See help.
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4600064
# phrap: 4412771
# db:
altered.
4506417 +/- 93646
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 40555
Number of reads with percent X's >= 20%: 1651 = 2.0%
Number of reads with percent X's >= 50%: 1328 = 1.6%
Number of reads with percent X's >= 80%: 284 = 0.3%
Total reads in project: 83179
Total bp X'd : 2883519
reads >= 20% >= 50% >= 80% screened
Nr with L09136 27268 269 142 12
Nr with pCC1Fos 2450 1 0 0
Nr with pMCL200_JGI_XZX+XZK 10837 1381 1186 272
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 75
Number of reads with percent X's >= 20%: 13 = 9.8%
Number of reads with percent X's >= 50%: 7 = 5.3%
Number of reads with percent X's >= 80%: 3 = 2.3%
Total reads in project: 133
Total bp X'd : 11569
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3 0 0 0
Nr with pCC1Fos 6 1 0 0
Nr with pMCL200_JGI_XZX+XZK 66 12 7 3
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 13215184
C = 26621217
G = 26587622
T = 13160217
N = 419710
X = 2883519
GC fraction = 0.64
Total = 82887469
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3436553_fasta.screen.contigs
-------------------------------------------------------------------
A 724099
C 1587225
G 1578375
T 718550
N 85
fraction GC = 0.69
total bases = 4608334
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 AAXI reads.list > grep.reads.list.AAXI
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAXI 4 500
-------------------------------------------------------------------
#Found 25960 total values totalling 116719440.0000. <4496.126348 +/- 19199.579530>
#Range: [ 774 - 905235 ]
#Most likely bin: [ 3000 - 3500 ] 9701 counts
#Median bin: [ 3500 - 4000 ] 7403 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 15 0.00 0.00 ]
| 1000 - 1500 : [ 63 0.00 0.00 ]
| 1500 - 2000 : [ 69 0.00 0.01 ]
|X 2000 - 2500 : [ 168 0.01 0.01 ]
|XXXXXXXXXXX 2500 - 3000 : [ 2689 0.10 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 9701 0.37 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 7403 0.29 0.77 ]
|XXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 4749 0.18 0.96 ]
|XXXX 4500 - 5000 : [ 1007 0.04 1.00 ]
#...
| 6500 - 7000 : [ 1 0.00 1.00 ]
| 7000 - 7500 : [ 1 0.00 1.00 ]
#...
| 14500 - 15000 : [ 1 0.00 1.00 ]
#...
| 20000 - 20500 : [ 1 0.00 1.00 ]
#...
| 21000 - 21500 : [ 1 0.00 1.00 ]
| 21500 - 22000 : [ 2 0.00 1.00 ]
#...
| 24000 - 24500 : [ 1 0.00 1.00 ]
#...
| 27000 - 27500 : [ 1 0.00 1.00 ]
#...
| 30000 - 30500 : [ 1 0.00 1.00 ]
#...
| 35000 - 35500 : [ 1 0.00 1.00 ]
#...
| 36000 - 36500 : [ 3 0.00 1.00 ]
| 36500 - 37000 : [ 2 0.00 1.00 ]
#...
| 37500 - 38000 : [ 1 0.00 1.00 ]
#...
| 50000 - 50500 : [ 1 0.00 1.00 ]
#...
| 54000 - 54500 : [ 1 0.00 1.00 ]
#...
| 57000 - 57500 : [ 1 0.00 1.00 ]
#...
| 60000 - 60500 : [ 1 0.00 1.00 ]
#...
| 68500 - 69000 : [ 1 0.00 1.00 ]
#...
| 97000 - 97500 : [ 1 0.00 1.00 ]
#...
| 102500 - 103000 : [ 1 0.00 1.00 ]
#...
| 106500 - 107000 : [ 1 0.00 1.00 ]
#...
| 108000 - 108500 : [ 1 0.00 1.00 ]
#...
| 120500 - 121000 : [ 1 0.00 1.00 ]
#...
| 121500 - 122000 : [ 1 0.00 1.00 ]
#...
| 123500 - 124000 : [ 1 0.00 1.00 ]
#...
| 134000 - 134500 : [ 2 0.00 1.00 ]
| 134500 - 135000 : [ 1 0.00 1.00 ]
#...
| 142500 - 143000 : [ 1 0.00 1.00 ]
#...
| 162500 - 163000 : [ 1 0.00 1.00 ]
#...
| 164500 - 165000 : [ 1 0.00 1.00 ]
#...
| 167000 - 167500 : [ 1 0.00 1.00 ]
#...
| 175500 - 176000 : [ 1 0.00 1.00 ]
#...
| 178000 - 178500 : [ 1 0.00 1.00 ]
#...
| 202500 - 203000 : [ 1 0.00 1.00 ]
#...
| 209500 - 210000 : [ 1 0.00 1.00 ]
#...
| 211000 - 211500 : [ 1 0.00 1.00 ]
#...
| 214500 - 215000 : [ 1 0.00 1.00 ]
#...
| 216000 - 216500 : [ 1 0.00 1.00 ]
#...
| 224000 - 224500 : [ 1 0.00 1.00 ]
#...
| 228000 - 228500 : [ 1 0.00 1.00 ]
#...
| 230500 - 231000 : [ 1 0.00 1.00 ]
#...
| 241500 - 242000 : [ 1 0.00 1.00 ]
#...
| 245500 - 246000 : [ 1 0.00 1.00 ]
#...
| 253500 - 254000 : [ 1 0.00 1.00 ]
#...
