See help.
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 4401518
# phrap: 4409418
# db:
altered.
9000000
4500000
5577734 +/- 1976225
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 14964
Number of reads with percent X's >= 20%: 232 = 0.4%
Number of reads with percent X's >= 50%: 95 = 0.1%
Number of reads with percent X's >= 80%: 5 = 0.0%
Total reads in project: 65141
Total bp X'd : 656948
reads >= 20% >= 50% >= 80% screened
Nr with L09136 12447 138 62 5
Nr with pCC1Fos 2305 1 1 0
Nr with pMCL200_JGI_XZX+XZK 212 93 32 0
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 7
Number of reads with percent X's >= 20%: 1 = 5.9%
Number of reads with percent X's >= 50%: 1 = 5.9%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 17
Total bp X'd : 730
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3 0 0 0
Nr with pCC1Fos 4 1 1 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 12577153
C = 18675122
G = 19225925
T = 11688381
N = 353899
X = 656948
GC fraction = 0.60
Total = 63177428
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634500_fasta.screen.contigs
-------------------------------------------------------------------
A 829618
C 1357938
G 1384419
T 834132
N 35
fraction GC = 0.62
total bases = 4406142
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 AICF reads.list > grep.reads.list.AICF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICF 4 500
-------------------------------------------------------------------
#Found 10994 total values totalling 63078598.0000. <5737.547571 +/- 39807.939382>
#Range: [ 701 - 1493796 ]
#Most likely bin: [ 3500 - 4000 ] 5098 counts
#Median bin: [ 3500 - 4000 ] 5098 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 6 0.00 0.00 ]
|X 1000 - 1500 : [ 66 0.01 0.01 ]
|X 1500 - 2000 : [ 67 0.01 0.01 ]
|X 2000 - 2500 : [ 111 0.01 0.02 ]
|XX 2500 - 3000 : [ 218 0.02 0.04 ]
|XXXXXXX 3000 - 3500 : [ 936 0.09 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 5098 0.46 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 4029 0.37 0.96 ]
|XXX 4500 - 5000 : [ 416 0.04 1.00 ]
| 5000 - 5500 : [ 1 0.00 1.00 ]
#...
| 8500 - 9000 : [ 1 0.00 1.00 ]
#...
| 15000 - 15500 : [ 1 0.00 1.00 ]
#...
| 18000 - 18500 : [ 1 0.00 1.00 ]
#...
| 33000 - 33500 : [ 1 0.00 1.00 ]
#...
| 63500 - 64000 : [ 1 0.00 1.00 ]
#...
| 66500 - 67000 : [ 1 0.00 1.00 ]
#...
| 99000 - 99500 : [ 1 0.00 1.00 ]
#...
| 111500 - 112000 : [ 1 0.00 1.00 ]
#...
| 112500 - 113000 : [ 1 0.00 1.00 ]
#...
| 141000 - 141500 : [ 1 0.00 1.00 ]
#...
| 145000 - 145500 : [ 1 0.00 1.00 ]
#...
| 146000 - 146500 : [ 1 0.00 1.00 ]
#...
| 150500 - 151000 : [ 1 0.00 1.00 ]
#...
| 167000 - 167500 : [ 1 0.00 1.00 ]
#...
| 184500 - 185000 : [ 1 0.00 1.00 ]
#...
| 187000 - 187500 : [ 1 0.00 1.00 ]
#...
| 189000 - 189500 : [ 1 0.00 1.00 ]
#...
| 201500 - 202000 : [ 1 0.00 1.00 ]
#...
| 215500 - 216000 : [ 1 0.00 1.00 ]
#...
| 219000 - 219500 : [ 1 0.00 1.00 ]
#...
| 227000 - 227500 : [ 1 0.00 1.00 ]
#...
| 230000 - 230500 : [ 1 0.00 1.00 ]
#...
| 238500 - 239000 : [ 1 0.00 1.00 ]
#...
| 249000 - 249500 : [ 1 0.00 1.00 ]
#...
| 254000 - 254500 : [ 1 0.00 1.00 ]
#...
| 315000 - 315500 : [ 1 0.00 1.00 ]
#...
| 352000 - 352500 : [ 1 0.00 1.00 ]
#...
| 440500 - 441000 : [ 1 0.00 1.00 ]
#...
