See help.
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4533662
# phrap: 3052361
# db:
altered.
6700000
4762007 +/- 1497870
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 2737
Number of reads with percent X's >= 20%: 456 = 3.0%
Number of reads with percent X's >= 50%: 412 = 2.7%
Number of reads with percent X's >= 80%: 344 = 2.3%
Total reads in project: 15236
Total bp X'd : 481373
reads >= 20% >= 50% >= 80% screened
Nr with L09136 2316 50 43 23
Nr with LRS 18 18 16 14
Nr with pMCL200_JGI_XZX+XZK 403 388 353 307
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 531
Number of reads with percent X's >= 20%: 356 = 13.5%
Number of reads with percent X's >= 50%: 347 = 13.2%
Number of reads with percent X's >= 80%: 323 = 12.3%
Total reads in project: 2635
Total bp X'd : 341740
reads >= 20% >= 50% >= 80% screened
Nr with L09136 202 30 29 20
Nr with LRS 18 18 16 14
Nr with pMCL200_JGI_XZX+XZK 311 308 302 289
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 4915204
C = 2561863
G = 2475086
T = 4783678
N = 103290
X = 481373
GC fraction = 0.33
Total = 15320494
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634512_fasta.screen.contigs
-------------------------------------------------------------------
A 1674315
C 799798
G 774624
T 1699249
N 3902
fraction GC = 0.32
total bases = 4951888
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 AHYP reads.list > grep.reads.list.AHYP
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHYP 4 500
-------------------------------------------------------------------
#Found 146 total values totalling 761225.0000. <5213.869863 +/- 1791.711634>
#Range: [ 1044 - 7333 ]
#Most likely bin: [ 5500 - 6000 ] 46 counts
#Median bin: [ 5500 - 6000 ] 46 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 1000 - 1500 : [ 10 0.07 0.07 ]
|XXXXXXXXXX 1500 - 2000 : [ 11 0.08 0.14 ]
|XXX 2000 - 2500 : [ 3 0.02 0.16 ]
|XXX 2500 - 3000 : [ 3 0.02 0.18 ]
|XXX 3000 - 3500 : [ 3 0.02 0.21 ]
|X 3500 - 4000 : [ 1 0.01 0.21 ]
|X 4000 - 4500 : [ 1 0.01 0.22 ]
|XX 4500 - 5000 : [ 2 0.01 0.23 ]
|XXXXX 5000 - 5500 : [ 6 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 46 0.32 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 38 0.26 0.85 ]
|XXXXXXXXXXXX 6500 - 7000 : [ 14 0.10 0.95 ]
|XXXXXXX 7000 - 7500 : [ 8 0.05 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFZ reads.list > grep.reads.list.AIFZ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFZ 4 500
-------------------------------------------------------------------
#Found 652 total values totalling 2073053.0000. <3179.529141 +/- 642.427887>
#Range: [ 881 - 4996 ]
#Most likely bin: [ 3000 - 3500 ] 214 counts
#Median bin: [ 3000 - 3500 ] 214 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
|XX 1000 - 1500 : [ 13 0.02 0.02 ]
|XXX 1500 - 2000 : [ 15 0.02 0.05 ]
|XXXXX 2000 - 2500 : [ 29 0.04 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 188 0.29 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 214 0.33 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 123 0.19 0.90 ]
|XXXXXXXXXXX 4000 - 4500 : [ 60 0.09 0.99 ]
|X 4500 - 5000 : [ 8 0.01 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIFZ 3017 +- 752 (n=336)
# AHYP 4087 +- 2562 (n=109)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634512_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
AIGB 7680 79 548 87 488 96 92 603 95 626
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIGB 0 0 0 0 0 96 92 603 95 626
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634512_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
40 7556 3834 95.85 99.84 AIFZ @
40 7680 3840 96.00 100.00 AHYP @
] 15236 7674 95.92 cumulative total@@
LIBRARY PLATE ID COUNT [ AIFZ 40 AHYP 40 ] for 80 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 3634512_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 96 total values totalling 53173.0000. <553.885417 +/- 245.235893>
#Range: [ 0 - 881 ]
#Most likely bin: [ 600 - 650 ] 13 counts
#Median bin: [ 600 - 650 ] 13 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 7 0.07 0.07 ]
|XXX 50 - 100 : [ 1 0.01 0.08 ]
|XXXXXXXXX 100 - 150 : [ 3 0.03 0.11 ]
|XXXXXXXXX 150 - 200 : [ 3 0.03 0.15 ]
#...
