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
3634513	3000	NULL	Acidobacterium sp.


-------------------------------------------------------------------
Taxonomy summary

Command: /home/copeland/scripts/tax2tree.sh Acidobacterium_sp.
-------------------------------------------------------------------




Error occurred: Empty result - nothing todo


pmfetch need params:



  • (id=NNNNNN[,NNNN,etc]) or (query_key=NNN, where NNN - number in the history, 0 - clipboard content for current database)
    • 

  • db=db_name (mandatory)
    • 

  • report=[docsum, brief, abstract, citation, medline, asn.1, mlasn1, uilist, sgml, gen] (Optional; default is asn.1)
    • 

  • mode=[html, file, text, asn.1, xml] (Optional; default is html)
    • 

  • dispstart - first element to display, from 0 to count - 1, (Optional; default is 0)
    • 

  • dispmax - number of items to display (Optional; default is all elements, from dispstart)
    • 

    See help.



-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------

# contigs: 9460029
# phrap: 9101725
# db: 
altered.

3000000
7187251 +/- 2964444

-------------------------------------------------------------------
Contam Summary with *.contigs:

Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------


Number of reads with X's: 12865
Number of reads with percent X's >= 20%:   349 = 0.6%
Number of reads with percent X's >= 50%:   175 = 0.3%
Number of reads with percent X's >= 80%:    17 = 0.0%
Total reads in project: 54382
Total bp X'd : 657526
                                  reads  >= 20% >= 50% >= 80% screened
Nr with L09136                    11644     55     39      1
Nr with pCC1Fos                     819      7      4      0
Nr with pMCL200_JGI_XZX+XZK         402    287    132     16

-------------------------------------------------------------------
Contam Summary with *.singlets:

Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------


Number of reads with X's: 21
Number of reads with percent X's >= 20%:     4 = 3.4%
Number of reads with percent X's >= 50%:     2 = 1.7%
Number of reads with percent X's >= 80%:     0 = 0.0%
Total reads in project: 119
Total bp X'd : 2642
                                  reads  >= 20% >= 50% >= 80% screened
Nr with L09136                       14      0      0      0
Nr with pCC1Fos                       3      0      0      0
Nr with pMCL200_JGI_XZX+XZK           4      4      2      0


-------------------------------------------------------------------
Base Count for Project:

Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------

A = 10351084
C = 15308039
G = 15648121
T = 9523243
N = 287484
X = 657526
GC fraction = 0.60
Total = 51775497

-------------------------------------------------------------------
Base Count for contigs:

Command: /psf/QC/bin/sparc/faCount 3634513_fasta.screen.contigs
-------------------------------------------------------------------


A	1845569
C	3006413
G	2989300
T	1849228
N	1853
fraction GC = 0.62
total bases = 9692363



    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 AIFW reads.list > grep.reads.list.AIFW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFW 4 500
-------------------------------------------------------------------


#Found 8847 total values totalling 28945509.0000. <3271.788064 +/- 437.765863>
#Range: [ 519 - 4497 ]
#Most likely bin: [ 3000 - 3500 ] 3304 counts
#Median bin: [ 3000 - 3500 ] 3304 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|                                         500 - 1000 : [ 4 0.00 0.00 ]
|                                         1000 - 1500 : [ 9 0.00 0.00 ]
|                                         1500 - 2000 : [ 7 0.00 0.00 ]
|X                                        2000 - 2500 : [ 116 0.01 0.02 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX          2500 - 3000 : [ 2534 0.29 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3304 0.37 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX           3500 - 4000 : [ 2479 0.28 0.96 ]
|XXXXX                                    4000 - 4500 : [ 394 0.04 1.00 ]

-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFX reads.list > grep.reads.list.AIFX
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFX 4 500
-------------------------------------------------------------------


