Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-13-2005
Runby: Kerrie Barry
Description: analysis of libraries completely sequenced (well, complete at this time)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3635728 2400 1219 Prochlorococcus marinus
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Prochlorococcus_marinus
-------------------------------------------------------------------
Prochlorococcus marinus, species, cyanobacteria
Prochlorococcus, genus, cyanobacteria
Prochlorococcaceae, family, cyanobacteria
Prochlorales (prochlorophytes), order, cyanobacteria
Cyanobacteria (blue-green algae), phylum, cyanobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 1842827
# phrap: 1837955
# db:
altered.
2400000
2026927 +/- 263809
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 0
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: 33515
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 0
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: 5510
Total bp X'd :
reads >= 20% >= 50% >= 80% screened
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 9495923
C = 6291652
G = 6238833
T = 9287501
N = 195183
X = 301617
GC fraction = 0.39
Total = 31810709
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3635728_fasta.screen.contigs
-------------------------------------------------------------------
A 616945
C 329080
G 318370
T 578947
N 9
fraction GC = 0.35
total bases = 1843351
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 APZF reads.list > grep.reads.list.APZF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APZF 4 500
-------------------------------------------------------------------
#Found 5968 total values totalling 34361237.0000. <5757.579926 +/- 42698.805050>
#Range: [ 606 - 1050125 ]
#Most likely bin: [ 3500 - 4000 ] 2489 counts
#Median bin: [ 3500 - 4000 ] 2489 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 12 0.00 0.00 ]
| 1000 - 1500 : [ 28 0.00 0.01 ]
|X 1500 - 2000 : [ 40 0.01 0.01 ]
|X 2000 - 2500 : [ 76 0.01 0.03 ]
|XXXX 2500 - 3000 : [ 251 0.04 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2452 0.41 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2489 0.42 0.90 ]
|XXXXXXXXX 4000 - 4500 : [ 586 0.10 0.99 ]
| 4500 - 5000 : [ 5 0.00 1.00 ]
#...
| 10000 - 10500 : [ 4 0.00 1.00 ]
| 10500 - 11000 : [ 1 0.00 1.00 ]
| 11000 - 11500 : [ 1 0.00 1.00 ]
#...
| 21000 - 21500 : [ 1 0.00 1.00 ]
| 21500 - 22000 : [ 1 0.00 1.00 ]
#...
| 25000 - 25500 : [ 1 0.00 1.00 ]
#...
| 118000 - 118500 : [ 1 0.00 1.00 ]
#...
| 132500 - 133000 : [ 1 0.00 1.00 ]
#...
| 185500 - 186000 : [ 1 0.00 1.00 ]
#...
| 250500 - 251000 : [ 1 0.00 1.00 ]
#...
| 302500 - 303000 : [ 1 0.00 1.00 ]
#...
| 406500 - 407000 : [ 1 0.00 1.00 ]
#...
| 471500 - 472000 : [ 1 0.00 1.00 ]
#...
| 718000 - 718500 : [ 1 0.00 1.00 ]
#...
| 730500 - 731000 : [ 1 0.00 1.00 ]
#...
| 875500 - 876000 : [ 1 0.00 1.00 ]
#...
| 876500 - 877000 : [ 4 0.00 1.00 ]
| 877000 - 877500 : [ 3 0.00 1.00 ]
#...
| 994500 - 995000 : [ 1 0.00 1.00 ]
#...
