See help.
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 5905397
# phrap: 5541835
# db:
altered.
4500000
5315744 +/- 595607
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
-------------------------------------------------------------------
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 = 12966444
C = 20703633
G = 20760356
T = 12933780
N = 324065
X = 793996
GC fraction = 0.61
Total = 68482274
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634502_fasta.screen.contigs
-------------------------------------------------------------------
A 1131704
C 1848892
G 1814675
T 1116948
N 76
fraction GC = 0.62
total bases = 5912295
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 AICO reads.list > grep.reads.list.AICO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICO 4 500
-------------------------------------------------------------------
#Found 13560 total values totalling 48989533.0000. <3612.797419 +/- 12460.595768>
#Range: [ 919 - 768898 ]
#Most likely bin: [ 3000 - 3500 ] 5262 counts
#Median bin: [ 3000 - 3500 ] 5262 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 4 0.00 0.00 ]
| 1000 - 1500 : [ 49 0.00 0.00 ]
|X 1500 - 2000 : [ 114 0.01 0.01 ]
|XXX 2000 - 2500 : [ 395 0.03 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 3810 0.28 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 5262 0.39 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 3563 0.26 0.97 ]
|XXX 4000 - 4500 : [ 334 0.02 1.00 ]
#...
| 5000 - 5500 : [ 1 0.00 1.00 ]
#...
| 6500 - 7000 : [ 1 0.00 1.00 ]
#...
| 13500 - 14000 : [ 1 0.00 1.00 ]
| 14000 - 14500 : [ 1 0.00 1.00 ]
#...
| 24500 - 25000 : [ 1 0.00 1.00 ]
| 25000 - 25500 : [ 1 0.00 1.00 ]
#...
| 35500 - 36000 : [ 1 0.00 1.00 ]
#...
| 45000 - 45500 : [ 1 0.00 1.00 ]
#...
| 46000 - 46500 : [ 1 0.00 1.00 ]
#...
| 47500 - 48000 : [ 1 0.00 1.00 ]
#...
| 83000 - 83500 : [ 1 0.00 1.00 ]
#...
| 93000 - 93500 : [ 1 0.00 1.00 ]
#...
| 114000 - 114500 : [ 1 0.00 1.00 ]
#...
| 127500 - 128000 : [ 1 0.00 1.00 ]
#...
| 136000 - 136500 : [ 1 0.00 1.00 ]
#...
| 147500 - 148000 : [ 1 0.00 1.00 ]
#...
| 148500 - 149000 : [ 1 0.00 1.00 ]
#...
| 155500 - 156000 : [ 1 0.00 1.00 ]
#...
| 192000 - 192500 : [ 1 0.00 1.00 ]
#...
| 201000 - 201500 : [ 1 0.00 1.00 ]
#...
| 205000 - 205500 : [ 1 0.00 1.00 ]
#...
| 214000 - 214500 : [ 1 0.00 1.00 ]
#...
| 268500 - 269000 : [ 1 0.00 1.00 ]
#...
| 269500 - 270000 : [ 1 0.00 1.00 ]
#...
| 291000 - 291500 : [ 1 0.00 1.00 ]
#...
| 311000 - 311500 : [ 1 0.00 1.00 ]
#...
| 583500 - 584000 : [ 1 0.00 1.00 ]
#...
| 757000 - 757500 : [ 1 0.00 1.00 ]
#...
