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: 12-12-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634482 8000 1854 Frankia sp.
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Frankia_sp.
-------------------------------------------------------------------
Actinobacteria, phylum, actinobacteria
Frankineae, suborder, high GC Gram+
Actinobacteridae, subclass, high GC Gram+
Frankiaceae, family, high GC Gram+
Actinomycetales, order, high GC Gram+
Frankia sp., species, high GC Gram+
Frankia, genus, high GC Gram+
Actinobacteria (class) (high G+C Gram-positive bacteria), class, high GC Gram+
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 5431277
# phrap: 5217047
# db:
altered.
8000000
6216108 +/- 1264430
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 19702
Number of reads with percent X's >= 20%: 1200 = 1.5%
Number of reads with percent X's >= 50%: 675 = 0.8%
Number of reads with percent X's >= 80%: 106 = 0.1%
Total reads in project: 82636
Total bp X'd : 1369137
reads >= 20% >= 50% >= 80% screened
Nr with L09136 15268 779 434 92
Nr with pCC1Fos 1813 8 6 1
Nr with pMCL200_JGI_XZX+XZK 2621 413 235 13
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 12356098
C = 26813841
G = 26209050
T = 13102332
N = 440588
X = 1369137
GC fraction = 0.66
Total = 80291046
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634482_fasta.screen.contigs
-------------------------------------------------------------------
A 843407
C 1950823
G 1897472
T 816112
N 763
fraction GC = 0.70
total bases = 5508577
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 AHZF reads.list > grep.reads.list.AHZF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZF 4 500
-------------------------------------------------------------------
#Found 15223 total values totalling 52185925.0000. <3428.097287 +/- 3253.981106>
#Range: [ 932 - 174835 ]
#Most likely bin: [ 3000 - 3500 ] 7298 counts
#Median bin: [ 3000 - 3500 ] 7298 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 21 0.00 0.00 ]
|XX 1000 - 1500 : [ 309 0.02 0.02 ]
|XX 1500 - 2000 : [ 333 0.02 0.04 ]
|XX 2000 - 2500 : [ 308 0.02 0.06 ]
|XXXXXX 2500 - 3000 : [ 1032 0.07 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 7298 0.48 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 5376 0.35 0.96 ]
|XXX 4000 - 4500 : [ 510 0.03 1.00 ]
| 4500 - 5000 : [ 15 0.00 1.00 ]
| 5000 - 5500 : [ 1 0.00 1.00 ]
#...
| 29500 - 30000 : [ 1 0.00 1.00 ]
#...
| 34500 - 35000 : [ 1 0.00 1.00 ]
#...
| 66500 - 67000 : [ 1 0.00 1.00 ]
#...
| 71500 - 72000 : [ 1 0.00 1.00 ]
#...
| 77000 - 77500 : [ 4 0.00 1.00 ]
| 77500 - 78000 : [ 3 0.00 1.00 ]
| 78000 - 78500 : [ 5 0.00 1.00 ]
#...
| 86500 - 87000 : [ 1 0.00 1.00 ]
#...
| 132000 - 132500 : [ 1 0.00 1.00 ]
#...
| 167500 - 168000 : [ 1 0.00 1.00 ]
#...
| 174500 - 175000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZG reads.list > grep.reads.list.AHZG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZG 4 500
-------------------------------------------------------------------
#Found 12990 total values totalling 111498786.0000. <8583.432333 +/- 4325.914844>
#Range: [ 567 - 152147 ]
#Most likely bin: [ 8500 - 9000 ] 2214 counts
#Median bin: [ 8500 - 9000 ] 2214 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 27 0.00 0.00 ]
|XXX 1000 - 1500 : [ 164 0.01 0.01 ]
|XXX 1500 - 2000 : [ 173 0.01 0.03 ]
|XXXX 2000 - 2500 : [ 199 0.02 0.04 ]
|XXX 2500 - 3000 : [ 192 0.01 0.06 ]
|XXX 3000 - 3500 : [ 183 0.01 0.07 ]
|XXX 3500 - 4000 : [ 184 0.01 0.09 ]
|XXXX 4000 - 4500 : [ 194 0.01 0.10 ]
|XXX 4500 - 5000 : [ 157 0.01 0.11 ]
|XXX 5000 - 5500 : [ 166 0.01 0.13 ]
|XX 5500 - 6000 : [ 133 0.01 0.14 ]
|XX 6000 - 6500 : [ 138 0.01 0.15 ]
|XX 6500 - 7000 : [ 118 0.01 0.16 ]
|XXXX 7000 - 7500 : [ 199 0.02 0.17 ]
|XXXXXXXXX 7500 - 8000 : [ 504 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1587 0.12 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 2214 0.17 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 2151 0.17 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 1887 0.15 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 1363 0.10 0.92 ]
|XXXXXXXXXXXXX 10500 - 11000 : [ 704 0.05 0.97 ]
|XXXXX 11000 - 11500 : [ 268 0.02 0.99 ]
|X 11500 - 12000 : [ 44 0.00 1.00 ]
| 12000 - 12500 : [ 5 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
#...
