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: 12-12-2005
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
3435908 2200 32046 Synechococcus elongatus
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Synechococcus_elongatus
-------------------------------------------------------------------
Synechococcus elongatus, 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: 2761877
# phrap: 2593598
# db:
altered.
2200000
2518491 +/- 235452
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 30418
Number of reads with percent X's >= 20%: 277 = 0.6%
Number of reads with percent X's >= 50%: 96 = 0.2%
Number of reads with percent X's >= 80%: 4 = 0.0%
Total reads in project: 44642
Total bp X'd : 1726339
reads >= 20% >= 50% >= 80% screened
Nr with L09136 7717 84 32 2
Nr with LRS 1 1 0 0
Nr with MuCam 2118 39 17 0
Nr with MuKam 3445 46 20 0
Nr with SCOSI 26 12 5 0
Nr with Tn5KmCTGTC 311 44 5 0
Nr with pACYC184 30 2 0 0
Nr with pBR328 85 16 1 0
Nr with pCC1Fos 1398 2 0 0
Nr with pMCL200_JGI_XZX+XZK 15287 31 16 2
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 141
Number of reads with percent X's >= 20%: 2 = 1.0%
Number of reads with percent X's >= 50%: 1 = 0.5%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 197
Total bp X'd : 7580
reads >= 20% >= 50% >= 80% screened
Nr with L09136 92 0 0 0
Nr with pCC1Fos 2 0 0 0
Nr with pMCL200_JGI_XZX+XZK 47 2 1 0
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Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 7886104
C = 9950513
G = 9564402
T = 8154163
N = 438365
X = 1738594
GC fraction = 0.52
Total = 37793824
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3435908_fasta.screen.contigs
-------------------------------------------------------------------
A 612219
C 764928
G 771474
T 622992
N 2209
fraction GC = 0.55
total bases = 2773822
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 AABT reads.list > grep.reads.list.AABT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AABT 4 500
-------------------------------------------------------------------
#Found 7407 total values totalling 56742188.0000. <7660.616714 +/- 54883.741513>
#Range: [ 820 - 1361877 ]
#Most likely bin: [ 3000 - 3500 ] 1641 counts
#Median bin: [ 3000 - 3500 ] 1641 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 16 0.00 0.00 ]
|X 1000 - 1500 : [ 53 0.01 0.01 ]
|X 1500 - 2000 : [ 41 0.01 0.01 ]
|XXXXXXXXXXXX 2000 - 2500 : [ 501 0.07 0.08 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 1531 0.21 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 1641 0.22 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 1387 0.19 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1034 0.14 0.84 ]
|XXXXXXXXXXXXXXXX 4500 - 5000 : [ 644 0.09 0.92 ]
|XXXXXXXX 5000 - 5500 : [ 346 0.05 0.97 ]
|XXX 5500 - 6000 : [ 120 0.02 0.99 ]
|X 6000 - 6500 : [ 28 0.00 0.99 ]
| 6500 - 7000 : [ 7 0.00 0.99 ]
| 7000 - 7500 : [ 1 0.00 0.99 ]
| 7500 - 8000 : [ 2 0.00 0.99 ]
#...
| 24000 - 24500 : [ 1 0.00 0.99 ]
#...
| 33000 - 33500 : [ 1 0.00 0.99 ]
#...
| 46500 - 47000 : [ 1 0.00 0.99 ]
#...
| 84500 - 85000 : [ 1 0.00 0.99 ]
#...
| 86500 - 87000 : [ 1 0.00 0.99 ]
#...
| 117000 - 117500 : [ 1 0.00 0.99 ]
#...
| 142500 - 143000 : [ 1 0.00 0.99 ]
#...
| 149000 - 149500 : [ 1 0.00 0.99 ]
#...
| 153000 - 153500 : [ 1 0.00 0.99 ]
#...
| 154000 - 154500 : [ 1 0.00 0.99 ]
#...
| 223000 - 223500 : [ 1 0.00 0.99 ]
#...
| 242500 - 243000 : [ 1 0.00 0.99 ]
#...
| 267500 - 268000 : [ 1 0.00 0.99 ]
#...
| 365500 - 366000 : [ 1 0.00 0.99 ]
#...
| 378500 - 379000 : [ 1 0.00 0.99 ]
#...