| 768500 - 769000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICP reads.list > grep.reads.list.AICP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICP 4 500
-------------------------------------------------------------------
#Found 14234 total values totalling 107583340.0000. <7558.194464 +/- 8379.076741>
#Range: [ 200 - 557474 ]
#Most likely bin: [ 7000 - 7500 ] 3644 counts
#Median bin: [ 7000 - 7500 ] 3644 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 500 : [ 1 0.00 0.00 ]
| 500 - 1000 : [ 6 0.00 0.00 ]
| 1000 - 1500 : [ 13 0.00 0.00 ]
| 1500 - 2000 : [ 19 0.00 0.00 ]
| 2000 - 2500 : [ 30 0.00 0.00 ]
|X 2500 - 3000 : [ 52 0.00 0.01 ]
|X 3000 - 3500 : [ 75 0.01 0.01 ]
|X 3500 - 4000 : [ 115 0.01 0.02 ]
|X 4000 - 4500 : [ 105 0.01 0.03 ]
|XX 4500 - 5000 : [ 137 0.01 0.04 ]
|X 5000 - 5500 : [ 66 0.00 0.04 ]
|XX 5500 - 6000 : [ 170 0.01 0.06 ]
|XXXXX 6000 - 6500 : [ 421 0.03 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 3197 0.22 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 3644 0.26 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 2601 0.18 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 2062 0.14 0.89 ]
|XXXXXXXXXXXXXXX 8500 - 9000 : [ 1407 0.10 0.99 ]
|X 9000 - 9500 : [ 96 0.01 1.00 ]
| 9500 - 10000 : [ 2 0.00 1.00 ]
#...
| 23500 - 24000 : [ 2 0.00 1.00 ]
#...
| 83000 - 83500 : [ 1 0.00 1.00 ]
| 83500 - 84000 : [ 1 0.00 1.00 ]
#...
| 102500 - 103000 : [ 1 0.00 1.00 ]
#...
| 106500 - 107000 : [ 1 0.00 1.00 ]
#...
| 125000 - 125500 : [ 1 0.00 1.00 ]
#...
| 187500 - 188000 : [ 1 0.00 1.00 ]
#...
| 195500 - 196000 : [ 1 0.00 1.00 ]
#...
| 207000 - 207500 : [ 1 0.00 1.00 ]
#...
| 272000 - 272500 : [ 1 0.00 1.00 ]
| 272500 - 273000 : [ 1 0.00 1.00 ]
#...
| 418000 - 418500 : [ 1 0.00 1.00 ]
#...
| 476000 - 476500 : [ 1 0.00 1.00 ]
#...
| 557000 - 557500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICS reads.list > grep.reads.list.AICS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICS 4 500
-------------------------------------------------------------------
#Found 1664 total values totalling 64460395.0000. <38738.218149 +/- 3722.290839>
#Range: [ 26303 - 109295 ]
#Most likely bin: [ 38000 - 38500 ] 97 counts
#Median bin: [ 38500 - 39000 ] 89 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 26000 - 26500 : [ 2 0.00 0.00 ]
| 26500 - 27000 : [ 1 0.00 0.00 ]
#...
| 27500 - 28000 : [ 1 0.00 0.00 ]
#...
|X 28500 - 29000 : [ 2 0.00 0.00 ]
#...
|XX 29500 - 30000 : [ 6 0.00 0.01 ]
|XX 30000 - 30500 : [ 4 0.00 0.01 ]
|X 30500 - 31000 : [ 3 0.00 0.01 ]
|XX 31000 - 31500 : [ 6 0.00 0.02 ]
|XXXX 31500 - 32000 : [ 10 0.01 0.02 ]
|XXXX 32000 - 32500 : [ 10 0.01 0.03 ]
|XXXXXXXXX 32500 - 33000 : [ 23 0.01 0.04 ]
|XXXXXXXXXXX 33000 - 33500 : [ 26 0.02 0.06 ]
|XXXXXXXXXXXX 33500 - 34000 : [ 30 0.02 0.07 ]
|XXXXXXXXXXXXXXXXX 34000 - 34500 : [ 42 0.03 0.10 ]
|XXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 48 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 55 0.03 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 85 0.05 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 76 0.05 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 94 0.06 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 90 0.05 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 87 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 97 0.06 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 89 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 96 0.06 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 89 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 79 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 71 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 82 0.05 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 60 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 69 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 63 0.04 0.90 ]
|XXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 45 0.03 0.93 ]
|XXXXXXXXXXXXXX 43500 - 44000 : [ 35 0.02 0.95 ]
|XXXXXXXXXXXXXXX 44000 - 44500 : [ 37 0.02 0.97 ]
|XXXXXX 44500 - 45000 : [ 14 0.01 0.98 ]
|XXXXXXXXX 45000 - 45500 : [ 22 0.01 0.99 ]
|XXX 45500 - 46000 : [ 8 0.00 1.00 ]
|XX 46000 - 46500 : [ 6 0.00 1.00 ]
#...
