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
3634476 3000 1100 Pelodictyon luteolum
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Pelodictyon_luteolum
-------------------------------------------------------------------
Chlorobium/Pelodictyon group, green sulfur bacteria
Chlorobiaceae, family, green sulfur bacteria
Chlorobiales, order, green sulfur bacteria
Chlorobia, class, green sulfur bacteria
Bacteroidetes/Chlorobi group, superphylum, eubacteria
Pelodictyon luteolum, species, green sulfur bacteria
Pelodictyon, genus, green sulfur bacteria
Chlorobi, phylum, green sulfur bacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2348335
# phrap: 2243885
# db:
altered.
3000000
2530740 +/- 334545
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 6765
Number of reads with percent X's >= 20%: 145 = 0.4%
Number of reads with percent X's >= 50%: 75 = 0.2%
Number of reads with percent X's >= 80%: 13 = 0.0%
Total reads in project: 34101
Total bp X'd : 317810
reads >= 20% >= 50% >= 80% screened
Nr with L09136 6143 47 25 7
Nr with pCC1Fos 487 10 1 0
Nr with pMCL200_JGI_XZX+XZK 135 88 49 6
-------------------------------------------------------------------
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%: 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: 42
Total bp X'd : 61
reads >= 20% >= 50% >= 80% screened
Nr with L09136 2 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 6961221
C = 9126753
G = 9178464
T = 6758524
N = 181855
X = 317810
GC fraction = 0.56
Total = 32524627
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634476_fasta.screen.contigs
-------------------------------------------------------------------
A 517308
C 689279
G 660921
T 487676
N 297
fraction GC = 0.57
total bases = 2355481
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 AHYF reads.list > grep.reads.list.AHYF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYF 4 500
-------------------------------------------------------------------
#Found 6845 total values totalling 21699436.0000. <3170.114828 +/- 4828.476128>
#Range: [ 900 - 348872 ]
#Most likely bin: [ 3000 - 3500 ] 4474 counts
#Median bin: [ 3000 - 3500 ] 4474 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 3 0.00 0.00 ]
| 1000 - 1500 : [ 47 0.01 0.01 ]
|X 1500 - 2000 : [ 121 0.02 0.02 ]
|X 2000 - 2500 : [ 156 0.02 0.05 ]
|XXXXXXXXXXXXXXXXX 2500 - 3000 : [ 1920 0.28 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4474 0.65 0.98 ]
|X 3500 - 4000 : [ 111 0.02 1.00 ]
| 4000 - 4500 : [ 1 0.00 1.00 ]
| 4500 - 5000 : [ 1 0.00 1.00 ]
#...
| 5500 - 6000 : [ 1 0.00 1.00 ]
| 6000 - 6500 : [ 2 0.00 1.00 ]
#...
| 14500 - 15000 : [ 1 0.00 1.00 ]
#...
| 28000 - 28500 : [ 1 0.00 1.00 ]
#...
| 48500 - 49000 : [ 1 0.00 1.00 ]
#...
| 82500 - 83000 : [ 1 0.00 1.00 ]
#...
| 83500 - 84000 : [ 1 0.00 1.00 ]
#...
| 101500 - 102000 : [ 1 0.00 1.00 ]
#...
| 120000 - 120500 : [ 1 0.00 1.00 ]
#...