| 1049500 - 1050000 : [ 1 0.00 1.00 ]
| 1050000 - 1050500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APZG reads.list > grep.reads.list.APZG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APZG 4 500
-------------------------------------------------------------------
#Found 6395 total values totalling 76601294.0000. <11978.310242 +/- 67191.588675>
#Range: [ 1078 - 1269291 ]
#Most likely bin: [ 6000 - 6500 ] 1614 counts
#Median bin: [ 6000 - 6500 ] 1614 counts
#Histogram Bins Count Fraction Cum_Fraction
| 1000 - 1500 : [ 18 0.00 0.00 ]
| 1500 - 2000 : [ 14 0.00 0.01 ]
| 2000 - 2500 : [ 19 0.00 0.01 ]
| 2500 - 3000 : [ 19 0.00 0.01 ]
|X 3000 - 3500 : [ 28 0.00 0.02 ]
|X 3500 - 4000 : [ 42 0.01 0.02 ]
|X 4000 - 4500 : [ 53 0.01 0.03 ]
|XXX 4500 - 5000 : [ 113 0.02 0.05 ]
|XXXXXXXXXXXXX 5000 - 5500 : [ 532 0.08 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1577 0.25 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1614 0.25 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1191 0.19 0.82 ]
|XXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 781 0.12 0.94 ]
|XXXXXXXX 7500 - 8000 : [ 311 0.05 0.99 ]
| 8000 - 8500 : [ 6 0.00 0.99 ]
| 8500 - 9000 : [ 1 0.00 0.99 ]
#...
| 9500 - 10000 : [ 1 0.00 0.99 ]
#...
| 12000 - 12500 : [ 1 0.00 0.99 ]
| 12500 - 13000 : [ 4 0.00 0.99 ]
| 13000 - 13500 : [ 4 0.00 0.99 ]
| 13500 - 14000 : [ 5 0.00 0.99 ]
| 14000 - 14500 : [ 1 0.00 0.99 ]
#...
| 33000 - 33500 : [ 1 0.00 0.99 ]
#...
| 66500 - 67000 : [ 1 0.00 0.99 ]
#...
| 73500 - 74000 : [ 1 0.00 0.99 ]
#...
| 89000 - 89500 : [ 1 0.00 0.99 ]
#...
| 95500 - 96000 : [ 1 0.00 0.99 ]
#...
| 107500 - 108000 : [ 1 0.00 0.99 ]
#...
| 140500 - 141000 : [ 1 0.00 0.99 ]
#...
| 162000 - 162500 : [ 1 0.00 0.99 ]
#...
| 175000 - 175500 : [ 1 0.00 0.99 ]
#...
| 194000 - 194500 : [ 1 0.00 0.99 ]
#...
| 195500 - 196000 : [ 1 0.00 0.99 ]
#...
| 243500 - 244000 : [ 1 0.00 0.99 ]
#...
| 247500 - 248000 : [ 1 0.00 0.99 ]
#...
| 260000 - 260500 : [ 1 0.00 0.99 ]
#...
| 293500 - 294000 : [ 1 0.00 0.99 ]
#...
| 294500 - 295000 : [ 1 0.00 0.99 ]
#...
| 326500 - 327000 : [ 1 0.00 0.99 ]
#...
| 347500 - 348000 : [ 1 0.00 0.99 ]
#...
| 367500 - 368000 : [ 1 0.00 0.99 ]
#...
| 370500 - 371000 : [ 1 0.00 0.99 ]
#...
| 436000 - 436500 : [ 1 0.00 0.99 ]
#...
| 445500 - 446000 : [ 1 0.00 0.99 ]
#...
| 528500 - 529000 : [ 1 0.00 0.99 ]
#...
| 548500 - 549000 : [ 1 0.00 0.99 ]
#...
| 577500 - 578000 : [ 1 0.00 0.99 ]
#...
| 606000 - 606500 : [ 1 0.00 0.99 ]
#...
| 621000 - 621500 : [ 1 0.00 0.99 ]
#...
| 640500 - 641000 : [ 1 0.00 0.99 ]
#...
| 696000 - 696500 : [ 1 0.00 1.00 ]
#...
| 705500 - 706000 : [ 1 0.00 1.00 ]
#...
| 740000 - 740500 : [ 1 0.00 1.00 ]
#...
| 750000 - 750500 : [ 1 0.00 1.00 ]
#...
| 820000 - 820500 : [ 1 0.00 1.00 ]
#...
| 850000 - 850500 : [ 1 0.00 1.00 ]
#...
| 877000 - 877500 : [ 1 0.00 1.00 ]
#...