#Found 6091 total values totalling 32810146.0000. <5386.659990 +/- 1475.417122>
#Range: [ 145 - 8979 ]
#Most likely bin: [ 5500 - 6000 ] 1412 counts
#Median bin: [ 5500 - 6000 ] 1412 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|X                                        0 - 500 : [ 32 0.01 0.01 ]
|X                                        500 - 1000 : [ 33 0.01 0.01 ]
|XXXX                                     1000 - 1500 : [ 139 0.02 0.03 ]
|XXXX                                     1500 - 2000 : [ 138 0.02 0.06 ]
|XXXX                                     2000 - 2500 : [ 133 0.02 0.08 ]
|XXX                                      2500 - 3000 : [ 118 0.02 0.10 ]
|XXXX                                     3000 - 3500 : [ 146 0.02 0.12 ]
|XXXXX                                    3500 - 4000 : [ 193 0.03 0.15 ]
|XXXXXXX                                  4000 - 4500 : [ 233 0.04 0.19 ]
|XXXXXXXXX                                4500 - 5000 : [ 316 0.05 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  5000 - 5500 : [ 803 0.13 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 1412 0.23 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     6000 - 6500 : [ 1269 0.21 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXX                   6500 - 7000 : [ 772 0.13 0.94 ]
|XXXXXXXXX                                7000 - 7500 : [ 324 0.05 1.00 ]
|X                                        7500 - 8000 : [ 29 0.00 1.00 ]
#...
|                                         8500 - 9000 : [ 1 0.00 1.00 ]

-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFY reads.list > grep.reads.list.AIFY
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIFY 4 500
-------------------------------------------------------------------


#Found 25 total values totalling 737959.0000. <29518.360000 +/- 8154.743007>
#Range: [ 6626 - 36101 ]
#Most likely bin: [ 33500 - 34000 ] 4 counts
#Median bin: [ 32500 - 33000 ] 1 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXX                               6500 - 7000 : [ 1 0.04 0.04 ]
#...
|XXXXXXXXXX                               8500 - 9000 : [ 1 0.04 0.08 ]
#...
|XXXXXXXXXX                               9500 - 10000 : [ 1 0.04 0.12 ]
#...
|XXXXXXXXXX                               26500 - 27000 : [ 1 0.04 0.16 ]
#...
|XXXXXXXXXX                               28000 - 28500 : [ 1 0.04 0.20 ]
|XXXXXXXXXX                               28500 - 29000 : [ 1 0.04 0.24 ]
#...
|XXXXXXXXXX                               29500 - 30000 : [ 1 0.04 0.28 ]
|XXXXXXXXXX                               30000 - 30500 : [ 1 0.04 0.32 ]
|XXXXXXXXXX                               30500 - 31000 : [ 1 0.04 0.36 ]
|XXXXXXXXXX                               31000 - 31500 : [ 1 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXX                     31500 - 32000 : [ 2 0.08 0.48 ]
#...
|XXXXXXXXXX                               32500 - 33000 : [ 1 0.04 0.52 ]
|XXXXXXXXXXXXXXXXXXXX                     33000 - 33500 : [ 2 0.08 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 4 0.16 0.76 ]
|XXXXXXXXXX                               34000 - 34500 : [ 1 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX           34500 - 35000 : [ 3 0.12 0.92 ]
|XXXXXXXXXX                               35000 - 35500 : [ 1 0.04 0.96 ]
#...
|XXXXXXXXXX                               36000 - 36500 : [ 1 0.04 1.00 ]



-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:

Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------

# AIFX 5195 +- 1603 (n=3015)
# AIFW 3112 +- 457 (n=4818)
# AIFY 25848 +- 11490 (n=11)


-------------------------------------------------------------------
Library / Read Quality summary

extracted from 3634513_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 
AIFW    59520     -1    -1     95   703   30946     89   632     93   644
AIFX    53760     -1    -1     97   692   27493     87   625     93   640
AIFY     3840     -1    -1     79   474    3839     71   622     80   591

        FWD    |----J15---| |----Q20---|  REV    |----J15---| |----Q20---|
LIB    Reads   %pass AvgLen %pass AvgNum  Reads  %pass AvgLen %pass AvgNun
AIFW    15308     89   628     93   642   15638     90   637     94   647
AIFX    13759     86   625     93   640   13734     88   625     94   640
AIFY     1920     70   634     77   603    1919     71   610     82   579


-------------------------------------------------------------------
reads2plates summary

extracted from file: 3634513_fasta.screen.r2p  [ from "READ/CLONE COUNT SUMMARY"  to end ]
-------------------------------------------------------------------


plate(s)        reads           clones  N/plate   avg%  LIBRARY	@

140		28033		12730	 90.93  94.72	AIFW	@
144		23571		12469	 86.59  90.20	AIFX	@
20		2778		1463	 73.15  76.20	AIFY	@

]		54382		26662	 87.70     	cumulative total@@

LIBRARY PLATE ID COUNT [ AIFW 140 AIFX 144 AIFY 20 ] for 304 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 3634513_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------