| 386000 - 386500 : [ 1 0.00 0.99 ]
#...
| 397000 - 397500 : [ 1 0.00 0.99 ]
#...
| 401500 - 402000 : [ 1 0.00 1.00 ]
#...
| 403000 - 403500 : [ 1 0.00 1.00 ]
#...
| 418000 - 418500 : [ 1 0.00 1.00 ]
#...
| 428000 - 428500 : [ 1 0.00 1.00 ]
#...
| 438500 - 439000 : [ 1 0.00 1.00 ]
#...
| 459500 - 460000 : [ 1 0.00 1.00 ]
#...
| 494500 - 495000 : [ 1 0.00 1.00 ]
#...
| 513000 - 513500 : [ 1 0.00 1.00 ]
#...
| 530000 - 530500 : [ 1 0.00 1.00 ]
#...
| 542500 - 543000 : [ 1 0.00 1.00 ]
#...
| 552500 - 553000 : [ 1 0.00 1.00 ]
#...
| 570000 - 570500 : [ 1 0.00 1.00 ]
#...
| 579500 - 580000 : [ 1 0.00 1.00 ]
#...
| 588500 - 589000 : [ 1 0.00 1.00 ]
#...
| 591000 - 591500 : [ 1 0.00 1.00 ]
#...
| 598000 - 598500 : [ 1 0.00 1.00 ]
#...
| 599500 - 600000 : [ 1 0.00 1.00 ]
#...
| 624000 - 624500 : [ 1 0.00 1.00 ]
#...
| 631000 - 631500 : [ 1 0.00 1.00 ]
#...
| 642000 - 642500 : [ 1 0.00 1.00 ]
#...
| 683500 - 684000 : [ 1 0.00 1.00 ]
#...
| 699500 - 700000 : [ 1 0.00 1.00 ]
#...
| 731500 - 732000 : [ 1 0.00 1.00 ]
#...
| 746000 - 746500 : [ 1 0.00 1.00 ]
#...
| 769000 - 769500 : [ 1 0.00 1.00 ]
#...
| 776000 - 776500 : [ 1 0.00 1.00 ]
#...
| 783500 - 784000 : [ 1 0.00 1.00 ]
#...
| 889500 - 890000 : [ 1 0.00 1.00 ]
#...
| 918500 - 919000 : [ 1 0.00 1.00 ]
#...
| 946500 - 947000 : [ 1 0.00 1.00 ]
#...
| 958500 - 959000 : [ 1 0.00 1.00 ]
#...
| 976000 - 976500 : [ 1 0.00 1.00 ]
#...
| 996500 - 997000 : [ 1 0.00 1.00 ]
#...
| 1034000 - 1034500 : [ 1 0.00 1.00 ]
#...
| 1052500 - 1053000 : [ 1 0.00 1.00 ]
#...
| 1165500 - 1166000 : [ 1 0.00 1.00 ]
#...
| 1166500 - 1167000 : [ 1 0.00 1.00 ]
#...
| 1361500 - 1362000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AABU reads.list > grep.reads.list.AABU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AABU 4 500
-------------------------------------------------------------------
#Found 7250 total values totalling 72571839.0000. <10009.908828 +/- 17465.110928>
#Range: [ 871 - 849114 ]
#Most likely bin: [ 9000 - 9500 ] 1004 counts
#Median bin: [ 9500 - 10000 ] 973 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 4 0.00 0.00 ]
|X 1000 - 1500 : [ 30 0.00 0.00 ]
|XX 1500 - 2000 : [ 49 0.01 0.01 ]
|XX 2000 - 2500 : [ 46 0.01 0.02 ]
|X 2500 - 3000 : [ 25 0.00 0.02 ]
|X 3000 - 3500 : [ 21 0.00 0.02 ]
|X 3500 - 4000 : [ 25 0.00 0.03 ]
|X 4000 - 4500 : [ 15 0.00 0.03 ]
|X 4500 - 5000 : [ 27 0.00 0.03 ]
|X 5000 - 5500 : [ 27 0.00 0.04 ]
|X 5500 - 6000 : [ 29 0.00 0.04 ]
|XX 6000 - 6500 : [ 47 0.01 0.05 ]
|XXXX 6500 - 7000 : [ 106 0.01 0.06 ]
|XXXXXXXXX 7000 - 7500 : [ 236 0.03 0.09 ]
|XXXXXXXXXXXXXXXXX 7500 - 8000 : [ 417 0.06 0.15 ]
|XXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 534 0.07 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 828 0.11 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 1004 0.14 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 973 0.13 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 825 0.11 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 10500 - 11000 : [ 645 0.09 0.82 ]
|XXXXXXXXXXXXXXXXXX 11000 - 11500 : [ 457 0.06 0.88 ]
|XXXXXXXXXXXXX 11500 - 12000 : [ 331 0.05 0.92 ]
|XXXXXXXXX 12000 - 12500 : [ 227 0.03 0.96 ]
|XXXXXX 12500 - 13000 : [ 147 0.02 0.98 ]
|XXX 13000 - 13500 : [ 75 0.01 0.99 ]
|XX 13500 - 14000 : [ 52 0.01 0.99 ]
|X 14000 - 14500 : [ 27 0.00 1.00 ]
| 14500 - 15000 : [ 10 0.00 1.00 ]
#...