| 878500 - 879000 : [ 3 0.00 1.00 ]
| 879000 - 879500 : [ 8 0.00 1.00 ]
| 879500 - 880000 : [ 2 0.00 1.00 ]
| 880000 - 880500 : [ 2 0.00 1.00 ]
| 880500 - 881000 : [ 3 0.00 1.00 ]
#...
| 928000 - 928500 : [ 1 0.00 1.00 ]
#...
| 930000 - 930500 : [ 1 0.00 1.00 ]
#...
| 961500 - 962000 : [ 1 0.00 1.00 ]
#...
| 1053000 - 1053500 : [ 1 0.00 1.00 ]
#...
| 1107500 - 1108000 : [ 1 0.00 1.00 ]
#...
| 1109000 - 1109500 : [ 1 0.00 1.00 ]
#...
| 1269000 - 1269500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APZH reads.list > grep.reads.list.APZH
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.APZH 4 500
-------------------------------------------------------------------
#Found 191 total values totalling 7111312.0000. <37232.000000 +/- 4235.229373>
#Range: [ 26904 - 55567 ]
#Most likely bin: [ 34500 - 35000 ] 16 counts
#Median bin: [ 36500 - 37000 ] 6 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 26500 - 27000 : [ 1 0.01 0.01 ]
#...
|XXXXX 28000 - 28500 : [ 2 0.01 0.02 ]
|XX 28500 - 29000 : [ 1 0.01 0.02 ]
#...
|XX 29500 - 30000 : [ 1 0.01 0.03 ]
#...
|XXXXXXXX 30500 - 31000 : [ 3 0.02 0.04 ]
|XXXXXXXXXX 31000 - 31500 : [ 4 0.02 0.06 ]
|XXXXXXXXXX 31500 - 32000 : [ 4 0.02 0.08 ]
|XXXXXXXXXX 32000 - 32500 : [ 4 0.02 0.10 ]
|XXXXXXXXXXXXXXX 32500 - 33000 : [ 6 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 8 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 7 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 8 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 16 0.08 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 11 0.06 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 13 0.07 0.47 ]
|XXXXXXXX 36000 - 36500 : [ 3 0.02 0.48 ]
|XXXXXXXXXXXXXXX 36500 - 37000 : [ 6 0.03 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 9 0.05 0.56 ]
|XXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 7 0.04 0.60 ]
|XXXXXXXXXX 38000 - 38500 : [ 4 0.02 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 9 0.05 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 11 0.06 0.72 ]
|XXXXXXXXXX 39500 - 40000 : [ 4 0.02 0.74 ]
|XXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 8 0.04 0.79 ]
|XXXXXXXXXXXXXXX 40500 - 41000 : [ 6 0.03 0.82 ]
|XXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 7 0.04 0.85 ]
|XXXXXXXXXXXX 41500 - 42000 : [ 5 0.03 0.88 ]
|XXXXXXXX 42000 - 42500 : [ 3 0.02 0.90 ]
|XXXXXXXXXX 42500 - 43000 : [ 4 0.02 0.92 ]
|XX 43000 - 43500 : [ 1 0.01 0.92 ]
|XX 43500 - 44000 : [ 1 0.01 0.93 ]
|XXXXXXXXXXXXXXX 44000 - 44500 : [ 6 0.03 0.96 ]
|XXXXXXXX 44500 - 45000 : [ 3 0.02 0.97 ]
|XX 45000 - 45500 : [ 1 0.01 0.98 ]
#...
|XX 46000 - 46500 : [ 1 0.01 0.98 ]
#...
|XX 48000 - 48500 : [ 1 0.01 0.99 ]
#...
|XX 49500 - 50000 : [ 1 0.01 0.99 ]
#...