| 460000 - 460500 : [ 1 0.00 1.00 ]
#...
| 478000 - 478500 : [ 1 0.00 1.00 ]
| 478500 - 479000 : [ 1 0.00 1.00 ]
#...
| 483500 - 484000 : [ 1 0.00 1.00 ]
#...
| 485000 - 485500 : [ 1 0.00 1.00 ]
#...
| 489500 - 490000 : [ 1 0.00 1.00 ]
#...
| 538500 - 539000 : [ 1 0.00 1.00 ]
#...
| 742000 - 742500 : [ 1 0.00 1.00 ]
#...
| 820500 - 821000 : [ 1 0.00 1.00 ]
#...
| 924500 - 925000 : [ 1 0.00 1.00 ]
#...
| 1105000 - 1105500 : [ 1 0.00 1.00 ]
#...
| 1124500 - 1125000 : [ 1 0.00 1.00 ]
#...
| 1218000 - 1218500 : [ 1 0.00 1.00 ]
| 1218500 - 1219000 : [ 1 0.00 1.00 ]
#...
| 1229500 - 1230000 : [ 1 0.00 1.00 ]
#...
| 1305500 - 1306000 : [ 1 0.00 1.00 ]
#...
| 1363000 - 1363500 : [ 1 0.00 1.00 ]
#...
| 1493500 - 1494000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICG reads.list > grep.reads.list.AICG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICG 4 500
-------------------------------------------------------------------
#Found 11908 total values totalling 123218498.0000. <10347.539301 +/- 52144.487507>
#Range: [ 822 - 1315234 ]
#Most likely bin: [ 6500 - 7000 ] 2550 counts
#Median bin: [ 6500 - 7000 ] 2550 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 6 0.00 0.00 ]
|X 1000 - 1500 : [ 40 0.00 0.00 ]
|X 1500 - 2000 : [ 47 0.00 0.01 ]
|X 2000 - 2500 : [ 66 0.01 0.01 ]
|X 2500 - 3000 : [ 51 0.00 0.02 ]
|X 3000 - 3500 : [ 74 0.01 0.02 ]
|X 3500 - 4000 : [ 67 0.01 0.03 ]
|X 4000 - 4500 : [ 67 0.01 0.04 ]
|X 4500 - 5000 : [ 78 0.01 0.04 ]
|XX 5000 - 5500 : [ 135 0.01 0.05 ]
|XXXXXXXXXXXXXX 5500 - 6000 : [ 897 0.08 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2505 0.21 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 2550 0.21 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 2378 0.20 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1803 0.15 0.90 ]
|XXXXXXXXXXXXXXXX 8000 - 8500 : [ 995 0.08 0.99 ]
|X 8500 - 9000 : [ 52 0.00 0.99 ]
| 9000 - 9500 : [ 4 0.00 0.99 ]
| 9500 - 10000 : [ 2 0.00 0.99 ]
| 10000 - 10500 : [ 1 0.00 0.99 ]
| 10500 - 11000 : [ 1 0.00 0.99 ]
| 11000 - 11500 : [ 1 0.00 0.99 ]
| 11500 - 12000 : [ 1 0.00 0.99 ]
| 12000 - 12500 : [ 1 0.00 0.99 ]
#...
| 16000 - 16500 : [ 1 0.00 0.99 ]
#...
| 25500 - 26000 : [ 1 0.00 0.99 ]
#...
| 28000 - 28500 : [ 1 0.00 0.99 ]
#...
| 29000 - 29500 : [ 1 0.00 0.99 ]
#...
| 31500 - 32000 : [ 1 0.00 0.99 ]
| 32000 - 32500 : [ 1 0.00 0.99 ]
#...
| 61000 - 61500 : [ 1 0.00 0.99 ]
#...
| 62500 - 63000 : [ 1 0.00 0.99 ]
#...
| 83000 - 83500 : [ 1 0.00 0.99 ]
#...
| 84500 - 85000 : [ 1 0.00 0.99 ]
#...
| 86000 - 86500 : [ 1 0.00 0.99 ]
| 86500 - 87000 : [ 1 0.00 0.99 ]
#...
| 92000 - 92500 : [ 1 0.00 0.99 ]
#...