| 17500 - 18000 : [ 2 0.00 1.00 ]
#...
| 20000 - 20500 : [ 1 0.00 1.00 ]
#...
| 26000 - 26500 : [ 1 0.00 1.00 ]
#...
| 37500 - 38000 : [ 1 0.00 1.00 ]
#...
| 43500 - 44000 : [ 1 0.00 1.00 ]
#...
| 51000 - 51500 : [ 1 0.00 1.00 ]
#...
| 67500 - 68000 : [ 1 0.00 1.00 ]
#...
| 79500 - 80000 : [ 1 0.00 1.00 ]
#...
| 82000 - 82500 : [ 1 0.00 1.00 ]
| 82500 - 83000 : [ 4 0.00 1.00 ]
| 83000 - 83500 : [ 5 0.00 1.00 ]
| 83500 - 84000 : [ 4 0.00 1.00 ]
| 84000 - 84500 : [ 5 0.00 1.00 ]
| 84500 - 85000 : [ 3 0.00 1.00 ]
| 85000 - 85500 : [ 1 0.00 1.00 ]
| 85500 - 86000 : [ 1 0.00 1.00 ]
#...
| 94000 - 94500 : [ 1 0.00 1.00 ]
#...
| 152000 - 152500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZH reads.list > grep.reads.list.AHZH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZH 4 500
-------------------------------------------------------------------
#Found 1090 total values totalling 44038750.0000. <40402.522936 +/- 11355.122095>
#Range: [ 3833 - 157926 ]
#Most likely bin: [ 36500 - 37000 ] 59 counts
#Median bin: [ 39000 - 39500 ] 43 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 3500 - 4000 : [ 1 0.00 0.00 ]
#...
|X 15500 - 16000 : [ 1 0.00 0.00 ]
#...
|X 19000 - 19500 : [ 1 0.00 0.00 ]
#...
|X 27500 - 28000 : [ 1 0.00 0.00 ]
|X 28000 - 28500 : [ 1 0.00 0.00 ]
#...
|XX 29500 - 30000 : [ 3 0.00 0.01 ]
|XXXX 30000 - 30500 : [ 6 0.01 0.01 ]
|XXX 30500 - 31000 : [ 4 0.00 0.02 ]
|XXXXX 31000 - 31500 : [ 8 0.01 0.02 ]
|XXXXXX 31500 - 32000 : [ 9 0.01 0.03 ]
|XXXXXXXXXXXXX 32000 - 32500 : [ 19 0.02 0.05 ]
|XXXXXXXXXXXXXXXX 32500 - 33000 : [ 23 0.02 0.07 ]
|XXXXXXXXXXXXXX 33000 - 33500 : [ 21 0.02 0.09 ]
|XXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 27 0.02 0.11 ]
|XXXXXXXXXXXXXXXXX 34000 - 34500 : [ 25 0.02 0.14 ]
|XXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 27 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 32 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 33 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 38 0.03 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 59 0.05 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 53 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 49 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 56 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 44 0.04 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 43 0.04 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 45 0.04 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 53 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 38 0.03 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 40 0.04 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 39 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 40 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 42 0.04 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 40 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 27 0.02 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXX 44000 - 44500 : [ 33 0.03 0.90 ]
|XXXXXXXXXXXXXXXXXXXXX 44500 - 45000 : [ 31 0.03 0.93 ]
|XXXXXXXXXXXXXXXX 45000 - 45500 : [ 23 0.02 0.95 ]
|XXXXXXXXXX 45500 - 46000 : [ 15 0.01 0.96 ]
|XXXXX 46000 - 46500 : [ 8 0.01 0.97 ]
|XXXXX 46500 - 47000 : [ 7 0.01 0.98 ]
|XXX 47000 - 47500 : [ 4 0.00 0.98 ]
#...
|X 106500 - 107000 : [ 1 0.00 0.98 ]
#...
|X 109000 - 109500 : [ 1 0.00 0.98 ]
|X 109500 - 110000 : [ 1 0.00 0.98 ]
|X 110000 - 110500 : [ 1 0.00 0.98 ]
|X 110500 - 111000 : [ 1 0.00 0.99 ]
#...