|XXXXXX 250 - 300 : [ 2 0.02 0.17 ]
|XXXXXXXXX 300 - 350 : [ 3 0.03 0.20 ]
|XXXXXXXXXXXXXXX 350 - 400 : [ 5 0.05 0.25 ]
|XXXXXX 400 - 450 : [ 2 0.02 0.27 ]
|XXXXXXXXX 450 - 500 : [ 3 0.03 0.30 ]
|XXXXXXXXX 500 - 550 : [ 3 0.03 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 12 0.12 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 13 0.14 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 8 0.08 0.68 ]
|XXXXXXXXXXXXXXXXXX 700 - 750 : [ 6 0.06 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 12 0.12 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 10 0.10 0.97 ]
|XXXXXXXXX 850 - 900 : [ 3 0.03 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYP
trimt JAZZ trim 15 readlength histogram for AHYS
trimt JAZZ trim 15 readlength histogram for AIFZ
trimt JAZZ trim 15 readlength histogram for AWGG
trimt JAZZ trim 15 readlength histogram for BAOF
trimt JAZZ trim 15 readlength histogram for BAOG
trimt JAZZ trim 15 readlength histogram for BAOH
trimt JAZZ trim 15 readlength histogram for BFTN
trimt JAZZ trim 15 readlength histogram for SCNC
trimt JAZZ trim 15 readlength histogram for SCOU
trimt JAZZ trim 15 readlength histogram for SCOW
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634512
-------------------------------------------------------------------
AHYP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIFZ.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIFZ.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIFZ.000201.000300 pUC18.fa pUC18.fa LRS.fasta
AIFZ.000301.000400 pUC18.fa pUC18.fa LRS.fasta
AIFZ.000401.000500 pUC18.fa pUC18.fa LRS.fasta
AWGG.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
BAOF.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
BFTN.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
AHYP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
AIFZ.000001.000100 pUC18.fa pUC18.fa LRS.fasta
AIFZ.000101.000200 pUC18.fa pUC18.fa LRS.fasta
AIFZ.000201.000300 pUC18.fa pUC18.fa LRS.fasta
AIFZ.000301.000400 pUC18.fa pUC18.fa LRS.fasta
AIFZ.000401.000500 pUC18.fa pUC18.fa LRS.fasta
AWGG.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
BAOF.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
BFTN.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634512_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634512_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 13446 total values totalling 4213.5877. <0.313371 +/- 0.065117>
#Range: [ 0.0455 - 0.6667 ]
#Most likely bin: [ 0.29 - 0.295 ] 634 counts
#Median bin: [ 0.3 - 0.305 ] 625 counts
#Entropy = 5.4874 bits
| 0.045 - 0.05 : [ 1 0.00 0.00 ]
#...
| 0.075 - 0.08 : [ 1 0.00 0.00 ]
#...
| 0.085 - 0.09 : [ 1 0.00 0.00 ]
#...
| 0.095 - 0.1 : [ 3 0.00 0.00 ]
| 0.1 - 0.105 : [ 1 0.00 0.00 ]
#...
| 0.11 - 0.115 : [ 1 0.00 0.00 ]
| 0.115 - 0.12 : [ 1 0.00 0.00 ]
#...
| 0.125 - 0.13 : [ 6 0.00 0.00 ]
#...