| 348500 - 349000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYG reads.list > grep.reads.list.AHYG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYG 4 500
-------------------------------------------------------------------
#Found 7584 total values totalling 54950045.0000. <7245.522811 +/- 12890.418219>
#Range: [ 676 - 446815 ]
#Most likely bin: [ 6000 - 6500 ] 1581 counts
#Median bin: [ 6500 - 7000 ] 1439 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 8 0.00 0.00 ]
|X 1000 - 1500 : [ 56 0.01 0.01 ]
|XX 1500 - 2000 : [ 68 0.01 0.02 ]
|XX 2000 - 2500 : [ 65 0.01 0.03 ]
|XX 2500 - 3000 : [ 63 0.01 0.03 ]
|X 3000 - 3500 : [ 58 0.01 0.04 ]
|XX 3500 - 4000 : [ 89 0.01 0.05 ]
|XXX 4000 - 4500 : [ 111 0.01 0.07 ]
|XXX 4500 - 5000 : [ 124 0.02 0.08 ]
|XXXXX 5000 - 5500 : [ 217 0.03 0.11 ]
|XXXXXXXXXXXXXXXX 5500 - 6000 : [ 620 0.08 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1581 0.21 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1439 0.19 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1251 0.16 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 919 0.12 0.88 ]
|XXXXXXXXXXXXXXXX 8000 - 8500 : [ 644 0.08 0.96 ]
|XXXXXX 8500 - 9000 : [ 237 0.03 1.00 ]
| 9000 - 9500 : [ 3 0.00 1.00 ]
| 9500 - 10000 : [ 2 0.00 1.00 ]
| 10000 - 10500 : [ 1 0.00 1.00 ]
#...
| 11500 - 12000 : [ 2 0.00 1.00 ]
#...
| 52000 - 52500 : [ 1 0.00 1.00 ]
#...
| 55000 - 55500 : [ 1 0.00 1.00 ]
#...
| 56000 - 56500 : [ 1 0.00 1.00 ]
#...
| 74000 - 74500 : [ 1 0.00 1.00 ]
#...
| 78000 - 78500 : [ 1 0.00 1.00 ]
#...
| 90000 - 90500 : [ 1 0.00 1.00 ]
| 90500 - 91000 : [ 1 0.00 1.00 ]
| 91000 - 91500 : [ 1 0.00 1.00 ]
#...
| 96500 - 97000 : [ 1 0.00 1.00 ]
#...
| 98500 - 99000 : [ 1 0.00 1.00 ]
#...
| 106000 - 106500 : [ 2 0.00 1.00 ]
#...
| 150500 - 151000 : [ 1 0.00 1.00 ]
#...
| 172500 - 173000 : [ 1 0.00 1.00 ]
#...
| 176500 - 177000 : [ 1 0.00 1.00 ]
#...
| 179000 - 179500 : [ 1 0.00 1.00 ]
#...
| 230500 - 231000 : [ 1 0.00 1.00 ]
#...
| 250500 - 251000 : [ 1 0.00 1.00 ]
#...
| 273000 - 273500 : [ 1 0.00 1.00 ]
#...
| 278000 - 278500 : [ 1 0.00 1.00 ]
#...
| 295000 - 295500 : [ 1 0.00 1.00 ]
#...
| 314500 - 315000 : [ 1 0.00 1.00 ]
#...
| 324000 - 324500 : [ 1 0.00 1.00 ]
#...
| 417000 - 417500 : [ 1 0.00 1.00 ]
#...
| 420500 - 421000 : [ 1 0.00 1.00 ]
#...
| 446500 - 447000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYH reads.list > grep.reads.list.AHYH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYH 4 500
-------------------------------------------------------------------
#Found 706 total values totalling 27775650.0000. <39342.280453 +/- 5577.052672>
#Range: [ 23623 - 155338 ]
#Most likely bin: [ 40000 - 40500 ] 46 counts
#Median bin: [ 39000 - 39500 ] 33 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 23500 - 24000 : [ 1 0.00 0.00 ]
#...
|X 29000 - 29500 : [ 1 0.00 0.00 ]
#...
