See help.
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 7275262
# phrap: 6624103
# db:
altered.
6700000
6866455 +/- 290726
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 23346
Number of reads with percent X's >= 20%: 211 = 0.2%
Number of reads with percent X's >= 50%: 135 = 0.1%
Number of reads with percent X's >= 80%: 19 = 0.0%
Total reads in project: 96309
Total bp X'd : 928878
reads >= 20% >= 50% >= 80% screened
Nr with L09136 19192 168 111 11
Nr with pCC1Fos 4100 0 0 0
Nr with pMCL200_JGI_XZX+XZK 54 43 24 8
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 196
Number of reads with percent X's >= 20%: 0 = 0.0%
Number of reads with percent X's >= 50%: 0 = 0.0%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 754
Total bp X'd : 7516
reads >= 20% >= 50% >= 80% screened
Nr with L09136 8 0 0 0
Nr with pCC1Fos 188 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 34413006
C = 15788864
G = 15437900
T = 33247673
N = 882535
X = 928878
GC fraction = 0.31
Total = 100698856
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634512_fasta.screen.contigs
-------------------------------------------------------------------
A 2436724
C 1280086
G 1018708
T 2681028
N 1130
fraction GC = 0.31
total bases = 7417676
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 2653 total values totalling 17244234.0000. <6499.899736 +/- 11969.108659>
#Range: [ 1044 - 620982 ]
#Most likely bin: [ 6000 - 6500 ] 830 counts
#Median bin: [ 6000 - 6500 ] 830 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 10 0.00 0.00 ]
|X 1500 - 2000 : [ 11 0.00 0.01 ]
| 2000 - 2500 : [ 7 0.00 0.01 ]
|X 2500 - 3000 : [ 13 0.00 0.02 ]
| 3000 - 3500 : [ 8 0.00 0.02 ]
| 3500 - 4000 : [ 9 0.00 0.02 ]
| 4000 - 4500 : [ 4 0.00 0.02 ]
| 4500 - 5000 : [ 7 0.00 0.03 ]
|XXXX 5000 - 5500 : [ 75 0.03 0.05 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 747 0.28 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 830 0.31 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 556 0.21 0.86 ]
|XXXXXXXXXXXXXX 7000 - 7500 : [ 287 0.11 0.97 ]
|XXXX 7500 - 8000 : [ 87 0.03 1.00 ]
#...
| 30500 - 31000 : [ 1 0.00 1.00 ]
#...
| 620500 - 621000 : [ 1 0.00 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 32086 total values totalling 112124759.0000. <3494.507231 +/- 3897.600826>
#Range: [ 571 - 544998 ]
#Most likely bin: [ 3000 - 3500 ] 11023 counts
#Median bin: [ 3000 - 3500 ] 11023 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 4 0.00 0.00 ]
|X 1000 - 1500 : [ 141 0.00 0.00 ]
|X 1500 - 2000 : [ 262 0.01 0.01 ]
|XXX 2000 - 2500 : [ 718 0.02 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 6328 0.20 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 11023 0.34 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 7691 0.24 0.82 ]
|XXXXXXXXXXXXXXXX 4000 - 4500 : [ 4496 0.14 0.96 ]
|XXXXX 4500 - 5000 : [ 1302 0.04 1.00 ]
| 5000 - 5500 : [ 98 0.00 1.00 ]
| 5500 - 6000 : [ 3 0.00 1.00 ]
#...
| 32500 - 33000 : [ 1 0.00 1.00 ]
| 33000 - 33500 : [ 2 0.00 1.00 ]
| 33500 - 34000 : [ 1 0.00 1.00 ]
| 34000 - 34500 : [ 3 0.00 1.00 ]
| 34500 - 35000 : [ 2 0.00 1.00 ]
| 35000 - 35500 : [ 3 0.00 1.00 ]
#...
| 83000 - 83500 : [ 1 0.00 1.00 ]
#...
| 88000 - 88500 : [ 1 0.00 1.00 ]
#...
| 108000 - 108500 : [ 1 0.00 1.00 ]
#...
| 110500 - 111000 : [ 1 0.00 1.00 ]
#...
| 137500 - 138000 : [ 1 0.00 1.00 ]
#...
| 140000 - 140500 : [ 1 0.00 1.00 ]
#...
| 317500 - 318000 : [ 1 0.00 1.00 ]
#...