|XX 55500 - 56000 : [ 1 0.01 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# APZF 3355 +- 664 (n=2939)
# APZH 36862 +- 4432 (n=97)
# APZG 6154 +- 1052 (n=3201)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3635728_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
APZF 19200 85 446 90 530 19030 83 521 88 536
APZG 18432 93 756 97 727 18432 94 754 98 746
APZH 3072 83 567 94 556 3072 83 570 94 592
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
APZF 9514 85 531 90 544 9516 80 510 86 527
APZG 9216 94 753 98 744 9216 94 756 97 747
APZH 1536 81 542 93 577 1536 85 597 95 608
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3635728_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
96 16028 8367 87.16 90.79 APZG @
16 2021 1275 79.69 83.01 APZH @
100 15466 8858 88.58 92.27 APZF @
] 33515 18500 87.26 cumulative total@@
LIBRARY PLATE ID COUNT [ APZG 96 APZH 16 APZF 100 ] for 212 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 3635728_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 40534 total values totalling 22781224.0000. <562.027532 +/- 267.961353>
#Range: [ 0 - 916 ]
#Most likely bin: [ 750 - 800 ] 6988 counts
#Median bin: [ 650 - 700 ] 3623 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 4177 0.10 0.10 ]
|XXXXX 50 - 100 : [ 799 0.02 0.12 ]
|XXXX 100 - 150 : [ 661 0.02 0.14 ]
|XXX 150 - 200 : [ 603 0.01 0.15 ]
|XXXX 200 - 250 : [ 746 0.02 0.17 ]
|XXXXX 250 - 300 : [ 912 0.02 0.19 ]
|XXXXXX 300 - 350 : [ 1013 0.02 0.22 ]
|XXXXXX 350 - 400 : [ 1031 0.03 0.25 ]
|XXXXXXX 400 - 450 : [ 1188 0.03 0.27 ]
|XXXXXXXX 450 - 500 : [ 1385 0.03 0.31 ]
|XXXXXXXXX 500 - 550 : [ 1570 0.04 0.35 ]
|XXXXXXXXXXXX 550 - 600 : [ 2099 0.05 0.40 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 2683 0.07 0.47 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3623 0.09 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5191 0.13 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6988 0.17 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4885 0.12 0.98 ]
|XXXXXX 850 - 900 : [ 964 0.02 1.00 ]
| 900 - 950 : [ 16 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APZF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APZF 3635728_fasta.screen.trimQ15.SaF > reads.trim15.APZF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APZF.rl 2 50
-------------------------------------------------------------------
#Found 19030 total values totalling 8254229.0000. <433.748240 +/- 249.433285>
#Range: [ 0 - 858 ]
#Most likely bin: [ 0 - 50 ] 2691 counts
#Median bin: [ 500 - 550 ] 1301 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 2691 0.14 0.14 ]
|XXXXXXXXX 50 - 100 : [ 634 0.03 0.17 ]
|XXXXXXXX 100 - 150 : [ 554 0.03 0.20 ]
|XXXXXXXX 150 - 200 : [ 525 0.03 0.23 ]
|XXXXXXXXX 200 - 250 : [ 616 0.03 0.26 ]
|XXXXXXXXXX 250 - 300 : [ 676 0.04 0.30 ]
|XXXXXXXXXXX 300 - 350 : [ 739 0.04 0.34 ]
|XXXXXXXXXXXX 350 - 400 : [ 798 0.04 0.38 ]
|XXXXXXXXXXXXXXX 400 - 450 : [ 984 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXX 450 - 500 : [ 1190 0.06 0.49 ]
|XXXXXXXXXXXXXXXXXXX 500 - 550 : [ 1301 0.07 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1684 0.09 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 2045 0.11 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 2193 0.12 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1704 0.09 0.96 ]
|XXXXXXXXXX 750 - 800 : [ 647 0.03 1.00 ]
|X 800 - 850 : [ 47 0.00 1.00 ]
| 850 - 900 : [ 2 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APZG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APZG 3635728_fasta.screen.trimQ15.SaF > reads.trim15.APZG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APZG.rl 2 50