|XX 30500 - 31000 : [ 2 0.00 0.01 ]
|XXX 31000 - 31500 : [ 3 0.00 0.01 ]
|XXX 31500 - 32000 : [ 4 0.01 0.02 ]
|XXXXXXXXXXX 32000 - 32500 : [ 13 0.02 0.03 ]
|XXXX 32500 - 33000 : [ 5 0.01 0.04 ]
|XXXXXXXXXX 33000 - 33500 : [ 12 0.02 0.06 ]
|XXXXXXXXXXX 33500 - 34000 : [ 13 0.02 0.08 ]
|XXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 23 0.03 0.11 ]
|XXXXXXXXXX 34500 - 35000 : [ 11 0.02 0.12 ]
|XXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 21 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 31 0.04 0.20 ]
|XXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 23 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 33 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 34 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 35 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 33 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 25 0.04 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 33 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 33 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 46 0.07 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 36 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 31 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 36 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 35 0.05 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 31 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 30 0.04 0.90 ]
|XXXXXXXXXXXXXXXXX 43500 - 44000 : [ 20 0.03 0.93 ]
|XXXXXXXXXXXXXXXXX 44000 - 44500 : [ 19 0.03 0.95 ]
|XXXXXXXXXX 44500 - 45000 : [ 11 0.02 0.97 ]
|XXXXXXXX 45000 - 45500 : [ 9 0.01 0.98 ]
|XXXXXX 45500 - 46000 : [ 7 0.01 0.99 ]
|XXXX 46000 - 46500 : [ 5 0.01 1.00 ]
#...
|X 155000 - 155500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHYH 39152 +- 3475 (n=360)
# AHYG 6521 +- 1455 (n=3836)
# AHYF 2939 +- 433 (n=3560)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634476_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
AHYF 15360 -1 -1 98 730 14542 99 681 100 692
AHYG 19968 -1 -1 95 657 17252 99 641 100 646
AHYH 3072 -1 -1 90 505 2307 96 567 100 592
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHYF 7255 99 673 100 691 7287 99 690 100 692
AHYG 8484 99 635 100 640 8768 99 646 100 651
AHYH 1274 96 569 100 586 1033 96 565 100 600
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634476_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
80 14542 7424 92.80 96.67 AHYF @
104 17252 8976 86.31 89.90 AHYG @
15 2307 1317 87.80 91.46 AHYH @
] 34101 17717 89.03 cumulative total@@
LIBRARY PLATE ID COUNT [ AHYF 80 AHYG 104 AHYH 15 ] for 199 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 3634476_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 34101 total values totalling 22039493.0000. <646.300490 +/- 175.980228>
#Range: [ 20 - 933 ]
#Most likely bin: [ 750 - 800 ] 6521 counts
#Median bin: [ 700 - 750 ] 6037 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 88 0.00 0.00 ]
|XX 50 - 100 : [ 307 0.01 0.01 ]
|XXX 100 - 150 : [ 439 0.01 0.02 ]
|XXX 150 - 200 : [ 423 0.01 0.04 ]
|XXX 200 - 250 : [ 486 0.01 0.05 ]
|XXXX 250 - 300 : [ 611 0.02 0.07 ]
|XXXX 300 - 350 : [ 697 0.02 0.09 ]
|XXXXX 350 - 400 : [ 734 0.02 0.11 ]
|XXXXXX 400 - 450 : [ 900 0.03 0.14 ]
|XXXXXX 450 - 500 : [ 1028 0.03 0.17 ]
|XXXXXXXXX 500 - 550 : [ 1467 0.04 0.21 ]
|XXXXXXXXXXXXX 550 - 600 : [ 2116 0.06 0.27 ]
|XXXXXXXXXXXXXXXXXXX 600 - 650 : [ 3099 0.09 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4585 0.13 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6037 0.18 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6521 0.19 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3837 0.11 0.98 ]
|XXXX 850 - 900 : [ 704 0.02 1.00 ]
| 900 - 950 : [ 22 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYF 3634476_fasta.screen.trimQ15.SaF > reads.trim15.AHYF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYF.rl 2 50
-------------------------------------------------------------------
#Found 14542 total values totalling 9834828.0000. <676.305047 +/- 167.513939>
#Range: [ 20 - 933 ]
#Most likely bin: [ 750 - 800 ] 2867 counts