| 109000 - 109500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AICS 38595 +- 3404 (n=852)
# AICO 3156 +- 1057 (n=6858)
# AICP 7278 +- 1107 (n=7175)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634502_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
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634502_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 70166 35416 92.23 cumulative total @@
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 3634502_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found -1 total values totalling 0.0000. <-0.000000 +/- 0.000000>
#Range: [ - ]
#Most likely bin: [ 0 - 50 ] 1 counts
#Median bin: [ 0 - 50 ] counts
#Histogram Bins Count Fraction Cum_Fraction
trimt JAZZ trim 15 readlength histogram for AICO
trimt JAZZ trim 15 readlength histogram for AICP
trimt JAZZ trim 15 readlength histogram for AICS
trimt JAZZ trim 15 readlength histogram for BGNZ
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634502
-------------------------------------------------------------------
AICO.000001.000100 pUC18.fa.4 LRS.fasta
AICO.000101.000200 pUC18.fa.4 LRS.fasta
AICO.000201.000300 pUC18.fa LRS.fasta
AICP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AICP.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AICP.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
AICS.000001.000100 pCC1Fos.fa.4 LRS.fasta
AICO.000001.000100 pUC18.fa.4 LRS.fasta
AICO.000101.000200 pUC18.fa.4 LRS.fasta
AICO.000201.000300 pUC18.fa LRS.fasta
AICP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AICP.000101.000200 pMCL200.fa pMCL200.fa LRS.fasta
AICP.000201.000300 pMCL200.fa pMCL200.fa LRS.fasta
AICS.000001.000100 pCC1Fos.fa.4 LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634502_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634502_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 70013 total values totalling 43281.3717. <0.618191 +/- 0.046527>
#Range: [ 0.1539 - 0.8888 ]
#Most likely bin: [ 0.625 - 0.63 ] 3447 counts
#Median bin: [ 0.62 - 0.625 ] 3164 counts
| 0.15 - 0.155 : [ 1 0.00 0.00 ]
#...
| 0.275 - 0.28 : [ 1 0.00 0.00 ]
#...
| 0.285 - 0.29 : [ 1 0.00 0.00 ]
#...
| 0.315 - 0.32 : [ 1 0.00 0.00 ]
| 0.32 - 0.325 : [ 2 0.00 0.00 ]
| 0.325 - 0.33 : [ 1 0.00 0.00 ]
| 0.33 - 0.335 : [ 2 0.00 0.00 ]
#...
| 0.34 - 0.345 : [ 1 0.00 0.00 ]
#...
| 0.35 - 0.355 : [ 2 0.00 0.00 ]
#...
| 0.36 - 0.365 : [ 6 0.00 0.00 ]
#...
