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
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Project Size(KB) TaxID GenusSpecies
3635543 2500 1129 Synechococcus sp.
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Synechococcus_sp.
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Synechococcus sp., species, cyanobacteria
Synechococcus, genus, cyanobacteria
Chroococcales, order, cyanobacteria
Cyanobacteria (blue-green algae), phylum, cyanobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 2230730
# phrap: 2152026
# db:
altered.
2500000
2294252 +/- 148991
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 5734
Number of reads with percent X's >= 20%: 104 = 0.3%
Number of reads with percent X's >= 50%: 60 = 0.2%
Number of reads with percent X's >= 80%: 5 = 0.0%
Total reads in project: 30400
Total bp X'd : 264826
reads >= 20% >= 50% >= 80% screened
Nr with L09136 5197 57 35 2
Nr with pCC1Fos 434 4 1 0
Nr with pMCL200_JGI_XZX+XZK 103 43 24 3
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 1
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: 47
Total bp X'd : 49
reads >= 20% >= 50% >= 80% screened
Nr with L09136 1 0 0 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 6740345
C = 7915838
G = 7883812
T = 6642298
N = 117187
X = 264826
GC fraction = 0.53
Total = 29564306
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Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3635543_fasta.screen.contigs
-------------------------------------------------------------------
A 520385
C 608709
G 600253
T 502540
N 0
fraction GC = 0.54
total bases = 2231887
Libraries and Reads
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Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
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-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOZK reads.list > grep.reads.list.AOZK
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOZK 4 500
-------------------------------------------------------------------
#Found 5876 total values totalling 50641521.0000. <8618.366406 +/- 63012.551351>
#Range: [ 809 - 1258568 ]
#Most likely bin: [ 3000 - 3500 ] 3302 counts
#Median bin: [ 3000 - 3500 ] 3302 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 33 0.01 0.01 ]
|X 1500 - 2000 : [ 58 0.01 0.02 ]
|XX 2000 - 2500 : [ 139 0.02 0.04 ]
|XXXXXXXXXXXXXXX 2500 - 3000 : [ 1222 0.21 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3302 0.56 0.81 ]
|XXXXXXXXXXXXX 3500 - 4000 : [ 1042 0.18 0.99 ]
| 4000 - 4500 : [ 9 0.00 0.99 ]
#...
| 7000 - 7500 : [ 1 0.00 0.99 ]
#...
| 9000 - 9500 : [ 1 0.00 0.99 ]
#...
| 19000 - 19500 : [ 1 0.00 0.99 ]
#...
| 22000 - 22500 : [ 1 0.00 0.99 ]
#...
| 23500 - 24000 : [ 1 0.00 0.99 ]
#...
| 43500 - 44000 : [ 1 0.00 0.99 ]
#...
| 51500 - 52000 : [ 1 0.00 0.99 ]
#...
| 57000 - 57500 : [ 1 0.00 0.99 ]
#...
| 71500 - 72000 : [ 1 0.00 0.99 ]
#...
| 79500 - 80000 : [ 1 0.00 0.99 ]
#...
| 99500 - 100000 : [ 1 0.00 0.99 ]
#...
| 111000 - 111500 : [ 1 0.00 0.99 ]
#...
| 112500 - 113000 : [ 1 0.00 0.99 ]
#...
| 116000 - 116500 : [ 1 0.00 0.99 ]
#...
| 122500 - 123000 : [ 1 0.00 0.99 ]
#...
| 128000 - 128500 : [ 1 0.00 0.99 ]
#...
| 142500 - 143000 : [ 1 0.00 0.99 ]
#...
| 144500 - 145000 : [ 1 0.00 0.99 ]
#...
| 188500 - 189000 : [ 1 0.00 0.99 ]
#...
| 195500 - 196000 : [ 1 0.00 0.99 ]
#...
| 203000 - 203500 : [ 1 0.00 0.99 ]
| 203500 - 204000 : [ 1 0.00 0.99 ]
#...
| 227500 - 228000 : [ 1 0.00 0.99 ]
#...
| 231500 - 232000 : [ 1 0.00 0.99 ]
#...
| 233000 - 233500 : [ 1 0.00 0.99 ]
#...
| 237500 - 238000 : [ 1 0.00 0.99 ]
#...
