See help.
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4502123
# phrap: 2637188
# db:
altered.
3000000
3379770 +/- 807326
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 3564
Number of reads with percent X's >= 20%: 689 = 4.5%
Number of reads with percent X's >= 50%: 608 = 4.0%
Number of reads with percent X's >= 80%: 270 = 1.8%
Total reads in project: 15303
Total bp X'd : 581485
reads >= 20% >= 50% >= 80% screened
Nr with L09136 2979 151 141 115
Nr with LRS 2 2 2 2
Nr with pMCL200_JGI_XZX+XZK 583 536 465 153
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 739
Number of reads with percent X's >= 20%: 261 = 7.8%
Number of reads with percent X's >= 50%: 256 = 7.7%
Number of reads with percent X's >= 80%: 199 = 6.0%
Total reads in project: 3343
Total bp X'd : 226469
reads >= 20% >= 50% >= 80% screened
Nr with L09136 608 137 135 115
Nr with LRS 2 2 2 2
Nr with pMCL200_JGI_XZX+XZK 129 122 119 82
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 3020500
C = 4140621
G = 4237682
T = 2650422
N = 148812
X = 581485
GC fraction = 0.57
Total = 14779522
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634513_fasta.screen.contigs
-------------------------------------------------------------------
A 967463
C 1567953
G 1558351
T 976543
N 7393
fraction GC = 0.62
total bases = 5077703
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 AIFW reads.list > grep.reads.list.AIFW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFW 4 500
-------------------------------------------------------------------
#Found 247 total values totalling 730864.0000. <2958.963563 +/- 446.988097>
#Range: [ 798 - 4141 ]
#Most likely bin: [ 2500 - 3000 ] 119 counts
#Median bin: [ 2500 - 3000 ] 119 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
|X 1000 - 1500 : [ 3 0.01 0.02 ]
| 1500 - 2000 : [ 1 0.00 0.02 ]
|XXXXX 2000 - 2500 : [ 14 0.06 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 119 0.48 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 86 0.35 0.91 ]
|XXXXXXX 3500 - 4000 : [ 21 0.09 0.99 ]
|X 4000 - 4500 : [ 2 0.01 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFX reads.list > grep.reads.list.AIFX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFX 4 500
-------------------------------------------------------------------
#Found 122 total values totalling 176049.0000. <1443.024590 +/- 1263.448815>
#Range: [ 94 - 6557 ]
#Most likely bin: [ 0 - 500 ] 38 counts
#Median bin: [ 1000 - 1500 ] 26 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 500 : [ 38 0.31 0.31 ]
|XXXXXXXX 500 - 1000 : [ 8 0.07 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 1500 : [ 26 0.21 0.59 ]
|XXXXXXXXXXXXXXXXXXX 1500 - 2000 : [ 18 0.15 0.74 ]
|XXXXXXXXXXXX 2000 - 2500 : [ 11 0.09 0.83 ]
|XXXXXXXXX 2500 - 3000 : [ 9 0.07 0.90 ]
|XXXX 3000 - 3500 : [ 4 0.03 0.93 ]
|XXX 3500 - 4000 : [ 3 0.02 0.96 ]
|X 4000 - 4500 : [ 1 0.01 0.97 ]
|XX 4500 - 5000 : [ 2 0.02 0.98 ]
#...
|X 6000 - 6500 : [ 1 0.01 0.99 ]
|X 6500 - 7000 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIFX 684 +- 896 (n=134)
# AIFW 2787 +- 648 (n=134)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634513_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
AIFW 59520 -1 -1 95 703 7659 89 589 93 606
AIFX 53760 -1 -1 97 692 7644 87 605 92 625
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIFW 3833 89 595 94 610 3826 89 583 92 602
AIFX 3826 87 612 92 631 3818 87 598 92 618
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634513_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
40 7659 3839 95.97 99.97 AIFW @
40 7644 3835 95.88 99.87 AIFX @
] 15303 7674 95.92 cumulative total@@
LIBRARY PLATE ID COUNT [ AIFW 40 AIFX 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 3634513_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 15303 total values totalling 8062102.0000. <526.831471 +/- 246.291093>
#Range: [ 0 - 881 ]
#Most likely bin: [ 700 - 750 ] 2389 counts
#Median bin: [ 600 - 650 ] 1867 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1517 0.10 0.10 ]
|XXXXXX 50 - 100 : [ 334 0.02 0.12 ]
|XXXXX 100 - 150 : [ 275 0.02 0.14 ]
|XXXXX 150 - 200 : [ 323 0.02 0.16 ]
|XXXX 200 - 250 : [ 266 0.02 0.18 ]
|XXXXX 250 - 300 : [ 328 0.02 0.20 ]
|XXXXXX 300 - 350 : [ 332 0.02 0.22 ]
|XXXXXX 350 - 400 : [ 386 0.03 0.25 ]
|XXXXXXXX 400 - 450 : [ 460 0.03 0.28 ]
|XXXXXXXXXX 450 - 500 : [ 609 0.04 0.32 ]