| 104000 - 104500 : [ 1 0.00 0.99 ]
#...
| 105500 - 106000 : [ 1 0.00 0.99 ]
| 106000 - 106500 : [ 1 0.00 0.99 ]
#...
| 115000 - 115500 : [ 1 0.00 0.99 ]
#...
| 127500 - 128000 : [ 1 0.00 0.99 ]
#...
| 135000 - 135500 : [ 1 0.00 0.99 ]
#...
| 149500 - 150000 : [ 1 0.00 0.99 ]
#...
| 152500 - 153000 : [ 1 0.00 0.99 ]
#...
| 164500 - 165000 : [ 1 0.00 0.99 ]
#...
| 175000 - 175500 : [ 1 0.00 0.99 ]
#...
| 179000 - 179500 : [ 1 0.00 0.99 ]
#...
| 193500 - 194000 : [ 1 0.00 0.99 ]
#...
| 212000 - 212500 : [ 1 0.00 0.99 ]
#...
| 226000 - 226500 : [ 1 0.00 1.00 ]
#...
| 236500 - 237000 : [ 1 0.00 1.00 ]
#...
| 241500 - 242000 : [ 1 0.00 1.00 ]
#...
| 257500 - 258000 : [ 1 0.00 1.00 ]
#...
| 261000 - 261500 : [ 1 0.00 1.00 ]
#...
| 262500 - 263000 : [ 1 0.00 1.00 ]
#...
| 272000 - 272500 : [ 1 0.00 1.00 ]
#...
| 273500 - 274000 : [ 1 0.00 1.00 ]
#...
| 285000 - 285500 : [ 1 0.00 1.00 ]
#...
| 288000 - 288500 : [ 1 0.00 1.00 ]
#...
| 311500 - 312000 : [ 1 0.00 1.00 ]
#...
| 316000 - 316500 : [ 1 0.00 1.00 ]
#...
| 350500 - 351000 : [ 1 0.00 1.00 ]
#...
| 386500 - 387000 : [ 1 0.00 1.00 ]
#...
| 392500 - 393000 : [ 1 0.00 1.00 ]
#...
| 443500 - 444000 : [ 1 0.00 1.00 ]
#...
| 446500 - 447000 : [ 2 0.00 1.00 ]
#...
| 464000 - 464500 : [ 1 0.00 1.00 ]
#...
| 469500 - 470000 : [ 1 0.00 1.00 ]
#...
| 479500 - 480000 : [ 1 0.00 1.00 ]
#...
| 492000 - 492500 : [ 1 0.00 1.00 ]
#...
| 499500 - 500000 : [ 1 0.00 1.00 ]
#...
| 521000 - 521500 : [ 1 0.00 1.00 ]
#...
| 539500 - 540000 : [ 1 0.00 1.00 ]
#...
| 543000 - 543500 : [ 1 0.00 1.00 ]
#...
| 568500 - 569000 : [ 1 0.00 1.00 ]
#...
| 578500 - 579000 : [ 1 0.00 1.00 ]
#...
| 624500 - 625000 : [ 1 0.00 1.00 ]
#...
| 625500 - 626000 : [ 1 0.00 1.00 ]
#...
| 686000 - 686500 : [ 1 0.00 1.00 ]
#...
| 687000 - 687500 : [ 1 0.00 1.00 ]
#...
| 703000 - 703500 : [ 1 0.00 1.00 ]
#...
| 740000 - 740500 : [ 1 0.00 1.00 ]
#...
| 741500 - 742000 : [ 1 0.00 1.00 ]
#...
| 773000 - 773500 : [ 1 0.00 1.00 ]
#...
| 774000 - 774500 : [ 1 0.00 1.00 ]
#...
| 806000 - 806500 : [ 1 0.00 1.00 ]
#...
| 833500 - 834000 : [ 1 0.00 1.00 ]
#...
| 841000 - 841500 : [ 1 0.00 1.00 ]
#...
| 844000 - 844500 : [ 1 0.00 1.00 ]
#...
| 859000 - 859500 : [ 1 0.00 1.00 ]
#...
| 860000 - 860500 : [ 1 0.00 1.00 ]
#...
| 873500 - 874000 : [ 1 0.00 1.00 ]
#...