| 245500 - 246000 : [ 1 0.00 0.99 ]
#...
| 248000 - 248500 : [ 1 0.00 0.99 ]
#...
| 254500 - 255000 : [ 1 0.00 0.99 ]
#...
| 268000 - 268500 : [ 1 0.00 0.99 ]
#...
| 283000 - 283500 : [ 1 0.00 0.99 ]
#...
| 292500 - 293000 : [ 1 0.00 0.99 ]
#...
| 315000 - 315500 : [ 1 0.00 0.99 ]
#...
| 337000 - 337500 : [ 1 0.00 0.99 ]
#...
| 403000 - 403500 : [ 1 0.00 0.99 ]
#...
| 420000 - 420500 : [ 1 0.00 0.99 ]
#...
| 446500 - 447000 : [ 1 0.00 0.99 ]
#...
| 462000 - 462500 : [ 1 0.00 0.99 ]
#...
| 463500 - 464000 : [ 1 0.00 0.99 ]
#...
| 465500 - 466000 : [ 1 0.00 0.99 ]
#...
| 478000 - 478500 : [ 1 0.00 1.00 ]
#...
| 485000 - 485500 : [ 1 0.00 1.00 ]
#...
| 491000 - 491500 : [ 1 0.00 1.00 ]
#...
| 499000 - 499500 : [ 1 0.00 1.00 ]
#...
| 521500 - 522000 : [ 1 0.00 1.00 ]
#...
| 531000 - 531500 : [ 1 0.00 1.00 ]
#...
| 544500 - 545000 : [ 1 0.00 1.00 ]
#...
| 549000 - 549500 : [ 1 0.00 1.00 ]
#...
| 559000 - 559500 : [ 1 0.00 1.00 ]
#...
| 592000 - 592500 : [ 1 0.00 1.00 ]
#...
| 691000 - 691500 : [ 1 0.00 1.00 ]
#...
| 708000 - 708500 : [ 1 0.00 1.00 ]
#...
| 738500 - 739000 : [ 2 0.00 1.00 ]
#...
| 760500 - 761000 : [ 1 0.00 1.00 ]
#...
| 773000 - 773500 : [ 1 0.00 1.00 ]
#...
| 823000 - 823500 : [ 1 0.00 1.00 ]
#...
| 868000 - 868500 : [ 1 0.00 1.00 ]
#...
| 873000 - 873500 : [ 1 0.00 1.00 ]
#...
| 881000 - 881500 : [ 1 0.00 1.00 ]
#...
| 979500 - 980000 : [ 1 0.00 1.00 ]
#...
| 1030000 - 1030500 : [ 1 0.00 1.00 ]
#...
| 1037500 - 1038000 : [ 1 0.00 1.00 ]
#...
| 1040500 - 1041000 : [ 1 0.00 1.00 ]
#...
| 1056500 - 1057000 : [ 1 0.00 1.00 ]
#...
| 1111000 - 1111500 : [ 1 0.00 1.00 ]
#...
| 1155500 - 1156000 : [ 1 0.00 1.00 ]
#...
| 1188000 - 1188500 : [ 1 0.00 1.00 ]
#...
| 1231500 - 1232000 : [ 1 0.00 1.00 ]
#...
| 1258500 - 1259000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOZN reads.list > grep.reads.list.AOZN
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOZN 4 500
-------------------------------------------------------------------
#Found 6235 total values totalling 69512580.0000. <11148.769848 +/- 56018.738136>
#Range: [ 718 - 1377580 ]
#Most likely bin: [ 6500 - 7000 ] 1471 counts
#Median bin: [ 6500 - 7000 ] 1471 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 3 0.00 0.00 ]
|X 1000 - 1500 : [ 29 0.00 0.01 ]
|X 1500 - 2000 : [ 26 0.00 0.01 ]
|X 2000 - 2500 : [ 46 0.01 0.02 ]
|X 2500 - 3000 : [ 53 0.01 0.03 ]
|XX 3000 - 3500 : [ 66 0.01 0.04 ]
|XX 3500 - 4000 : [ 78 0.01 0.05 ]
|XXX 4000 - 4500 : [ 94 0.02 0.06 ]
|XXXX 4500 - 5000 : [ 158 0.03 0.09 ]
|XXXXXX 5000 - 5500 : [ 229 0.04 0.13 ]
|XXXXXXXXXXXXXXXXX 5500 - 6000 : [ 617 0.10 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1212 0.19 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1471 0.24 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 1002 0.16 0.82 ]
|XXXXXXXXXXXXXXXXX 7500 - 8000 : [ 643 0.10 0.92 ]
|XXXXXXXXX 8000 - 8500 : [ 314 0.05 0.97 ]
|XXXX 8500 - 9000 : [ 129 0.02 0.99 ]
| 9000 - 9500 : [ 4 0.00 0.99 ]
#...