| 20500 - 21000 : [ 1 0.00 1.00 ]
#...
| 59500 - 60000 : [ 1 0.00 1.00 ]
#...
| 108500 - 109000 : [ 1 0.00 1.00 ]
#...
| 159000 - 159500 : [ 1 0.00 1.00 ]
#...
| 184000 - 184500 : [ 1 0.00 1.00 ]
#...
| 200000 - 200500 : [ 1 0.00 1.00 ]
#...
| 392000 - 392500 : [ 1 0.00 1.00 ]
#...
| 593500 - 594000 : [ 1 0.00 1.00 ]
#...
| 621000 - 621500 : [ 1 0.00 1.00 ]
#...
| 727500 - 728000 : [ 1 0.00 1.00 ]
#...
| 849000 - 849500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AABW reads.list > grep.reads.list.AABW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AABW 4 500
-------------------------------------------------------------------
#Found 1265 total values totalling 44382145.0000. <35084.699605 +/- 3780.798709>
#Range: [ 23581 - 46491 ]
#Most likely bin: [ 35000 - 35500 ] 88 counts
#Median bin: [ 34500 - 35000 ] 71 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 23500 - 24000 : [ 4 0.00 0.00 ]
| 24000 - 24500 : [ 1 0.00 0.00 ]
#...
|XX 25000 - 25500 : [ 4 0.00 0.01 ]
|X 25500 - 26000 : [ 3 0.00 0.01 ]
|XX 26000 - 26500 : [ 5 0.00 0.01 ]
|XX 26500 - 27000 : [ 4 0.00 0.02 ]
|XXX 27000 - 27500 : [ 6 0.00 0.02 ]
|XXXXX 27500 - 28000 : [ 11 0.01 0.03 ]
|XXXXXXX 28000 - 28500 : [ 15 0.01 0.04 ]
|XXXXXX 28500 - 29000 : [ 13 0.01 0.05 ]
|XXXXXXXX 29000 - 29500 : [ 17 0.01 0.07 ]
|XXXXXX 29500 - 30000 : [ 13 0.01 0.08 ]
|XXXXXXXXXXXX 30000 - 30500 : [ 26 0.02 0.10 ]
|XXXXXXXXXXXXXXX 30500 - 31000 : [ 33 0.03 0.12 ]
|XXXXXXXXXXXXXXXX 31000 - 31500 : [ 35 0.03 0.15 ]
|XXXXXXXXXXXXXXXX 31500 - 32000 : [ 36 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 56 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 65 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33000 - 33500 : [ 77 0.06 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 79 0.06 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 83 0.07 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 71 0.06 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 88 0.07 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 60 0.05 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 58 0.05 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 57 0.05 0.73 ]
|XXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 41 0.03 0.76 ]
|XXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 39 0.03 0.79 ]
|XXXXXXXXXXXXXXXX 38000 - 38500 : [ 36 0.03 0.82 ]
|XXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 43 0.03 0.85 ]
|XXXXXXXXXXXXX 39000 - 39500 : [ 28 0.02 0.88 ]
|XXXXXXXXXX 39500 - 40000 : [ 22 0.02 0.89 ]
|XXXXXXXX 40000 - 40500 : [ 18 0.01 0.91 ]
|XXXXXXXX 40500 - 41000 : [ 17 0.01 0.92 ]
|XXXXXXXXXXX 41000 - 41500 : [ 24 0.02 0.94 ]
|XXXXXXXXXXXXX 41500 - 42000 : [ 28 0.02 0.96 ]
|XXX 42000 - 42500 : [ 6 0.00 0.97 ]
|XXX 42500 - 43000 : [ 7 0.01 0.97 ]
|XXXXXX 43000 - 43500 : [ 13 0.01 0.98 ]
|XXX 43500 - 44000 : [ 6 0.00 0.99 ]
|X 44000 - 44500 : [ 3 0.00 0.99 ]
|XX 44500 - 45000 : [ 4 0.00 0.99 ]