|X 111500 - 112000 : [ 1 0.00 0.99 ]
|XX 112000 - 112500 : [ 3 0.00 0.99 ]
#...
|X 113000 - 113500 : [ 2 0.00 0.99 ]
|X 113500 - 114000 : [ 2 0.00 0.99 ]
#...
|X 115500 - 116000 : [ 2 0.00 0.99 ]
|X 116000 - 116500 : [ 2 0.00 1.00 ]
#...
|X 117000 - 117500 : [ 1 0.00 1.00 ]
|X 117500 - 118000 : [ 1 0.00 1.00 ]
|X 118000 - 118500 : [ 1 0.00 1.00 ]
#...
|X 157500 - 158000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHZH 38814 +- 4386 (n=524)
# AHZF 3172 +- 790 (n=7892)
# AHZG 8159 +- 2537 (n=6646)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634482_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
AHZF 38400 -1 -1 98 681 36793 100 690 100 699
AHZG 49920 -1 -1 91 553 40151 97 562 100 577
AHZH 7008 -1 -1 84 501 5692 97 598 100 610
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHZF 18344 99 677 100 695 18449 100 704 100 703
AHZG 19935 97 569 100 583 20216 97 556 100 570
AHZH 2904 98 612 100 615 2788 97 583 100 606
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634482_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
256 40151 21881 85.47 89.03 AHZG @
36 5692 3119 86.64 90.25 AHZH @
200 36793 18756 93.78 97.69 AHZF @
] 82636 43756 88.93 cumulative total@@
LIBRARY PLATE ID COUNT [ AHZG 256 AHZH 36 AHZF 200 ] for 492 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 3634482_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 82636 total values totalling 50592157.0000. <612.229016 +/- 197.209334>
#Range: [ 21 - 937 ]
#Most likely bin: [ 750 - 800 ] 13506 counts
#Median bin: [ 650 - 700 ] 10080 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 263 0.00 0.00 ]
|XXXX 50 - 100 : [ 1253 0.02 0.02 ]
|XXXXX 100 - 150 : [ 1610 0.02 0.04 ]
|XXXXX 150 - 200 : [ 1644 0.02 0.06 ]
|XXXXX 200 - 250 : [ 1839 0.02 0.08 ]
|XXXXXX 250 - 300 : [ 2116 0.03 0.11 ]
|XXXXXXX 300 - 350 : [ 2209 0.03 0.13 ]
|XXXXXXX 350 - 400 : [ 2459 0.03 0.16 ]
|XXXXXXXX 400 - 450 : [ 2834 0.03 0.20 ]
|XXXXXXXXXX 450 - 500 : [ 3233 0.04 0.24 ]
|XXXXXXXXXXXX 500 - 550 : [ 4077 0.05 0.28 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 5449 0.07 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 7548 0.09 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 10080 0.12 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 12698 0.15 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 13506 0.16 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 8050 0.10 0.98 ]
|XXXXX 850 - 900 : [ 1709 0.02 1.00 ]
| 900 - 950 : [ 59 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZF 3634482_fasta.screen.trimQ15.SaF > reads.trim15.AHZF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZF.rl 2 50
-------------------------------------------------------------------
#Found 36793 total values totalling 25280775.0000. <687.108281 +/- 161.646511>
#Range: [ 22 - 937 ]
#Most likely bin: [ 750 - 800 ] 8926 counts
#Median bin: [ 700 - 750 ] 6297 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 35 0.00 0.00 ]
|X 50 - 100 : [ 140 0.00 0.00 ]
|X 100 - 150 : [ 275 0.01 0.01 ]
|XX 150 - 200 : [ 364 0.01 0.02 ]
|XX 200 - 250 : [ 440 0.01 0.03 ]
|XX 250 - 300 : [ 491 0.01 0.05 ]
|XX 300 - 350 : [ 551 0.01 0.06 ]
|XXX 350 - 400 : [ 653 0.02 0.08 ]
|XXX 400 - 450 : [ 766 0.02 0.10 ]
|XXXX 450 - 500 : [ 862 0.02 0.12 ]
|XXXXX 500 - 550 : [ 1089 0.03 0.15 ]
|XXXXXXX 550 - 600 : [ 1557 0.04 0.20 ]
|XXXXXXXXXXX 600 - 650 : [ 2449 0.07 0.26 ]
|XXXXXXXXXXXXXXXXXX 650 - 700 : [ 3906 0.11 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6297 0.17 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8926 0.24 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6391 0.17 0.96 ]
|XXXXXXX 850 - 900 : [ 1542 0.04 1.00 ]
| 900 - 950 : [ 59 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZG 3634482_fasta.screen.trimQ15.SaF > reads.trim15.AHZG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZG.rl 2 50
-------------------------------------------------------------------
#Found 40151 total values totalling 21984342.0000. <547.541581 +/- 202.244702>
#Range: [ 21 - 896 ]
#Most likely bin: [ 700 - 750 ] 5382 counts
#Median bin: [ 600 - 650 ] 4542 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 50 : [ 207 0.01 0.01 ]