| 40000 - 40500 : [ 1 0.00 0.99 ]
#...
| 41000 - 41500 : [ 1 0.00 0.99 ]
#...
| 55500 - 56000 : [ 1 0.00 0.99 ]
#...
| 67000 - 67500 : [ 1 0.00 0.99 ]
#...
| 84500 - 85000 : [ 1 0.00 0.99 ]
#...
| 99500 - 100000 : [ 1 0.00 0.99 ]
#...
| 117000 - 117500 : [ 1 0.00 0.99 ]
#...
| 127000 - 127500 : [ 1 0.00 0.99 ]
#...
| 128500 - 129000 : [ 1 0.00 0.99 ]
#...
| 146500 - 147000 : [ 1 0.00 0.99 ]
#...
| 175000 - 175500 : [ 1 0.00 0.99 ]
#...
| 195000 - 195500 : [ 1 0.00 0.99 ]
#...
| 203500 - 204000 : [ 1 0.00 0.99 ]
#...
| 222500 - 223000 : [ 1 0.00 0.99 ]
#...
| 232500 - 233000 : [ 1 0.00 0.99 ]
#...
| 237000 - 237500 : [ 1 0.00 0.99 ]
#...
| 238500 - 239000 : [ 1 0.00 0.99 ]
#...
| 247000 - 247500 : [ 1 0.00 0.99 ]
#...
| 320500 - 321000 : [ 1 0.00 0.99 ]
#...
| 325000 - 325500 : [ 1 0.00 0.99 ]
#...
| 326000 - 326500 : [ 1 0.00 0.99 ]
#...
| 332000 - 332500 : [ 1 0.00 0.99 ]
#...
| 350500 - 351000 : [ 1 0.00 0.99 ]
#...
| 354500 - 355000 : [ 1 0.00 0.99 ]
#...
| 355500 - 356000 : [ 1 0.00 0.99 ]
#...
| 357000 - 357500 : [ 1 0.00 0.99 ]
#...
| 359500 - 360000 : [ 2 0.00 0.99 ]
#...
| 384000 - 384500 : [ 1 0.00 0.99 ]
#...
| 386500 - 387000 : [ 1 0.00 1.00 ]
#...
| 402500 - 403000 : [ 1 0.00 1.00 ]
#...
| 409000 - 409500 : [ 1 0.00 1.00 ]
#...
| 420500 - 421000 : [ 1 0.00 1.00 ]
#...
| 422500 - 423000 : [ 1 0.00 1.00 ]
#...
| 453000 - 453500 : [ 1 0.00 1.00 ]
#...
| 469500 - 470000 : [ 1 0.00 1.00 ]
#...
| 503000 - 503500 : [ 1 0.00 1.00 ]
#...
| 528000 - 528500 : [ 1 0.00 1.00 ]
#...
| 537000 - 537500 : [ 1 0.00 1.00 ]
#...
| 552500 - 553000 : [ 1 0.00 1.00 ]
#...
| 578000 - 578500 : [ 1 0.00 1.00 ]
#...
| 596500 - 597000 : [ 1 0.00 1.00 ]
#...
| 610000 - 610500 : [ 1 0.00 1.00 ]
#...
| 630000 - 630500 : [ 1 0.00 1.00 ]
#...
| 654000 - 654500 : [ 1 0.00 1.00 ]
#...
| 659000 - 659500 : [ 1 0.00 1.00 ]
#...
| 663000 - 663500 : [ 1 0.00 1.00 ]
#...
| 693500 - 694000 : [ 1 0.00 1.00 ]
#...
| 751500 - 752000 : [ 1 0.00 1.00 ]
#...