#Median bin: [ 700 - 750 ] 2562 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 20 0.00 0.00 ]
|X 50 - 100 : [ 94 0.01 0.01 ]
|XX 100 - 150 : [ 158 0.01 0.02 ]
|XX 150 - 200 : [ 156 0.01 0.03 ]
|XXX 200 - 250 : [ 184 0.01 0.04 ]
|XX 250 - 300 : [ 162 0.01 0.05 ]
|XXX 300 - 350 : [ 212 0.01 0.07 ]
|XXXX 350 - 400 : [ 253 0.02 0.09 ]
|XXXX 400 - 450 : [ 305 0.02 0.11 ]
|XXXXX 450 - 500 : [ 372 0.03 0.13 ]
|XXXXXXX 500 - 550 : [ 476 0.03 0.16 ]
|XXXXXXXXX 550 - 600 : [ 679 0.05 0.21 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 1137 0.08 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1860 0.13 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2562 0.18 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2867 0.20 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2393 0.16 0.96 ]
|XXXXXXXXX 850 - 900 : [ 630 0.04 1.00 ]
| 900 - 950 : [ 22 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYG 3634476_fasta.screen.trimQ15.SaF > reads.trim15.AHYG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYG.rl 2 50
-------------------------------------------------------------------
#Found 17252 total values totalling 10945902.0000. <634.471482 +/- 171.337565>
#Range: [ 20 - 891 ]
#Most likely bin: [ 750 - 800 ] 3449 counts
#Median bin: [ 650 - 700 ] 2337 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 41 0.00 0.00 ]
|XX 50 - 100 : [ 141 0.01 0.01 ]
|XXX 100 - 150 : [ 220 0.01 0.02 ]
|XXX 150 - 200 : [ 219 0.01 0.04 ]
|XXX 200 - 250 : [ 250 0.01 0.05 ]
|XXX 250 - 300 : [ 299 0.02 0.07 ]
|XXXX 300 - 350 : [ 334 0.02 0.09 ]
|XXXXX 350 - 400 : [ 414 0.02 0.11 ]
|XXXXXX 400 - 450 : [ 537 0.03 0.14 ]
|XXXXXXX 450 - 500 : [ 587 0.03 0.18 ]
|XXXXXXXXXX 500 - 550 : [ 899 0.05 0.23 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 1276 0.07 0.30 ]
|XXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1721 0.10 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2337 0.14 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3035 0.18 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3449 0.20 0.91 ]
|XXXXXXXXXXXXXXXX 800 - 850 : [ 1420 0.08 1.00 ]
|X 850 - 900 : [ 73 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYH 3634476_fasta.screen.trimQ15.SaF > reads.trim15.AHYH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYH.rl 2 50
-------------------------------------------------------------------
#Found 2307 total values totalling 1258763.0000. <545.627655 +/- 210.955577>
#Range: [ 22 - 860 ]
#Most likely bin: [ 700 - 750 ] 440 counts
#Median bin: [ 600 - 650 ] 241 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 50 : [ 27 0.01 0.01 ]
|XXXXXXX 50 - 100 : [ 72 0.03 0.04 ]
|XXXXXX 100 - 150 : [ 61 0.03 0.07 ]
|XXXX 150 - 200 : [ 48 0.02 0.09 ]
|XXXXX 200 - 250 : [ 52 0.02 0.11 ]
|XXXXXXXXXXXXXX 250 - 300 : [ 150 0.07 0.18 ]
|XXXXXXXXXXXXXX 300 - 350 : [ 151 0.07 0.24 ]
|XXXXXX 350 - 400 : [ 67 0.03 0.27 ]
|XXXXX 400 - 450 : [ 58 0.03 0.30 ]
|XXXXXX 450 - 500 : [ 69 0.03 0.33 ]
|XXXXXXXX 500 - 550 : [ 92 0.04 0.37 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 161 0.07 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 241 0.10 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 388 0.17 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 440 0.19 0.90 ]
|XXXXXXXXXXXXXXXXXXX 750 - 800 : [ 205 0.09 0.99 ]
|XX 800 - 850 : [ 24 0.01 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634476
-------------------------------------------------------------------
AHYF.000001.000100 pUC18.fa LRS.fasta
AHYG.000001.000100 pMCL200.fa LRS.fasta
AHYG.000101.000200 pMCL200.fa LRS.fasta
AHYH.000001.000100 pCC1Fos.fa LRS.fasta
AHYF.000001.000100 pUC18.fa LRS.fasta
AHYG.000001.000100 pMCL200.fa LRS.fasta
AHYG.000101.000200 pMCL200.fa LRS.fasta
AHYH.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634476_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634476_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 34013 total values totalling 19511.8479. <0.573659 +/- 0.044272>
#Range: [ 0 - 0.7838 ]
#Most likely bin: [ 0.59 - 0.595 ] 1864 counts
#Median bin: [ 0.58 - 0.585 ] 1844 counts
| 0 - 0.005 : [ 2 0.00 0.00 ]
#...