|X 45000 - 45500 : [ 3 0.00 0.99 ]
|XX 45500 - 46000 : [ 5 0.00 1.00 ]
|X 46000 - 46500 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AHUI 3145 +- 513 (n=113)
# AABW 34951 +- 3793 (n=640)
# AHUH 3130 +- 524 (n=92)
# AABT 3487 +- 928 (n=3717)
# AABU 9274 +- 2010 (n=3630)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3435908_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
??? 0 0 0 0 0 8865 94 224 100 233
AABT 16896 -1 -1 99 687 16583 99 697 99 699
AABU 16896 -1 -1 98 659 15401 100 621 100 677
AABW 6144 84 618 93 611 2876 99 684 100 699
AHUH 768 -1 -1 80 515 435 99 631 100 670
AHUI 768 -1 -1 81 543 482 99 679 100 685
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
??? 0 0 0 0 0 0 0 0 0 0
AABT 8344 98 685 99 696 8239 100 708 100 701
AABU 7738 99 613 99 679 7663 100 629 100 676
AABW 1426 99 707 100 700 1450 99 662 100 699
AHUH 234 99 628 100 669 201 99 635 100 673
AHUI 253 98 667 100 684 229 99 692 100 685
8865 reads had indecipherable directionality
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3435908_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
1 30 12 12.00 12.50 NNN @
1 8 8 8.00 8.33 SSS @
1 27 12 12.00 12.50 KKK @
1 46 12 12.00 12.50 DDD @
1 12 8 8.00 8.33 PPP @
1 18 11 11.00 11.46 OOO @
1 1 1 1.00 1.04 _EF @
1 20 10 10.00 10.42 MMM @
1 146 1 1.00 1.04 m_Tn @
1 1 1 1.00 1.04 pANL @
16 2876 1491 93.19 97.07 AABW @
1 7 7 7.00 7.29 VVV @
1 24 11 11.00 11.46 JJJ @
1 37 12 12.00 12.50 BBB @
1 30 11 11.00 11.46 EEE @
88 15401 7762 88.20 91.88 AABU @
1 4 4 4.00 4.17 WWW @
1 32 12 12.00 12.50 HHH @
1 1 1 1.00 1.04 _pAM @
1 3 3 3.00 3.12 _LC @
1 8 8 8.00 8.33 QQQ @
1 2 2 2.00 2.08 TTT @
1 28 12 12.00 12.50 III @
1 34 11 11.00 11.46 FFF @
4 435 252 63.00 65.62 AHUH @
1 1 1 1.00 1.04 _PAM @
1 26 10 10.00 10.42 LLL @
1 1 1 1.00 1.04 _ZE @
1 34 11 11.00 11.46 GGG @
1 56 12 12.00 12.50 CCC @
1 1 1 1.00 1.04 HelU @
1 5 5 5.00 5.21 UUU @
1 31 31 31.00 32.29 ile_ @
88 16583 8324 94.59 98.53 AABT @
1 10 6 6.00 6.25 _OE @
4 482 252 63.00 65.62 AHUI @
1 40 11 11.00 11.46 AAA @
1 2 1 1.00 1.04 _put @
1 3 3 3.00 3.12 CON @
1 10 9 9.00 9.38 RRR @
] 36516 18353 78.10 cumulative total@@
LIBRARY PLATE ID COUNT [ NNN 1 DDD 1 KKK 1 SSS 1 PPP 1 OOO 1 _EF 0 EF 1 MMM 1 m_Tn 0 pANL 0 AABW 16 LC 1 VVV 1 JJJ 1 BBB 1 EEE 1 AABU 88 ZE 1 HHH 1 WWW 1 _pAM 0 U 1 _LC 0 QQQ 1 TTT 1 III 1 FFF 1 AHUH 4 _PAM 0 OE 1 LLL 1 _ZE 0 PAM 1 GGG 1 CCC 1 HelU 0 AM 1 ANL 1 UUU 1 ile_ 0 AABT 88 _OE 0 AHUI 4 AAA 1 _put 0 RRR 1 CON 1 ] for 232 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 3435908_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 44642 total values totalling 25426651.0000. <569.567918 +/- 242.230495>
#Range: [ 0 - 18001 ]
#Most likely bin: [ 650 - 700 ] 10850 counts
#Median bin: [ 600 - 650 ] 7565 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 220 0.00 0.00 ]
|XX 50 - 100 : [ 567 0.01 0.02 ]
|XXXXXXXX 100 - 150 : [ 2157 0.05 0.07 ]
|XXXXXXXXX 150 - 200 : [ 2365 0.05 0.12 ]