| 776000 - 776500 : [ 1 0.00 1.00 ]
#...
| 846500 - 847000 : [ 1 0.00 1.00 ]
#...
| 852000 - 852500 : [ 1 0.00 1.00 ]
#...
| 862500 - 863000 : [ 1 0.00 1.00 ]
#...
| 915500 - 916000 : [ 1 0.00 1.00 ]
#...
| 937500 - 938000 : [ 1 0.00 1.00 ]
#...
| 946500 - 947000 : [ 1 0.00 1.00 ]
#...
| 980500 - 981000 : [ 1 0.00 1.00 ]
#...
| 984500 - 985000 : [ 1 0.00 1.00 ]
#...
| 1106000 - 1106500 : [ 1 0.00 1.00 ]
#...
| 1263000 - 1263500 : [ 1 0.00 1.00 ]
#...
| 1377500 - 1378000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOZO reads.list > grep.reads.list.AOZO
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AOZO 4 500
-------------------------------------------------------------------
#Found 1025 total values totalling 38415687.0000. <37478.719024 +/- 3648.124908>
#Range: [ 24652 - 47138 ]
#Most likely bin: [ 36500 - 37000 ] 64 counts
#Median bin: [ 37000 - 37500 ] 49 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 24500 - 25000 : [ 1 0.00 0.00 ]
|X 25000 - 25500 : [ 1 0.00 0.00 ]
#...
|X 29000 - 29500 : [ 1 0.00 0.00 ]
|X 29500 - 30000 : [ 2 0.00 0.00 ]
|XX 30000 - 30500 : [ 3 0.00 0.01 ]
|XXXXX 30500 - 31000 : [ 8 0.01 0.02 ]
|XXXXXXXXX 31000 - 31500 : [ 14 0.01 0.03 ]
|XXXXXXXXXXXXX 31500 - 32000 : [ 21 0.02 0.05 ]
|XXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 30 0.03 0.08 ]
|XXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 31 0.03 0.11 ]
|XXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 32 0.03 0.14 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 43 0.04 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 43 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 52 0.05 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 51 0.05 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 59 0.06 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 42 0.04 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 64 0.06 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 49 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 56 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 42 0.04 0.63 ]
|XXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 34 0.03 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 38 0.04 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 37 0.04 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 37 0.04 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 43 0.04 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 38 0.04 0.85 ]
|XXXXXXXXXXXXXXXXX 41500 - 42000 : [ 27 0.03 0.88 ]
|XXXXXXXXXXXXXX 42000 - 42500 : [ 23 0.02 0.90 ]
|XXXXXXXXXXXXXXXXX 42500 - 43000 : [ 27 0.03 0.93 ]
|XXXXXXXX 43000 - 43500 : [ 13 0.01 0.94 ]
|XXXXXXXXXXXX 43500 - 44000 : [ 20 0.02 0.96 ]
|XXXXX 44000 - 44500 : [ 8 0.01 0.97 ]
|XXXXX 44500 - 45000 : [ 8 0.01 0.97 ]
|XXXXXXX 45000 - 45500 : [ 11 0.01 0.98 ]
|XX 45500 - 46000 : [ 4 0.00 0.99 ]
|XXXXX 46000 - 46500 : [ 8 0.01 1.00 ]
|XX 46500 - 47000 : [ 3 0.00 1.00 ]
|X 47000 - 47500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AOZN 6404 +- 1615 (n=3102)
# AOZO 37582 +- 3659 (n=472)
# AOZK 3088 +- 676 (n=2935)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3635543_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
AOZK 14976 -1 -1 96 719 14484 92 692 94 697