| 0.215 - 0.22 : [ 1 0.00 0.00 ]
#...
| 0.29 - 0.295 : [ 2 0.00 0.00 ]
#...
| 0.3 - 0.305 : [ 1 0.00 0.00 ]
#...
| 0.315 - 0.32 : [ 1 0.00 0.00 ]
| 0.32 - 0.325 : [ 1 0.00 0.00 ]
| 0.325 - 0.33 : [ 1 0.00 0.00 ]
#...
| 0.34 - 0.345 : [ 2 0.00 0.00 ]
| 0.345 - 0.35 : [ 1 0.00 0.00 ]
| 0.35 - 0.355 : [ 1 0.00 0.00 ]
| 0.355 - 0.36 : [ 2 0.00 0.00 ]
| 0.36 - 0.365 : [ 1 0.00 0.00 ]
| 0.365 - 0.37 : [ 3 0.00 0.00 ]
| 0.37 - 0.375 : [ 6 0.00 0.00 ]
| 0.375 - 0.38 : [ 5 0.00 0.00 ]
| 0.38 - 0.385 : [ 12 0.00 0.00 ]
| 0.385 - 0.39 : [ 10 0.00 0.00 ]
| 0.39 - 0.395 : [ 17 0.00 0.00 ]
| 0.395 - 0.4 : [ 10 0.00 0.00 ]
| 0.4 - 0.405 : [ 23 0.00 0.00 ]
| 0.405 - 0.41 : [ 21 0.00 0.00 ]
| 0.41 - 0.415 : [ 18 0.00 0.00 ]
|X 0.415 - 0.42 : [ 24 0.00 0.00 ]
| 0.42 - 0.425 : [ 16 0.00 0.01 ]
|X 0.425 - 0.43 : [ 32 0.00 0.01 ]
|X 0.43 - 0.435 : [ 26 0.00 0.01 ]
|X 0.435 - 0.44 : [ 46 0.00 0.01 ]
|X 0.44 - 0.445 : [ 57 0.00 0.01 ]
|X 0.445 - 0.45 : [ 59 0.00 0.01 ]
|XX 0.45 - 0.455 : [ 74 0.00 0.01 ]
|XX 0.455 - 0.46 : [ 82 0.00 0.02 ]
|XXX 0.46 - 0.465 : [ 126 0.00 0.02 ]
|XXX 0.465 - 0.47 : [ 125 0.00 0.02 ]
|XXX 0.47 - 0.475 : [ 161 0.00 0.03 ]
|XXXX 0.475 - 0.48 : [ 183 0.01 0.03 ]
|XXXXX 0.48 - 0.485 : [ 216 0.01 0.04 ]
|XXXXX 0.485 - 0.49 : [ 248 0.01 0.05 ]
|XXXXXX 0.49 - 0.495 : [ 275 0.01 0.06 ]
|XXXXXXX 0.495 - 0.5 : [ 304 0.01 0.06 ]
|XXXXXXXXX 0.5 - 0.505 : [ 429 0.01 0.08 ]
|XXXXXXXX 0.505 - 0.51 : [ 394 0.01 0.09 ]
|XXXXXXXXXX 0.51 - 0.515 : [ 447 0.01 0.10 ]
|XXXXXXXXXXX 0.515 - 0.52 : [ 496 0.01 0.12 ]
|XXXXXXXXXXXXX 0.52 - 0.525 : [ 586 0.02 0.13 ]
|XXXXXXXXXXXXXX 0.525 - 0.53 : [ 663 0.02 0.15 ]
|XXXXXXXXXXXXXX 0.53 - 0.535 : [ 653 0.02 0.17 ]
|XXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 753 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 847 0.02 0.22 ]
|XXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 959 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1095 0.03 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1199 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1376 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1497 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1650 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1718 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1844 0.05 