|XXXXXX 200 - 250 : [ 1625 0.04 0.16 ]
|XXXX 250 - 300 : [ 1068 0.02 0.18 ]
|XXX 300 - 350 : [ 786 0.02 0.20 ]
|XX 350 - 400 : [ 496 0.01 0.21 ]
|X 400 - 450 : [ 374 0.01 0.22 ]
|X 450 - 500 : [ 402 0.01 0.23 ]
|XXXX 500 - 550 : [ 1061 0.02 0.25 ]
|XXXXXXXXXXXXXX 550 - 600 : [ 3731 0.08 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 7565 0.17 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 10850 0.24 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 7518 0.17 0.91 ]
|XXXXXXXXXXXXX 750 - 800 : [ 3411 0.08 0.99 ]
|XX 800 - 850 : [ 430 0.01 1.00 ]
| 850 - 900 : [ 7 0.00 1.00 ]
| 900 - 950 : [ 4 0.00 1.00 ]
#...
| 8000 - 8050 : [ 1 0.00 1.00 ]
#...
| 9000 - 9050 : [ 1 0.00 1.00 ]
#...
| 11650 - 11700 : [ 1 0.00 1.00 ]
#...
| 15000 - 15050 : [ 1 0.00 1.00 ]
#...
| 18000 - 18050 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AGXK
trimt JAZZ trim 15 readlength histogram for AABT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AABT 3435908_fasta.screen.trimQ15.SaF > reads.trim15.AABT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AABT.rl 2 50
-------------------------------------------------------------------
#Found 16583 total values totalling 11454899.0000. <690.761563 +/- 95.145672>
#Range: [ 0 - 927 ]
#Most likely bin: [ 650 - 700 ] 5375 counts
#Median bin: [ 700 - 750 ] 5196 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 0 - 50 : [ 124 0.01 0.01 ]
| 50 - 100 : [ 24 0.00 0.01 ]
| 100 - 150 : [ 19 0.00 0.01 ]
| 150 - 200 : [ 28 0.00 0.01 ]
| 200 - 250 : [ 21 0.00 0.01 ]
| 250 - 300 : [ 29 0.00 0.01 ]
| 300 - 350 : [ 20 0.00 0.02 ]
| 350 - 400 : [ 43 0.00 0.02 ]
| 400 - 450 : [ 32 0.00 0.02 ]
| 450 - 500 : [ 59 0.00 0.02 ]
|X 500 - 550 : [ 115 0.01 0.03 ]
|XXX 550 - 600 : [ 347 0.02 0.05 ]
|XXXXXXXXXXXXXX 600 - 650 : [ 1937 0.12 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5375 0.32 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5196 0.31 0.81 ]
|XXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2803 0.17 0.98 ]
|XXX 800 - 850 : [ 402 0.02 1.00 ]
| 850 - 900 : [ 6 0.00 1.00 ]
| 900 - 950 : [ 3 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AABU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AABU 3435908_fasta.screen.trimQ15.SaF > reads.trim15.AABU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AABU.rl 2 50
-------------------------------------------------------------------
#Found 15401 total values totalling 9516686.0000. <617.926498 +/- 76.322253>
#Range: [ 0 - 903 ]
#Most likely bin: [ 600 - 650 ] 5391 counts
#Median bin: [ 600 - 650 ] 5391 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 50 0.00 0.00 ]
| 50 - 100 : [ 19 0.00 0.00 ]
| 100 - 150 : [ 17 0.00 0.01 ]
| 150 - 200 : [ 26 0.00 0.01 ]
| 200 - 250 : [ 25 0.00 0.01 ]
| 250 - 300 : [ 33 0.00 0.01 ]
| 300 - 350 : [ 41 0.00 0.01 ]
| 350 - 400 : [ 56 0.00 0.02 ]
|X 400 - 450 : [ 69 0.00 0.02 ]
|X 450 - 500 : [ 201 0.01 0.03 ]