-------------------------------------------------------------------
#Found 18432 total values totalling 13056323.0000. <708.350857 +/- 205.217217>
#Range: [ 0 - 916 ]
#Most likely bin: [ 750 - 800 ] 6034 counts
#Median bin: [ 750 - 800 ] 6034 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXX 0 - 50 : [ 1071 0.06 0.06 ]
| 50 - 100 : [ 61 0.00 0.06 ]
| 100 - 150 : [ 65 0.00 0.06 ]
| 150 - 200 : [ 36 0.00 0.07 ]
| 200 - 250 : [ 60 0.00 0.07 ]
| 250 - 300 : [ 68 0.00 0.07 ]
|X 300 - 350 : [ 81 0.00 0.08 ]
| 350 - 400 : [ 74 0.00 0.08 ]
|X 400 - 450 : [ 106 0.01 0.09 ]
|X 450 - 500 : [ 119 0.01 0.09 ]
|X 500 - 550 : [ 165 0.01 0.10 ]
|XX 550 - 600 : [ 253 0.01 0.12 ]
|XXX 600 - 650 : [ 410 0.02 0.14 ]
|XXXXXXX 650 - 700 : [ 1094 0.06 0.20 ]
|XXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3052 0.17 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6034 0.33 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4720 0.26 0.95 ]
|XXXXXX 850 - 900 : [ 947 0.05 1.00 ]
| 900 - 950 : [ 16 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for APZH
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep APZH 3635728_fasta.screen.trimQ15.SaF > reads.trim15.APZH.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.APZH.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 1470672.0000. <478.734375 +/- 268.299877>
#Range: [ 0 - 865 ]
#Most likely bin: [ 700 - 750 ] 435 counts
#Median bin: [ 550 - 600 ] 162 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 415 0.14 0.14 ]
|XXXXXXXXXX 50 - 100 : [ 104 0.03 0.17 ]
|XXXX 100 - 150 : [ 42 0.01 0.18 ]
|XXXX 150 - 200 : [ 42 0.01 0.20 ]
|XXXXXX 200 - 250 : [ 70 0.02 0.22 ]
|XXXXXXXXXXXXXXX 250 - 300 : [ 168 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXX 300 - 350 : [ 193 0.06 0.34 ]
|XXXXXXXXXXXXXXX 350 - 400 : [ 159 0.05 0.39 ]
|XXXXXXXXX 400 - 450 : [ 98 0.03 0.42 ]
|XXXXXXX 450 - 500 : [ 76 0.02 0.44 ]
|XXXXXXXXXX 500 - 550 : [ 104 0.03 0.48 ]
|XXXXXXXXXXXXXXX 550 - 600 : [ 162 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 228 0.07 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 336 0.11 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 435 0.14 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 307 0.10 0.96 ]
|XXXXXXXXXXX 800 - 850 : [ 118 0.04 1.00 ]
|X 850 - 900 : [ 15 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ATUF
trimt JAZZ trim 15 readlength histogram for ATYS
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3635728
-------------------------------------------------------------------
APZF.000001.000100 pUC18.fa pUC18.fa LRS.fasta
APZF.000101.000200 pUC18.fa pUC18.fa LRS.fasta
APZG.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
APZG.000101.000200 pMCL200.fa LRS.fasta
APZH.000001.000100 pCC1Fos.fa LRS.fasta
APZF.000001.000100 pUC18.fa pUC18.fa LRS.fasta
APZF.000101.000200 pUC18.fa pUC18.fa LRS.fasta
APZG.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta
APZG.000101.000200 pMCL200.fa LRS.fasta
APZH.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3635728_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3635728_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 33358 total values totalling 12982.4613. <0.389186 +/- 0.098116>
#Range: [ 0.025 - 0.9615 ]
#Most likely bin: [ 0.36 - 0.365 ] 1309 counts
#Median bin: [ 0.365 - 0.37 ] 1266 counts
| 0.025 - 0.03 : [ 1 0.00 0.00 ]
#...
| 0.04 - 0.045 : [ 1 0.00 0.00 ]
#...
| 0.09 - 0.095 : [ 1 0.00 0.00 ]
#...
| 0.105 - 0.11 : [ 1 0.00 0.00 ]
#...
| 0.115 - 0.12 : [ 1 0.00 0.00 ]
| 0.12 - 0.125 : [ 1 0.00 0.00 ]
| 0.125 - 0.13 : [ 1 0.00 0.00 ]
#...