AOZN 16128 -1 -1 97 705 16104 88 667 93 658
AOZO 3072 -1 -1 84 410 3072 73 472 85 483
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AOZK 7463 92 682 94 697 7021 92 702 94 698
AOZN 8053 82 654 89 634 8051 95 678 97 680
AOZO 1536 74 465 84 488 1536 73 478 85 477
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3635543_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
72 13441 6739 93.60 97.50 AOZK @
84 14537 7773 92.54 96.39 AOZN @
16 2422 1316 82.25 85.68 AOZO @
] 30400 15828 92.02 cumulative total@@
LIBRARY PLATE ID COUNT [ AOZK 72 AOZN 84 AOZO 16 ] for 172 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 3635543_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 33660 total values totalling 19851185.0000. <589.755942 +/- 265.567465>
#Range: [ 0 - 936 ]
#Most likely bin: [ 750 - 800 ] 6096 counts
#Median bin: [ 650 - 700 ] 3042 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 3229 0.10 0.10 ]
|XXXX 50 - 100 : [ 611 0.02 0.11 ]
|XXX 100 - 150 : [ 485 0.01 0.13 ]
|XXX 150 - 200 : [ 432 0.01 0.14 ]
|XXX 200 - 250 : [ 507 0.02 0.16 ]
|XXXXX 250 - 300 : [ 789 0.02 0.18 ]
|XXXX 300 - 350 : [ 634 0.02 0.20 ]
|XXXX 350 - 400 : [ 588 0.02 0.22 ]
|XXXX 400 - 450 : [ 650 0.02 0.24 ]
|XXXXX 450 - 500 : [ 837 0.02 0.26 ]
|XXXXXXX 500 - 550 : [ 1103 0.03 0.29 ]
|XXXXXXXXXX 550 - 600 : [ 1580 0.05 0.34 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 2473 0.07 0.41 ]
|XXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3042 0.09 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 3978 0.12 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6096 0.18 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 5543 0.16 0.97 ]
|XXXXXXX 850 - 900 : [ 1056 0.03 1.00 ]
| 900 - 950 : [ 27 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOZK
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOZK 3635543_fasta.screen.trimQ15.SaF > reads.trim15.AOZK.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOZK.rl 2 50
-------------------------------------------------------------------
#Found 14484 total values totalling 9242857.0000. <638.142571 +/- 237.597265>
#Range: [ 0 - 936 ]
#Most likely bin: [ 750 - 800 ] 2948 counts
#Median bin: [ 700 - 750 ] 2027 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXX 0 - 50 : [ 1021 0.07 0.07 ]
|XX 50 - 100 : [ 124 0.01 0.08 ]
|XX 100 - 150 : [ 130 0.01 0.09 ]
|XX 150 - 200 : [ 125 0.01 0.10 ]
|XX 200 - 250 : [ 154 0.01 0.11 ]
|XX 250 - 300 : [ 155 0.01 0.12 ]
|XXX 300 - 350 : [ 202 0.01 0.13 ]
|XXX 350 - 400 : [ 217 0.01 0.15 ]
|XXX 400 - 450 : [ 241 0.02 0.16 ]
|XXXXX 450 - 500 : [ 337 0.02 0.19 ]
|XXXXXX 500 - 550 : [ 409 0.03 0.22 ]
|XXXXXXXX 550 - 600 : [ 581 0.04 0.26 ]
|XXXXXXXXXXXXXX 600 - 650 : [ 1035 0.07 0.33 ]
|XXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1462 0.10 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2027 0.14 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2948 0.20 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2670 0.18 0.96 ]
|XXXXXXXX 850 - 900 : [ 622 0.04 1.00 ]
| 900 - 950 : [ 24 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOZN
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOZN 3635543_fasta.screen.trimQ15.SaF > reads.trim15.AOZN.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOZN.rl 2 50