| 922500 - 923000 : [ 1 0.00 1.00 ]
#...
| 929500 - 930000 : [ 1 0.00 1.00 ]
#...
| 950500 - 951000 : [ 1 0.00 1.00 ]
#...
| 963500 - 964000 : [ 1 0.00 1.00 ]
#...
| 985000 - 985500 : [ 1 0.00 1.00 ]
#...
| 990000 - 990500 : [ 1 0.00 1.00 ]
#...
| 1008000 - 1008500 : [ 1 0.00 1.00 ]
#...
| 1023000 - 1023500 : [ 1 0.00 1.00 ]
#...
| 1064500 - 1065000 : [ 1 0.00 1.00 ]
#...
| 1106000 - 1106500 : [ 1 0.00 1.00 ]
#...
| 1129500 - 1130000 : [ 1 0.00 1.00 ]
#...
| 1164000 - 1164500 : [ 1 0.00 1.00 ]
#...
| 1168500 - 1169000 : [ 1 0.00 1.00 ]
#...
| 1209000 - 1209500 : [ 1 0.00 1.00 ]
#...
| 1239000 - 1239500 : [ 1 0.00 1.00 ]
#...
| 1315000 - 1315500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICH reads.list > grep.reads.list.AICH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICH 4 500
-------------------------------------------------------------------
#Found 2069 total values totalling 78548452.0000. <37964.452392 +/- 4513.426508>
#Range: [ 5717 - 48344 ]
#Most likely bin: [ 35000 - 35500 ] 91 counts
#Median bin: [ 37500 - 38000 ] 71 counts
#Histogram Bins Count Fraction Cum_Fraction
| 5500 - 6000 : [ 1 0.00 0.00 ]
#...
| 6500 - 7000 : [ 1 0.00 0.00 ]
#...
| 9000 - 9500 : [ 1 0.00 0.00 ]
#...
| 10000 - 10500 : [ 1 0.00 0.00 ]
#...
| 11000 - 11500 : [ 1 0.00 0.00 ]
#...
| 13000 - 13500 : [ 1 0.00 0.00 ]
| 13500 - 14000 : [ 1 0.00 0.00 ]
#...
| 18500 - 19000 : [ 1 0.00 0.00 ]
#...
| 25500 - 26000 : [ 1 0.00 0.00 ]
#...
|X 27000 - 27500 : [ 3 0.00 0.01 ]
| 27500 - 28000 : [ 1 0.00 0.01 ]
|X 28000 - 28500 : [ 3 0.00 0.01 ]
|XXX 28500 - 29000 : [ 6 0.00 0.01 ]
|XX 29000 - 29500 : [ 5 0.00 0.01 ]
|XXXX 29500 - 30000 : [ 10 0.00 0.02 ]
|XXXXXXX 30000 - 30500 : [ 17 0.01 0.03 ]
|XXXXXXXXXXXX 30500 - 31000 : [ 28 0.01 0.04 ]
|XXXXXXXXXXXXXX 31000 - 31500 : [ 32 0.02 0.06 ]
|XXXXXXXXXXXXXXXXXX 31500 - 32000 : [ 40 0.02 0.07 ]
|XXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 43 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 58 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 64 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 72 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 72 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 83 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 91 0.04 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 91 0.04 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 87 0.04 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 71 0.03 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 88 0.04 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 71 0.03 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 84 0.04 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 74 0.04 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 85 0.04 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 73 0.04 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 59 0.03 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 84 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 77 0.04 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 68 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 62 0.03 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 70 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 53 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 45 0.02 0.91 ]
|XXXXXXXXXXXXXXXXX 44000 - 44500 : [ 39 0.02 0.93 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 44500 - 45000 : [ 54 0.03 0.95 ]
|XXXXXXXXXXXXX 45000 - 45500 : [ 30 0.01 0.97 ]
