases = 17.99 +- 6.80 = 0.27 +- 7.36
Contig 277 761 reads 34307 bases = 18.19 +- 6.90 = 1.24 +- 6.75
Contig 291 2933 reads 133726 bases = 18.22 +- 8.72 = 0.08 +- 6.89
Contig 283 1517 reads 68398 bases = 18.23 +- 7.74 = 0.00 +- 6.67
Contig 288 2151 reads 95780 bases = 18.63 +- 9.31 = 0.03 +- 6.57
Contig 279 962 reads 41956 bases = 18.79 +- 8.62 = 1.04 +- 6.60
Contig 295 3820 reads 166343 bases = 18.90 +- 7.96 = 0.01 +- 7.69
Contig 289 2540 reads 110124 bases = 19.03 +- 7.83 = 0.14 +- 7.06
Contig 293 3544 reads 149988 bases = 19.44 +- 8.26 = 0.14 +- 7.14
Contig 294 3555 reads 146641 bases = 20.13 +- 8.23 = 0.31 +- 8.02
Contig 271 273 reads 9933 bases = 22.38 +- 9.89 = 8.41 +- 5.20
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1414
HQ Discrepant reads = 31
Chimeric reads = 99
Suspect alignments = 539
-------------------------------------------------------------------
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/finished1/microbe/3436494/edit_dir.08Jun04.QD