-------------------------------------------------------------------
#Found 16104 total values totalling 9523685.0000. <591.386302 +/- 265.809773>
#Range: [ 0 - 911 ]
#Most likely bin: [ 750 - 800 ] 3040 counts
#Median bin: [ 700 - 750 ] 1746 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1561 0.10 0.10 ]
|XXXX 50 - 100 : [ 318 0.02 0.12 ]
|XXX 100 - 150 : [ 241 0.01 0.13 ]
|XXX 150 - 200 : [ 196 0.01 0.14 ]
|XXX 200 - 250 : [ 224 0.01 0.16 ]
|XXX 250 - 300 : [ 263 0.02 0.17 ]
|XXXX 300 - 350 : [ 280 0.02 0.19 ]
|XXXX 350 - 400 : [ 314 0.02 0.21 ]
|XXXX 400 - 450 : [ 322 0.02 0.23 ]
|XXXXX 450 - 500 : [ 393 0.02 0.26 ]
|XXXXXXX 500 - 550 : [ 566 0.04 0.29 ]
|XXXXXXXXXXX 550 - 600 : [ 813 0.05 0.34 ]
|XXXXXXXXXXXXXXXX 600 - 650 : [ 1219 0.08 0.42 ]
|XXXXXXXXXXXXXXXXX 650 - 700 : [ 1325 0.08 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1746 0.11 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3040 0.19 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2847 0.18 0.97 ]
|XXXXXX 850 - 900 : [ 433 0.03 1.00 ]
| 900 - 950 : [ 3 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AOZO
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOZO 3635543_fasta.screen.trimQ15.SaF > reads.trim15.AOZO.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOZO.rl 2 50
-------------------------------------------------------------------
#Found 3072 total values totalling 1084643.0000. <353.073893 +/- 262.935342>
#Range: [ 0 - 859 ]
#Most likely bin: [ 0 - 50 ] 647 counts
#Median bin: [ 250 - 300 ] 371 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 647 0.21 0.21 ]
|XXXXXXXXXX 50 - 100 : [ 169 0.06 0.27 ]
|XXXXXXX 100 - 150 : [ 114 0.04 0.30 ]
|XXXXXXX 150 - 200 : [ 111 0.04 0.34 ]
|XXXXXXXX 200 - 250 : [ 129 0.04 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXX 250 - 300 : [ 371 0.12 0.50 ]
|XXXXXXXXX 300 - 350 : [ 152 0.05 0.55 ]
|XXXX 350 - 400 : [ 57 0.02 0.57 ]
|XXXXX 400 - 450 : [ 87 0.03 0.60 ]
|XXXXXXX 450 - 500 : [ 107 0.03 0.63 ]
|XXXXXXXX 500 - 550 : [ 128 0.04 0.67 ]
|XXXXXXXXXXX 550 - 600 : [ 186 0.06 0.74 ]
|XXXXXXXXXXXXXX 600 - 650 : [ 219 0.07 0.81 ]
|XXXXXXXXXXXXXXXX 650 - 700 : [ 255 0.08 0.89 ]
|XXXXXXXXXXXXX 700 - 750 : [ 205 0.07 0.96 ]
|XXXXXXX 750 - 800 : [ 108 0.04 0.99 ]
|XX 800 - 850 : [ 26 0.01 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for ASYH
trimt JAZZ trim 15 readlength histogram for ASWY
trimt JAZZ trim 15 readlength histogram for ATTU
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3635543
-------------------------------------------------------------------
AOZK.000001.000100 pUC18.fa LRS.fasta
AOZN.000001.000100 pMCL200.fa LRS.fasta
AOZO.000001.000100 pCC1Fos.fa LRS.fasta
AOZK.000001.000100 pUC18.fa LRS.fasta
AOZN.000001.000100 pMCL200.fa LRS.fasta
AOZO.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3635543_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3635543_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 30210 total values totalling 16382.9241. <0.542301 +/- 0.060773>
#Range: [ 0 - 1 ]
#Most likely bin: [ 0.56 - 0.565 ] 1559 counts
#Median bin: [ 0.555 - 0.56 ] 1447 counts
| 0 - 0.005 : [ 1 0.00 0.00 ]
#...
| 0.18 - 0.185 : [ 1 0.00 0.00 ]
#...
| 0.26 - 0.265 : [ 1 0.00 0.00 ]
#...