#Found 62278 total values totalling 34356160.0000. <551.658049 +/- 255.076359>
#Range: [ 0 - 975 ]
#Most likely bin: [ 700 - 750 ] 10873 counts
#Median bin: [ 650 - 700 ] 9213 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXX                 0 - 50 : [ 6497 0.10 0.10 ]
|XXXXX                                    50 - 100 : [ 1352 0.02 0.13 ]
|XXX                                      100 - 150 : [ 947 0.02 0.14 ]
|XXXX                                     150 - 200 : [ 1027 0.02 0.16 ]
|XXX                                      200 - 250 : [ 851 0.01 0.17 ]
|XXXX                                     250 - 300 : [ 1124 0.02 0.19 ]
|XXXX                                     300 - 350 : [ 1040 0.02 0.21 ]
|XXXX                                     350 - 400 : [ 1216 0.02 0.23 ]
|XXXXX                                    400 - 450 : [ 1395 0.02 0.25 ]
|XXXXXXX                                  450 - 500 : [ 1930 0.03 0.28 ]
|XXXXXXXXXX                               500 - 550 : [ 2676 0.04 0.32 ]
|XXXXXXXXXXXXXXX                          550 - 600 : [ 4024 0.06 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  600 - 650 : [ 6372 0.10 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX       650 - 700 : [ 9213 0.15 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 10873 0.17 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX            750 - 800 : [ 7898 0.13 0.94 ]
|XXXXXXXXXXXX                             800 - 850 : [ 3211 0.05 0.99 ]
|XX                                       850 - 900 : [ 557 0.01 1.00 ]
|                                         900 - 950 : [ 72 0.00 1.00 ]
|                                         950 - 1000 : [ 3 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for AIFW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFW 3634513_fasta.screen.trimQ15.SaF > reads.trim15.AIFW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFW.rl 2 50
-------------------------------------------------------------------


#Found 30946 total values totalling 17548592.0000. <567.071415 +/- 243.306269>
#Range: [ 0 - 975 ]
#Most likely bin: [ 700 - 750 ] 5928 counts
#Median bin: [ 650 - 700 ] 5018 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXX                      0 - 50 : [ 2785 0.09 0.09 ]
|XXX                                      50 - 100 : [ 492 0.02 0.11 ]
|XXX                                      100 - 150 : [ 470 0.02 0.12 ]
|XXX                                      150 - 200 : [ 415 0.01 0.13 ]
|XXX                                      200 - 250 : [ 417 0.01 0.15 ]
|XXX                                      250 - 300 : [ 441 0.01 0.16 ]
|XXX                                      300 - 350 : [ 504 0.02 0.18 ]
|XXXX                                     350 - 400 : [ 632 0.02 0.20 ]
|XXXXX                                    400 - 450 : [ 747 0.02 0.22 ]
|XXXXXXX                                  450 - 500 : [ 972 0.03 0.25 ]
|XXXXXXXXX                                500 - 550 : [ 1312 0.04 0.30 ]
|XXXXXXXXXXXXX                            550 - 600 : [ 1973 0.06 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXX                   600 - 650 : [ 3256 0.11 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX       650 - 700 : [ 5018 0.16 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5928 0.19 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX               750 - 800 : [ 3881 0.13 0.94 ]
|XXXXXXXX                                 800 - 850 : [ 1245 0.04 0.99 ]
|XXX                                      850 - 900 : [ 383 0.01 1.00 ]
|                                         900 - 950 : [ 72 0.00 1.00 ]
|                                         950 - 1000 : [ 3 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for AIFX
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFX 3634513_fasta.screen.trimQ15.SaF > reads.trim15.AIFX.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFX.rl 2 50
-------------------------------------------------------------------


#Found 27493 total values totalling 15096664.0000. <549.109373 +/- 255.269605>
#Range: [ 0 - 894 ]
#Most likely bin: [ 700 - 750 ] 4395 counts
#Median bin: [ 600 - 650 ] 2883 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXX                 0 - 50 : [ 2660 0.10 0.10 ]
|XXXXXXX                                  50 - 100 : [ 793 0.03 0.13 ]
|XXXX                                     100 - 150 : [ 437 0.02 0.14 ]
|XXXXX                                    150 - 200 : [ 572 0.02 0.16 ]
|XXXX                                     200 - 250 : [ 388 0.01 0.18 ]
|XXXXX                                    250 - 300 : [ 534 0.02 0.20 ]
|XXXX                                     300 - 350 : [ 423 0.02 0.21 ]
|XXXXX                                    350 - 400 : [ 530 0.02 0.23 ]
|XXXXX                                    400 - 450 : [ 599 0.02 0.25 ]
|XXXXXXXX                                 450 - 500 : [ 859 0.03 0.28 ]
|XXXXXXXXXXXX                             500 - 550 : [ 1277 0.05 0.33 ]
|XXXXXXXXXXXXXXXXX                        550 - 600 : [ 1876 0.07 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX               600 - 650 : [ 2883 0.10 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX      650 - 700 : [ 3800 0.14 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4395 0.16 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX         750 - 800 : [ 3528 0.13 0.93 ]
|XXXXXXXXXXXXXXXX                         800 - 850 : [ 1780 0.06 0.99 ]
|X                                        850 - 900 : [ 159 0.01 1.00 ]