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1791 0.05 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 1864 0.05 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 1744 0.05 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 1805 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 1581 0.05 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 1323 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 1175 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 925 0.03 0.91 ]
|XXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 725 0.02 0.93 ]
|XXXXXXXXXXXXXX 0.63 - 0.635 : [ 636 0.02 0.95 ]
|XXXXXXXXXXX 0.635 - 0.64 : [ 500 0.01 0.97 ]
|XXXXXXXX 0.64 - 0.645 : [ 362 0.01 0.98 ]
|XXXXX 0.645 - 0.65 : [ 247 0.01 0.98 ]
|XXXX 0.65 - 0.655 : [ 167 0.00 0.99 ]
|XX 0.655 - 0.66 : [ 115 0.00 0.99 ]
|XX 0.66 - 0.665 : [ 82 0.00 1.00 ]
|X 0.665 - 0.67 : [ 51 0.00 1.00 ]
|X 0.67 - 0.675 : [ 32 0.00 1.00 ]
| 0.675 - 0.68 : [ 19 0.00 1.00 ]
| 0.68 - 0.685 : [ 18 0.00 1.00 ]
| 0.685 - 0.69 : [ 11 0.00 1.00 ]
| 0.69 - 0.695 : [ 11 0.00 1.00 ]
| 0.695 - 0.7 : [ 5 0.00 1.00 ]
| 0.7 - 0.705 : [ 5 0.00 1.00 ]
| 0.705 - 0.71 : [ 7 0.00 1.00 ]
| 0.71 - 0.715 : [ 1 0.00 1.00 ]
#...
| 0.72 - 0.725 : [ 1 0.00 1.00 ]
| 0.725 - 0.73 : [ 1 0.00 1.00 ]
| 0.73 - 0.735 : [ 2 0.00 1.00 ]
| 0.735 - 0.74 : [ 2 0.00 1.00 ]
#...
| 0.75 - 0.755 : [ 1 0.00 1.00 ]
#...
| 0.765 - 0.77 : [ 1 0.00 1.00 ]
| 0.77 - 0.775 : [ 1 0.00 1.00 ]
#...
| 0.78 - 0.785 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 3. 1 read; 657 bp (untrimmed), 485 (trimmed).
Contig 4. 1 read; 1444 bp (untrimmed), 0 (trimmed).
Contig 5. 1 read; 942 bp (untrimmed), 640 (trimmed).
Contig 6. 1 read; 1030 bp (untrimmed), 261 (trimmed).
Contig 7. 2 reads; 189 bp (untrimmed), 189 (trimmed).
Contig 8. 2 reads; 961 bp (untrimmed), 454 (trimmed).
Contig 9. 5 reads; 1325 bp (untrimmed), 1285 (trimmed).
Contig 10. 18 reads; 3840 bp (untrimmed), 3623 (trimmed).
Contig 11. 47 reads; 6371 bp (untrimmed), 6352 (trimmed).
Contig 12. 140 reads; 13081 bp (untrimmed), 12835 (trimmed).
Contig 13. 297 reads; 22449 bp (untrimmed), 22341 (trimmed).
Contig 14. 304 reads; 23769 bp (untrimmed), 23719 (trimmed).
Contig 15. 423 reads; 36886 bp (untrimmed), 36875 (trimmed).
Contig 16. 453 reads; 36185 bp (untrimmed), 36173 (trimmed).