|XXXXXX 500 - 550 : [ 864 0.06 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 3294 0.21 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 5391 0.35 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4514 0.29 0.95 ]
|XXXXXX 700 - 750 : [ 788 0.05 1.00 ]
| 750 - 800 : [ 10 0.00 1.00 ]
| 800 - 850 : [ 1 0.00 1.00 ]
| 850 - 900 : [ 1 0.00 1.00 ]
| 900 - 950 : [ 1 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AABW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AABW 3435908_fasta.screen.trimQ15.SaF > reads.trim15.AABW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AABW.rl 2 50
-------------------------------------------------------------------
#Found 2876 total values totalling 1949702.0000. <677.921419 +/- 128.703536>
#Range: [ 0 - 843 ]
#Most likely bin: [ 700 - 750 ] 1174 counts
#Median bin: [ 700 - 750 ] 1174 counts
#Histogram Bins Count Fraction Cum_Fraction
| 0 - 50 : [ 7 0.00 0.00 ]
|X 50 - 100 : [ 23 0.01 0.01 ]
|X 100 - 150 : [ 20 0.01 0.02 ]
|X 150 - 200 : [ 29 0.01 0.03 ]
|X 200 - 250 : [ 28 0.01 0.04 ]
|X 250 - 300 : [ 23 0.01 0.05 ]
| 300 - 350 : [ 8 0.00 0.05 ]
| 350 - 400 : [ 8 0.00 0.05 ]
|X 400 - 450 : [ 18 0.01 0.06 ]
|X 450 - 500 : [ 35 0.01 0.07 ]
|X 500 - 550 : [ 30 0.01 0.08 ]
|XX 550 - 600 : [ 60 0.02 0.10 ]
|XXXXXX 600 - 650 : [ 173 0.06 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 728 0.25 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1174 0.41 0.82 ]
|XXXXXXXXXXXXXXXXX 750 - 800 : [ 494 0.17 0.99 ]
|X 800 - 850 : [ 18 0.01 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3435908
-------------------------------------------------------------------
AAA.000001.000100
AABT.000001.000100 pUC18.fa LRS.fasta
AABU.000001.000100 pMCL200.fa LRS.fasta
AABW.000001.000100 pCC1Fos.fa LRS.fasta
AHUH.000001.000100 pUC18.fa pCC1Fos.fa ecoli.k12.m45.8_pieces LRS.fasta
AHUI.000001.000100 pUC18.fa pCC1Fos.fa LRS.fasta
COL.000001.000100 vector.ychen.fa LRS.fasta
AAA.000001.000100
AABT.000001.000100 pUC18.fa LRS.fasta
AABU.000001.000100 pMCL200.fa LRS.fasta
AABW.000001.000100 pCC1Fos.fa LRS.fasta
AHUH.000001.000100 pUC18.fa pCC1Fos.fa ecoli.k12.m45.8_pieces LRS.fasta
AHUI.000001.000100 pUC18.fa pCC1Fos.fa LRS.fasta
COL.000001.000100 vector.ychen.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3435908_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3435908_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 1 total values totalling 0.0000. <0.000000 +/- 0.000000>
#Range: [ 0 - 0 ]
#Most likely bin: [ 0 - 0.005 ] 1 counts
#Median bin: [ 0 - 0.005 ] 1 counts
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 0.005 : [ 1 1.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 13. 2 reads; 338 bp (untrimmed), 337 (trimmed).
Contig 14. 2 reads; 725 bp (untrimmed), 455 (trimmed).
Contig 15. 2 reads; 1242 bp (untrimmed), 510 (trimmed).
Contig 16. 2 reads; 1114 bp (untrimmed), 390 (trimmed).
Contig 17. 2 reads; 268 bp (untrimmed), 268 (trimmed).