| 0.38 - 0.385 : [ 2 0.00 0.00 ]
| 0.385 - 0.39 : [ 2 0.00 0.00 ]
| 0.39 - 0.395 : [ 2 0.00 0.00 ]
| 0.395 - 0.4 : [ 6 0.00 0.00 ]
| 0.4 - 0.405 : [ 4 0.00 0.00 ]
| 0.405 - 0.41 : [ 12 0.00 0.00 ]
| 0.41 - 0.415 : [ 11 0.00 0.00 ]
| 0.415 - 0.42 : [ 10 0.00 0.00 ]
| 0.42 - 0.425 : [ 8 0.00 0.00 ]
| 0.425 - 0.43 : [ 13 0.00 0.00 ]
| 0.43 - 0.435 : [ 12 0.00 0.00 ]
| 0.435 - 0.44 : [ 17 0.00 0.00 ]
| 0.44 - 0.445 : [ 24 0.00 0.00 ]
| 0.445 - 0.45 : [ 25 0.00 0.00 ]
| 0.45 - 0.455 : [ 30 0.00 0.00 ]
| 0.455 - 0.46 : [ 38 0.00 0.00 ]
| 0.46 - 0.465 : [ 43 0.00 0.00 ]
|X 0.465 - 0.47 : [ 48 0.00 0.00 ]
| 0.47 - 0.475 : [ 40 0.00 0.01 ]
|X 0.475 - 0.48 : [ 61 0.00 0.01 ]
|X 0.48 - 0.485 : [ 74 0.00 0.01 ]
|X 0.485 - 0.49 : [ 91 0.00 0.01 ]
|X 0.49 - 0.495 : [ 118 0.00 0.01 ]
|XX 0.495 - 0.5 : [ 139 0.00 0.01 ]
|XXX 0.5 - 0.505 : [ 229 0.00 0.02 ]
|XXX 0.505 - 0.51 : [ 234 0.00 0.02 ]
|XXXX 0.51 - 0.515 : [ 304 0.00 0.02 ]
|XXXX 0.515 - 0.52 : [ 314 0.00 0.03 ]
|XXXXX 0.52 - 0.525 : [ 400 0.01 0.03 ]
|XXXXXX 0.525 - 0.53 : [ 491 0.01 0.04 ]
|XXXXXXX 0.53 - 0.535 : [ 577 0.01 0.05 ]
|XXXXXXXX 0.535 - 0.54 : [ 680 0.01 0.06 ]
|XXXXXXXX 0.54 - 0.545 : [ 715 0.01 0.07 ]
|XXXXXXXXXXX 0.545 - 0.55 : [ 930 0.01 0.08 ]
|XXXXXXXXXXX 0.55 - 0.555 : [ 953 0.01 0.10 ]
|XXXXXXXXXXXXX 0.555 - 0.56 : [ 1142 0.02 0.11 ]
|XXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1273 0.02 0.13 ]
|XXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1410 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1532 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1581 0.02 0.19 ]
|XXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1760 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1997 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 2125 0.03 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 2227 0.03 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 2607 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 2750 0.04 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 2901 0.04 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 3085 0.04 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 3164 0.05 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 3447 0.05 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 3418 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 3281 0.05 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 3178 0.05 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 2949 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 2740 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 2546 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 2221 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 1894 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 1683 0.02 0.91 ]
|XXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 1477 0.02 0.93 ]
|XXXXXXXXXXXXXX 0.68 - 0.685 : [ 1213 0.02 0.95 ]
|XXXXXXXXXXX 0.685 - 0.69 : [ 916 0.01 0.96 ]
|XXXXXXXXX 0.69 - 0.695 : [ 743 0.01 0.97 ]
|XXXXXXX 0.695 - 0.7 : [ 574 0.01 0.98 ]
|XXXXX 0.7 - 0.705 : [ 394 0.01 0.98 ]
|XXXX 0.705 - 0.71 : [ 310 0.00 0.99 ]
|XXX 0.71 - 0.715 : [ 241 0.00 0.99 ]
|XX 0.715 - 0.72 : [ 147 0.00 0.99 ]
|X 0.72 - 0.725 : [ 118 0.00 1.00 ]
|X 0.725 - 0.73 : [ 84 0.00 1.00 ]
|X 0.73 - 0.735 : [ 63 0.00 1.00 ]
| 0.735 - 0.74 : [ 36 0.00 1.00 ]
| 0.74 - 0.745 : [ 25 0.00 1.00 ]
| 0.745 - 0.75 : [ 19 0.00 1.00 ]
| 0.75 - 0.755 : [ 18 0.00 1.00 ]
| 0.755 - 0.76 : [ 11 0.00 1.00 ]
| 0.76 - 0.765 : [ 5 0.00 1.00 ]
| 0.765 - 0.77 : [ 3 0.00 1.00 ]
| 0.77 - 0.775 : [ 6 0.00 1.00 ]
| 0.775 - 0.78 : [ 4 0.00 1.00 ]
| 0.78 - 0.785 : [ 2 0.00 1.00 ]
| 0.785 - 0.79 : [ 3 0.00 1.00 ]
| 0.79 - 0.795 : [ 1 0.00 1.00 ]
#...