|XXXXXXXXXX 45500 - 46000 : [ 23 0.01 0.98 ]
|XXXXXXXX 46000 - 46500 : [ 19 0.01 0.99 ]
|XXXXXXXX 46500 - 47000 : [ 19 0.01 1.00 ]
|XX 47000 - 47500 : [ 4 0.00 1.00 ]
| 47500 - 48000 : [ 1 0.00 1.00 ]
| 48000 - 48500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AICF 3719 +- 597 (n=5885)
# AICH 38088 +- 4401 (n=1042)
# AICG 6657 +- 1284 (n=6085)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634500_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
AICF 30720 -1 -1 97 731 30210 93 667 95 684
AICG 36480 -1 -1 91 574 36225 85 543 90 560
AICH 5376 -1 -1 99 679 5376 97 644 99 689
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AICF 16448 93 678 95 699 13762 92 655 94 666
AICG 18308 82 539 88 550 17917 88 547 92 570
AICH 2688 97 647 99 688 2688 97 642 99 689
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634500_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
140 28286 13015 92.96 96.84 AICF @
184 31598 16638 90.42 94.19 AICG @
28 5257 2665 95.18 99.14 AICH @
] 65141 32318 91.81 cumulative total@@
LIBRARY PLATE ID COUNT [ AICF 140 AICG 184 AICH 28 ] for 352 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 3634500_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 71811 total values totalling 38933228.0000. <542.162454 +/- 243.303581>
#Range: [ 0 - 943 ]
#Most likely bin: [ 650 - 700 ] 10737 counts
#Median bin: [ 600 - 650 ] 8591 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 6543 0.09 0.09 ]
|XXXX 50 - 100 : [ 1192 0.02 0.11 ]
|XXXX 100 - 150 : [ 1129 0.02 0.12 ]
|XXXX 150 - 200 : [ 1166 0.02 0.14 ]
|XXXXX 200 - 250 : [ 1213 0.02 0.16 ]
|XXXXXX 250 - 300 : [ 1577 0.02 0.18 ]
|XXXXXXX 300 - 350 : [ 1836 0.03 0.20 ]
|XXXXXXX 350 - 400 : [ 1944 0.03 0.23 ]
|XXXXXXXX 400 - 450 : [ 2262 0.03 0.26 ]
|XXXXXXXXXX 450 - 500 : [ 2767 0.04 0.30 ]
|XXXXXXXXXXXXXXX 500 - 550 : [ 3918 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 5883 0.08 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 8591 0.12 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 10737 0.15 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 9570 0.13 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6565 0.09 0.93 ]
|XXXXXXXXXXXXXXX 800 - 850 : [ 4041 0.06 0.99 ]
|XXX 850 - 900 : [ 854 0.01 1.00 ]
| 900 - 950 : [ 23 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICF 3634500_fasta.screen.trimQ15.SaF > reads.trim15.AICF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICF.rl 2 50
-------------------------------------------------------------------
#Found 30210 total values totalling 18748481.0000. <620.605131 +/- 224.406298>
#Range: [ 0 - 943 ]
#Most likely bin: [ 700 - 750 ] 5169 counts
#Median bin: [ 650 - 700 ] 4355 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 0 - 50 : [ 1903 0.06 0.06 ]
|XX 50 - 100 : [ 252 0.01 0.07 ]
|XX 100 - 150 : [ 272 0.01 0.08 ]
|XX 150 - 200 : [ 313 0.01 0.09 ]
|XX 200 - 250 : [ 312 0.01 0.10 ]
|XXX 250 - 300 : [ 366 0.01 0.11 ]
|XXX 300 - 350 : [ 386 0.01 0.13 ]
|XXXX 350 - 400 : [ 485 0.02 0.14 ]
|XXXXX 400 - 450 : [ 620 0.02 0.16 ]
|XXXXXX 450 - 500 : [ 812 0.03 0.19 ]
|XXXXXXXX 500 - 550 : [ 1059 0.04 0.22 ]
|XXXXXXXXXXXXX 550 - 600 : [ 1734 0.06 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2794 0.09 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4355 0.14 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5169 0.17 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4900 0.16 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 3650 0.12 0.97 ]