| 255000 - 255500 : [ 1 0.00 1.00 ]
#...
| 261500 - 262000 : [ 1 0.00 1.00 ]
#...
| 299000 - 299500 : [ 1 0.00 1.00 ]
#...
| 308500 - 309000 : [ 6 0.00 1.00 ]
| 309000 - 309500 : [ 4 0.00 1.00 ]
| 309500 - 310000 : [ 5 0.00 1.00 ]
| 310000 - 310500 : [ 2 0.00 1.00 ]
#...
| 317000 - 317500 : [ 1 0.00 1.00 ]
#...
| 322000 - 322500 : [ 1 0.00 1.00 ]
#...
| 327000 - 327500 : [ 1 0.00 1.00 ]
#...
| 348500 - 349000 : [ 1 0.00 1.00 ]
#...
| 356000 - 356500 : [ 1 0.00 1.00 ]
#...
| 368000 - 368500 : [ 1 0.00 1.00 ]
#...
| 373500 - 374000 : [ 1 0.00 1.00 ]
#...
| 381000 - 381500 : [ 1 0.00 1.00 ]
#...
| 386000 - 386500 : [ 1 0.00 1.00 ]
#...
| 388500 - 389000 : [ 1 0.00 1.00 ]
#...
| 399000 - 399500 : [ 1 0.00 1.00 ]
#...
| 400500 - 401000 : [ 1 0.00 1.00 ]
#...
| 403500 - 404000 : [ 1 0.00 1.00 ]
#...
| 413500 - 414000 : [ 1 0.00 1.00 ]
#...
| 434500 - 435000 : [ 1 0.00 1.00 ]
#...
| 447500 - 448000 : [ 1 0.00 1.00 ]
#...
| 448500 - 449000 : [ 1 0.00 1.00 ]
#...
| 512000 - 512500 : [ 1 0.00 1.00 ]
#...
| 522500 - 523000 : [ 1 0.00 1.00 ]
#...
| 540500 - 541000 : [ 1 0.00 1.00 ]
#...
| 587500 - 588000 : [ 1 0.00 1.00 ]
#...
| 606500 - 607000 : [ 1 0.00 1.00 ]
#...
| 653500 - 654000 : [ 1 0.00 1.00 ]
#...
| 689000 - 689500 : [ 1 0.00 1.00 ]
#...
| 706000 - 706500 : [ 1 0.00 1.00 ]
#...
| 849000 - 849500 : [ 1 0.00 1.00 ]
#...
| 905000 - 905500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAXJ reads.list > grep.reads.list.AAXJ
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAXJ 4 500
-------------------------------------------------------------------
#Found 1980 total values totalling 18191563.0000. <9187.658081 +/- 12254.132977>
#Range: [ 738 - 316402 ]
#Most likely bin: [ 8500 - 9000 ] 278 counts
#Median bin: [ 8500 - 9000 ] 278 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 500 - 1000 : [ 8 0.00 0.00 ]
|XXX 1000 - 1500 : [ 23 0.01 0.02 ]
|XXX 1500 - 2000 : [ 24 0.01 0.03 ]
|XXX 2000 - 2500 : [ 19 0.01 0.04 ]
|XX 2500 - 3000 : [ 16 0.01 0.05 ]
|XXX 3000 - 3500 : [ 23 0.01 0.06 ]
|XXX 3500 - 4000 : [ 21 0.01 0.07 ]
|XXX 4000 - 4500 : [ 21 0.01 0.08 ]
|XX 4500 - 5000 : [ 16 0.01 0.09 ]
|XXX 5000 - 5500 : [ 21 0.01 0.10 ]
|XXX 5500 - 6000 : [ 18 0.01 0.11 ]
|XXXX 6000 - 6500 : [ 31 0.02 0.12 ]
|XXXXX 6500 - 7000 : [ 38 0.02 0.14 ]
|XXXXXXXXXXXX 7000 - 7500 : [ 81 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 166 0.08 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 231 0.12 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 278 0.14 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 213 0.11 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 203 0.10 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 174 0.09 0.82 ]
|XXXXXXXXXXXXXXXXXXXXX 10500 - 11000 : [ 149 0.08 0.90 ]
|XXXXXXXXXXXX 11000 - 11500 : [ 80 0.04 0.94 ]
|XXXXX 11500 - 12000 : [ 36 0.02 0.95 ]
|XXXX 12000 - 12500 : [ 27 0.01 0.97 ]
|XX 12500 - 13000 : [ 13 0.01 0.97 ]
|XX 13000 - 13500 : [ 13 0.01 0.98 ]
|XX 13500 - 14000 : [ 12 0.01 0.99 ]
|XX 14000 - 14500 : [ 12 0.01 0.99 ]
| 14500 - 15000 : [ 3 0.00 0.99 ]
#...
| 15500 - 16000 : [ 1 0.00 1.00 ]
#...
| 16500 - 17000 : [ 1 0.00 1.00 ]
| 17000 - 17500 : [ 1 0.00 1.00 ]
#...
| 18000 - 18500 : [ 2 0.00 1.00 ]
#...
| 21500 - 22000 : [ 1 0.00 1.00 ]
#...
| 74500 - 75000 : [ 1 0.00 1.00 ]
#...
| 314000 - 314500 : [ 1 0.00 1.00 ]
#...
| 315000 - 315500 : [ 1 0.00 1.00 ]
#...