| 544500 - 545000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AWGG reads.list > grep.reads.list.AWGG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AWGG 4 500
-------------------------------------------------------------------
#Found 2875 total values totalling 19459603.0000. <6768.557565 +/- 863.876927>
#Range: [ 1016 - 10500 ]
#Most likely bin: [ 6000 - 6500 ] 772 counts
#Median bin: [ 6500 - 7000 ] 705 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 9 0.00 0.00 ]
| 1500 - 2000 : [ 5 0.00 0.00 ]
| 2000 - 2500 : [ 6 0.00 0.01 ]
| 2500 - 3000 : [ 9 0.00 0.01 ]
|X 3000 - 3500 : [ 13 0.00 0.01 ]
|X 3500 - 4000 : [ 13 0.00 0.02 ]
|X 4000 - 4500 : [ 10 0.00 0.02 ]
| 4500 - 5000 : [ 6 0.00 0.02 ]
#...
|XXXXXXXXX 5500 - 6000 : [ 167 0.06 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 772 0.27 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 705 0.25 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 648 0.23 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 455 0.16 0.98 ]
|XX 8000 - 8500 : [ 47 0.02 1.00 ]
| 8500 - 9000 : [ 4 0.00 1.00 ]
| 9000 - 9500 : [ 3 0.00 1.00 ]
| 9500 - 10000 : [ 1 0.00 1.00 ]
| 10000 - 10500 : [ 1 0.00 1.00 ]
| 10500 - 11000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep BAOF reads.list > grep.reads.list.BAOF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BAOF 4 500
-------------------------------------------------------------------
#Found 1137 total values totalling 41273782.0000. <36300.599824 +/- 3690.633661>
#Range: [ 1834 - 45361 ]
#Most likely bin: [ 36500 - 37000 ] 73 counts
#Median bin: [ 36000 - 36500 ] 59 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1500 - 2000 : [ 1 0.00 0.00 ]
#...
|X 23000 - 23500 : [ 2 0.00 0.00 ]
#...
|X 25500 - 26000 : [ 2 0.00 0.00 ]
|X 26000 - 26500 : [ 1 0.00 0.01 ]
|X 26500 - 27000 : [ 1 0.00 0.01 ]
|X 27000 - 27500 : [ 2 0.00 0.01 ]
|XX 27500 - 28000 : [ 3 0.00 0.01 ]
|XX 28000 - 28500 : [ 4 0.00 0.01 ]
|XX 28500 - 29000 : [ 4 0.00 0.02 ]
|XXXXXXX 29000 - 29500 : [ 12 0.01 0.03 ]
|XXXX 29500 - 30000 : [ 7 0.01 0.03 ]
|XXXXXXXXX 30000 - 30500 : [ 16 0.01 0.05 ]
|XXXXXXXXX 30500 - 31000 : [ 17 0.01 0.06 ]
|XXXXXXXXXXXX 31000 - 31500 : [ 21 0.02 0.08 ]
|XXXXXXXXXXXXX 31500 - 32000 : [ 23 0.02 0.10 ]
|XXXXXXXXXXXXXXXX 32000 - 32500 : [ 30 0.03 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 49 0.04 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 55 0.05 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 49 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 54 0.05 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 66 0.06 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 60 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 57 0.05 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 59 0.05 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 73 0.06 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 55 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 56 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 43 0.04 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 48 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 41 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 42 0.04 0.84 ]
|XXXXXXXXXXXXXXX 40000 - 40500 : [ 28 0.02 0.86 ]
|XXXXXXXXXXXXXXX 40500 - 41000 : [ 27 0.02 0.89 ]
|XXXXXXXXXXXXXXXXX 41000 - 41500 : [ 31 0.03 0.91 ]
|XXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 33 0.03 0.94 ]
|XXXXXXXXXXX 42000 - 42500 : [ 20 0.02 0.96 ]
|XXXXXXXX 42500 - 43000 : [ 15 0.01 0.97 ]
|XXXXXXX 43000 - 43500 : [ 12 0.01 0.98 ]
|XXXX 43500 - 44000 : [ 8 0.01 0.99 ]
|XX 44000 - 44500 : [ 4 0.00 0.99 ]
|XX 44500 - 45000 : [ 3 0.00 1.00 ]
|XX 45000 - 45500 : [ 3 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep BFTN reads.list > grep.reads.list.BFTN
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.BFTN 4 500
-------------------------------------------------------------------
#Found 1080 total values totalling 39377544.0000. <36460.688889 +/- 4125.489202>
#Range: [ 1910 - 71488 ]
#Most likely bin: [ 35500 - 36000 ] 70 counts
#Median bin: [ 36000 - 36500 ] 53 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1500 - 2000 : [ 1 0.00 0.00 ]
#...
|X 11500 - 12000 : [ 1 0.00 0.00 ]
|X 12000 - 12500 : [ 1 0.00 0.00 ]
#...
|X 17500 - 18000 : [ 1 0.00 0.00 ]
#...
|X 19500 - 20000 : [ 1 0.00 0.00 ]
#...
|X 24000 - 24500 : [ 1 0.00 0.01 ]
|X 24500 - 25000 : [ 1 0.00 0.01 ]
#...