|XXXXXX 850 - 900 : [ 806 0.03 1.00 ]
| 900 - 950 : [ 22 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICG 3634500_fasta.screen.trimQ15.SaF > reads.trim15.AICG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICG.rl 2 50
-------------------------------------------------------------------
#Found 36225 total values totalling 16819823.0000. <464.315335 +/- 240.415250>
#Range: [ 0 - 846 ]
#Most likely bin: [ 650 - 700 ] 5415 counts
#Median bin: [ 550 - 600 ] 3965 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 4514 0.12 0.12 ]
|XXXXXXX 50 - 100 : [ 905 0.02 0.15 ]
|XXXXXX 100 - 150 : [ 833 0.02 0.17 ]
|XXXXXX 150 - 200 : [ 833 0.02 0.20 ]
|XXXXXX 200 - 250 : [ 870 0.02 0.22 ]
|XXXXXXX 250 - 300 : [ 977 0.03 0.25 ]
|XXXXXXXX 300 - 350 : [ 1143 0.03 0.28 ]
|XXXXXXXXXX 350 - 400 : [ 1307 0.04 0.31 ]
|XXXXXXXXXXXX 400 - 450 : [ 1583 0.04 0.36 ]
|XXXXXXXXXXXXXX 450 - 500 : [ 1893 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 2738 0.08 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 3965 0.11 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 5296 0.15 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5415 0.15 0.89 ]
|XXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3132 0.09 0.98 ]
|XXXXXX 750 - 800 : [ 769 0.02 1.00 ]
| 800 - 850 : [ 52 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICH 3634500_fasta.screen.trimQ15.SaF > reads.trim15.AICH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICH.rl 2 50
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#Found 5376 total values totalling 3364924.0000. <625.915923 +/- 189.341961>
#Range: [ 0 - 900 ]
#Most likely bin: [ 700 - 750 ] 1269 counts
#Median bin: [ 650 - 700 ] 967 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 0 - 50 : [ 126 0.02 0.02 ]
|X 50 - 100 : [ 35 0.01 0.03 ]
|X 100 - 150 : [ 24 0.00 0.03 ]
|X 150 - 200 : [ 20 0.00 0.04 ]
|X 200 - 250 : [ 31 0.01 0.04 ]
|XXXXXXX 250 - 300 : [ 234 0.04 0.09 ]
|XXXXXXXXXX 300 - 350 : [ 307 0.06 0.14 ]
|XXXXX 350 - 400 : [ 152 0.03 0.17 ]
|XX 400 - 450 : [ 59 0.01 0.18 ]
|XX 450 - 500 : [ 62 0.01 0.20 ]
|XXXX 500 - 550 : [ 121 0.02 0.22 ]
|XXXXXX 550 - 600 : [ 184 0.03 0.25 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 501 0.09 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 967 0.18 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1269 0.24 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 896 0.17 0.93 ]
|XXXXXXXXXXX 800 - 850 : [ 339 0.06 0.99 ]
|XX 850 - 900 : [ 48 0.01 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634500
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AICF.000001.000100 pUC18.fa LRS.fasta
AICF.000101.000200 pUC18.fa LRS.fasta
AICG.000001.000100 pMCL200.fa LRS.fasta
AICG.000101.000200 pMCL200.fa LRS.fasta
AICH.000001.000100 pCC1Fos.fa LRS.fasta
AICF.000001.000100 pUC18.fa LRS.fasta
AICF.000101.000200 pUC18.fa LRS.fasta
AICG.000001.000100 pMCL200.fa LRS.fasta
AICG.000101.000200 pMCL200.fa LRS.fasta
AICH.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634500_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
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# GC.3634500_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 64911 total values totalling 40150.0881. <0.618541 +/- 0.040801>
#Range: [ 0.3 - 0.8438 ]
#Most likely bin: [ 0.625 - 0.63 ] 3903 counts
#Median bin: [ 0.62 - 0.625 ] 3738 counts
| 0.3 - 0.305 : [ 1 0.00 0.00 ]
#...
| 0.31 - 0.315 : [ 1 0.00 0.00 ]
#...
| 0.35 - 0.355 : [ 1 0.00 0.00 ]
#...