|XXXXXXX 50 - 100 : [ 990 0.02 0.03 ]
|XXXXXXXXX 100 - 150 : [ 1209 0.03 0.06 ]
|XXXXXXXXX 150 - 200 : [ 1164 0.03 0.09 ]
|XXXXXXXXX 200 - 250 : [ 1269 0.03 0.12 ]
|XXXXXXXXXX 250 - 300 : [ 1341 0.03 0.15 ]
|XXXXXXXXXXX 300 - 350 : [ 1443 0.04 0.19 ]
|XXXXXXXXXXXX 350 - 400 : [ 1656 0.04 0.23 ]
|XXXXXXXXXXXXXX 400 - 450 : [ 1901 0.05 0.28 ]
|XXXXXXXXXXXXXXXX 450 - 500 : [ 2172 0.05 0.33 ]
|XXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 2724 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 3501 0.09 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 4542 0.11 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5378 0.13 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5382 0.13 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3753 0.09 0.96 ]
|XXXXXXXXXX 800 - 850 : [ 1373 0.03 1.00 ]
|X 850 - 900 : [ 146 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHZH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHZH 3634482_fasta.screen.trimQ15.SaF > reads.trim15.AHZH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZH.rl 2 50
-------------------------------------------------------------------
#Found 5692 total values totalling 3327040.0000. <584.511595 +/- 201.663100>
#Range: [ 29 - 879 ]
#Most likely bin: [ 700 - 750 ] 1019 counts
#Median bin: [ 650 - 700 ] 796 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 21 0.00 0.00 ]
|XXXXX 50 - 100 : [ 123 0.02 0.03 ]
|XXXXX 100 - 150 : [ 126 0.02 0.05 ]
|XXXXX 150 - 200 : [ 116 0.02 0.07 ]
|XXXXX 200 - 250 : [ 130 0.02 0.09 ]
|XXXXXXXXXXX 250 - 300 : [ 284 0.05 0.14 ]
|XXXXXXXX 300 - 350 : [ 215 0.04 0.18 ]
|XXXXXX 350 - 400 : [ 150 0.03 0.20 ]
|XXXXXXX 400 - 450 : [ 167 0.03 0.23 ]
|XXXXXXXX 450 - 500 : [ 199 0.03 0.27 ]
|XXXXXXXXXX 500 - 550 : [ 264 0.05 0.32 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 391 0.07 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 557 0.10 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 796 0.14 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1019 0.18 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 827 0.15 0.95 ]
|XXXXXXXXXXX 800 - 850 : [ 286 0.05 1.00 ]
|X 850 - 900 : [ 21 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APZI
trimt JAZZ trim 15 readlength histogram for APZK
trimt JAZZ trim 15 readlength histogram for AZOO
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634482
-------------------------------------------------------------------
AHZF.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHZF.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AHZF.000201.000300 pUC18.fa pUC18.fa LRS.fasta
AHZG.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AHZG.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AHZG.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
AHZG.001701.001800 pMCL200.fa pMCL200.fa LRS.fasta
AHZG.002501.002600 pMCL200.fa pMCL200.fa LRS.fasta
AHZH.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AZOO.000001.000100
BCUT.000001.000100 pCC1Fos.fa pUC18.fa U00096.2.fa.4_pieces pCC1Fos.fa pUC18.fa LRS.fasta
AHZF.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AHZF.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AHZF.000201.000300 pUC18.fa pUC18.fa LRS.fasta
AHZG.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AHZG.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AHZG.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
AHZG.001701.001800 pMCL200.fa pMCL200.fa LRS.fasta
AHZG.002501.002600 pMCL200.fa pMCL200.fa LRS.fasta
AHZH.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AZOO.000001.000100
BCUT.000001.000100 pCC1Fos.fa pUC18.fa U00096.2.fa.4_pieces pCC1Fos.fa pUC18.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634482_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634482_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 82351 total values totalling 57142.3309. <0.693888 +/- 0.042728>
#Range: [ 0 - 0.9286 ]
#Most likely bin: [ 0.7 - 0.705 ] 4383 counts
#Median bin: [ 0.695 - 0.7 ] 4283 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.185 - 0.19 : [ 1 0.00 0.00 ]
#...