| 316000 - 316500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAXK reads.list > grep.reads.list.AAXK
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AAXK 4 500
-------------------------------------------------------------------
#Found 1747 total values totalling 61690209.0000. <35312.082999 +/- 13778.788474>
#Range: [ 1389 - 347596 ]
#Most likely bin: [ 35500 - 36000 ] 153 counts
#Median bin: [ 35000 - 35500 ] 152 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 1 0.00 0.00 ]
|X 1500 - 2000 : [ 3 0.00 0.00 ]
|X 2000 - 2500 : [ 3 0.00 0.00 ]
| 2500 - 3000 : [ 1 0.00 0.00 ]
|X 3000 - 3500 : [ 4 0.00 0.01 ]
|XX 3500 - 4000 : [ 6 0.00 0.01 ]
|X 4000 - 4500 : [ 2 0.00 0.01 ]
|X 4500 - 5000 : [ 4 0.00 0.01 ]
| 5000 - 5500 : [ 1 0.00 0.01 ]
| 5500 - 6000 : [ 1 0.00 0.01 ]
| 6000 - 6500 : [ 1 0.00 0.02 ]
| 6500 - 7000 : [ 1 0.00 0.02 ]
#...
| 8000 - 8500 : [ 1 0.00 0.02 ]
| 8500 - 9000 : [ 1 0.00 0.02 ]
#...
|X 10500 - 11000 : [ 2 0.00 0.02 ]
#...
|X 26500 - 27000 : [ 3 0.00 0.02 ]
| 27000 - 27500 : [ 1 0.00 0.02 ]
| 27500 - 28000 : [ 1 0.00 0.02 ]
|X 28000 - 28500 : [ 3 0.00 0.02 ]
|X 28500 - 29000 : [ 5 0.00 0.03 ]
|XXX 29000 - 29500 : [ 11 0.01 0.03 ]
|XXX 29500 - 30000 : [ 10 0.01 0.04 ]
|XXXX 30000 - 30500 : [ 14 0.01 0.05 ]
|XXXX 30500 - 31000 : [ 15 0.01 0.05 ]
|XXXXXXX 31000 - 31500 : [ 26 0.01 0.07 ]
|XXXXXXXXXXXXX 31500 - 32000 : [ 49 0.03 0.10 ]
|XXXXXXXXXXXXXXXX 32000 - 32500 : [ 63 0.04 0.13 ]
|XXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 76 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 102 0.06 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 120 0.07 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 148 0.08 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 146 0.08 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 152 0.09 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 153 0.09 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 130 0.07 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 97 0.06 0.78 ]
|XXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 79 0.05 0.82 ]
|XXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 69 0.04 0.86 ]
|XXXXXXXXXXXXXX 38000 - 38500 : [ 55 0.03 0.89 ]
|XXXXXXXXXXXX 38500 - 39000 : [ 44 0.03 0.92 ]
|XXXXXXXXX 39000 - 39500 : [ 35 0.02 0.94 ]
|XXXXXXX 39500 - 40000 : [ 27 0.02 0.95 ]
|XXXX 40000 - 40500 : [ 17 0.01 0.96 ]
|XXXX 40500 - 41000 : [ 17 0.01 0.97 ]
|XXXXX 41000 - 41500 : [ 21 0.01 0.99 ]
|XX 41500 - 42000 : [ 8 0.00 0.99 ]
|XX 42000 - 42500 : [ 6 0.00 0.99 ]
|X 42500 - 43000 : [ 3 0.00 0.99 ]
|X 43000 - 43500 : [ 3 0.00 1.00 ]
#...
|X 44500 - 45000 : [ 2 0.00 1.00 ]
#...
| 90500 - 91000 : [ 1 0.00 1.00 ]
#...
| 340500 - 341000 : [ 1 0.00 1.00 ]
#...
| 344500 - 345000 : [ 1 0.00 1.00 ]
#...
| 347500 - 348000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AFHO reads.list > grep.reads.list.AFHO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AFHO 4 500
-------------------------------------------------------------------
#Found 1708 total values totalling 16115556.0000. <9435.337237 +/- 8585.410918>
#Range: [ 100 - 315187 ]
#Most likely bin: [ 9500 - 10000 ] 266 counts
#Median bin: [ 9500 - 10000 ] 266 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXX 0 - 500 : [ 79 0.05 0.05 ]
|X 500 - 1000 : [ 8 0.00 0.05 ]
|XXX 1000 - 1500 : [ 17 0.01 0.06 ]
|XXX 1500 - 2000 : [ 22 0.01 0.07 ]
|XX 2000 - 2500 : [ 13 0.01 0.08 ]
|XXX 2500 - 3000 : [ 18 0.01 0.09 ]
|XX 3000 - 3500 : [ 14 0.01 0.10 ]
|XXX 3500 - 4000 : [ 19 0.01 0.11 ]
|XX 4000 - 4500 : [ 13 0.01 0.12 ]
|XXX 4500 - 5000 : [ 19 0.01 0.13 ]
|XXX 5000 - 5500 : [ 21 0.01 0.14 ]
|XX 5500 - 6000 : [ 11 0.01 0.15 ]
|XX 6000 - 6500 : [ 13 0.01 0.16 ]
|XX 6500 - 7000 : [ 13 0.01 0.16 ]
|XX 7000 - 7500 : [ 15 0.01 0.17 ]
|XXX 7500 - 8000 : [ 17 0.01 0.18 ]
|XXXXX 8000 - 8500 : [ 33 0.02 0.20 ]
|XXXXXXXXXXX 8500 - 9000 : [ 71 0.04 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 186 0.11 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 266 0.16 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 254 0.15 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 10500 - 11000 : [ 174 0.10 0.76 ]
|XXXXXXXXXXXXXXXXXXX 11000 - 11500 : [ 127 0.07 0.83 ]
|XXXXXXXXXXXXXXX 11500 - 12000 : [ 98 0.06 0.89 ]
|XXXXXXXXXXX 12000 - 12500 : [ 74 0.04 0.93 ]
|XXXXXX 12500 - 13000 : [ 37 0.02 0.96 ]
|XX 13000 - 13500 : [ 15 0.01 0.96 ]
|XXXX 13500 - 14000 : [ 28 0.02 0.98 ]
|XX 14000 - 14500 : [ 15 0.01 0.99 ]
|X 14500 - 15000 : [ 9 0.01 0.99 ]
|X 15000 - 15500 : [ 6 0.00 1.00 ]
| 15500 - 16000 : [ 1 0.00 1.00 ]
#...