| 0.14 - 0.145 : [ 3 0.00 0.00 ]
| 0.145 - 0.15 : [ 3 0.00 0.00 ]
| 0.15 - 0.155 : [ 4 0.00 0.00 ]
| 0.155 - 0.16 : [ 1 0.00 0.00 ]
| 0.16 - 0.165 : [ 6 0.00 0.00 ]
| 0.165 - 0.17 : [ 6 0.00 0.00 ]
|X 0.17 - 0.175 : [ 9 0.00 0.00 ]
|X 0.175 - 0.18 : [ 17 0.00 0.00 ]
|X 0.18 - 0.185 : [ 12 0.00 0.01 ]
|X 0.185 - 0.19 : [ 14 0.00 0.01 ]
|X 0.19 - 0.195 : [ 13 0.00 0.01 ]
|X 0.195 - 0.2 : [ 16 0.00 0.01 ]
|XX 0.2 - 0.205 : [ 38 0.00 0.01 ]
|XXX 0.205 - 0.21 : [ 42 0.00 0.01 ]
|XXXX 0.21 - 0.215 : [ 64 0.00 0.02 ]
|XXXX 0.215 - 0.22 : [ 59 0.00 0.02 ]
|XXXXXX 0.22 - 0.225 : [ 100 0.01 0.03 ]
|XXXXXXXX 0.225 - 0.23 : [ 120 0.01 0.04 ]
|XXXXXXXX 0.23 - 0.235 : [ 134 0.01 0.05 ]
|XXXXXXXXXXXXXX 0.235 - 0.24 : [ 228 0.02 0.07 ]
|XXXXXXXXXXXXXXX 0.24 - 0.245 : [ 243 0.02 0.09 ]
|XXXXXXXXXXXXXXX 0.245 - 0.25 : [ 245 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.25 - 0.255 : [ 371 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.255 - 0.26 : [ 360 0.03 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.26 - 0.265 : [ 439 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.265 - 0.27 : [ 480 0.04 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.27 - 0.275 : [ 511 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.275 - 0.28 : [ 570 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.28 - 0.285 : [ 590 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.285 - 0.29 : [ 586 0.04 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 634 0.05 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.295 - 0.3 : [ 572 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 625 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 576 0.04 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 583 0.04 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 521 0.04 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 462 0.03 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 412 0.03 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 402 0.03 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 372 0.03 0.78 ]
|XXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 315 0.02 0.80 ]
|XXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 247 0.02 0.82 ]
|XXXXXXXXXXXXX 0.35 - 0.355 : [ 199 0.01 0.83 ]
|XXXXXXXXXXXX 0.355 - 0.36 : [ 184 0.01 0.85 ]
|XXXXXXX 0.36 - 0.365 : [ 113 0.01 0.86 ]
|XXXXXXX 0.365 - 0.37 : [ 113 0.01 0.86 ]
|XXXXXX 0.37 - 0.375 : [ 100 0.01 0.87 ]
|XXXXX 0.375 - 0.38 : [ 85 0.01 0.88 ]
|XXXX 0.38 - 0.385 : [ 69 0.01 0.88 ]
|XXX 0.385 - 0.39 : [ 52 0.00 0.89 ]
|XXX 0.39 - 0.395 : [ 54 0.00 0.89 ]
|XXX 0.395 - 0.4 : [ 46 0.00 0.90 ]
|XXXX 0.4 - 0.405 : [ 65 0.00 0.90 ]
|XXX 0.405 - 0.41 : [ 47 0.00 0.90 ]
|XXX 0.41 - 0.415 : [ 50 0.00 0.91 ]
|XXX 0.415 - 0.42 : [ 50 0.00 0.91 ]
|XXX 0.42 - 0.425 : [ 55 0.00 0.91 ]
|XXXX 0.425 - 0.43 : [ 67 0.00 0.92 ]
|XXXX 0.43 - 0.435 : [ 62 0.00 0.92 ]
|XXXX 0.435 - 0.44 : [ 57 0.00 0.93 ]
|XXX 0.44 - 0.445 : [ 50 0.00 0.93 ]
|XXXXX 0.445 - 0.45 : [ 75 0.01 0.94 ]
|XXXX 0.45 - 0.455 : [ 67 0.00 0.94 ]
|XXXX 0.455 - 0.46 : [ 64 0.00 0.95 ]
|XXXX 0.46 - 0.465 : [ 56 0.00 0.95 ]
|XXXX 0.465 - 0.47 : [ 56 0.00 0.96 ]
|XXXX 0.47 - 0.475 : [ 61 0.00 0.96 ]
|XXX 0.475 - 0.48 : [ 54 0.00 0.96 ]
|XXXX 0.48 - 0.485 : [ 59 0.00 0.97 ]
|XXX 0.485 - 0.49 : [ 54 0.00 0.97 ]
|XXX 0.49 - 0.495 : [ 48 0.00 0.98 ]
|XX 0.495 - 0.5 : [ 36 0.00 0.98 ]
|XXX 0.5 - 0.505 : [ 45 0.00 0.98 ]
|XX 0.505 - 0.51 : [ 25 0.00 0.98 ]
|XX 0.51 - 0.515 : [ 34 0.00 0.99 ]
|XX 0.515 - 0.52 : [ 39 0.00 0.99 ]
|XXX 0.52 - 0.525 : [ 41 0.00 0.99 ]
|X 0.525 - 0.53 : [ 21 0.00 0.99 ]
|X 0.53 - 0.535 : [ 17 0.00 1.00 ]
|X 0.535 - 0.54 : [ 12 0.00 1.00 ]
|X 0.54 - 0.545 : [ 13 0.00 1.00 ]
|X 0.545 - 0.55 : [ 8 0.00 1.00 ]
| 0.55 - 0.555 : [ 7 0.00 1.00 ]
| 0.555 - 0.56 : [ 3 0.00 1.00 ]
| 0.56 - 0.565 : [ 3 0.00 1.00 ]
#...