|X 25500 - 26000 : [ 2 0.00 0.01 ]
#...
|X 27000 - 27500 : [ 1 0.00 0.01 ]
|X 27500 - 28000 : [ 1 0.00 0.01 ]
|X 28000 - 28500 : [ 2 0.00 0.01 ]
|XXX 28500 - 29000 : [ 5 0.00 0.02 ]
|XXX 29000 - 29500 : [ 6 0.01 0.02 ]
|XXX 29500 - 30000 : [ 5 0.00 0.03 ]
|XXXXX 30000 - 30500 : [ 9 0.01 0.04 ]
|XXXXXXX 30500 - 31000 : [ 13 0.01 0.05 ]
|XXXXXXXXXXX 31000 - 31500 : [ 20 0.02 0.07 ]
|XXXXXXXXXXXXXXXX 31500 - 32000 : [ 28 0.03 0.09 ]
|XXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 35 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 49 0.05 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 49 0.05 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 49 0.05 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 55 0.05 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 60 0.06 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 57 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 70 0.06 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 53 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 55 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 53 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 39 0.04 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 43 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 37 0.03 0.74 ]
|XXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 37 0.03 0.78 ]
|XXXXXXXXXXXXXXXX 39500 - 40000 : [ 28 0.03 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 44 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 36 0.03 0.88 ]
|XXXXXXXXXXXX 41000 - 41500 : [ 21 0.02 0.90 ]
|XXXXXXXXXXXXXX 41500 - 42000 : [ 24 0.02 0.92 ]
|XXXXXXXXXX 42000 - 42500 : [ 18 0.02 0.94 ]
|XXXXXXX 42500 - 43000 : [ 13 0.01 0.95 ]
|XXXXXXXXX 43000 - 43500 : [ 16 0.01 0.96 ]
|XXXXXXXXXX 43500 - 44000 : [ 17 0.02 0.98 ]
|XXXXX 44000 - 44500 : [ 8 0.01 0.99 ]
|XXX 44500 - 45000 : [ 5 0.00 0.99 ]
|XXX 45000 - 45500 : [ 5 0.00 1.00 ]
|X 45500 - 46000 : [ 1 0.00 1.00 ]
|XX 46000 - 46500 : [ 3 0.00 1.00 ]
#...
|X 71000 - 71500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# BFTN 36308 +- 3847 (n=795)
# AIFZ 3288 +- 684 (n=15083)
# AHYP 6233 +- 772 (n=1263)
# AWGG 6746 +- 846 (n=1392)
# BAOF 36237 +- 3493 (n=486)
-------------------------------------------------------------------
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
AHYP 7680 93 813 97 788 5769 100 819 100 820
AIFZ 79104 88 710 95 729 70578 97 698 100 724
AWGG 7968 84 693 92 642 6682 100 713 100 705
BAOF 15360 83 650 91 597 5981 93 616 100 642
BFTN 15360 64 517 78 408 7299 90 508 100 547
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AHYP 2866 100 823 100 822 2903 100 815 100 818
AIFZ 35504 97 692 100 717 35074 97 704 100 730
AWGG 3379 100 709 100 701 3303 99 718 100 709
BAOF 2942 93 611 100 632 3039 94 620 100 652
BFTN 3662 89 510 100 542 3637 90 506 100 551
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634512_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
72 7299 4434 61.58 64.15 BFTN @
408 70578 38029 93.21 97.09 AIFZ @
40 6682 3354 83.85 87.34 AWGG @
40 5769 2917 72.92 75.96 AHYP @
80 5981 4342 54.27 56.54 BAOF @
] 96309 53076 82.93 cumulative total@@
LIBRARY PLATE ID COUNT [ BFTN 72 AIFZ 408 AHYP 40 AWGG 40 BAOF 80 ] for 640 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 96309 total values totalling 64199697.0000. <666.601221 +/- 226.297638>
#Range: [ 11 - 999 ]
#Most likely bin: [ 800 - 850 ] 20309 counts
#Median bin: [ 750 - 800 ] 15376 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 50 : [ 953 0.01 0.01 ]
|XXXXX 50 - 100 : [ 2409 0.03 0.03 ]
|XXXX 100 - 150 : [ 1962 0.02 0.06 ]
|XXXX 150 - 200 : [ 1800 0.02 0.07 ]
|XXX 200 - 250 : [ 1666 0.02 0.09 ]
|XXXX 250 - 300 : [ 1819 0.02 0.11 ]
|XXXX 300 - 350 : [ 2114 0.02 0.13 ]
|XXXX 350 - 400 : [ 1993 0.02 0.15 ]
|XXXX 400 - 450 : [ 2147 0.02 0.18 ]
|XXXXX 450 - 500 : [ 2302 0.02 0.20 ]
|XXXXX 500 - 550 : [ 2610 0.03 0.23 ]