| 128500 - 129000 : [ 1 0.00 1.00 ]
#...
| 315000 - 315500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACGW reads.list > grep.reads.list.ACGW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACGW 4 500
-------------------------------------------------------------------
#Found 252 total values totalling 284964.0000. <1130.809524 +/- 565.148916>
#Range: [ 789 - 4909 ]
#Most likely bin: [ 1000 - 1500 ] 127 counts
#Median bin: [ 1000 - 1500 ] 127 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 500 - 1000 : [ 110 0.44 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 1500 : [ 127 0.50 0.94 ]
|X 1500 - 2000 : [ 2 0.01 0.95 ]
|X 2000 - 2500 : [ 3 0.01 0.96 ]
|X 2500 - 3000 : [ 2 0.01 0.97 ]
|X 3000 - 3500 : [ 3 0.01 0.98 ]
| 3500 - 4000 : [ 1 0.00 0.98 ]
| 4000 - 4500 : [ 1 0.00 0.99 ]
|X 4500 - 5000 : [ 3 0.01 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACGX reads.list > grep.reads.list.ACGX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.ACGX 4 500
-------------------------------------------------------------------
#Found 284 total values totalling 494239.0000. <1740.278169 +/- 661.394257>
#Range: [ 1149 - 4811 ]
#Most likely bin: [ 1500 - 2000 ] 143 counts
#Median bin: [ 1500 - 2000 ] 143 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 1500 : [ 106 0.37 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1500 - 2000 : [ 143 0.50 0.88 ]
| 2000 - 2500 : [ 1 0.00 0.88 ]
|XXXXX 2500 - 3000 : [ 18 0.06 0.94 ]
|X 3000 - 3500 : [ 4 0.01 0.96 ]
|X 3500 - 4000 : [ 2 0.01 0.96 ]
|XX 4000 - 4500 : [ 6 0.02 0.99 ]
|X 4500 - 5000 : [ 4 0.01 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# ACGW 1017 +- 667 (n=145)
# AAXI 3465 +- 865 (n=13535)
# AAXK 34746 +- 4709 (n=856)
# ACGX 1660 +- 774 (n=156)
# AFHO 7469 +- 4394 (n=1091)
# AAXJ 7955 +- 3065 (n=1070)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3436553_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
AAXI 67968 -1 -1 98 685 65865 99 652 100 661
AAXJ 7680 -1 -1 97 586 5120 98 555 100 621
AAXK 5376 -1 -1 97 638 5120 99 655 100 665
ACGW 768 -1 -1 89 570 567 100 620 100 644
ACGX 768 -1 -1 93 688 603 100 660 100 679
AFHO 9600 -1 -1 94 649 5904 97 499 100 632
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AAXI 31661 99 651 100 665 34204 99 653 100 659
AAXJ 2500 98 547 100 623 2620 99 562 100 620
AAXK 2546 99 663 100 660 2574 99 647 100 670
ACGW 285 100 617 100 646 282 100 624 100 643
ACGX 302 100 650 100 676 301 99 671 100 682
AFHO 2336 98 480 100 617 3568 97 512 100 642
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3436553_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones LIBRARY @
] 83179 38802 89.00 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 3436553_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 83179 total values totalling 52459225.0000. <630.678717 +/- 170.340569>
#Range: [ 15 - 950 ]
#Most likely bin: [ 650 - 700 ] 14783 counts
#Median bin: [ 650 - 700 ] 14783 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 153 0.00 0.00 ]
|XX 50 - 100 : [ 584 0.01 0.01 ]
|XXXX 100 - 150 : [ 1360 0.02 0.03 ]
|XXX 150 - 200 : [ 1131 0.01 0.04 ]
|XXX 200 - 250 : [ 1282 0.02 0.05 ]
|XXXX 250 - 300 : [ 1307 0.02 0.07 ]
|XXXX 300 - 350 : [ 1494 0.02 0.09 ]
|XXXXX 350 - 400 : [ 1732 0.02 0.11 ]
|XXXXXX 400 - 450 : [ 2203 0.03 0.14 ]
|XXXXXXXX 450 - 500 : [ 2830 0.03 0.17 ]
|XXXXXXXXXXX 500 - 550 : [ 3895 0.05 0.22 ]
|XXXXXXXXXXXXXXXXX 550 - 600 : [ 6342 0.08 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 10899 0.13 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 14783 0.18 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 14011 0.17 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 10469 0.13 0.90 ]
|XXXXXXXXXXXXXXXXXX 800 - 850 : [ 6773 0.08 0.98 ]
|XXXXX 850 - 900 : [ 1828 0.02 1.00 ]
| 900 - 950 : [ 102 0.00 1.00 ]
| 950 - 1000 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAXI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAXI 3436553_fasta.screen.trimQ15.SaF > reads.trim15.AAXI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAXI.rl 2 50
-------------------------------------------------------------------
#Found 65865 total values totalling 42714847.0000. <648.521172 +/- 159.833484>