| 0.57 - 0.575 : [ 2 0.00 1.00 ]
#...
| 0.59 - 0.595 : [ 1 0.00 1.00 ]
#...
| 0.6 - 0.605 : [ 1 0.00 1.00 ]
| 0.605 - 0.61 : [ 1 0.00 1.00 ]
| 0.61 - 0.615 : [ 1 0.00 1.00 ]
#...
| 0.62 - 0.625 : [ 1 0.00 1.00 ]
| 0.625 - 0.63 : [ 1 0.00 1.00 ]
| 0.63 - 0.635 : [ 1 0.00 1.00 ]
#...
| 0.665 - 0.67 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 2274. 25 reads; 6785 bp (untrimmed), 6741 (trimmed).
Contig 2275. 25 reads; 7688 bp (untrimmed), 7438 (trimmed).
Contig 2276. 26 reads; 6718 bp (untrimmed), 6708 (trimmed).
Contig 2277. 26 reads; 6741 bp (untrimmed), 6720 (trimmed).
Contig 2278. 26 reads; 5626 bp (untrimmed), 5372 (trimmed).
Contig 2279. 26 reads; 7379 bp (untrimmed), 7324 (trimmed).
Contig 2280. 26 reads; 7075 bp (untrimmed), 6911 (trimmed).
Contig 2281. 27 reads; 7336 bp (untrimmed), 7298 (trimmed).
Contig 2282. 27 reads; 10045 bp (untrimmed), 9840 (trimmed).
Contig 2283. 28 reads; 7544 bp (untrimmed), 7461 (trimmed).
Contig 2284. 30 reads; 8122 bp (untrimmed), 7879 (trimmed).
Contig 2285. 30 reads; 9111 bp (untrimmed), 8989 (trimmed).
Contig 2286. 31 reads; 9774 bp (untrimmed), 9559 (trimmed).
Contig 2287. 32 reads; 8418 bp (untrimmed), 8124 (trimmed).
Contig 2288. 33 reads; 9180 bp (untrimmed), 9113 (trimmed).
Contig 2289. 34 reads; 11218 bp (untrimmed), 11084 (trimmed).
Contig 2290. 36 reads; 9491 bp (untrimmed), 9124 (trimmed).
Contig 2291. 37 reads; 8016 bp (untrimmed), 7858 (trimmed).
Contig 2292. 39 reads; 8691 bp (untrimmed), 8556 (trimmed).
Contig 2293. 43 reads; 12241 bp (untrimmed), 11946 (trimmed).
Contig 2294. 45 reads; 12005 bp (untrimmed), 11999 (trimmed).
Contig 2295. 48 reads; 11560 bp (untrimmed), 11491 (trimmed).
Contig 2296. 51 reads; 15998 bp (untrimmed), 15833 (trimmed).
Contig 2297. 52 reads; 8779 bp (untrimmed), 8417 (trimmed).
Contig 2298. 53 reads; 12369 bp (untrimmed), 12337 (trimmed).
Contig 2299. 57 reads; 11852 bp (untrimmed), 11773 (trimmed).
Contig 2300. 95 reads; 7354 bp (untrimmed), 7130 (trimmed).
--------------------------------------------------------------
Totals 12601 reads; 4951888 bp (untrimmed), 4533662 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4897907 bases Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 201
HQ Discrepant reads = 379
Chimeric reads = 62
Suspect alignments = 29
-------------------------------------------------------------------
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/microbe4/3634512/edit_dir.02Dec04.QC