|XXXXXXX 550 - 600 : [ 3433 0.04 0.26 ]
|XXXXXXXXX 600 - 650 : [ 4555 0.05 0.31 ]
|XXXXXXXXXXXXX 650 - 700 : [ 6553 0.07 0.38 ]
|XXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 9935 0.10 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 15376 0.16 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 20309 0.21 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 850 - 900 : [ 12541 0.13 0.98 ]
|XXXX 900 - 950 : [ 1798 0.02 1.00 ]
| 950 - 1000 : [ 34 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYP
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AHYP 3634512_fasta.screen.trimQ15.SaF > reads.trim15.AHYP.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHYP.rl 2 50
-------------------------------------------------------------------
#Found 5769 total values totalling 4715646.0000. <817.411336 +/- 85.627310>
#Range: [ 29 - 957 ]
#Most likely bin: [ 800 - 850 ] 2567 counts
#Median bin: [ 800 - 850 ] 2567 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 7 0.00 0.00 ]
| 50 - 100 : [ 7 0.00 0.00 ]
| 100 - 150 : [ 7 0.00 0.00 ]
| 150 - 200 : [ 11 0.00 0.01 ]
| 200 - 250 : [ 5 0.00 0.01 ]
| 250 - 300 : [ 12 0.00 0.01 ]
| 300 - 350 : [ 11 0.00 0.01 ]
| 350 - 400 : [ 9 0.00 0.01 ]
| 400 - 450 : [ 14 0.00 0.01 ]
| 450 - 500 : [ 7 0.00 0.02 ]
| 500 - 550 : [ 11 0.00 0.02 ]
| 550 - 600 : [ 19 0.00 0.02 ]
| 600 - 650 : [ 24 0.00 0.02 ]
|X 650 - 700 : [ 50 0.01 0.03 ]
|XXX 700 - 750 : [ 194 0.03 0.07 ]
|XXXXXXXXXXXXXXX 750 - 800 : [ 984 0.17 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2567 0.44 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 850 - 900 : [ 1703 0.30 0.98 ]
|XX 900 - 950 : [ 126 0.02 1.00 ]
| 950 - 1000 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AHYS
trimt JAZZ trim 15 readlength histogram for AIFZ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFZ 3634512_fasta.screen.trimQ15.SaF > reads.trim15.AIFZ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFZ.rl 2 50
-------------------------------------------------------------------
#Found 70578 total values totalling 47902948.0000. <678.723512 +/- 221.472434>
#Range: [ 17 - 999 ]
#Most likely bin: [ 800 - 850 ] 15465 counts
#Median bin: [ 750 - 800 ] 11167 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 558 0.01 0.01 ]
|XXXX 50 - 100 : [ 1608 0.02 0.03 ]
|XXXX 100 - 150 : [ 1491 0.02 0.05 ]
|XXX 150 - 200 : [ 1238 0.02 0.07 ]
|XXX 200 - 250 : [ 1162 0.02 0.09 ]
|XXX 250 - 300 : [ 1085 0.02 0.10 ]
|XXX 300 - 350 : [ 1193 0.02 0.12 ]
|XXX 350 - 400 : [ 1291 0.02 0.14 ]
|XXXX 400 - 450 : [ 1535 0.02 0.16 ]
|XXXX 450 - 500 : [ 1735 0.02 0.18 ]
|XXXXX 500 - 550 : [ 1950 0.03 0.21 ]
|XXXXXX 550 - 600 : [ 2438 0.03 0.24 ]
|XXXXXXXX 600 - 650 : [ 3227 0.05 0.29 ]
|XXXXXXXXXXXX 650 - 700 : [ 4522 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXX 700 - 750 : [ 7010 0.10 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 11167 0.16 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 15465 0.22 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 850 - 900 : [ 10228 0.14 0.98 ]
|XXXX 900 - 950 : [ 1643 0.02 1.00 ]
| 950 - 1000 : [ 32 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AWGG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AWGG 3634512_fasta.screen.trimQ15.SaF > reads.trim15.AWGG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AWGG.rl 2 50
-------------------------------------------------------------------
#Found 6682 total values totalling 4745967.0000. <710.261449 +/- 131.793350>
#Range: [ 19 - 922 ]
#Most likely bin: [ 750 - 800 ] 1821 counts
#Median bin: [ 700 - 750 ] 1246 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 10 0.00 0.00 ]
| 50 - 100 : [ 22 0.00 0.00 ]
| 100 - 150 : [ 13 0.00 0.01 ]
| 150 - 200 : [ 16 0.00 0.01 ]
|X 200 - 250 : [ 24 0.00 0.01 ]
|X 250 - 300 : [ 45 0.01 0.02 ]
|X 300 - 350 : [ 54 0.01 0.03 ]
|X 350 - 400 : [ 67 0.01 0.04 ]
|XXX 400 - 450 : [ 131 0.02 0.06 ]