| 0.27 - 0.275 : [ 1 0.00 0.00 ]
| 0.275 - 0.28 : [ 3 0.00 0.00 ]
| 0.28 - 0.285 : [ 1 0.00 0.00 ]
| 0.285 - 0.29 : [ 9 0.00 0.00 ]
| 0.29 - 0.295 : [ 8 0.00 0.00 ]
| 0.295 - 0.3 : [ 13 0.00 0.00 ]
| 0.3 - 0.305 : [ 14 0.00 0.00 ]
| 0.305 - 0.31 : [ 17 0.00 0.00 ]
| 0.31 - 0.315 : [ 14 0.00 0.00 ]
|X 0.315 - 0.32 : [ 22 0.00 0.00 ]
|X 0.32 - 0.325 : [ 22 0.00 0.00 ]
|X 0.325 - 0.33 : [ 33 0.00 0.01 ]
|X 0.33 - 0.335 : [ 28 0.00 0.01 ]
|X 0.335 - 0.34 : [ 29 0.00 0.01 ]
|X 0.34 - 0.345 : [ 39 0.00 0.01 ]
|X 0.345 - 0.35 : [ 30 0.00 0.01 ]
|X 0.35 - 0.355 : [ 38 0.00 0.01 ]
|X 0.355 - 0.36 : [ 48 0.00 0.01 ]
|X 0.36 - 0.365 : [ 57 0.00 0.01 ]
|XX 0.365 - 0.37 : [ 61 0.00 0.02 ]
|XX 0.37 - 0.375 : [ 61 0.00 0.02 ]
|XX 0.375 - 0.38 : [ 81 0.00 0.02 ]
|XX 0.38 - 0.385 : [ 68 0.00 0.02 ]
|XX 0.385 - 0.39 : [ 91 0.00 0.03 ]
|XXX 0.39 - 0.395 : [ 107 0.00 0.03 ]
|XXX 0.395 - 0.4 : [ 135 0.00 0.03 ]
|XXX 0.4 - 0.405 : [ 125 0.00 0.04 ]
|XXX 0.405 - 0.41 : [ 135 0.00 0.04 ]
|XXXX 0.41 - 0.415 : [ 150 0.00 0.05 ]
|XXXX 0.415 - 0.42 : [ 139 0.00 0.05 ]
|XXXXX 0.42 - 0.425 : [ 176 0.01 0.06 ]
|XXXXX 0.425 - 0.43 : [ 210 0.01 0.07 ]
|XXXXX 0.43 - 0.435 : [ 208 0.01 0.07 ]
|XXXXXX 0.435 - 0.44 : [ 228 0.01 0.08 ]
|XXXXXX 0.44 - 0.445 : [ 238 0.01 0.09 ]
|XXXXXX 0.445 - 0.45 : [ 241 0.01 0.10 ]
|XXXXXXX 0.45 - 0.455 : [ 281 0.01 0.10 ]
|XXXXXXXX 0.455 - 0.46 : [ 300 0.01 0.11 ]
|XXXXXXX 0.46 - 0.465 : [ 263 0.01 0.12 ]
|XXXXXXX 0.465 - 0.47 : [ 271 0.01 0.13 ]
|XXXXXXX 0.47 - 0.475 : [ 266 0.01 0.14 ]
|XXXXXXX 0.475 - 0.48 : [ 271 0.01 0.15 ]
|XXXXXXXXX 0.48 - 0.485 : [ 342 0.01 0.16 ]
|XXXXXXXXXX 0.485 - 0.49 : [ 377 0.01 0.17 ]
|XXXXXXXXXX 0.49 - 0.495 : [ 374 0.01 0.19 ]
|XXXXXXXX 0.495 - 0.5 : [ 312 0.01 0.20 ]
|XXXXXXXXXXXX 0.5 - 0.505 : [ 474 0.02 0.21 ]
|XXXXXXXXXXX 0.505 - 0.51 : [ 427 0.01 0.23 ]
|XXXXXXXXXXXX 0.51 - 0.515 : [ 481 0.02 0.24 ]
|XXXXXXXXXXXXX 0.515 - 0.52 : [ 519 0.02 0.26 ]
|XXXXXXXXXXXXXXX 0.52 - 0.525 : [ 583 0.02 0.28 ]
|XXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 712 0.02 0.30 ]
|XXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 771 0.03 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 941 0.03 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 1069 0.04 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 1169 0.04 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 1315 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 1447 0.05 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 1559 0.05 0.58 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 1538 0.05 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 1529 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 1480 0.05 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 1383 0.05 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 1327 0.04 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 1188 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 959 0.03 0.89 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 850 0.03 0.92 ]
|XXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 661 0.02 0.94 ]
|XXXXXXXXXXXXX 0.61 - 0.615 : [ 488 0.02 0.95 ]
|XXXXXXXXX 0.615 - 0.62 : [ 335 0.01 0.96 ]
|XXXXXXX 0.62 - 0.625 : [ 291 0.01 0.97 ]
|XXXXX 0.625 - 0.63 : [ 213 0.01 0.98 ]
|XXXX 0.63 - 0.635 : [ 164 0.01 0.99 ]