| 0.3 - 0.305 : [ 3 0.00 0.00 ]
#...
| 0.325 - 0.33 : [ 1 0.00 0.00 ]
| 0.33 - 0.335 : [ 1 0.00 0.00 ]
#...
| 0.35 - 0.355 : [ 1 0.00 0.00 ]
#...
| 0.37 - 0.375 : [ 2 0.00 0.00 ]
#...
| 0.39 - 0.395 : [ 3 0.00 0.00 ]
| 0.395 - 0.4 : [ 2 0.00 0.00 ]
| 0.4 - 0.405 : [ 1 0.00 0.00 ]
| 0.405 - 0.41 : [ 4 0.00 0.00 ]
| 0.41 - 0.415 : [ 1 0.00 0.00 ]
#...
| 0.42 - 0.425 : [ 4 0.00 0.00 ]
| 0.425 - 0.43 : [ 5 0.00 0.00 ]
| 0.43 - 0.435 : [ 7 0.00 0.00 ]
#...
| 0.44 - 0.445 : [ 9 0.00 0.00 ]
| 0.445 - 0.45 : [ 1 0.00 0.00 ]
| 0.45 - 0.455 : [ 1 0.00 0.00 ]
| 0.455 - 0.46 : [ 2 0.00 0.00 ]
| 0.46 - 0.465 : [ 7 0.00 0.00 ]
| 0.465 - 0.47 : [ 5 0.00 0.00 ]
| 0.47 - 0.475 : [ 3 0.00 0.00 ]
| 0.475 - 0.48 : [ 6 0.00 0.00 ]
| 0.48 - 0.485 : [ 13 0.00 0.00 ]
| 0.485 - 0.49 : [ 7 0.00 0.00 ]
| 0.49 - 0.495 : [ 3 0.00 0.00 ]
| 0.495 - 0.5 : [ 3 0.00 0.00 ]
| 0.5 - 0.505 : [ 18 0.00 0.00 ]
| 0.505 - 0.51 : [ 12 0.00 0.00 ]
| 0.51 - 0.515 : [ 21 0.00 0.00 ]
| 0.515 - 0.52 : [ 16 0.00 0.00 ]
| 0.52 - 0.525 : [ 26 0.00 0.00 ]
| 0.525 - 0.53 : [ 17 0.00 0.00 ]
| 0.53 - 0.535 : [ 32 0.00 0.00 ]
| 0.535 - 0.54 : [ 44 0.00 0.00 ]
| 0.54 - 0.545 : [ 40 0.00 0.00 ]
|X 0.545 - 0.55 : [ 59 0.00 0.00 ]
|X 0.55 - 0.555 : [ 73 0.00 0.01 ]
|X 0.555 - 0.56 : [ 80 0.00 0.01 ]
|X 0.56 - 0.565 : [ 120 0.00 0.01 ]
|X 0.565 - 0.57 : [ 129 0.00 0.01 ]
|X 0.57 - 0.575 : [ 145 0.00 0.01 ]
|XX 0.575 - 0.58 : [ 204 0.00 0.01 ]
|XX 0.58 - 0.585 : [ 203 0.00 0.02 ]
|XX 0.585 - 0.59 : [ 231 0.00 0.02 ]
|XX 0.59 - 0.595 : [ 268 0.00 0.02 ]
|XX 0.595 - 0.6 : [ 253 0.00 0.03 ]
|XXX 0.6 - 0.605 : [ 356 0.00 0.03 ]
|XXX 0.605 - 0.61 : [ 368 0.00 0.03 ]
|XXXX 0.61 - 0.615 : [ 468 0.01 0.04 ]
|XXXXX 0.615 - 0.62 : [ 586 0.01 0.05 ]
|XXXXXX 0.62 - 0.625 : [ 649 0.01 0.05 ]
|XXXXXXXX 0.625 - 0.63 : [ 903 0.01 0.07 ]
|XXXXXXXXX 0.63 - 0.635 : [ 993 0.01 0.08 ]
|XXXXXXXXXXX 0.635 - 0.64 : [ 1165 0.01 0.09 ]
|XXXXXXXXXXXXX 0.64 - 0.645 : [ 1387 0.02 0.11 ]
|XXXXXXXXXXXXXXX 0.645 - 0.65 : [ 1680 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 1929 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 2297 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 2698 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 3031 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 3343 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 3563 0.04 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 3886 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 4171 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 4245 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 4283 0.05 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 4383 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 4220 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 4088 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 3752 0.05 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 3798 0.05 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.725 - 0.73 : [ 3235 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.73 - 0.735 : [ 2928 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.735 - 0.74 : [ 2443 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXX 0.74 - 0.745 : [ 2030 0.02 0.91 ]