|XXX 450 - 500 : [ 134 0.02 0.08 ]
|XXXX 500 - 550 : [ 196 0.03 0.11 ]
|XXXXXXXX 550 - 600 : [ 346 0.05 0.16 ]
|XXXXXXXX 600 - 650 : [ 377 0.06 0.21 ]
|XXXXXXXXXXXXXXX 650 - 700 : [ 674 0.10 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1246 0.19 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 1821 0.27 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1266 0.19 0.96 ]
|XXXXX 850 - 900 : [ 234 0.04 1.00 ]
| 900 - 950 : [ 6 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for BAOF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep BAOF 3634512_fasta.screen.trimQ15.SaF > reads.trim15.BAOF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.BAOF.rl 2 50
-------------------------------------------------------------------
#Found 5981 total values totalling 3458713.0000. <578.283397 +/- 245.463398>
#Range: [ 11 - 967 ]
#Most likely bin: [ 750 - 800 ] 837 counts
#Median bin: [ 650 - 700 ] 640 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 0 - 50 : [ 190 0.03 0.03 ]
|XXXXXXXXXX 50 - 100 : [ 210 0.04 0.07 ]
|XXXXXXX 100 - 150 : [ 148 0.02 0.09 ]
|XXXXXXXXX 150 - 200 : [ 180 0.03 0.12 ]
|XXXXXXX 200 - 250 : [ 154 0.03 0.15 ]
|XXXXXXXXX 250 - 300 : [ 195 0.03 0.18 ]
|XXXXXXXXXXX 300 - 350 : [ 240 0.04 0.22 ]
|XXXXXXXXX 350 - 400 : [ 183 0.03 0.25 ]
|XXXXXXXX 400 - 450 : [ 159 0.03 0.28 ]
|XXXXXXXXX 450 - 500 : [ 179 0.03 0.31 ]
|XXXXXXXXX 500 - 550 : [ 188 0.03 0.34 ]
|XXXXXXXXXXXXX 550 - 600 : [ 278 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 439 0.07 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 640 0.11 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 798 0.13 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 837 0.14 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 666 0.11 0.95 ]
|XXXXXXXXXXXXX 850 - 900 : [ 274 0.05 1.00 ]
|X 900 - 950 : [ 22 0.00 1.00 ]
| 950 - 1000 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for BAOG
trimt JAZZ trim 15 readlength histogram for BAOH
trimt JAZZ trim 15 readlength histogram for BFTN
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep BFTN 3634512_fasta.screen.trimQ15.SaF > reads.trim15.BFTN.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.BFTN.rl 2 50
-------------------------------------------------------------------
#Found 7299 total values totalling 3376423.0000. <462.587067 +/- 247.384793>
#Range: [ 11 - 917 ]
#Most likely bin: [ 700 - 750 ] 687 counts
#Median bin: [ 450 - 500 ] 247 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 0 - 50 : [ 188 0.03 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 50 - 100 : [ 562 0.08 0.10 ]
|XXXXXXXXXXXXXXXXXX 100 - 150 : [ 303 0.04 0.14 ]
|XXXXXXXXXXXXXXXXXXXXX 150 - 200 : [ 355 0.05 0.19 ]
|XXXXXXXXXXXXXXXXXXX 200 - 250 : [ 321 0.04 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 482 0.07 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 300 - 350 : [ 616 0.08 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 350 - 400 : [ 443 0.06 0.45 ]
|XXXXXXXXXXXXXXXXXX 400 - 450 : [ 308 0.04 0.49 ]
|XXXXXXXXXXXXXX 450 - 500 : [ 247 0.03 0.52 ]
|XXXXXXXXXXXXXXX 500 - 550 : [ 265 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 352 0.05 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 488 0.07 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 667 0.09 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 687 0.09 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 567 0.08 0.94 ]
|XXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 345 0.05 0.99 ]
|XXXXXX 850 - 900 : [ 102 0.01 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
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 95451 total values totalling 28597.5714. <0.299605 +/- 0.047529>
#Range: [ 0 - 0.8182 ]
#Most likely bin: [ 0.29 - 0.295 ] 4746 counts
#Median bin: [ 0.295 - 0.3 ] 4628 counts
#Entropy = 5.1689 bits
| 0 - 0.005 : [ 1 1.05e-05 1.05e-05 ]
#...
| 0.03 - 0.035 : [ 1 1.05e-05 2.10e-05 ]
#...