Contig 17. 559 reads; 36516 bp (untrimmed), 36323 (trimmed).
Contig 18. 639 reads; 45213 bp (untrimmed), 45086 (trimmed).
Contig 19. 705 reads; 49339 bp (untrimmed), 49264 (trimmed).
Contig 20. 796 reads; 58947 bp (untrimmed), 58839 (trimmed).
Contig 21. 1031 reads; 84218 bp (untrimmed), 83896 (trimmed).
Contig 22. 1238 reads; 86308 bp (untrimmed), 86308 (trimmed).
Contig 23. 1241 reads; 86014 bp (untrimmed), 85725 (trimmed).
Contig 24. 1327 reads; 92944 bp (untrimmed), 92877 (trimmed).
Contig 25. 1491 reads; 107458 bp (untrimmed), 107393 (trimmed).
Contig 26. 3171 reads; 215412 bp (untrimmed), 215323 (trimmed).
Contig 27. 3464 reads; 222838 bp (untrimmed), 222770 (trimmed).
Contig 28. 7205 reads; 495016 bp (untrimmed), 494967 (trimmed).
Contig 29. 9495 reads; 623594 bp (untrimmed), 623486 (trimmed).
--------------------------------------------------------------
Totals 34059 reads; 2355481 bp (untrimmed), 2348335 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2348684 bases = 12.62 +- 4.57 = 0.14 +- 4.24
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 22 total values totalling 229.8200. <10.446364 +/- 3.461082>
#Range: [ 1.37 - 13.53 ]
#Most likely bin: [ 12.5 - 13 ] 4 counts
#Median bin: [ 11.5 - 12 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 1 - 1.5 : [ 1 0.05 0.05 ]
#...
|XXXXXXXXXX 2.5 - 3 : [ 1 0.05 0.09 ]
#...
|XXXXXXXXXX 4 - 4.5 : [ 1 0.05 0.14 ]
#...
|XXXXXXXXXX 6 - 6.5 : [ 1 0.05 0.18 ]
#...
|XXXXXXXXXX 9 - 9.5 : [ 1 0.05 0.23 ]
#...
|XXXXXXXXXX 10 - 10.5 : [ 1 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 2 0.09 0.36 ]
|XXXXXXXXXX 11 - 11.5 : [ 1 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 2 0.09 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 4 0.18 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.18 0.86 ]
|XXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 2 0.09 0.95 ]
|XXXXXXXXXX 13.5 - 14 : [ 1 0.05 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 20 total values totalling 225.5200. <11.276000 +/- 2.354760>
#Range: [ 4.04 - 13.53 ]
#Most likely bin: [ 12.5 - 13 ] 4 counts
#Median bin: [ 12 - 12.5 ] 4 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXX 4 - 4.5 : [ 1 0.05 0.05 ]
#...
|XXXXXXXXXX 6 - 6.5 : [ 1 0.05 0.10 ]
#...
|XXXXXXXXXX 9 - 9.5 : [ 1 0.05 0.15 ]
#...