trimt JAZZ trim 15 readlength histogram for AIFY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFY 3634513_fasta.screen.trimQ15.SaF > reads.trim15.AIFY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFY.rl 2 50
-------------------------------------------------------------------


#Found 3839 total values totalling 1710904.0000. <445.663975 +/- 313.762595>
#Range: [ 0 - 887 ]
#Most likely bin: [ 0 - 50 ] 1052 counts
#Median bin: [ 550 - 600 ] 175 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1052 0.27 0.27 ]
|XXX                                      50 - 100 : [ 67 0.02 0.29 ]
|XX                                       100 - 150 : [ 40 0.01 0.30 ]
|XX                                       150 - 200 : [ 40 0.01 0.31 ]
|XX                                       200 - 250 : [ 46 0.01 0.32 ]
|XXXXXX                                   250 - 300 : [ 149 0.04 0.36 ]
|XXXX                                     300 - 350 : [ 113 0.03 0.39 ]
|XX                                       350 - 400 : [ 54 0.01 0.41 ]
|XX                                       400 - 450 : [ 49 0.01 0.42 ]
|XXXX                                     450 - 500 : [ 99 0.03 0.45 ]
|XXX                                      500 - 550 : [ 87 0.02 0.47 ]
|XXXXXXX                                  550 - 600 : [ 175 0.05 0.51 ]
|XXXXXXXXX                                600 - 650 : [ 233 0.06 0.57 ]
|XXXXXXXXXXXXXXX                          650 - 700 : [ 395 0.10 0.68 ]
|XXXXXXXXXXXXXXXXXXXXX                    700 - 750 : [ 550 0.14 0.82 ]
|XXXXXXXXXXXXXXXXXXX                      750 - 800 : [ 489 0.13 0.95 ]
|XXXXXXX                                  800 - 850 : [ 186 0.05 1.00 ]
|X                                        850 - 900 : [ 15 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for BFBO
trimt JAZZ trim 15 readlength histogram for BFBP
trimt JAZZ trim 15 readlength histogram for BFBS

-------------------------------------------------------------------
Library vector screening

Command: /home/copeland/scripts/checkScreen.sh 3634513
-------------------------------------------------------------------

AIFW.000001.000100 pUC18.fa LRS.fasta 
AIFW.000101.000200 pUC18.fa LRS.fasta 
AIFW.000201.000300 pUC18.fa LRS.fasta 
AIFW.000301.000400 pUC18.fa LRS.fasta 
AIFX.000001.000100 pMCL200.fa LRS.fasta 
AIFX.000101.000200 pMCL200.fa LRS.fasta 
AIFX.000201.000300 pMCL200.fa LRS.fasta 
AIFY.000001.000100 pCC1Fos.fa LRS.fasta 
AIFW.000001.000100 pUC18.fa LRS.fasta 
AIFW.000101.000200 pUC18.fa LRS.fasta 
AIFW.000201.000300 pUC18.fa LRS.fasta 
AIFW.000301.000400 pUC18.fa LRS.fasta 
AIFX.000001.000100 pMCL200.fa LRS.fasta 
AIFX.000101.000200 pMCL200.fa LRS.fasta 
AIFX.000201.000300 pMCL200.fa LRS.fasta 
AIFY.000001.000100 pCC1Fos.fa LRS.fasta 


-------------------------------------------------------------------
GC content histogram:

Command: 	/bin/nawk '{print $5+$6}' GC.3634513_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------