| 0.36 - 0.365 : [ 2 0.00 0.00 ]
| 0.365 - 0.37 : [ 1 0.00 0.00 ]
| 0.37 - 0.375 : [ 2 0.00 0.00 ]
| 0.375 - 0.38 : [ 1 0.00 0.00 ]
| 0.38 - 0.385 : [ 2 0.00 0.00 ]
| 0.385 - 0.39 : [ 5 0.00 0.00 ]
| 0.39 - 0.395 : [ 4 0.00 0.00 ]
| 0.395 - 0.4 : [ 5 0.00 0.00 ]
| 0.4 - 0.405 : [ 5 0.00 0.00 ]
| 0.405 - 0.41 : [ 3 0.00 0.00 ]
| 0.41 - 0.415 : [ 8 0.00 0.00 ]
| 0.415 - 0.42 : [ 14 0.00 0.00 ]
| 0.42 - 0.425 : [ 11 0.00 0.00 ]
| 0.425 - 0.43 : [ 11 0.00 0.00 ]
| 0.43 - 0.435 : [ 12 0.00 0.00 ]
| 0.435 - 0.44 : [ 13 0.00 0.00 ]
| 0.44 - 0.445 : [ 18 0.00 0.00 ]
| 0.445 - 0.45 : [ 18 0.00 0.00 ]
| 0.45 - 0.455 : [ 36 0.00 0.00 ]
| 0.455 - 0.46 : [ 41 0.00 0.00 ]
|X 0.46 - 0.465 : [ 54 0.00 0.00 ]
|X 0.465 - 0.47 : [ 53 0.00 0.00 ]
|X 0.47 - 0.475 : [ 57 0.00 0.01 ]
|X 0.475 - 0.48 : [ 68 0.00 0.01 ]
|X 0.48 - 0.485 : [ 75 0.00 0.01 ]
|X 0.485 - 0.49 : [ 89 0.00 0.01 ]
|X 0.49 - 0.495 : [ 75 0.00 0.01 ]
|X 0.495 - 0.5 : [ 56 0.00 0.01 ]
|X 0.5 - 0.505 : [ 139 0.00 0.01 ]
|X 0.505 - 0.51 : [ 141 0.00 0.02 ]
|XX 0.51 - 0.515 : [ 157 0.00 0.02 ]
|XX 0.515 - 0.52 : [ 219 0.00 0.02 ]
|XX 0.52 - 0.525 : [ 223 0.00 0.02 ]
|XXX 0.525 - 0.53 : [ 271 0.00 0.03 ]
|XXX 0.53 - 0.535 : [ 323 0.00 0.03 ]
|XXXX 0.535 - 0.54 : [ 380 0.01 0.04 ]
|XXXX 0.54 - 0.545 : [ 437 0.01 0.05 ]
|XXXXXX 0.545 - 0.55 : [ 539 0.01 0.06 ]
|XXXXXX 0.55 - 0.555 : [ 555 0.01 0.06 ]
|XXXXXXX 0.555 - 0.56 : [ 727 0.01 0.07 ]
|XXXXXXXXX 0.56 - 0.565 : [ 873 0.01 0.09 ]
|XXXXXXXXXX 0.565 - 0.57 : [ 1015 0.02 0.10 ]
|XXXXXXXXXXXX 0.57 - 0.575 : [ 1191 0.02 0.12 ]
|XXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1430 0.02 0.14 ]
|XXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1699 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1865 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 2268 0.03 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 2511 0.04 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 2986 0.05 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 3114 0.05 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 3425 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 3603 0.06 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 3738 0.06 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 3903 0.06 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 3655 0.06 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 3516 0.05 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 3288 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 3038 0.05 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 2649 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 2165 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 1735 0.03 0.90 ]
|XXXXXXXXXXXXXXX 0.665 - 0.67 : [ 1463 0.02 0.92 ]
|XXXXXXXXXXXX 0.67 - 0.675 : [ 1153 0.02 0.94 ]
|XXXXXXXXXX 0.675 - 0.68 : [ 964 0.01 0.96 ]
|XXXXXXX 0.68 - 0.685 : [ 695 0.01 0.97 ]
|XXXXX 0.685 - 0.69 : [ 517 0.01 0.98 ]
|XXXX 0.69 - 0.695 : [ 418 0.01 0.98 ]
|XXX 0.695 - 0.7 : [ 316 0.00 0.99 ]
|XX 0.7 - 0.705 : [ 238 0.00 0.99 ]
|XX 0.705 - 0.71 : [ 156 0.00 0.99 ]
|X 0.71 - 0.715 : [ 114 0.00 0.99 ]
|X 0.715 - 0.72 : [ 86 0.00 1.00 ]
|X 0.72 - 0.725 : [ 50 0.00 1.00 ]
| 0.725 - 0.73 : [ 41 0.00 1.00 ]
| 0.73 - 0.735 : [ 42 0.00 1.00 ]
| 0.735 - 0.74 : [ 34 0.00 1.00 ]
| 0.74 - 0.745 : [ 24 0.00 1.00 ]
| 0.745 - 0.75 : [ 15 0.00 1.00 ]
| 0.75 - 0.755 : [ 17 0.00 1.00 ]
| 0.755 - 0.76 : [ 12 0.00 1.00 ]
| 0.76 - 0.765 : [ 11 0.00 1.00 ]
| 0.765 - 0.77 : [ 4 0.00 1.00 ]
| 0.77 - 0.775 : [ 4 0.00 1.00 ]
| 0.775 - 0.78 : [ 2 0.00 1.00 ]
| 0.78 - 0.785 : [ 3 0.00 1.00 ]
| 0.785 - 0.79 : [ 2 0.00 1.00 ]
| 0.79 - 0.795 : [ 2 0.00 1.00 ]
| 0.795 - 0.8 : [ 1 0.00 1.00 ]
| 0.8 - 0.805 : [ 4 0.00 1.00 ]
#...