| 0.04 - 0.045 : [ 1 1.05e-05 3.14e-05 ]
| 0.045 - 0.05 : [ 1 1.05e-05 4.19e-05 ]
| 0.05 - 0.055 : [ 1 1.05e-05 5.24e-05 ]
#...
| 0.06 - 0.065 : [ 2 2.10e-05 7.33e-05 ]
| 0.065 - 0.07 : [ 4 4.19e-05 1.15e-04 ]
| 0.07 - 0.075 : [ 2 2.10e-05 1.36e-04 ]
| 0.075 - 0.08 : [ 3 3.14e-05 1.68e-04 ]
| 0.08 - 0.085 : [ 7 7.33e-05 2.41e-04 ]
| 0.085 - 0.09 : [ 5 5.24e-05 2.93e-04 ]
| 0.09 - 0.095 : [ 10 1.05e-04 3.98e-04 ]
| 0.095 - 0.1 : [ 6 6.29e-05 4.61e-04 ]
| 0.1 - 0.105 : [ 12 1.26e-04 5.87e-04 ]
| 0.105 - 0.11 : [ 4 4.19e-05 6.29e-04 ]
| 0.11 - 0.115 : [ 7 7.33e-05 7.02e-04 ]
| 0.115 - 0.12 : [ 10 1.05e-04 8.07e-04 ]
| 0.12 - 0.125 : [ 11 1.15e-04 9.22e-04 ]
| 0.125 - 0.13 : [ 17 1.78e-04 1.10e-03 ]
| 0.13 - 0.135 : [ 19 1.99e-04 1.30e-03 ]
| 0.135 - 0.14 : [ 27 2.83e-04 1.58e-03 ]
| 0.14 - 0.145 : [ 23 2.41e-04 1.82e-03 ]
| 0.145 - 0.15 : [ 30 3.14e-04 2.14e-03 ]
| 0.15 - 0.155 : [ 43 4.50e-04 2.59e-03 ]
| 0.155 - 0.16 : [ 40 4.19e-04 3.01e-03 ]
| 0.16 - 0.165 : [ 52 5.45e-04 3.55e-03 ]
| 0.165 - 0.17 : [ 42 4.40e-04 3.99e-03 ]
|X 0.17 - 0.175 : [ 65 6.81e-04 4.67e-03 ]
|X 0.175 - 0.18 : [ 82 8.59e-04 5.53e-03 ]
|X 0.18 - 0.185 : [ 107 1.12e-03 6.65e-03 ]
|X 0.185 - 0.19 : [ 141 1.48e-03 8.13e-03 ]
|X 0.19 - 0.195 : [ 154 1.61e-03 9.74e-03 ]
|X 0.195 - 0.2 : [ 156 1.63e-03 1.14e-02 ]
|XXX 0.2 - 0.205 : [ 300 3.14e-03 1.45e-02 ]
|XXX 0.205 - 0.21 : [ 341 3.57e-03 1.81e-02 ]
|XXXX 0.21 - 0.215 : [ 479 5.02e-03 2.31e-02 ]
|XXXXX 0.215 - 0.22 : [ 541 5.67e-03 2.88e-02 ]
|XXXXXX 0.22 - 0.225 : [ 715 7.49e-03 3.63e-02 ]
|XXXXXXXX 0.225 - 0.23 : [ 902 9.45e-03 4.57e-02 ]
|XXXXXXXXXX 0.23 - 0.235 : [ 1154 1.21e-02 5.78e-02 ]
|XXXXXXXXXXXXX 0.235 - 0.24 : [ 1533 1.61e-02 7.39e-02 ]
|XXXXXXXXXXXXXXX 0.24 - 0.245 : [ 1812 1.90e-02 9.29e-02 ]
|XXXXXXXXXXXXXXXX 0.245 - 0.25 : [ 1924 2.02e-02 1.13e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.25 - 0.255 : [ 2715 2.84e-02 1.41e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.255 - 0.26 : [ 2858 2.99e-02 1.71e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.26 - 0.265 : [ 3367 3.53e-02 2.07e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.265 - 0.27 : [ 3657 3.83e-02 2.45e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.27 - 0.275 : [ 3877 4.06e-02 2.86e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.275 - 0.28 : [ 4280 4.48e-02 3.30e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.28 - 0.285 : [ 4521 4.74e-02 3.78e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.285 - 0.29 : [ 4558 4.78e-02 4.26e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 4746 4.97e-02 4.75e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.295 - 0.3 : [ 4628 4.85e-02 5.24e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 4633 4.85e-02 