#Range: [ 15 - 950 ]
#Most likely bin: [ 700 - 750 ] 11482 counts
#Median bin: [ 650 - 700 ] 11049 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 72 0.00 0.00 ]
|X 50 - 100 : [ 362 0.01 0.01 ]
|XX 100 - 150 : [ 554 0.01 0.02 ]
|XX 150 - 200 : [ 681 0.01 0.03 ]
|XXX 200 - 250 : [ 761 0.01 0.04 ]
|XXX 250 - 300 : [ 955 0.01 0.05 ]
|XXXX 300 - 350 : [ 1085 0.02 0.07 ]
|XXXXX 350 - 400 : [ 1385 0.02 0.09 ]
|XXXXXX 400 - 450 : [ 1705 0.03 0.11 ]
|XXXXXXXX 450 - 500 : [ 2213 0.03 0.15 ]
|XXXXXXXXXX 500 - 550 : [ 2935 0.04 0.19 ]
|XXXXXXXXXXXXXXXX 550 - 600 : [ 4720 0.07 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 7902 0.12 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 11049 0.17 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 11482 0.17 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 9609 0.15 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6507 0.10 0.97 ]
|XXXXXX 850 - 900 : [ 1787 0.03 1.00 ]
| 900 - 950 : [ 100 0.00 1.00 ]
| 950 - 1000 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAXJ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAXJ 3436553_fasta.screen.trimQ15.SaF > reads.trim15.AAXJ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAXJ.rl 2 50
-------------------------------------------------------------------
#Found 5120 total values totalling 2798630.0000. <546.607422 +/- 155.753277>
#Range: [ 28 - 766 ]
#Most likely bin: [ 600 - 650 ] 1313 counts
#Median bin: [ 600 - 650 ] 1313 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 24 0.00 0.00 ]
|XX 50 - 100 : [ 60 0.01 0.02 ]
|XXXX 100 - 150 : [ 137 0.03 0.04 ]
|XXX 150 - 200 : [ 98 0.02 0.06 ]
|XXX 200 - 250 : [ 111 0.02 0.08 ]
|XXX 250 - 300 : [ 109 0.02 0.11 ]
|XXXXX 300 - 350 : [ 148 0.03 0.13 ]
|XXXX 350 - 400 : [ 129 0.03 0.16 ]
|XXXXX 400 - 450 : [ 168 0.03 0.19 ]
|XXXXXXXX 450 - 500 : [ 258 0.05 0.24 ]
|XXXXXXXXXXXXX 500 - 550 : [ 428 0.08 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 798 0.16 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1313 0.26 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1171 0.23 0.97 ]
|XXXXX 700 - 750 : [ 165 0.03 1.00 ]
| 750 - 800 : [ 3 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AAXK
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AAXK 3436553_fasta.screen.trimQ15.SaF > reads.trim15.AAXK.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AAXK.rl 2 50
-------------------------------------------------------------------
#Found 5120 total values totalling 3314348.0000. <647.333594 +/- 154.620488>
#Range: [ 18 - 867 ]
#Most likely bin: [ 700 - 750 ] 1530 counts
#Median bin: [ 650 - 700 ] 1256 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 24 0.00 0.00 ]
|X 50 - 100 : [ 41 0.01 0.01 ]
|X 100 - 150 : [ 48 0.01 0.02 ]
|X 150 - 200 : [ 57 0.01 0.03 ]
|XX 200 - 250 : [ 80 0.02 0.05 ]
|XX 250 - 300 : [ 86 0.02 0.07 ]
|XX 300 - 350 : [ 81 0.02 0.08 ]
|XX 350 - 400 : [ 62 0.01 0.09 ]
|XX 400 - 450 : [ 63 0.01 0.11 ]
|XXX 450 - 500 : [ 98 0.02 0.12 ]
|XXX 500 - 550 : [ 116 0.02 0.15 ]
|XXXXX 550 - 600 : [ 205 0.04 0.19 ]
|XXXXXXXXXXXXXX 600 - 650 : [ 530 0.10 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1256 0.25 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1530 0.30 0.84 ]
|XXXXXXXXXXXXXXXXX 750 - 800 : [ 633 0.12 0.96 ]
|XXXXX 800 - 850 : [ 193 0.04 1.00 ]
| 850 - 900 : [ 17 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ASNX
trimt JAZZ trim 15 readlength histogram for AFHN
trimt JAZZ trim 15 readlength histogram for AFHO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AFHO 3436553_fasta.screen.trimQ15.SaF > reads.trim15.AFHO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AFHO.rl 2 50
-------------------------------------------------------------------
#Found 5904 total values totalling 2883243.0000. <488.354167 +/- 220.385692>
#Range: [ 17 - 912 ]
#Most likely bin: [ 600 - 650 ] 987 counts
#Median bin: [ 550 - 600 ] 560 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 33 0.01 0.01 ]
|XXXXX 50 - 100 : [ 118 0.02 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 100 - 150 : [ 609 0.10 0.13 ]
|XXXXXXXXXXX 150 - 200 : [ 283 0.05 0.18 ]
|XXXXXXXXXXXXX 200 - 250 : [ 316 0.05 0.23 ]
|XXXXXX 250 - 300 : [ 143 0.02 0.25 ]