# GC.3634513_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 54221 total values totalling 33497.9288. <0.617804 +/- 0.039110>
#Range: [ 0.2887 - 0.9231 ]
#Most likely bin: [ 0.615 - 0.62 ] 3082 counts
#Median bin: [ 0.615 - 0.62 ] 3082 counts
|                                         0.285 - 0.29 : [ 1 0.00 0.00 ]
#...
|                                         0.295 - 0.3 : [ 1 0.00 0.00 ]
#...
|                                         0.32 - 0.325 : [ 1 0.00 0.00 ]
|                                         0.325 - 0.33 : [ 3 0.00 0.00 ]
#...
|                                         0.34 - 0.345 : [ 1 0.00 0.00 ]
#...
|                                         0.35 - 0.355 : [ 1 0.00 0.00 ]
|                                         0.355 - 0.36 : [ 1 0.00 0.00 ]
|                                         0.36 - 0.365 : [ 5 0.00 0.00 ]
|                                         0.365 - 0.37 : [ 1 0.00 0.00 ]
|                                         0.37 - 0.375 : [ 2 0.00 0.00 ]
|                                         0.375 - 0.38 : [ 1 0.00 0.00 ]
|                                         0.38 - 0.385 : [ 1 0.00 0.00 ]
#...
|                                         0.39 - 0.395 : [ 1 0.00 0.00 ]
|                                         0.395 - 0.4 : [ 2 0.00 0.00 ]
|                                         0.4 - 0.405 : [ 5 0.00 0.00 ]
|                                         0.405 - 0.41 : [ 4 0.00 0.00 ]
|                                         0.41 - 0.415 : [ 5 0.00 0.00 ]
|                                         0.415 - 0.42 : [ 6 0.00 0.00 ]
|                                         0.42 - 0.425 : [ 5 0.00 0.00 ]
|                                         0.425 - 0.43 : [ 3 0.00 0.00 ]
|                                         0.43 - 0.435 : [ 5 0.00 0.00 ]
|                                         0.435 - 0.44 : [ 2 0.00 0.00 ]
|                                         0.44 - 0.445 : [ 5 0.00 0.00 ]
|                                         0.445 - 0.45 : [ 1 0.00 0.00 ]
|                                         0.45 - 0.455 : [ 11 0.00 0.00 ]
|                                         0.455 - 0.46 : [ 10 0.00 0.00 ]
|                                         0.46 - 0.465 : [ 13 0.00 0.00 ]
|                                         0.465 - 0.47 : [ 14 0.00 0.00 ]
|                                         0.47 - 0.475 : [ 17 0.00 0.00 ]
|                                         0.475 - 0.48 : [ 15 0.00 0.00 ]
|                                         0.48 - 0.485 : [ 36 0.00 0.00 ]
|                                         0.485 - 0.49 : [ 30 0.00 0.00 ]
|                                         0.49 - 0.495 : [ 31 0.00 0.00 ]
|                                         0.495 - 0.5 : [ 30 0.00 0.00 ]
|X                                        0.5 - 0.505 : [ 96 0.00 0.01 ]
|X                                        0.505 - 0.51 : [ 70 0.00 0.01 ]
|X                                        0.51 - 0.515 : [ 108 0.00 0.01 ]
|XX                                       0.515 - 0.52 : [ 126 0.00 0.01 ]
|XX                                       0.52 - 0.525 : [ 154 0.00 0.02 ]
|XXX                                      0.525 - 0.53 : [ 201 0.00 0.02 ]
|XXX                                      0.53 - 0.535 : [ 255 0.00 0.02 ]
|XXXX                                     0.535 - 0.54 : [ 317 0.01 0.03 ]
|XXXXX                                    0.54 - 0.545 : [ 383 0.01 0.04 ]
|XXXXXXX                                  0.545 - 0.55 : [ 540 0.01 0.05 ]
|XXXXXXXX                                 0.55 - 0.555 : [ 602 0.01 0.06 ]
|XXXXXXXXX                                0.555 - 0.56 : [ 704 0.01 0.07 ]
|XXXXXXXXXXX                              0.56 - 0.565 : [ 848 0.02 0.09 ]
|XXXXXXXXXXXXXX                           0.565 - 0.57 : [ 1043 0.02 0.11 ]