5.72e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 4473 4.69e-02 6.19e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 4315 4.52e-02 6.64e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 4110 4.31e-02 7.07e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 3741 3.92e-02 7.47e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 3486 3.65e-02 7.83e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 3144 3.29e-02 8.16e-01 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 2875 3.01e-02 8.46e-01 ]
|XXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 2504 2.62e-02 8.72e-01 ]
|XXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 2192 2.30e-02 8.95e-01 ]
|XXXXXXXXXXXXXXX 0.35 - 0.355 : [ 1824 1.91e-02 9.15e-01 ]
|XXXXXXXXXXXXX 0.355 - 0.36 : [ 1551 1.62e-02 9.31e-01 ]
|XXXXXXXXXXX 0.36 - 0.365 : [ 1316 1.38e-02 9.45e-01 ]
|XXXXXXXXX 0.365 - 0.37 : [ 1042 1.09e-02 9.55e-01 ]
|XXXXXX 0.37 - 0.375 : [ 662 6.94e-03 9.62e-01 ]
|XXXX 0.375 - 0.38 : [ 526 5.51e-03 9.68e-01 ]
|XXX 0.38 - 0.385 : [ 379 3.97e-03 9.72e-01 ]
|XX 0.385 - 0.39 : [ 251 2.63e-03 9.75e-01 ]
|XX 0.39 - 0.395 : [ 211 2.21e-03 9.77e-01 ]
|X 0.395 - 0.4 : [ 141 1.48e-03 9.78e-01 ]
|X 0.4 - 0.405 : [ 167 1.75e-03 9.80e-01 ]
|X 0.405 - 0.41 : [ 112 1.17e-03 9.81e-01 ]
|X 0.41 - 0.415 : [ 111 1.16e-03 9.82e-01 ]
|X 0.415 - 0.42 : [ 97 1.02e-03 9.83e-01 ]
|X 0.42 - 0.425 : [ 86 9.01e-04 9.84e-01 ]
|X 0.425 - 0.43 : [ 71 7.44e-04 9.85e-01 ]
| 0.43 - 0.435 : [ 51 5.34e-04 9.85e-01 ]
| 0.435 - 0.44 : [ 51 5.34e-04 9.86e-01 ]
|X 0.44 - 0.445 : [ 70 7.33e-04 9.87e-01 ]
| 0.445 - 0.45 : [ 59 6.18e-04 9.87e-01 ]
| 0.45 - 0.455 : [ 40 4.19e-04 9.88e-01 ]
| 0.455 - 0.46 : [ 32 3.35e-04 9.88e-01 ]
| 0.46 - 0.465 : [ 42 4.40e-04 9.89e-01 ]
| 0.465 - 0.47 : [ 45 4.71e-04 9.89e-01 ]
|X 0.47 - 0.475 : [ 80 8.38e-04 9.90e-01 ]
|X 0.475 - 0.48 : [ 101 1.06e-03 9.91e-01 ]
|X 0.48 - 0.485 : [ 96 1.01e-03 9.92e-01 ]
|X 0.485 - 0.49 : [ 74 7.75e-04 9.93e-01 ]
| 0.49 - 0.495 : [ 57 5.97e-04 9.93e-01 ]
| 0.495 - 0.5 : [ 41 4.30e-04 9.94e-01 ]
| 0.5 - 0.505 : [ 51 5.34e-04 9.94e-01 ]
| 0.505 - 0.51 : [ 55 5.76e-04 9.95e-01 ]
| 0.51 - 0.515 : [ 53 5.55e-04 9.95e-01 ]
|X 0.515 - 0.52 : [ 79 8.28e-04 9.96e-01 ]
|X 0.52 - 0.525 : [ 87 9.11e-04 9.97e-01 ]
|X 0.525 - 0.53 : [ 64 6.71e-04 9.98e-01 ]
| 0.53 - 0.535 : [ 33 3.46e-04 9.98e-01 ]
| 0.535 - 0.54 : [ 30 3.14e-04 9.98e-01 ]
| 0.54 - 0.545 : [ 24 2.51e-04 9.99e-01 ]
| 0.545 - 0.55 : [ 20 2.10e-04 9.99e-01 ]
| 0.55 - 0.555 : [ 13 1.36e-04 9.99e-01 ]
| 0.555 - 0.56 : [ 9 9.43e-05 9.99e-01 ]
| 0.56 - 0.565 : [ 8 8.38e-05 9.99e-01 ]
| 0.565 - 0.57 : [ 7 7.33e-05 9.99e-01 ]
| 0.57 - 0.575 : [ 3 3.14e-05 9.99e-01 ]
| 0.575 - 0.58 : [ 1 1.05e-05 9.99e-01 ]
| 0.58 - 0.585 : [ 1 1.05e-05 9.99e-01 ]
#...
| 0.59 - 0.595 : [ 8 8.38e-05 9.99e-01 ]
#...