|XXXXXXX 300 - 350 : [ 171 0.03 0.28 ]
|XXXXXX 350 - 400 : [ 143 0.02 0.31 ]
|XXXXXXXXXX 400 - 450 : [ 245 0.04 0.35 ]
|XXXXXXXXX 450 - 500 : [ 232 0.04 0.39 ]
|XXXXXXXXXXXXXXX 500 - 550 : [ 382 0.06 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 560 0.09 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 987 0.17 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 909 0.15 0.87 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 516 0.09 0.96 ]
|XXXXXXX 750 - 800 : [ 165 0.03 0.98 ]
|XXX 800 - 850 : [ 66 0.01 1.00 ]
|X 850 - 900 : [ 24 0.00 1.00 ]
| 900 - 950 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AGYN
trimt JAZZ trim 15 readlength histogram for ATGZ
trimt JAZZ trim 15 readlength histogram for ACGW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACGW 3436553_fasta.screen.trimQ15.SaF > reads.trim15.ACGW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACGW.rl 2 50
-------------------------------------------------------------------
#Found 567 total values totalling 351671.0000. <620.231041 +/- 130.199865>
#Range: [ 110 - 760 ]
#Most likely bin: [ 650 - 700 ] 237 counts
#Median bin: [ 650 - 700 ] 237 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 100 - 150 : [ 6 0.01 0.01 ]
|X 150 - 200 : [ 8 0.01 0.02 ]
|XX 200 - 250 : [ 10 0.02 0.04 ]
|X 250 - 300 : [ 8 0.01 0.06 ]
|X 300 - 350 : [ 6 0.01 0.07 ]
|X 350 - 400 : [ 8 0.01 0.08 ]
|XX 400 - 450 : [ 12 0.02 0.10 ]
|XXXX 450 - 500 : [ 22 0.04 0.14 ]
|XXX 500 - 550 : [ 19 0.03 0.17 ]
|XXXX 550 - 600 : [ 24 0.04 0.22 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 91 0.16 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 237 0.42 0.80 ]
|XXXXXXXXXXXXXXXXXXX 700 - 750 : [ 115 0.20 1.00 ]
| 750 - 800 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ACGX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep ACGX 3436553_fasta.screen.trimQ15.SaF > reads.trim15.ACGX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.ACGX.rl 2 50
-------------------------------------------------------------------
#Found 603 total values totalling 396486.0000. <657.522388 +/- 123.727127>
#Range: [ 78 - 828 ]
#Most likely bin: [ 700 - 750 ] 203 counts
#Median bin: [ 650 - 700 ] 161 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 50 - 100 : [ 3 0.00 0.00 ]
|X 100 - 150 : [ 6 0.01 0.01 ]
|X 150 - 200 : [ 4 0.01 0.02 ]
|X 200 - 250 : [ 4 0.01 0.03 ]
|X 250 - 300 : [ 6 0.01 0.04 ]
|X 300 - 350 : [ 3 0.00 0.04 ]
|X 350 - 400 : [ 5 0.01 0.05 ]
|XX 400 - 450 : [ 10 0.02 0.07 ]
|X 450 - 500 : [ 7 0.01 0.08 ]
|XXX 500 - 550 : [ 15 0.02 0.10 ]
|XXXXXXX 550 - 600 : [ 35 0.06 0.16 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 76 0.13 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 161 0.27 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 203 0.34 0.89 ]
|XXXXXXXXXXX 750 - 800 : [ 58 0.10 0.99 ]
|X 800 - 850 : [ 7 0.01 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3436553
-------------------------------------------------------------------
AAA.000001.000100 pMCL200.fa LRS.fasta
AAXI.000001.000100 pUC18.fa LRS.fasta
AAXI.000101.000200 pUC18.fa LRS.fasta
AAXI.000201.000300 pUC18.fa LRS.fasta
AAXI.000301.000400 pUC18.fa LRS.fasta
AAXJ.000001.000100 pMCL200.fa LRS.fasta
AAXK.000001.000100 pCC1Fos.fa LRS.fasta
ACGW.000001.000100 pUC18.fa LRS.fasta
ACGX.000001.000100 pUC18.fa LRS.fasta
AFHO.000001.000100 pMCL200.fa LRS.fasta
AAA.000001.000100 pMCL200.fa LRS.fasta
AAXI.000001.000100 pUC18.fa LRS.fasta
AAXI.000101.000200 pUC18.fa LRS.fasta
AAXI.000201.000300 pUC18.fa LRS.fasta
AAXI.000301.000400 pUC18.fa LRS.fasta
AAXJ.000001.000100 pMCL200.fa LRS.fasta
AAXK.000001.000100 pCC1Fos.fa LRS.fasta
ACGW.000001.000100 pUC18.fa LRS.fasta
ACGX.000001.000100 pUC18.fa LRS.fasta
AFHO.000001.000100 pMCL200.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3436553_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3436553_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 83005 total values totalling 56609.7623. <0.682004 +/- 0.047586>
#Range: [ 0.1212 - 0.9318 ]
#Most likely bin: [ 0.69 - 0.695 ] 4228 counts
#Median bin: [ 0.685 - 0.69 ] 4162 counts
| 0.12 - 0.125 : [ 1 0.00 0.00 ]
#...
| 0.13 - 0.135 : [ 1 0.00 0.00 ]
#...
| 0.16 - 0.165 : [ 1 0.00 0.00 ]
#...