Contig 18. 3 reads; 715 bp (untrimmed), 525 (trimmed).
Contig 19. 3 reads; 993 bp (untrimmed), 975 (trimmed).
Contig 20. 4 reads; 674 bp (untrimmed), 617 (trimmed).
Contig 21. 4 reads; 1064 bp (untrimmed), 905 (trimmed).
Contig 22. 4 reads; 910 bp (untrimmed), 909 (trimmed).
Contig 23. 4 reads; 1535 bp (untrimmed), 1535 (trimmed).
Contig 24. 4 reads; 741 bp (untrimmed), 422 (trimmed).
Contig 25. 7 reads; 645 bp (untrimmed), 341 (trimmed).
Contig 26. 8 reads; 753 bp (untrimmed), 560 (trimmed).
Contig 27. 8 reads; 1276 bp (untrimmed), 1012 (trimmed).
Contig 28. 10 reads; 756 bp (untrimmed), 351 (trimmed).
Contig 29. 11 reads; 690 bp (untrimmed), 533 (trimmed).
Contig 30. 17 reads; 648 bp (untrimmed), 648 (trimmed).
Contig 31. 21 reads; 1093 bp (untrimmed), 812 (trimmed).
Contig 32. 22 reads; 1386 bp (untrimmed), 1341 (trimmed).
Contig 33. 34 reads; 791 bp (untrimmed), 709 (trimmed).
Contig 34. 1449 reads; 46913 bp (untrimmed), 46913 (trimmed).
Contig 35. 1681 reads; 102874 bp (untrimmed), 102852 (trimmed).
Contig 36. 1810 reads; 77264 bp (untrimmed), 77220 (trimmed).
Contig 37. 2623 reads; 208702 bp (untrimmed), 208584 (trimmed).
Contig 38. 12327 reads; 817991 bp (untrimmed), 817868 (trimmed).
Contig 39. 24331 reads; 1490650 bp (untrimmed), 1490641 (trimmed).
--------------------------------------------------------------
Totals 44409 reads; 2773822 bp (untrimmed), 2761877 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 2763499 bases = 11.43 +- 5.08 = 0.01 +- 3.77
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 27 total values totalling 161.7200. <5.989630 +/- 4.779255>
#Range: [ 1.18 - 19.98 ]
#Most likely bin: [ 1.5 - 2 ] 4 counts
#Median bin: [ 4 - 4.5 ] 1 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 3 0.11 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 4 0.15 0.26 ]
|XXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 2 0.07 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 4 0.15 0.48 ]
#...
|XXXXXXXXXX 4 - 4.5 : [ 1 0.04 0.52 ]
#...
|XXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 2 0.07 0.59 ]
|XXXXXXXXXX 6 - 6.5 : [ 1 0.04 0.63 ]
#...
|XXXXXXXXXX 7.5 - 8 : [ 1 0.04 0.67 ]
|XXXXXXXXXX 8 - 8.5 : [ 1 0.04 0.70 ]
#...
|XXXXXXXXXX 9 - 9.5 : [ 1 0.04 0.74 ]
|XXXXXXXXXX 9.5 - 10 : [ 1 0.04 0.78 ]
#...
|XXXXXXXXXX 10.5 - 11 : [ 1 0.04 0.81 ]
|XXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 2 0.07 0.89 ]
|XXXXXXXXXX 11.5 - 12 : [ 1 0.04 0.93 ]
#...
|XXXXXXXXXX 14.5 - 15 : [ 1 0.04 0.96 ]
#...
|XXXXXXXXXX 19.5 - 20 : [ 1 0.04 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 6 total values totalling 77.9700. <12.995000 +/- 3.447505>
#Range: [ 9.67 - 19.98 ]
#Most likely bin: [ 11 - 11.5 ] 2 counts
#Median bin: [ 11 - 11.5 ] 2 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXX 9.5 - 10 : [ 1 0.17 0.17 ]
#...