|XXXXXXXXXXXXXX 0.745 - 0.75 : [ 1515 0.02 0.93 ]
|XXXXXXXXXXXXX 0.75 - 0.755 : [ 1421 0.02 0.95 ]
|XXXXXXXXX 0.755 - 0.76 : [ 1012 0.01 0.96 ]
|XXXXXXX 0.76 - 0.765 : [ 810 0.01 0.97 ]
|XXXXXX 0.765 - 0.77 : [ 618 0.01 0.98 ]
|XXXX 0.77 - 0.775 : [ 492 0.01 0.98 ]
|XXX 0.775 - 0.78 : [ 354 0.00 0.99 ]
|XX 0.78 - 0.785 : [ 267 0.00 0.99 ]
|XX 0.785 - 0.79 : [ 202 0.00 0.99 ]
|XX 0.79 - 0.795 : [ 170 0.00 0.99 ]
|X 0.795 - 0.8 : [ 89 0.00 0.99 ]
|X 0.8 - 0.805 : [ 106 0.00 1.00 ]
|X 0.805 - 0.81 : [ 64 0.00 1.00 ]
| 0.81 - 0.815 : [ 50 0.00 1.00 ]
| 0.815 - 0.82 : [ 40 0.00 1.00 ]
| 0.82 - 0.825 : [ 29 0.00 1.00 ]
| 0.825 - 0.83 : [ 26 0.00 1.00 ]
| 0.83 - 0.835 : [ 19 0.00 1.00 ]
| 0.835 - 0.84 : [ 16 0.00 1.00 ]
| 0.84 - 0.845 : [ 16 0.00 1.00 ]
| 0.845 - 0.85 : [ 3 0.00 1.00 ]
| 0.85 - 0.855 : [ 11 0.00 1.00 ]
| 0.855 - 0.86 : [ 6 0.00 1.00 ]
| 0.86 - 0.865 : [ 15 0.00 1.00 ]
| 0.865 - 0.87 : [ 4 0.00 1.00 ]
| 0.87 - 0.875 : [ 1 0.00 1.00 ]
| 0.875 - 0.88 : [ 4 0.00 1.00 ]
| 0.88 - 0.885 : [ 7 0.00 1.00 ]
| 0.885 - 0.89 : [ 3 0.00 1.00 ]
| 0.89 - 0.895 : [ 3 0.00 1.00 ]
| 0.895 - 0.9 : [ 1 0.00 1.00 ]
| 0.9 - 0.905 : [ 1 0.00 1.00 ]
| 0.905 - 0.91 : [ 5 0.00 1.00 ]
| 0.91 - 0.915 : [ 2 0.00 1.00 ]
| 0.915 - 0.92 : [ 1 0.00 1.00 ]
| 0.92 - 0.925 : [ 1 0.00 1.00 ]
| 0.925 - 0.93 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 163. 922 reads; 50687 bp (untrimmed), 50504 (trimmed).
Contig 164. 944 reads; 67709 bp (untrimmed), 67312 (trimmed).
Contig 165. 962 reads; 64602 bp (untrimmed), 64139 (trimmed).
Contig 166. 982 reads; 66309 bp (untrimmed), 65981 (trimmed).
Contig 167. 999 reads; 67262 bp (untrimmed), 66929 (trimmed).
Contig 168. 1026 reads; 71556 bp (untrimmed), 70729 (trimmed).
Contig 169. 1100 reads; 69270 bp (untrimmed), 69229 (trimmed).
Contig 170. 1110 reads; 66398 bp (untrimmed), 66237 (trimmed).
Contig 171. 1117 reads; 72132 bp (untrimmed), 71633 (trimmed).
Contig 172. 1266 reads; 91433 bp (untrimmed), 90676 (trimmed).
Contig 173. 1303 reads; 77363 bp (untrimmed), 76728 (trimmed).
Contig 174. 1338 reads; 88831 bp (untrimmed), 88004 (trimmed).
Contig 175. 1443 reads; 96672 bp (untrimmed), 96583 (trimmed).
Contig 176. 1447 reads; 104633 bp (untrimmed), 103210 (trimmed).
Contig 177. 1471 reads; 92186 bp (untrimmed), 92029 (trimmed).
Contig 178. 1744 reads; 109406 bp (untrimmed), 109034 (trimmed).
Contig 179. 1767 reads; 110659 bp (untrimmed), 110532 (trimmed).
Contig 180. 1799 reads; 102730 bp (untrimmed), 101864 (trimmed).
Contig 181. 2134 reads; 125808 bp (untrimmed), 124729 (trimmed).