|XXX 0.635 - 0.64 : [ 101 0.00 0.99 ]
|XX 0.64 - 0.645 : [ 67 0.00 0.99 ]
|X 0.645 - 0.65 : [ 44 0.00 0.99 ]
|X 0.65 - 0.655 : [ 45 0.00 1.00 ]
|X 0.655 - 0.66 : [ 27 0.00 1.00 ]
| 0.66 - 0.665 : [ 18 0.00 1.00 ]
|X 0.665 - 0.67 : [ 20 0.00 1.00 ]
| 0.67 - 0.675 : [ 8 0.00 1.00 ]
| 0.675 - 0.68 : [ 14 0.00 1.00 ]
| 0.68 - 0.685 : [ 5 0.00 1.00 ]
| 0.685 - 0.69 : [ 9 0.00 1.00 ]
| 0.69 - 0.695 : [ 8 0.00 1.00 ]
| 0.695 - 0.7 : [ 3 0.00 1.00 ]
| 0.7 - 0.705 : [ 10 0.00 1.00 ]
| 0.705 - 0.71 : [ 3 0.00 1.00 ]
| 0.71 - 0.715 : [ 2 0.00 1.00 ]
| 0.715 - 0.72 : [ 2 0.00 1.00 ]
| 0.72 - 0.725 : [ 3 0.00 1.00 ]
#...
| 0.73 - 0.735 : [ 1 0.00 1.00 ]
| 0.735 - 0.74 : [ 2 0.00 1.00 ]
| 0.74 - 0.745 : [ 1 0.00 1.00 ]
#...
| 0.76 - 0.765 : [ 1 0.00 1.00 ]
#...
| 0.77 - 0.775 : [ 1 0.00 1.00 ]
#...
| 1 - 1.005 : [ 2 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
--------------------------------------------------------------
Contig 1. 3 reads; 741 bp (untrimmed), 318 (trimmed).
Contig 2. 5 reads; 1057 bp (untrimmed), 654 (trimmed).
Contig 3. 10619 reads; 734161 bp (untrimmed), 733919 (trimmed).
Contig 4. 19726 reads; 1495928 bp (untrimmed), 1495839 (trimmed).
--------------------------------------------------------------
Totals 30353 reads; 2231887 bp (untrimmed), 2230730 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2231887 bases = 12.16 +- 3.88 = 0.01 +- 3.69
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 4 total values totalling 29.0500. <7.262500 +/- 5.189183>
#Range: [ 1.00 - 12.96 ]
#Most likely bin: [ 0 - 0.5 ] 1 counts
#Median bin: [ 3 - 3.5 ] 1 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 1 0.25 0.25 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 1 0.25 0.50 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 1 0.25 0.75 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 1 0.25 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 2 total values totalling 24.7400. <12.370000 +/- 0.590000>
#Range: [ 11.78 - 12.96 ]
#Most likely bin: [ 0 - 0.5 ] 1 counts
#Median bin: [ 11.5 - 12 ] 1 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 1 0.50 0.50 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 1 0.50 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 1 3 reads 741 bases = 1.00 +- 0.07 = -1.00 +- 0.07
Contig 2 5 reads 1057 bases = 3.31 +- 1.75 = 3.31 +- 1.75
Contig 4 19726 reads 1495928 bases = 11.78 +- 3.69 = 0.03 +- 3.68
Contig 3 10619 reads 734161 bases = 12.96 +- 4.10 = -0.02 +- 3.70
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 212
HQ Discrepant reads = 1
Chimeric reads = 57
Suspect alignments = 168
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 3.57 SUN/Ultra-2/3
Equivalent to Phil Green's version 0.990329
Score matrix (set by value of penalty: -2)
A C G T N X
A 1 -2 -2 -2 0 -3
C -2 1 -2 -2 0 -3
G -2 -2 1 -2 0 -3
T -2 -2 -2 1 0 -3
N 0 0 0 0 0 0
X -3 -3 -3 -3 0 -3
gap_init: -4
gap_ext: -3
ins_gap_ext: -3
del_gap_ext: -3
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 30
maxmatch: 55
max_group_size: 20
minscore: 55
bandwidth: 14
indexwordsize: 10
vector_bound: 20
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 13
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -5
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/finished2/microbe/3635543/edit_dir.16Aug04.QD