|XXXXXXXXXXXXXXX                          0.57 - 0.575 : [ 1154 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXX                       0.575 - 0.58 : [ 1409 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXXX                    0.58 - 0.585 : [ 1588 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXXX                 0.585 - 0.59 : [ 1834 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX              0.59 - 0.595 : [ 2042 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX            0.595 - 0.6 : [ 2236 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX        0.6 - 0.605 : [ 2566 0.05 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     0.605 - 0.61 : [ 2743 0.05 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    0.61 - 0.615 : [ 2845 0.05 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 3082 0.06 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  0.62 - 0.625 : [ 2969 0.05 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  0.625 - 0.63 : [ 3016 0.06 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX   0.63 - 0.635 : [ 2935 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     0.635 - 0.64 : [ 2736 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX        0.64 - 0.645 : [ 2523 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX           0.645 - 0.65 : [ 2319 0.04 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX               0.65 - 0.655 : [ 2032 0.04 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  0.655 - 0.66 : [ 1742 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXX                     0.66 - 0.665 : [ 1512 0.03 0.90 ]
|XXXXXXXXXXXXXXXX                         0.665 - 0.67 : [ 1251 0.02 0.93 ]
|XXXXXXXXXXXXX                            0.67 - 0.675 : [ 973 0.02 0.94 ]
|XXXXXXXXXX                               0.675 - 0.68 : [ 734 0.01 0.96 ]
|XXXXXXX                                  0.68 - 0.685 : [ 561 0.01 0.97 ]
|XXXXXX                                   0.685 - 0.69 : [ 495 0.01 0.98 ]
|XXXX                                     0.69 - 0.695 : [ 325 0.01 0.98 ]
|XXX                                      0.695 - 0.7 : [ 232 0.00 0.99 ]
|XX                                       0.7 - 0.705 : [ 184 0.00 0.99 ]
|X                                        0.705 - 0.71 : [ 111 0.00 0.99 ]
|X                                        0.71 - 0.715 : [ 87 0.00 1.00 ]
|X                                        0.715 - 0.72 : [ 57 0.00 1.00 ]
|X                                        0.72 - 0.725 : [ 47 0.00 1.00 ]
|                                         0.725 - 0.73 : [ 33 0.00 1.00 ]
|                                         0.73 - 0.735 : [ 31 0.00 1.00 ]
|                                         0.735 - 0.74 : [ 24 0.00 1.00 ]
|                                         0.74 - 0.745 : [ 12 0.00 1.00 ]
|                                         0.745 - 0.75 : [ 6 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 : [ 6 0.00 1.00 ]
|                                         0.765 - 0.77 : [ 7 0.00 1.00 ]
|                                         0.77 - 0.775 : [ 6 0.00 1.00 ]
|                                         0.775 - 0.78 : [ 2 0.00 1.00 ]
|                                         0.78 - 0.785 : [ 5 0.00 1.00 ]
|                                         0.785 - 0.79 : [ 1 0.00 1.00 ]
|                                         0.79 - 0.795 : [ 1 0.00 1.00 ]
|                                         0.795 - 0.8 : [ 2 0.00 1.00 ]
|                                         0.8 - 0.805 : [ 2 0.00 1.00 ]
|                                         0.805 - 0.81 : [ 2 0.00 1.00 ]
#...
|                                         0.815 - 0.82 : [ 2 0.00 1.00 ]
#...
|                                         0.825 - 0.83 : [ 1 0.00 1.00 ]
#...
|                                         0.84 - 0.845 : [ 3 0.00 1.00 ]
#...
|                                         0.85 - 0.855 : [ 1 0.00 1.00 ]
#...
|                                         0.865 - 0.87 : [ 2 0.00 1.00 ]
#...
|                                         0.92 - 0.925 : [ 1 0.00 1.00 ]