| 0.175 - 0.18 : [ 2 0.00 0.00 ]
| 0.18 - 0.185 : [ 1 0.00 0.00 ]
| 0.185 - 0.19 : [ 1 0.00 0.00 ]
| 0.19 - 0.195 : [ 1 0.00 0.00 ]
#...
| 0.215 - 0.22 : [ 1 0.00 0.00 ]
#...
| 0.23 - 0.235 : [ 1 0.00 0.00 ]
#...
| 0.245 - 0.25 : [ 1 0.00 0.00 ]
| 0.25 - 0.255 : [ 1 0.00 0.00 ]
| 0.255 - 0.26 : [ 4 0.00 0.00 ]
| 0.26 - 0.265 : [ 1 0.00 0.00 ]
| 0.265 - 0.27 : [ 7 0.00 0.00 ]
| 0.27 - 0.275 : [ 1 0.00 0.00 ]
#...
| 0.285 - 0.29 : [ 3 0.00 0.00 ]
| 0.29 - 0.295 : [ 2 0.00 0.00 ]
| 0.295 - 0.3 : [ 1 0.00 0.00 ]
| 0.3 - 0.305 : [ 1 0.00 0.00 ]
#...
| 0.31 - 0.315 : [ 2 0.00 0.00 ]
| 0.315 - 0.32 : [ 2 0.00 0.00 ]
| 0.32 - 0.325 : [ 3 0.00 0.00 ]
#...
| 0.33 - 0.335 : [ 1 0.00 0.00 ]
#...
| 0.34 - 0.345 : [ 5 0.00 0.00 ]
| 0.345 - 0.35 : [ 6 0.00 0.00 ]
| 0.35 - 0.355 : [ 6 0.00 0.00 ]
| 0.355 - 0.36 : [ 3 0.00 0.00 ]
| 0.36 - 0.365 : [ 5 0.00 0.00 ]
| 0.365 - 0.37 : [ 7 0.00 0.00 ]
| 0.37 - 0.375 : [ 9 0.00 0.00 ]
| 0.375 - 0.38 : [ 5 0.00 0.00 ]
| 0.38 - 0.385 : [ 40 0.00 0.00 ]
| 0.385 - 0.39 : [ 4 0.00 0.00 ]
|X 0.39 - 0.395 : [ 118 0.00 0.00 ]
| 0.395 - 0.4 : [ 4 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 : [ 4 0.00 0.00 ]
| 0.415 - 0.42 : [ 4 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 : [ 4 0.00 0.00 ]
| 0.435 - 0.44 : [ 9 0.00 0.00 ]
| 0.44 - 0.445 : [ 11 0.00 0.00 ]
| 0.445 - 0.45 : [ 4 0.00 0.00 ]
| 0.45 - 0.455 : [ 13 0.00 0.00 ]
| 0.455 - 0.46 : [ 5 0.00 0.00 ]
| 0.46 - 0.465 : [ 4 0.00 0.00 ]
| 0.465 - 0.47 : [ 6 0.00 0.00 ]
| 0.47 - 0.475 : [ 2 0.00 0.00 ]
| 0.475 - 0.48 : [ 19 0.00 0.00 ]
| 0.48 - 0.485 : [ 23 0.00 0.00 ]
| 0.485 - 0.49 : [ 18 0.00 0.00 ]
| 0.49 - 0.495 : [ 19 0.00 0.01 ]
| 0.495 - 0.5 : [ 12 0.00 0.01 ]
|X 0.5 - 0.505 : [ 62 0.00 0.01 ]
| 0.505 - 0.51 : [ 27 0.00 0.01 ]
| 0.51 - 0.515 : [ 31 0.00 0.01 ]
| 0.515 - 0.52 : [ 41 0.00 0.01 ]
|X 0.52 - 0.525 : [ 56 0.00 0.01 ]
|X 0.525 - 0.53 : [ 138 0.00 0.01 ]
|X 0.53 - 0.535 : [ 76 0.00 0.01 ]
|X 0.535 - 0.54 : [ 74 0.00 0.01 ]
|X 0.54 - 0.545 : [ 95 0.00 0.01 ]
|X 0.545 - 0.55 : [ 112 0.00 0.01 ]
|X 0.55 - 0.555 : [ 126 0.00 0.02 ]
|X 0.555 - 0.56 : [ 139 0.00 0.02 ]
|XX 0.56 - 0.565 : [ 203 0.00 0.02 ]
|XX 0.565 - 0.57 : [ 192 0.00 0.02 ]
|XX 0.57 - 0.575 : [ 228 0.00 0.02 ]
|XX 0.575 - 0.58 : [ 205 0.00 0.03 ]
|XX 0.58 - 0.585 : [ 250 0.00 0.03 ]
|XXX 0.585 - 0.59 : [ 347 0.00 0.03 ]
|XXX 0.59 - 0.595 : [ 348 0.00 0.04 ]
|XXXX 0.595 - 0.6 : [ 407 0.00 0.04 ]
|XXXXX 0.6 - 0.605 : [ 527 0.01 0.05 ]
|XXXXX 0.605 - 0.61 : [ 545 0.01 0.06 ]
|XXXXXXXXX 0.61 - 0.615 : [ 928 0.01 0.07 ]
|XXXXXXXXX 0.615 - 0.62 : [ 927 0.01 0.08 ]
|XXXXXXXXXX 0.62 - 0.625 : [ 1015 0.01 0.09 ]
|XXXXXXXXXXXX 0.625 - 0.63 : [ 1222 0.01 0.11 ]
|XXXXXXXXXXXXX 0.63 - 0.635 : [ 1402 0.02 0.12 ]
|XXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 1691 0.02 0.14 ]
|XXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 1965 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 2277 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 2508 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 3023 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 3195 0.04 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 3523 0.04 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 3752 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 3936 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 4063 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 4162 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 4228 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 4122 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 4122 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 3930 0.05 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 3690 0.04 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 3341 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 2964 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.725 - 0.73 : [ 2566 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXXX 0.73 - 0.735 : [ 2233 0.03 0.91 ]