|XXXXXXXXXXXXXX 500 - 550 : [ 858 0.06 0.37 ]
|XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1176 0.08 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1867 0.12 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2376 0.16 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2389 0.16 0.88 ]
|XXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1324 0.09 0.97 ]
|XXXXXXXX 800 - 850 : [ 448 0.03 1.00 ]
|X 850 - 900 : [ 35 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIFW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFW 3634513_fasta.screen.trimQ15.SaF > reads.trim15.AIFW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFW.rl 2 50
-------------------------------------------------------------------
#Found 7659 total values totalling 4026033.0000. <525.660400 +/- 238.029653>
#Range: [ 0 - 870 ]
#Most likely bin: [ 700 - 750 ] 1261 counts
#Median bin: [ 600 - 650 ] 932 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 717 0.09 0.09 ]
|XXXX 50 - 100 : [ 128 0.02 0.11 ]
|XXXXX 100 - 150 : [ 149 0.02 0.13 ]
|XXXX 150 - 200 : [ 129 0.02 0.15 ]
|XXXX 200 - 250 : [ 140 0.02 0.16 ]
|XXXXX 250 - 300 : [ 170 0.02 0.19 ]
|XXXXXX 300 - 350 : [ 196 0.03 0.21 ]
|XXXXXXX 350 - 400 : [ 224 0.03 0.24 ]
|XXXXXXXX 400 - 450 : [ 265 0.03 0.28 ]
|XXXXXXXXXXX 450 - 500 : [ 341 0.04 0.32 ]
|XXXXXXXXXXXXXX 500 - 550 : [ 457 0.06 0.38 ]
|XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 612 0.08 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 932 0.12 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1216 0.16 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1261 0.16 0.91 ]
|XXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 634 0.08 0.99 ]
|XXX 800 - 850 : [ 87 0.01 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIFX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFX 3634513_fasta.screen.trimQ15.SaF > reads.trim15.AIFX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFX.rl 2 50
-------------------------------------------------------------------
#Found 7644 total values totalling 4036069.0000. <528.004840 +/- 254.294297>
#Range: [ 0 - 881 ]
#Most likely bin: [ 650 - 700 ] 1160 counts
#Median bin: [ 600 - 650 ] 935 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 800 0.10 0.10 ]
|XXXXXXX 50 - 100 : [ 206 0.03 0.13 ]
|XXXX 100 - 150 : [ 126 0.02 0.15 ]
|XXXXXXX 150 - 200 : [ 194 0.03 0.17 ]
|XXXX 200 - 250 : [ 126 0.02 0.19 ]
|XXXXX 250 - 300 : [ 158 0.02 0.21 ]
|XXXXX 300 - 350 : [ 136 0.02 0.23 ]
|XXXXXX 350 - 400 : [ 162 0.02 0.25 ]
|XXXXXXX 400 - 450 : [ 195 0.03 0.28 ]
|XXXXXXXXX 450 - 500 : [ 268 0.04 0.31 ]
|XXXXXXXXXXXXXX 500 - 550 : [ 401 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXX 550 - 600 : [ 564 0.07 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 935 0.12 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1160 0.15 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1128 0.15 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 690 0.09 0.95 ]
|XXXXXXXXXXXX 800 - 850 : [ 361 0.05 1.00 ]
|X 850 - 900 : [ 34 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIFY
trimt JAZZ trim 15 readlength histogram for BFBO
trimt JAZZ trim 15 readlength histogram for BFBP
trimt JAZZ trim 15 readlength histogram for BFBS
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634513
-------------------------------------------------------------------
AIFW.000001.000100 pUC18.fa LRS.fasta
AIFW.000101.000200 pUC18.fa LRS.fasta
AIFW.000201.000300 pUC18.fa LRS.fasta
AIFW.000301.000400 pUC18.fa LRS.fasta
AIFX.000001.000100 pMCL200.fa LRS.fasta
AIFX.000101.000200 pMCL200.fa LRS.fasta
AIFX.000201.000300 pMCL200.fa LRS.fasta
AIFY.000001.000100 pCC1Fos.fa LRS.fasta
AIFW.000001.000100 pUC18.fa LRS.fasta
AIFW.000101.000200 pUC18.fa LRS.fasta
AIFW.000201.000300 pUC18.fa LRS.fasta
AIFW.000301.000400 pUC18.fa LRS.fasta
AIFX.000001.000100 pMCL200.fa LRS.fasta
AIFX.000101.000200 pMCL200.fa LRS.fasta
AIFX.000201.000300 pMCL200.fa LRS.fasta
AIFY.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634513_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634513_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 13807 total values totalling 8493.0537. <0.615127 +/- 0.044749>
#Range: [ 0 - 0.9231 ]
#Most likely bin: [ 0.625 - 0.63 ] 766 counts
#Median bin: [ 0.615 - 0.62 ] 738 counts
| 0 - 0.005 : [ 2 0.00 0.00 ]
#...