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 2 0.33 0.50 ]
|XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 1 0.17 0.67 ]
#...
|XXXXXXXXXXXXXXXXXXXX 14.5 - 15 : [ 1 0.17 0.83 ]
#...
|XXXXXXXXXXXXXXXXXXXX 19.5 - 20 : [ 1 0.17 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------
Contig 15 2 reads 1242 bases = 1.18 +- 0.39 = 0.50 +- 0.75
Contig 16 2 reads 1114 bases = 1.20 +- 0.40 = 0.64 +- 0.63
Contig 12 2 reads 832 bases = 1.36 +- 0.48 = 1.36 +- 0.48
Contig 21 4 reads 1064 bases = 1.52 +- 0.89 = 0.91 +- 0.50
Contig 23 4 reads 1535 bases = 1.72 +- 0.76 = 1.72 +- 0.76
Contig 14 2 reads 725 bases = 1.76 +- 0.43 = 1.76 +- 0.43
Contig 11 2 reads 522 bases = 1.99 +- 0.11 = 1.99 +- 0.11
Contig 18 3 reads 715 bases = 2.37 +- 0.80 = 2.37 +- 0.80
Contig 19 3 reads 993 bases = 2.38 +- 0.75 = 2.38 +- 0.75
Contig 22 4 reads 910 bases = 2.55 +- 1.23 = 1.10 +- 1.01
Contig 20 4 reads 674 bases = 2.60 +- 1.31 = 1.10 +- 0.92
Contig 24 4 reads 741 bases = 2.85 +- 1.29 = 2.85 +- 1.29
Contig 25 7 reads 645 bases = 2.90 +- 2.08 = -0.32 +- 1.13
Contig 27 8 reads 1276 bases = 4.35 +- 2.53 = 4.35 +- 2.53
Contig 28 10 reads 756 bases = 5.53 +- 4.08 = 5.53 +- 4.08
Contig 32 22 reads 1386 bases = 5.77 +- 7.34 = 4.79 +- 7.73
Contig 26 8 reads 753 bases = 6.03 +- 2.28 = 6.03 +- 2.28
Contig 29 11 reads 690 bases = 7.53 +- 4.05 = 7.53 +- 4.05
Contig 31 21 reads 1093 bases = 8.25 +- 6.37 = 4.45 +- 2.50
Contig 30 17 reads 648 bases = 9.40 +- 3.73 = 3.26 +- 0.62
Contig 18 3 reads 715 bases = 2.37 +- 0.80 = 2.37 +- 0.80
Contig 19 3 reads 993 bases = 2.38 +- 0.75 = 2.38 +- 0.75
Contig 22 4 reads 910 bases = 2.55 +- 1.23 = 1.10 +- 1.01
Contig 20 4 reads 674 bases = 2.60 +- 1.31 = 1.10 +- 0.92
Contig 24 4 reads 741 bases = 2.85 +- 1.29 = 2.85 +- 1.29
Contig 25 7 reads 645 bases = 2.90 +- 2.08 = -0.32 +- 1.13
Contig 27 8 reads 1276 bases = 4.35 +- 2.53 = 4.35 +- 2.53
Contig 28 10 reads 756 bases = 5.53 +- 4.08 = 5.53 +- 4.08
Contig 32 22 reads 1386 bases = 5.77 +- 7.34 = 4.79 +- 7.73
Contig 26 8 reads 753 bases = 6.03 +- 2.28 = 6.03 +- 2.28
Contig 29 11 reads 690 bases = 7.53 +- 4.05 = 7.53 +- 4.05
Contig 31 21 reads 1093 bases = 8.25 +- 6.37 = 4.45 +- 2.50
Contig 30 17 reads 648 bases = 9.40 +- 3.73 = 3.26 +- 0.62
Contig 37 2623 reads 208702 bases = 9.67 +- 3.42 = 0.06 +- 3.52
Contig 33 34 reads 791 bases = 10.51 +- 14.43 = 10.51 +- 14.43
Contig 38 12327 reads 817991 bases = 11.00 +- 5.05 = -0.02 +- 3.73
Contig 35 1681 reads 102874 bases = 11.21 +- 4.33 = 0.05 +- 3.59
Contig 39 24331 reads 1490650 bases = 11.59 +- 4.92 = -0.05 +- 3.71
Contig 36 1810 reads 77264 bases = 14.52 +- 5.10 = 0.33 +- 4.36
Contig 34 1449 reads 46913 bases = 19.98 +- 5.42 = 0.18 +- 5.39
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 1933
HQ Discrepant reads = 4
Chimeric reads = 53
Suspect alignments = 570
-------------------------------------------------------------------
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/3435908/edit_dir.07May05.QD