|XXXXXXXXXXXXXXXXXX 0.735 - 0.74 : [ 1862 0.02 0.93 ]
|XXXXXXXXXXXXX 0.74 - 0.745 : [ 1393 0.02 0.95 ]
|XXXXXXXXX 0.745 - 0.75 : [ 994 0.01 0.96 ]
|XXXXXXXX 0.75 - 0.755 : [ 892 0.01 0.97 ]
|XXXXXX 0.755 - 0.76 : [ 677 0.01 0.98 ]
|XXXX 0.76 - 0.765 : [ 466 0.01 0.98 ]
|XXX 0.765 - 0.77 : [ 341 0.00 0.99 ]
|XX 0.77 - 0.775 : [ 241 0.00 0.99 ]
|XX 0.775 - 0.78 : [ 183 0.00 0.99 ]
|X 0.78 - 0.785 : [ 113 0.00 1.00 ]
|X 0.785 - 0.79 : [ 84 0.00 1.00 ]
|X 0.79 - 0.795 : [ 74 0.00 1.00 ]
| 0.795 - 0.8 : [ 33 0.00 1.00 ]
|X 0.8 - 0.805 : [ 60 0.00 1.00 ]
| 0.805 - 0.81 : [ 33 0.00 1.00 ]
| 0.81 - 0.815 : [ 25 0.00 1.00 ]
| 0.815 - 0.82 : [ 22 0.00 1.00 ]
| 0.82 - 0.825 : [ 12 0.00 1.00 ]
| 0.825 - 0.83 : [ 7 0.00 1.00 ]
| 0.83 - 0.835 : [ 6 0.00 1.00 ]
| 0.835 - 0.84 : [ 11 0.00 1.00 ]
| 0.84 - 0.845 : [ 6 0.00 1.00 ]
| 0.845 - 0.85 : [ 2 0.00 1.00 ]
| 0.85 - 0.855 : [ 5 0.00 1.00 ]
| 0.855 - 0.86 : [ 3 0.00 1.00 ]
| 0.86 - 0.865 : [ 4 0.00 1.00 ]
| 0.865 - 0.87 : [ 2 0.00 1.00 ]
| 0.87 - 0.875 : [ 3 0.00 1.00 ]
#...
| 0.88 - 0.885 : [ 2 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 : [ 1 0.00 1.00 ]
#...
| 0.93 - 0.935 : [ 2 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 99. 114 reads; 639 bp (untrimmed), 639 (trimmed).
Contig 100. 129 reads; 100 bp (untrimmed), 100 (trimmed).
Contig 101. 186 reads; 10949 bp (untrimmed), 10232 (trimmed).
Contig 102. 209 reads; 19426 bp (untrimmed), 19396 (trimmed).
Contig 103. 212 reads; 101 bp (untrimmed), 101 (trimmed).
Contig 104. 361 reads; 20909 bp (untrimmed), 20906 (trimmed).
Contig 105. 411 reads; 22013 bp (untrimmed), 21998 (trimmed).
Contig 106. 424 reads; 21260 bp (untrimmed), 20919 (trimmed).
Contig 107. 640 reads; 42889 bp (untrimmed), 42889 (trimmed).
Contig 108. 1276 reads; 74594 bp (untrimmed), 74023 (trimmed).
Contig 109. 1344 reads; 67606 bp (untrimmed), 67460 (trimmed).
Contig 110. 1516 reads; 83852 bp (untrimmed), 83385 (trimmed).
Contig 111. 1792 reads; 106334 bp (untrimmed), 105844 (trimmed).
Contig 112. 2205 reads; 129849 bp (untrimmed), 129788 (trimmed).
Contig 113. 2385 reads; 139194 bp (untrimmed), 138760 (trimmed).
Contig 114. 2548 reads; 146853 bp (untrimmed), 146535 (trimmed).
Contig 115. 2554 reads; 148165 bp (untrimmed), 148165 (trimmed).
Contig 116. 2814 reads; 169305 bp (untrimmed), 169282 (trimmed).
Contig 117. 3058 reads; 177490 bp (untrimmed), 177012 (trimmed).
Contig 118. 3166 reads; 159375 bp (untrimmed), 159211 (trimmed).
Contig 119. 3285 reads; 186636 bp (untrimmed), 186426 (trimmed).
Contig 120. 3727 reads; 148373 bp (untrimmed), 148357 (trimmed).
Contig 121. 5025 reads; 276572 bp (untrimmed), 276510 (trimmed).
Contig 122. 6028 reads; 335204 bp (untrimmed), 335204 (trimmed).
Contig 123. 6559 reads; 380005 bp (untrimmed), 379280 (trimmed).
Contig 124. 12460 reads; 695666 bp (untrimmed), 695571 (trimmed).
Contig 125. 17894 reads; 1001657 bp (untrimmed), 1001657 (trimmed).
--------------------------------------------------------------
Totals 83046 reads; 4608334 bp (untrimmed), 4600064 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 4590462 bases Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 5082
HQ Discrepant reads = 76
Chimeric reads = 130
Suspect alignments = 303
-------------------------------------------------------------------
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/3436553/edit_dir.03Feb04.QD