| 0.82 - 0.825 : [ 1 0.00 1.00 ]
#...
| 0.83 - 0.835 : [ 1 0.00 1.00 ]
#...
| 0.84 - 0.845 : [ 1 0.00 1.00 ]
Contigs and Assemblies
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Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
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Contig 1. 3 reads; 1097 bp (untrimmed), 841 (trimmed).
Contig 2. 5 reads; 1225 bp (untrimmed), 1027 (trimmed).
Contig 3. 29 reads; 3436 bp (untrimmed), 2890 (trimmed).
Contig 4. 31 reads; 3387 bp (untrimmed), 3358 (trimmed).
Contig 5. 93 reads; 10009 bp (untrimmed), 9981 (trimmed).
Contig 6. 245 reads; 16989 bp (untrimmed), 16968 (trimmed).
Contig 7. 304 reads; 23371 bp (untrimmed), 23218 (trimmed).
Contig 8. 439 reads; 24258 bp (untrimmed), 24172 (trimmed).
Contig 9. 482 reads; 41009 bp (untrimmed), 40794 (trimmed).
Contig 10. 497 reads; 25284 bp (untrimmed), 25270 (trimmed).
Contig 11. 502 reads; 46415 bp (untrimmed), 46110 (trimmed).
Contig 12. 528 reads; 41891 bp (untrimmed), 41530 (trimmed).
Contig 13. 595 reads; 46211 bp (untrimmed), 46184 (trimmed).
Contig 14. 984 reads; 84303 bp (untrimmed), 84160 (trimmed).
Contig 15. 1051 reads; 58172 bp (untrimmed), 58078 (trimmed).
Contig 16. 1131 reads; 80172 bp (untrimmed), 79872 (trimmed).
Contig 17. 1216 reads; 82260 bp (untrimmed), 82219 (trimmed).
Contig 18. 1646 reads; 134651 bp (untrimmed), 134647 (trimmed).
Contig 19. 1976 reads; 147102 bp (untrimmed), 147002 (trimmed).
Contig 20. 2687 reads; 225275 bp (untrimmed), 225249 (trimmed).
Contig 21. 2984 reads; 219433 bp (untrimmed), 219102 (trimmed).
Contig 22. 3229 reads; 236310 bp (untrimmed), 236098 (trimmed).
Contig 23. 3420 reads; 240509 bp (untrimmed), 240323 (trimmed).
Contig 24. 3568 reads; 283674 bp (untrimmed), 283016 (trimmed).
Contig 25. 4572 reads; 367683 bp (untrimmed), 367639 (trimmed).
Contig 26. 4737 reads; 312059 bp (untrimmed), 311958 (trimmed).
Contig 27. 28170 reads; 1649957 bp (untrimmed), 1649812 (trimmed).
--------------------------------------------------------------
Totals 65124 reads; 4406142 bp (untrimmed), 4401518 (trimmed).
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Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
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depth.out contains 4406142 bases Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
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Small Inserts = 1
HQ Discrepant reads = 51
Chimeric reads = 110
Suspect alignments = 268
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Assembly parameters
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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/microbe4/3634500/edit_dir.18Jun04.QD