| 0.135 - 0.14 : [ 1 0.00 0.00 ]
| 0.14 - 0.145 : [ 2 0.00 0.00 ]
#...
| 0.15 - 0.155 : [ 3 0.00 0.00 ]
| 0.155 - 0.16 : [ 1 0.00 0.00 ]
| 0.16 - 0.165 : [ 5 0.00 0.00 ]
| 0.165 - 0.17 : [ 4 0.00 0.00 ]
| 0.17 - 0.175 : [ 1 0.00 0.00 ]
| 0.175 - 0.18 : [ 6 0.00 0.00 ]
| 0.18 - 0.185 : [ 4 0.00 0.00 ]
| 0.185 - 0.19 : [ 8 0.00 0.00 ]
| 0.19 - 0.195 : [ 12 0.00 0.00 ]
| 0.195 - 0.2 : [ 10 0.00 0.00 ]
|X 0.2 - 0.205 : [ 19 0.00 0.00 ]
| 0.205 - 0.21 : [ 16 0.00 0.00 ]
| 0.21 - 0.215 : [ 13 0.00 0.00 ]
| 0.215 - 0.22 : [ 11 0.00 0.00 ]
|X 0.22 - 0.225 : [ 37 0.00 0.00 ]
|X 0.225 - 0.23 : [ 43 0.00 0.01 ]
|X 0.23 - 0.235 : [ 42 0.00 0.01 ]
|XX 0.235 - 0.24 : [ 53 0.00 0.01 ]
|XX 0.24 - 0.245 : [ 77 0.00 0.01 ]
|XXX 0.245 - 0.25 : [ 82 0.00 0.01 ]
|XXXX 0.25 - 0.255 : [ 144 0.00 0.02 ]
|XXXXX 0.255 - 0.26 : [ 157 0.00 0.02 ]
|XXXXX 0.26 - 0.265 : [ 165 0.00 0.03 ]
|XXXXXXX 0.265 - 0.27 : [ 218 0.01 0.03 ]
|XXXXXXXX 0.27 - 0.275 : [ 256 0.01 0.04 ]
|XXXXXXXXXX 0.275 - 0.28 : [ 322 0.01 0.05 ]
|XXXXXXXXXXXX 0.28 - 0.285 : [ 391 0.01 0.06 ]
|XXXXXXXXXXXXX 0.285 - 0.29 : [ 427 0.01 0.08 ]
|XXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 522 0.02 0.09 ]
|XXXXXXXXXXXXXXXX 0.295 - 0.3 : [ 516 0.02 0.11 ]
|XXXXXXXXXXXXXXXXXXX 0.3 - 0.305 : [ 612 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.305 - 0.31 : [ 708 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.31 - 0.315 : [ 793 0.02 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.315 - 0.32 : [ 865 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.32 - 0.325 : [ 910 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.325 - 0.33 : [ 943 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.33 - 0.335 : [ 990 0.03 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.335 - 0.34 : [ 1062 0.03 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.34 - 0.345 : [ 1125 0.03 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.345 - 0.35 : [ 1216 0.04 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.35 - 0.355 : [ 1263 0.04 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.355 - 0.36 : [ 1302 0.04 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.36 - 0.365 : [ 1309 0.04 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.365 - 0.37 : [ 1266 0.04 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.37 - 0.375 : [ 1135 0.03 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.375 - 0.38 : [ 1230 0.04 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.38 - 0.385 : [ 1147 0.03 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.385 - 0.39 : [ 1041 0.03 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.39 - 0.395 : [ 912 0.03 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 798 0.02 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 769 0.02 0.75 ]
|XXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 577 0.02 0.77 ]
|XXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 508 0.02 0.78 ]
|XXXXXXXXXXX 0.415 - 0.42 : [ 359 0.01 0.79 ]
|XXXXXXXXXXX 0.42 - 0.425 : [ 352 0.01 0.80 ]
|XXXXXXXXXX 0.425 - 0.43 : [ 320 0.01 0.81 ]
|XXXXXXX 0.43 - 0.435 : [ 239 0.01 0.82 ]
|XXXXX 0.435 - 0.44 : [ 175 0.01 0.82 ]
|XXXXX 0.44 - 0.445 : [ 163 0.00 0.83 ]
|XXXXX 0.445 - 0.45 : [ 150 0.00 0.83 ]
|XXXX 0.45 - 0.455 : [ 116 0.00 0.84 ]
|XXX 0.455 - 0.46 : [ 106 0.00 0.84 ]
|XX 0.46 - 0.465 : [ 80 0.00 0.84 ]
|XX 0.465 - 0.47 : [ 77 0.00 0.85 ]
|XX 0.47 - 0.475 : [ 81 0.00 0.85 ]
|XXX 0.475 - 0.48 : [ 87 0.00 0.85 ]
|XX 0.48 - 0.485 : [ 68 0.00 0.85 ]
|XX 0.485 - 0.49 : [ 54 0.00 0.85 ]
|XX 0.49 - 0.495 : [ 52 0.00 0.86 ]
|XX 0.495 - 0.5 : [ 62 0.00 0.86 ]
|XX 0.5 - 0.505 : [ 65 0.00 0.86 ]
|XX 0.505 - 0.51 : [ 50 0.00 0.86 ]
|X 0.51 - 0.515 : [ 41 0.00 0.86 ]
|XX 0.515 - 0.52 : [ 64 0.00 0.86 ]
|XX 0.52 - 0.525 : [ 64 0.00 0.87 ]
|XXX 0.525 - 0.53 : [ 107 0.00 0.87 ]
|XX 0.53 - 0.535 : [ 71 0.00 0.87 ]
|XXXX 0.535 - 0.54 : [ 119 0.00 0.87 ]
|XXXX 0.54 - 0.545 : [ 125 0.00 0.88 ]
|XXXX 0.545 - 0.55 : [ 128 0.00 0.88 ]
|XXX 0.55 - 0.555 : [ 104 0.00 0.89 ]
|XXXX 0.555 - 0.56 : [ 143 0.00 0.89 ]
|XXXXX 0.56 - 0.565 : [ 151 0.00 0.89 ]
|XXXXX 0.565 - 0.57 : [ 159 0.00 0.90 ]
|XXXXX 0.57 - 0.575 : [ 178 0.01 0.90 ]
|XXXXXX 0.575 - 0.58 : [ 186 0.01 0.91 ]
|XXXXXX 0.58 - 0.585 : [ 197 0.01 0.92 ]
|XXXXXX 0.585 - 0.59 : [ 206 0.01 0.92 ]
|XXXXXX 0.59 - 0.595 : [ 204 0.01 0.93 ]
|XXXXXX 0.595 - 0.6 : [ 192 0.01 0.93 ]
|XXXXXXX 0.6 - 0.605 : [ 218 0.01 0.94 ]
|XXXXXX 0.605 - 0.61 : [ 186 0.01 0.95 ]
|XXXXXX 0.61 - 0.615 : [ 180 0.01 0.95 ]
|XXXXX 0.615 - 0.62 : [ 179 0.01 0.96 ]
|XXXXX 0.62 - 0.625 : [ 149 0.00 0.96 ]
|XXXXX 0.625 - 0.63 : [ 151 0.00 0.97 ]
|XXXX 0.63 - 0.635 : [ 124 0.00 0.97 ]
|XXXX 0.635 - 0.64 : [ 124 0.00 0.97 ]
|XXX 0.64 - 0.645 : [ 103 0.00 0.98 ]
|XXX 0.645 - 0.65 : [ 112 0.00 0.98 ]
|XXX 0.65 - 0.655 : [ 100 0.00 0.98 ]
|XX 0.655 - 0.66 : [ 80 0.00 0.98 ]
|XX 0.66 - 0.665 : [ 60 0.00 0.99 ]
|XX 0.665 - 0.67 : [ 73 0.00 0.99 ]
|X 0.67 - 0.675 : [ 49 0.00 0.99 ]
|XX 0.675 - 0.68 : [ 52 0.00 0.99 ]
|X 0.68 - 0.685 : [ 39 0.00 0.99 ]
|X 0.685 - 0.69 : [ 30 0.00 0.99 ]
|X 0.69 - 0.695 : [ 28 0.00 0.99 ]
|X 0.695 - 0.7 : [ 28 0.00 1.00 ]
|X 0.7 - 0.705 : [ 20 0.00 1.00 ]
|X 0.705 - 0.71 : [ 19 0.00 1.00 ]
| 0.71 - 0.715 : [ 10 0.00 1.00 ]
| 0.715 - 0.72 : [ 12 0.00 1.00 ]
| 0.72 - 0.725 : [ 8 0.00 1.00 ]