| 0.235 - 0.24 : [ 1 0.00 0.00 ]
#...
| 0.26 - 0.265 : [ 1 0.00 0.00 ]
| 0.265 - 0.27 : [ 1 0.00 0.00 ]
#...
| 0.28 - 0.285 : [ 1 0.00 0.00 ]
| 0.285 - 0.29 : [ 1 0.00 0.00 ]
| 0.29 - 0.295 : [ 1 0.00 0.00 ]
#...
| 0.3 - 0.305 : [ 1 0.00 0.00 ]
#...
| 0.32 - 0.325 : [ 1 0.00 0.00 ]
| 0.325 - 0.33 : [ 2 0.00 0.00 ]
#...
| 0.345 - 0.35 : [ 1 0.00 0.00 ]
#...
| 0.365 - 0.37 : [ 2 0.00 0.00 ]
| 0.37 - 0.375 : [ 3 0.00 0.00 ]
| 0.375 - 0.38 : [ 2 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 : [ 3 0.00 0.00 ]
| 0.395 - 0.4 : [ 3 0.00 0.00 ]
| 0.4 - 0.405 : [ 7 0.00 0.00 ]
| 0.405 - 0.41 : [ 5 0.00 0.00 ]
| 0.41 - 0.415 : [ 3 0.00 0.00 ]
| 0.415 - 0.42 : [ 1 0.00 0.00 ]
| 0.42 - 0.425 : [ 5 0.00 0.00 ]
| 0.425 - 0.43 : [ 4 0.00 0.00 ]
| 0.43 - 0.435 : [ 8 0.00 0.00 ]
|X 0.435 - 0.44 : [ 17 0.00 0.01 ]
| 0.44 - 0.445 : [ 5 0.00 0.01 ]
| 0.445 - 0.45 : [ 1 0.00 0.01 ]
| 0.45 - 0.455 : [ 6 0.00 0.01 ]
|X 0.455 - 0.46 : [ 12 0.00 0.01 ]
| 0.46 - 0.465 : [ 7 0.00 0.01 ]
|X 0.465 - 0.47 : [ 15 0.00 0.01 ]
| 0.47 - 0.475 : [ 9 0.00 0.01 ]
|X 0.475 - 0.48 : [ 14 0.00 0.01 ]
|X 0.48 - 0.485 : [ 20 0.00 0.01 ]
|X 0.485 - 0.49 : [ 16 0.00 0.01 ]
|X 0.49 - 0.495 : [ 12 0.00 0.01 ]
| 0.495 - 0.5 : [ 7 0.00 0.01 ]
|XX 0.5 - 0.505 : [ 41 0.00 0.02 ]
|X 0.505 - 0.51 : [ 22 0.00 0.02 ]
|XX 0.51 - 0.515 : [ 33 0.00 0.02 ]
|XX 0.515 - 0.52 : [ 35 0.00 0.02 ]
|XX 0.52 - 0.525 : [ 36 0.00 0.03 ]
|XXX 0.525 - 0.53 : [ 65 0.00 0.03 ]
|XXXXX 0.53 - 0.535 : [ 101 0.01 0.04 ]
|XXXXX 0.535 - 0.54 : [ 98 0.01 0.05 ]
|XXXXX 0.54 - 0.545 : [ 98 0.01 0.05 ]
|XXXXXXX 0.545 - 0.55 : [ 131 0.01 0.06 ]
|XXXXXXXXX 0.55 - 0.555 : [ 165 0.01 0.07 ]
|XXXXXXXXX 0.555 - 0.56 : [ 167 0.01 0.09 ]
|XXXXXXXXXXXX 0.56 - 0.565 : [ 228 0.02 0.10 ]
|XXXXXXXXXXXXXXX 0.565 - 0.57 : [ 291 0.02 0.12 ]
|XXXXXXXXXXXXXXX 0.57 - 0.575 : [ 291 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 376 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 408 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 486 0.04 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 521 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 552 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 652 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 682 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 669 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 738 0.05 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 696 0.05 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 766 0.06 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 681 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 691 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 634 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 594 0.04 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 503 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 412 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 368 0.03 0.90 ]
|XXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 313 0.02 0.92 ]
|XXXXXXXXXXXXXX 0.67 - 0.675 : [ 265 0.02 0.94 ]
|XXXXXXXXXX 0.675 - 0.68 : [ 189 0.01 0.96 ]
|XXXXXXXX 0.68 - 0.685 : [ 157 0.01 0.97 ]
|XXXXXXX 0.685 - 0.69 : [ 135 0.01 0.98 ]
|XXXX 0.69 - 0.695 : [ 81 0.01 0.98 ]
|XXX 0.695 - 0.7 : [ 53 0.00 0.99 ]
|XXX 0.7 - 0.705 : [ 52 0.00 0.99 ]
|XX 0.705 - 0.71 : [ 32 0.00 0.99 ]
|X 0.71 - 0.715 : [ 17 0.00 0.99 ]
|X 0.715 - 0.72 : [ 17 0.00 1.00 ]
|X 0.72 - 0.725 : [ 14 0.00 1.00 ]
|X 0.725 - 0.73 : [ 15 0.00 1.00 ]
|X 0.73 - 0.735 : [ 11 0.00 1.00 ]
| 0.735 - 0.74 : [ 4 0.00 1.00 ]
| 0.74 - 0.745 : [ 2 0.00 1.00 ]
| 0.745 - 0.75 : [ 2 0.00 1.00 ]
#...