| 0.8 - 0.805 : [ 4 0.00 1.00 ]
| 0.805 - 0.81 : [ 4 0.00 1.00 ]
#...
| 0.815 - 0.82 : [ 2 0.00 1.00 ]
| 0.82 - 0.825 : [ 1 0.00 1.00 ]
#...
| 0.845 - 0.85 : [ 1 0.00 1.00 ]
#...
| 0.865 - 0.87 : [ 1 0.00 1.00 ]
#...
| 0.885 - 0.89 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 24. 278 reads; 26582 bp (untrimmed), 26340 (trimmed).
Contig 25. 287 reads; 27445 bp (untrimmed), 26724 (trimmed).
Contig 26. 313 reads; 30815 bp (untrimmed), 30722 (trimmed).
Contig 27. 318 reads; 31520 bp (untrimmed), 31442 (trimmed).
Contig 28. 646 reads; 55057 bp (untrimmed), 54855 (trimmed).
Contig 29. 846 reads; 67738 bp (untrimmed), 67714 (trimmed).
Contig 30. 861 reads; 83479 bp (untrimmed), 83373 (trimmed).
Contig 31. 916 reads; 84969 bp (untrimmed), 84931 (trimmed).
Contig 32. 940 reads; 81269 bp (untrimmed), 81227 (trimmed).
Contig 33. 1250 reads; 107085 bp (untrimmed), 107072 (trimmed).
Contig 34. 1260 reads; 105200 bp (untrimmed), 105198 (trimmed).
Contig 35. 1261 reads; 99143 bp (untrimmed), 98276 (trimmed).
Contig 36. 1343 reads; 124099 bp (untrimmed), 124043 (trimmed).
Contig 37. 1919 reads; 166543 bp (untrimmed), 166441 (trimmed).
Contig 38. 1957 reads; 167038 bp (untrimmed), 166980 (trimmed).
Contig 39. 2335 reads; 196801 bp (untrimmed), 196522 (trimmed).
Contig 40. 2628 reads; 238916 bp (untrimmed), 238883 (trimmed).
Contig 41. 2806 reads; 241052 bp (untrimmed), 241004 (trimmed).
Contig 42. 3084 reads; 260251 bp (untrimmed), 260222 (trimmed).
Contig 43. 3544 reads; 329519 bp (untrimmed), 329307 (trimmed).
Contig 44. 3808 reads; 352054 bp (untrimmed), 351898 (trimmed).
Contig 45. 4716 reads; 367145 bp (untrimmed), 367091 (trimmed).
Contig 46. 4773 reads; 458209 bp (untrimmed), 458142 (trimmed).
Contig 47. 5013 reads; 399759 bp (untrimmed), 399556 (trimmed).
Contig 48. 5436 reads; 338694 bp (untrimmed), 338577 (trimmed).
Contig 49. 5727 reads; 495163 bp (untrimmed), 495093 (trimmed).
Contig 50. 10598 reads; 848529 bp (untrimmed), 848461 (trimmed).
--------------------------------------------------------------
Totals 70143 reads; 5912295 bp (untrimmed), 5905397 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 5910712 bases Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 27
Chimeric reads = 111
Suspect alignments = 318
-------------------------------------------------------------------
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/3634502/edit_dir.29Mar04.QD