    Contigs and Assemblies
    
    
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------

Contig 1325.  174 reads;  27103 bp (untrimmed),  27043 (trimmed).
Contig 1326.  174 reads;  27075 bp (untrimmed),  26771 (trimmed).
Contig 1327.  177 reads;  27768 bp (untrimmed),  27720 (trimmed).
Contig 1328.  177 reads;  32142 bp (untrimmed),  32008 (trimmed).
Contig 1329.  177 reads;  24541 bp (untrimmed),  24461 (trimmed).
Contig 1330.  182 reads;  23143 bp (untrimmed),  22802 (trimmed).
Contig 1331.  186 reads;  28487 bp (untrimmed),  28225 (trimmed).
Contig 1332.  186 reads;  24094 bp (untrimmed),  23790 (trimmed).
Contig 1333.  188 reads;  24517 bp (untrimmed),  24275 (trimmed).
Contig 1334.  188 reads;  22046 bp (untrimmed),  21917 (trimmed).
Contig 1335.  197 reads;  28868 bp (untrimmed),  28776 (trimmed).
Contig 1336.  197 reads;  31082 bp (untrimmed),  31053 (trimmed).
Contig 1337.  200 reads;  29605 bp (untrimmed),  29263 (trimmed).
Contig 1338.  210 reads;  33517 bp (untrimmed),  33174 (trimmed).
Contig 1339.  214 reads;  32352 bp (untrimmed),  31705 (trimmed).
Contig 1340.  214 reads;  27843 bp (untrimmed),  27505 (trimmed).
Contig 1341.  220 reads;  30808 bp (untrimmed),  30492 (trimmed).
Contig 1342.  225 reads;  36796 bp (untrimmed),  36525 (trimmed).
Contig 1343.  227 reads;  35293 bp (untrimmed),  35273 (trimmed).
Contig 1344.  237 reads;  33763 bp (untrimmed),  33637 (trimmed).
Contig 1345.  263 reads;  36237 bp (untrimmed),  36068 (trimmed).
Contig 1346.  285 reads;  40628 bp (untrimmed),  40516 (trimmed).
Contig 1347.  310 reads;  43671 bp (untrimmed),  43623 (trimmed).
Contig 1348.  361 reads;  47484 bp (untrimmed),  46970 (trimmed).
Contig 1349.  407 reads;  60643 bp (untrimmed),  60332 (trimmed).
Contig 1350.  416 reads;  58619 bp (untrimmed),  58544 (trimmed).
Contig 1351.  540 reads;  71143 bp (untrimmed),  70897 (trimmed).
--------------------------------------------------------------
Totals      54263 reads; 9692363 bp (untrimmed), 9460029 (trimmed).


-------------------------------------------------------------------
Depth Summary

Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------

depth.out contains 9691843 bases  = 4.72 +- 2.48   = 0.46 +- 2.34  


-------------------------------------------------------------------
Histogram of All Contig Depth Values:

Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------


#Found 1349 total values totalling 5436.7400. <4.030200 +/- 1.229901>
#Range: [ 1.16 - 7.60 ]
#Most likely bin: [ 4 - 4.5 ] 214 counts
#Median bin: [ 4 - 4.5 ] 214 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XX                                       1 - 1.5 : [ 9 0.01 0.01 ]
|XXXXXXXXXXXX                             1.5 - 2 : [ 64 0.05 0.05 ]
|XXXXXXXXXXXXXXXXXX                       2 - 2.5 : [ 95 0.07 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX                2.5 - 3 : [ 135 0.10 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX            3 - 3.5 : [ 157 0.12 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX          3.5 - 4 : [ 168 0.12 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 214 0.16 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    4.5 - 5 : [ 200 0.15 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX              5 - 5.5 : [ 143 0.11 0.88 ]
|XXXXXXXXXXXXXXXXX                        5.5 - 6 : [ 92 0.07 0.95 ]
|XXXXXXXXXX                               6 - 6.5 : [ 51 0.04 0.98 ]
|XXX                                      6.5 - 7 : [ 16 0.01 1.00 ]
|X                                        7 - 7.5 : [ 4 0.00 1.00 ]
|                                         7.5 - 8 : [ 1 0.00 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 975 total values totalling 4417.4600. <4.530728 +/- 0.950787>
#Range: [ 2.33 - 7.60 ]
#Most likely bin: [ 4 - 4.5 ] 200 counts
#Median bin: [ 4.5 - 5 ] 195 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XX                                       2 - 2.5 : [ 8 0.01 0.01 ]
|XXXXXXXXX                                2.5 - 3 : [ 45 0.05 0.05 ]
|XXXXXXXXXXXXXXXXXX                       3 - 3.5 : [ 91 0.09 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX              3.5 - 4 : [ 136 0.14 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 200 0.21 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  4.5 - 5 : [ 195 0.20 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX            5 - 5.5 : [ 143 0.15 0.84 ]
|XXXXXXXXXXXXXXXXXX                       5.5 - 6 : [ 90 0.09 0.93 ]
|XXXXXXXXX                                6 - 6.5 : [ 46 0.05 0.98 ]
|XXX                                      6.5 - 7 : [ 16 0.02 0.99 ]
|X                                        7 - 7.5 : [ 4 0.00 1.00 ]
|                                         7.5 - 8 : [ 1 0.00 1.00 ]


-------------------------------------------------------------------
Sorted Depth Values:

Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
-------------------------------------------------------------------