| 0.725 - 0.73 : [ 10 0.00 1.00 ]
| 0.73 - 0.735 : [ 10 0.00 1.00 ]
| 0.735 - 0.74 : [ 6 0.00 1.00 ]
| 0.74 - 0.745 : [ 4 0.00 1.00 ]
| 0.745 - 0.75 : [ 3 0.00 1.00 ]
| 0.75 - 0.755 : [ 8 0.00 1.00 ]
| 0.755 - 0.76 : [ 6 0.00 1.00 ]
| 0.76 - 0.765 : [ 4 0.00 1.00 ]
| 0.765 - 0.77 : [ 1 0.00 1.00 ]
| 0.77 - 0.775 : [ 2 0.00 1.00 ]
| 0.775 - 0.78 : [ 1 0.00 1.00 ]
#...
| 0.785 - 0.79 : [ 1 0.00 1.00 ]
| 0.79 - 0.795 : [ 4 0.00 1.00 ]
#...
| 0.8 - 0.805 : [ 2 0.00 1.00 ]
| 0.805 - 0.81 : [ 3 0.00 1.00 ]
#...
| 0.83 - 0.835 : [ 1 0.00 1.00 ]
| 0.835 - 0.84 : [ 1 0.00 1.00 ]
| 0.84 - 0.845 : [ 1 0.00 1.00 ]
#...
| 0.87 - 0.875 : [ 1 0.00 1.00 ]
| 0.875 - 0.88 : [ 1 0.00 1.00 ]
#...
| 0.91 - 0.915 : [ 1 0.00 1.00 ]
| 0.915 - 0.92 : [ 1 0.00 1.00 ]
#...
| 0.96 - 0.965 : [ 1 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
--------------------------------------------------------------
Contig 1. 293 reads; 25928 bp (untrimmed), 25536 (trimmed).
Contig 2. 7863 reads; 514821 bp (untrimmed), 514759 (trimmed).
Contig 3. 19849 reads; 1302602 bp (untrimmed), 1302532 (trimmed).
--------------------------------------------------------------
Totals 28005 reads; 1843351 bp (untrimmed), 1842827 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 1843351 bases = 13.08 +- 3.90 = 0.06 +- 3.78
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 3 total values totalling 35.8900. <11.963333 +/- 1.664238>
#Range: [ 9.61 - 13.17 ]
#Most likely bin: [ 13 - 13.5 ] 2 counts
#Median bin: [ 13 - 13.5 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 1 0.33 0.33 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 2 0.67 1.00 ]
-------------------------------------------------------------------
Histogram of Major Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000
-------------------------------------------------------------------
#Found 3 total values totalling 35.8900. <11.963333 +/- 1.664238>
#Range: [ 9.61 - 13.17 ]
#Most likely bin: [ 13 - 13.5 ] 2 counts
#Median bin: [ 13 - 13.5 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 1 0.33 0.33 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 2 0.67 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 1 293 reads 25928 bases = 9.61 +- 3.38 = 0.47 +- 3.18
Contig 3 19849 reads 1302602 bases = 13.11 +- 3.81 = 0.03 +- 3.74
Contig 2 7863 reads 514821 bases = 13.17 +- 4.05 = 0.13 +- 3.92
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1
HQ Discrepant reads = 0
Chimeric reads = 36
Suspect alignments = 298
-------------------------------------------------------------------
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/finished1/microbe/3635728/edit_dir.30Sep04.QD