|XXXXXXXXXX 10 - 10.5 : [ 1 0.05 0.20 ]
|XXXXXXXXXXXXXXXXXXXX 10.5 - 11 : [ 2 0.10 0.30 ]
|XXXXXXXXXX 11 - 11.5 : [ 1 0.05 0.35 ]
|XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 2 0.10 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 4 0.20 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 4 0.20 0.85 ]
|XXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 2 0.10 0.95 ]
|XXXXXXXXXX 13.5 - 14 : [ 1 0.05 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 8 2 reads 961 bases = 1.37 +- 0.48 = -0.63 +- 0.48
Contig 9 5 reads 1325 bases = 2.93 +- 1.14 = 0.42 +- 0.70
Contig 10 18 reads 3840 bases = 4.04 +- 1.84 = 0.24 +- 2.01
Contig 11 47 reads 6371 bases = 6.07 +- 3.08 = 2.71 +- 3.63
Contig 12 140 reads 13081 bases = 9.41 +- 4.20 = 0.32 +- 5.48
Contig 15 423 reads 36886 bases = 10.05 +- 4.14 = 0.22 +- 4.87
Contig 21 1031 reads 84218 bases = 10.64 +- 4.18 = 0.32 +- 4.51
Contig 16 453 reads 36185 bases = 10.74 +- 4.16 = 0.13 +- 4.53
Contig 14 304 reads 23769 bases = 11.02 +- 3.49 = 1.31 +- 4.44
Contig 20 796 reads 58947 bases = 11.59 +- 4.66 = 0.17 +- 4.23
Contig 13 297 reads 22449 bases = 11.87 +- 4.45 = 0.26 +- 4.73
Contig 25 1491 reads 107458 bases = 12.19 +- 4.97 = -0.05 +- 5.14
Contig 22 1238 reads 86308 bases = 12.44 +- 4.24 = 0.07 +- 4.60
Contig 24 1327 reads 92944 bases = 12.45 +- 3.89 = 0.29 +- 4.00
Contig 19 705 reads 49339 bases = 12.46 +- 4.22 = 0.39 +- 4.79
Contig 23 1241 reads 86014 bases = 12.50 +- 4.02 = 0.47 +- 3.75
Contig 18 639 reads 45213 bases = 12.54 +- 4.71 = 0.00 +- 3.71
Contig 28 7205 reads 495016 bases = 12.70 +- 5.05 = -0.00 +- 4.15
Contig 26 3171 reads 215412 bases = 12.77 +- 4.34 = 0.02 +- 4.08
Contig 29 9495 reads 623594 bases = 13.22 +- 4.34 = 0.11 +- 4.02
Contig 10 18 reads 3840 bases = 4.04 +- 1.84 = 0.24 +- 2.01
Contig 11 47 reads 6371 bases = 6.07 +- 3.08 = 2.71 +- 3.63
Contig 12 140 reads 13081 bases = 9.41 +- 4.20 = 0.32 +- 5.48
Contig 15 423 reads 36886 bases = 10.05 +- 4.14 = 0.22 +- 4.87
Contig 21 1031 reads 84218 bases = 10.64 +- 4.18 = 0.32 +- 4.51
Contig 16 453 reads 36185 bases = 10.74 +- 4.16 = 0.13 +- 4.53
Contig 14 304 reads 23769 bases = 11.02 +- 3.49 = 1.31 +- 4.44
Contig 20 796 reads 58947 bases = 11.59 +- 4.66 = 0.17 +- 4.23
Contig 13 297 reads 22449 bases = 11.87 +- 4.45 = 0.26 +- 4.73
Contig 25 1491 reads 107458 bases = 12.19 +- 4.97 = -0.05 +- 5.14
Contig 22 1238 reads 86308 bases = 12.44 +- 4.24 = 0.07 +- 4.60
Contig 24 1327 reads 92944 bases = 12.45 +- 3.89 = 0.29 +- 4.00
Contig 19 705 reads 49339 bases = 12.46 +- 4.22 = 0.39 +- 4.79
Contig 23 1241 reads 86014 bases = 12.50 +- 4.02 = 0.47 +- 3.75
Contig 18 639 reads 45213 bases = 12.54 +- 4.71 = 0.00 +- 3.71
Contig 28 7205 reads 495016 bases = 12.70 +- 5.05 = -0.00 +- 4.15
Contig 26 3171 reads 215412 bases = 12.77 +- 4.34 = 0.02 +- 4.08
Contig 29 9495 reads 623594 bases = 13.22 +- 4.34 = 0.11 +- 4.02
Contig 17 559 reads 36516 bases = 13.29 +- 4.66 = 0.54 +- 4.88
Contig 27 3464 reads 222838 bases = 13.53 +- 4.07 = 0.17 +- 4.29
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 15
Chimeric reads = 107
Suspect alignments = 178
-------------------------------------------------------------------
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/microbe4/3634476/edit_dir.06Aug04.QD