| 0.6 - 0.605 : [ 2 2.10e-05 9.99e-01 ]
| 0.605 - 0.61 : [ 3 3.14e-05 1.00e+00 ]
| 0.61 - 0.615 : [ 4 4.19e-05 1.00e+00 ]
| 0.615 - 0.62 : [ 4 4.19e-05 1.00e+00 ]
| 0.62 - 0.625 : [ 3 3.14e-05 1.00e+00 ]
| 0.625 - 0.63 : [ 4 4.19e-05 1.00e+00 ]
| 0.63 - 0.635 : [ 3 3.14e-05 1.00e+00 ]
#...
| 0.64 - 0.645 : [ 6 6.29e-05 1.00e+00 ]
#...
| 0.65 - 0.655 : [ 1 1.05e-05 1.00e+00 ]
| 0.655 - 0.66 : [ 3 3.14e-05 1.00e+00 ]
#...
| 0.665 - 0.67 : [ 1 1.05e-05 1.00e+00 ]
#...
| 0.675 - 0.68 : [ 1 1.05e-05 1.00e+00 ]
| 0.68 - 0.685 : [ 4 4.19e-05 1.00e+00 ]
| 0.685 - 0.69 : [ 1 1.05e-05 1.00e+00 ]
| 0.69 - 0.695 : [ 3 3.14e-05 1.00e+00 ]
| 0.695 - 0.7 : [ 1 1.05e-05 1.00e+00 ]
| 0.7 - 0.705 : [ 1 1.05e-05 1.00e+00 ]
#...
| 0.72 - 0.725 : [ 1 1.05e-05 1.00e+00 ]
| 0.725 - 0.73 : [ 2 2.10e-05 1.00e+00 ]
#...
| 0.735 - 0.74 : [ 1 1.05e-05 1.00e+00 ]
#...
| 0.75 - 0.755 : [ 1 1.05e-05 1.00e+00 ]
#...
| 0.8 - 0.805 : [ 1 1.05e-05 1.00e+00 ]
#...
| 0.815 - 0.82 : [ 1 1.05e-05 1.00e+00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 845. 944 reads; 69656 bp (untrimmed), 69449 (trimmed).
Contig 846. 966 reads; 67503 bp (untrimmed), 67404 (trimmed).
Contig 847. 1107 reads; 51151 bp (untrimmed), 51130 (trimmed).
Contig 848. 1209 reads; 82360 bp (untrimmed), 82205 (trimmed).
Contig 849. 1309 reads; 92927 bp (untrimmed), 92480 (trimmed).
Contig 850. 1314 reads; 100440 bp (untrimmed), 100343 (trimmed).
Contig 851. 1380 reads; 99355 bp (untrimmed), 99207 (trimmed).
Contig 852. 1389 reads; 97620 bp (untrimmed), 97424 (trimmed).
Contig 853. 1474 reads; 100321 bp (untrimmed), 100145 (trimmed).
Contig 854. 1663 reads; 108234 bp (untrimmed), 108091 (trimmed).
Contig 855. 1694 reads; 110002 bp (untrimmed), 109927 (trimmed).
Contig 856. 1929 reads; 111530 bp (untrimmed), 111433 (trimmed).
Contig 857. 1938 reads; 105985 bp (untrimmed), 105675 (trimmed).
Contig 858. 1954 reads; 139613 bp (untrimmed), 139151 (trimmed).
Contig 859. 2056 reads; 123752 bp (untrimmed), 123655 (trimmed).
Contig 860. 2152 reads; 141049 bp (untrimmed), 141019 (trimmed).
Contig 861. 2292 reads; 114634 bp (untrimmed), 114164 (trimmed).
Contig 862. 2413 reads; 179850 bp (untrimmed), 179664 (trimmed).
Contig 863. 2428 reads; 140866 bp (untrimmed), 140820 (trimmed).
Contig 864. 2484 reads; 183321 bp (untrimmed), 183238 (trimmed).
Contig 865. 2976 reads; 223578 bp (untrimmed), 223489 (trimmed).
Contig 866. 3425 reads; 241398 bp (untrimmed), 241089 (trimmed).
Contig 867. 3838 reads; 249359 bp (untrimmed), 249316 (trimmed).
Contig 868. 5824 reads; 352289 bp (untrimmed), 352055 (trimmed).
Contig 869. 7162 reads; 430817 bp (untrimmed), 430717 (trimmed).
Contig 870. 7376 reads; 492380 bp (untrimmed), 492273 (trimmed).
Contig 871. 16563 reads; 1000800 bp (untrimmed), 1000662 (trimmed).
--------------------------------------------------------------
Totals 95555 reads; 7417676 bp (untrimmed), 7275262 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 7405547 bases Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 828
HQ Discrepant reads = 311
Chimeric reads = 128
Suspect alignments = 526
-------------------------------------------------------------------
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.06Sep05.QD