Contig 182. 2138 reads; 125683 bp (untrimmed), 125657 (trimmed).
Contig 183. 2450 reads; 190489 bp (untrimmed), 189982 (trimmed).
Contig 184. 2597 reads; 161260 bp (untrimmed), 160544 (trimmed).
Contig 185. 3031 reads; 183375 bp (untrimmed), 182913 (trimmed).
Contig 186. 3494 reads; 207246 bp (untrimmed), 207232 (trimmed).
Contig 187. 3896 reads; 238722 bp (untrimmed), 238166 (trimmed).
Contig 188. 4186 reads; 290500 bp (untrimmed), 289449 (trimmed).
Contig 189. 9034 reads; 539509 bp (untrimmed), 538962 (trimmed).
--------------------------------------------------------------
Totals 82561 reads; 5508577 bp (untrimmed), 5431277 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 5488650 bases = 12.70 +- 5.30 = 0.32 +- 3.94
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 165 total values totalling 1520.6400. <9.216000 +/- 4.446577>
#Range: [ 1.08 - 15.98 ]
#Most likely bin: [ 12 - 12.5 ] 15 counts
#Median bin: [ 10.5 - 11 ] 3 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 11 0.07 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 10 0.06 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 9 0.05 0.18 ]
|XXXXXXXXXXX 2.5 - 3 : [ 4 0.02 0.21 ]
|XXX 3 - 3.5 : [ 1 0.01 0.21 ]
|XXX 3.5 - 4 : [ 1 0.01 0.22 ]
#...
|XXX 4.5 - 5 : [ 1 0.01 0.22 ]
|XXXXX 5 - 5.5 : [ 2 0.01 0.24 ]
|XXXXX 5.5 - 6 : [ 2 0.01 0.25 ]
|XXXXXXXX 6 - 6.5 : [ 3 0.02 0.27 ]
|XXXXX 6.5 - 7 : [ 2 0.01 0.28 ]
|XXXXXXXX 7 - 7.5 : [ 3 0.02 0.30 ]
|XXXXX 7.5 - 8 : [ 2 0.01 0.31 ]
|XXXXXXXXXXXXX 8 - 8.5 : [ 5 0.03 0.34 ]
|XXXXXXXXXXX 8.5 - 9 : [ 4 0.02 0.36 ]
|XXXXXXXXXXXXX 9 - 9.5 : [ 5 0.03 0.39 ]
|XXXXXXXXXXXXXXXX 9.5 - 10 : [ 6 0.04 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 11 0.07 0.50 ]
|XXXXXXXX 10.5 - 11 : [ 3 0.02 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 12 0.07 0.59 ]
|XXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 15 0.09 0.72 ]
|XXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 8 0.05 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 13 0.08 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 10 0.06 0.91 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 9 0.05 0.96 ]
|XXXXXXXX 14.5 - 15 : [ 3 0.02 0.98 ]
|XXXXX 15 - 15.5 : [ 2 0.01 0.99 ]
|XXX 15.5 - 16 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Histogram of Major Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000
-------------------------------------------------------------------
#Found 124 total values totalling 1397.2400. <11.268065 +/- 2.664983>
#Range: [ 2.09 - 15.98 ]
#Most likely bin: [ 12 - 12.5 ] 15 counts
#Median bin: [ 11.5 - 12 ] 7 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXX 2 - 2.5 : [ 1 0.01 0.01 ]
#...
|XXX 3.5 - 4 : [ 1 0.01 0.02 ]
#...