Contig 3           2 reads      1682 bases  =   1.16 +- 0.37     =   1.16 +-  0.37
Contig 10          3 reads      2051 bases  =   1.30 +- 0.46     =   0.40 +-  0.73
Contig 44          3 reads      1961 bases  =   1.40 +- 0.49     =   1.40 +-  0.49
Contig 173         5 reads      3243 bases  =   1.43 +- 0.50     =   0.23 +-  1.06
Contig 34          3 reads      1851 bases  =   1.43 +- 0.50     =   0.50 +-  0.56
Contig 9           3 reads      1830 bases  =   1.44 +- 0.57     =   0.42 +-  0.76
Contig 269         7 reads      4071 bases  =   1.46 +- 0.54     =   0.40 +-  1.32
Contig 112         4 reads      2202 bases  =   1.48 +- 0.50     =   0.67 +-  0.76
Contig 5           3 reads      1315 bases  =   1.49 +- 0.53     =   1.49 +-  0.53
Contig 12          3 reads      1857 bases  =   1.54 +- 0.65     =   0.63 +-  1.06
Contig 46          3 reads      1757 bases  =   1.54 +- 0.50     =   0.43 +-  0.53
Contig 1           2 reads      1251 bases  =   1.56 +- 0.50     =   1.56 +-  0.50
Contig 59          3 reads      1599 bases  =   1.56 +- 0.81     =   0.85 +-  0.36
Contig 97          4 reads      2289 bases  =   1.57 +- 0.65     =   0.82 +-  1.39
Contig 152         5 reads      2464 bases  =   1.59 +- 0.52     =   0.45 +-  1.48
Contig 31          3 reads      1267 bases  =   1.59 +- 0.63     =   1.59 +-  0.63
Contig 2           2 reads      1161 bases  =   1.60 +- 0.49     =  -0.07 +-  0.63
Contig 13          3 reads      1349 bases  =   1.61 +- 0.85     =   1.61 +-  0.85
Contig 21          3 reads      1618 bases  =   1.61 +- 0.65     =   0.58 +-  0.49
Contig 106         4 reads      1767 bases  =   1.62 +- 0.50     =   1.62 +-  0.50

Contig 1280      135 reads     17435 bases  =   6.54 +- 4.86     =   0.81 +-  3.40
Contig 1351      540 reads     71143 bases  =   6.55 +- 2.90     =   0.11 +-  2.73
Contig 1333      188 reads     24517 bases  =   6.57 +- 2.83     =  -0.10 +-  2.05
Contig 1106       68 reads      8484 bases  =   6.59 +- 2.95     =   1.18 +-  2.71
Contig 1303      153 reads     19711 bases  =   6.59 +- 2.77     =   0.52 +-  2.53
Contig 1214      100 reads     13362 bases  =   6.63 +- 2.95     =   0.17 +-  3.99
Contig 1310      158 reads     20202 bases  =   6.70 +- 3.38     =   0.02 +-  3.09
Contig 1332      186 reads     24094 bases  =   6.70 +- 2.88     =   0.71 +-  2.80
Contig 1330      182 reads     23143 bases  =   6.72 +- 3.16     =   0.08 +-  1.97
Contig 1113       69 reads      8320 bases  =   6.78 +- 2.98     =   0.09 +-  2.86
Contig 1320      169 reads     20907 bases  =   6.80 +- 2.78     =   0.02 +-  3.16
Contig 1304      154 reads     18353 bases  =   6.81 +- 7.64     =   0.29 +-  3.13
Contig 1072       62 reads      7732 bases  =   6.84 +- 2.59     =   0.50 +-  3.38
Contig 965        47 reads      5983 bases  =   6.87 +- 2.32     =  -0.10 +-  3.06
Contig 1151       81 reads     10207 bases  =   6.94 +- 2.57     =   0.20 +-  3.11
Contig 1313      160 reads     19206 bases  =   7.01 +- 2.39     =  -0.00 +-  3.03
Contig 894        39 reads      4903 bases  =   7.03 +- 3.50     =   2.37 +-  2.78
Contig 583        18 reads      2112 bases  =   7.04 +- 3.99     =   0.39 +-  1.32
Contig 1334      188 reads     22046 bases  =   7.20 +- 3.20     =   0.24 +-  3.16
Contig 1172       87 reads      9828 bases  =   7.60 +- 3.36     =   1.08 +-  2.12


    Assembler Specific Info
    
    
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------

Small Inserts = 1

HQ Discrepant reads = 868

Chimeric reads = 125

Suspect alignments = 151


-------------------------------------------------------------------
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/microbe3/3634513/edit_dir.28Jun04.QD