| 0.76 - 0.765 : [ 1 0.00 1.00 ]
| 0.765 - 0.77 : [ 1 0.00 1.00 ]
#...
| 0.78 - 0.785 : [ 3 0.00 1.00 ]
| 0.785 - 0.79 : [ 2 0.00 1.00 ]
#...
| 0.805 - 0.81 : [ 1 0.00 1.00 ]
| 0.81 - 0.815 : [ 1 0.00 1.00 ]
| 0.815 - 0.82 : [ 1 0.00 1.00 ]
#...
| 0.84 - 0.845 : [ 2 0.00 1.00 ]
#...
| 0.92 - 0.925 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 3123. 16 reads; 5873 bp (untrimmed), 5591 (trimmed).
Contig 3124. 16 reads; 5153 bp (untrimmed), 4849 (trimmed).
Contig 3125. 16 reads; 5005 bp (untrimmed), 4819 (trimmed).
Contig 3126. 16 reads; 2146 bp (untrimmed), 2088 (trimmed).
Contig 3127. 16 reads; 6306 bp (untrimmed), 5940 (trimmed).
Contig 3128. 16 reads; 5170 bp (untrimmed), 5035 (trimmed).
Contig 3129. 16 reads; 3157 bp (untrimmed), 2968 (trimmed).
Contig 3130. 16 reads; 3177 bp (untrimmed), 2832 (trimmed).
Contig 3131. 16 reads; 5510 bp (untrimmed), 5235 (trimmed).
Contig 3132. 17 reads; 5057 bp (untrimmed), 5036 (trimmed).
Contig 3133. 17 reads; 6756 bp (untrimmed), 6370 (trimmed).
Contig 3134. 17 reads; 5436 bp (untrimmed), 5343 (trimmed).
Contig 3135. 17 reads; 4920 bp (untrimmed), 4818 (trimmed).
Contig 3136. 17 reads; 4496 bp (untrimmed), 4469 (trimmed).
Contig 3137. 18 reads; 4081 bp (untrimmed), 3948 (trimmed).
Contig 3138. 18 reads; 5476 bp (untrimmed), 5099 (trimmed).
Contig 3139. 19 reads; 5961 bp (untrimmed), 5851 (trimmed).
Contig 3140. 20 reads; 510 bp (untrimmed), 510 (trimmed).
Contig 3141. 21 reads; 5634 bp (untrimmed), 5555 (trimmed).
Contig 3142. 23 reads; 154 bp (untrimmed), 154 (trimmed).
Contig 3143. 24 reads; 5649 bp (untrimmed), 5408 (trimmed).
Contig 3144. 27 reads; 7710 bp (untrimmed), 7621 (trimmed).
Contig 3145. 29 reads; 3059 bp (untrimmed), 2957 (trimmed).
Contig 3146. 41 reads; 6056 bp (untrimmed), 5774 (trimmed).
Contig 3147. 56 reads; 705 bp (untrimmed), 666 (trimmed).
Contig 3148. 96 reads; 1831 bp (untrimmed), 1791 (trimmed).
Contig 3149. 139 reads; 894 bp (untrimmed), 807 (trimmed).
--------------------------------------------------------------
Totals 11960 reads; 5077703 bp (untrimmed), 4502123 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 5041616 bases Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 179
HQ Discrepant reads = 712
Chimeric reads = 63
Suspect alignments = 61
-------------------------------------------------------------------
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/microbe3/3634513/edit_dir.03Jun04.QC