|XXX 4.5 - 5 : [ 1 0.01 0.02 ]
|XXXXX 5 - 5.5 : [ 2 0.02 0.04 ]
|XXXXX 5.5 - 6 : [ 2 0.02 0.06 ]
|XXXXXXXX 6 - 6.5 : [ 3 0.02 0.08 ]
|XXXXX 6.5 - 7 : [ 2 0.02 0.10 ]
|XXXXX 7 - 7.5 : [ 2 0.02 0.11 ]
|XXX 7.5 - 8 : [ 1 0.01 0.12 ]
|XXXXXXXXXXX 8 - 8.5 : [ 4 0.03 0.15 ]
|XXXXX 8.5 - 9 : [ 2 0.02 0.17 ]
|XXXXXXXXXXX 9 - 9.5 : [ 4 0.03 0.20 ]
|XXXXXXXXXXXXXXXX 9.5 - 10 : [ 6 0.05 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 10 0.08 0.33 ]
|XXXXXXXX 10.5 - 11 : [ 3 0.02 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 12 0.10 0.45 ]
|XXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.06 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 15 0.12 0.63 ]
|XXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 8 0.06 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 13 0.10 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 10 0.08 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 9 0.07 0.95 ]
|XXXXXXXX 14.5 - 15 : [ 3 0.02 0.98 ]
|XXXXX 15 - 15.5 : [ 2 0.02 0.99 ]
|XXX 15.5 - 16 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 22 2 reads 2059 bases = 1.08 +- 0.27 = 0.02 +- 0.96
Contig 37 2 reads 1690 bases = 1.10 +- 0.30 = -0.00 +- 0.95
Contig 28 2 reads 1101 bases = 1.15 +- 0.36 = -0.25 +- 0.89
Contig 33 2 reads 1108 bases = 1.18 +- 0.39 = 1.18 +- 0.39
Contig 24 2 reads 1654 bases = 1.20 +- 0.40 = -0.02 +- 0.89
Contig 25 2 reads 1722 bases = 1.21 +- 0.40 = -0.02 +- 0.89
Contig 32 2 reads 1086 bases = 1.22 +- 0.42 = 1.22 +- 0.42
Contig 31 2 reads 981 bases = 1.31 +- 0.46 = 0.69 +- 0.46
Contig 38 2 reads 769 bases = 1.31 +- 0.46 = 1.31 +- 0.46
Contig 36 2 reads 1141 bases = 1.32 +- 0.47 = 1.32 +- 0.47
Contig 21 2 reads 1220 bases = 1.49 +- 0.50 = 1.49 +- 0.50
Contig 35 2 reads 878 bases = 1.57 +- 0.49 = 1.57 +- 0.49
Contig 58 12 reads 1031 bases = 1.63 +- 2.51 = 1.63 +- 2.51
Contig 23 2 reads 1015 bases = 1.67 +- 0.47 = 1.67 +- 0.47
Contig 40 2 reads 1185 bases = 1.69 +- 0.46 = -0.04 +- 0.55
Contig 43 3 reads 986 bases = 1.73 +- 0.85 = 1.73 +- 0.85
Contig 47 4 reads 1482 bases = 1.90 +- 1.11 = 1.90 +- 1.11
Contig 27 2 reads 757 bases = 1.93 +- 0.26 = 0.01 +- 0.27
Contig 26 2 reads 584 bases = 1.95 +- 0.22 = -0.02 +- 0.22
Contig 20 2 reads 798 bases = 1.96 +- 0.20 = -0.02 +- 0.20
Contig 155 613 reads 38699 bases = 13.67 +- 4.74 = 0.25 +- 3.99
Contig 187 3896 reads 238722 bases = 13.70 +- 4.89 = 0.37 +- 4.34
Contig 90 79 reads 4704 bases = 13.77 +- 5.84 = 0.89 +- 3.62
Contig 185 3031 reads 183375 bases = 13.84 +- 4.62 = 0.29 +- 3.93
Contig 96 91 reads 5882 bases = 13.92 +- 7.56 = 2.49 +- 3.19
Contig 115 216 reads 13655 bases = 14.03 +- 5.38 = 0.58 +- 4.71
Contig 181 2134 reads 125808 bases = 14.17 +- 5.53 = 0.45 +- 4.12
Contig 110 178 reads 10866 bases = 14.27 +- 4.06 = 0.80 +- 3.84
Contig 135 398 reads 23931 bases = 14.29 +- 5.14 = 0.22 +- 3.82
Contig 173 1303 reads 77363 bases = 14.31 +- 5.20 = 0.37 +- 4.30
Contig 189 9034 reads 539509 bases = 14.31 +- 6.84 = 0.22 +- 4.36
Contig 186 3494 reads 207246 bases = 14.32 +- 5.01 = 0.18 +- 4.17
Contig 182 2138 reads 125683 bases = 14.38 +- 4.56 = 0.06 +- 3.83
Contig 170 1110 reads 66398 bases = 14.44 +- 4.57 = 0.55 +- 3.99
Contig 94 83 reads 4906 bases = 14.50 +- 5.03 = 0.49 +- 3.47
Contig 132 391 reads 22910 bases = 14.67 +- 5.26 = 0.98 +- 4.26
Contig 180 1799 reads 102730 bases = 14.74 +- 5.04 = 0.20 +- 4.13
Contig 144 490 reads 27352 bases = 15.16 +- 8.63 = 0.23 +- 4.73
Contig 150 541 reads 30873 bases = 15.31 +- 4.71 = 0.32 +- 4.26
Contig 163 922 reads 50687 bases = 15.98 +- 5.46 = 0.43 +- 4.74
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1548
HQ Discrepant reads = 127
Chimeric reads = 290
Suspect alignments = 455
-------------------------------------------------------------------
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/3634482/edit_dir.06Jul04.QD