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
3634501	9000	NULL	Silicibacter sp.
3634501	4500	NULL	Silicibacter sp.


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

Command: /home/copeland/scripts/tax2tree.sh Silicibacter_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: 4176047
# phrap: 3993843
# db: 
altered.

9000000
4500000
5417472 +/- 2076301

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

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


Number of reads with X's: 14070
Number of reads with percent X's >= 20%:   222 = 0.4%
Number of reads with percent X's >= 50%:    98 = 0.2%
Number of reads with percent X's >= 80%:     7 = 0.0%
Total reads in project: 57977
Total bp X'd : 672933
                                  reads  >= 20% >= 50% >= 80% screened
Nr with L09136                    10894     59     40      6
Nr with pCC1Fos                    3151    145     49      0
Nr with pEpiFos5                      2      0      0      0
Nr with pMCL200_JGI_XZX+XZK          23     18      9      1

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

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


Number of reads with X's: 243
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: 548
Total bp X'd : 10108
                                  reads  >= 20% >= 50% >= 80% screened
Nr with L09136                        3      0      0      0
Nr with pCC1Fos                     240      0      0      0


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

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

A = 13664411
C = 19465414
G = 19015557
T = 13472745
N = 478571
X = 672933
GC fraction = 0.58
Total = 66769631

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

Command: /psf/QC/bin/sparc/faCount 3634501_fasta.screen.contigs
-------------------------------------------------------------------


A	840356
C	1254701
G	1257878
T	844128
N	1208
fraction GC = 0.60
total bases = 4198271



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


#Found 11136 total values totalling 37573346.0000. <3374.043283 +/- 6025.183869>
#Range: [ 1162 - 426539 ]
#Most likely bin: [ 3000 - 3500 ] 4715 counts
#Median bin: [ 3000 - 3500 ] 4715 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|                                         1000 - 1500 : [ 15 0.00 0.00 ]
|                                         1500 - 2000 : [ 30 0.00 0.00 ]
|X                                        2000 - 2500 : [ 87 0.01 0.01 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX              2500 - 3000 : [ 3177 0.29 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 4715 0.42 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX               3500 - 4000 : [ 3033 0.27 0.99 ]
|X                                        4000 - 4500 : [ 68 0.01 1.00 ]
#...
|                                         10000 - 10500 : [ 1 0.00 1.00 ]
#...
|                                         13000 - 13500 : [ 1 0.00 1.00 ]
#...
|                                         32000 - 32500 : [ 1 0.00 1.00 ]
#...
|                                         47000 - 47500 : [ 1 0.00 1.00 ]
#...
|                                         64000 - 64500 : [ 1 0.00 1.00 ]
#...
|                                         76000 - 76500 : [ 1 0.00 1.00 ]
#...
|                                         188000 - 188500 : [ 1 0.00 1.00 ]
#...
|                                         190500 - 191000 : [ 1 0.00 1.00 ]
#...
|                                         212500 - 213000 : [ 1 0.00 1.00 ]
#...
|                                         316500 - 317000 : [ 1 0.00 1.00 ]
#...
|                                         426500 - 427000 : [ 1 0.00 1.00 ]

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


#Found 9884 total values totalling 84063662.0000. <8505.024484 +/- 6992.909579>
#Range: [ 1341 - 333700 ]
#Most likely bin: [ 8000 - 8500 ] 2589 counts
#Median bin: [ 8000 - 8500 ] 2589 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|                                         1000 - 1500 : [ 4 0.00 0.00 ]
|                                         1500 - 2000 : [ 5 0.00 0.00 ]
|                                         2000 - 2500 : [ 10 0.00 0.00 ]
|                                         2500 - 3000 : [ 17 0.00 0.00 ]
|                                         3000 - 3500 : [ 11 0.00 0.00 ]
|                                         3500 - 4000 : [ 16 0.00 0.01 ]
|                                         4000 - 4500 : [ 27 0.00 0.01 ]
|                                         4500 - 5000 : [ 24 0.00 0.01 ]
|X                                        5000 - 5500 : [ 45 0.00 0.02 ]
|X                                        5500 - 6000 : [ 71 0.01 0.02 ]
|X                                        6000 - 6500 : [ 83 0.01 0.03 ]
|XXX                                      6500 - 7000 : [ 178 0.02 0.05 ]
|XXXXXXXXXXX                              7000 - 7500 : [ 724 0.07 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX         7500 - 8000 : [ 2077 0.21 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 2589 0.26 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX        8500 - 9000 : [ 2133 0.22 0.81 ]
|XXXXXXXXXXXXXXXXXXX                      9000 - 9500 : [ 1252 0.13 0.94 ]
|XXXXXXXX                                 9500 - 10000 : [ 545 0.06 0.99 ]
|X                                        10000 - 10500 : [ 56 0.01 1.00 ]
#...
|                                         14000 - 14500 : [ 1 0.00 1.00 ]
#...
|                                         25500 - 26000 : [ 1 0.00 1.00 ]
#...
|                                         47500 - 48000 : [ 1 0.00 1.00 ]
#...
|                                         52000 - 52500 : [ 1 0.00 1.00 ]
#...
|                                         54000 - 54500 : [ 1 0.00 1.00 ]
#...
|                                         74500 - 75000 : [ 1 0.00 1.00 ]
#...
|                                         106000 - 106500 : [ 1 0.00 1.00 ]
#...
|                                         110000 - 110500 : [ 1 0.00 1.00 ]
#...
|                                         131000 - 131500 : [ 1 0.00 1.00 ]
#...
|                                         138000 - 138500 : [ 1 0.00 1.00 ]
#...
|                                         146000 - 146500 : [ 1 0.00 1.00 ]
#...
|                                         158500 - 159000 : [ 1 0.00 1.00 ]
#...
|                                         160500 - 161000 : [ 1 0.00 1.00 ]
#...
|                                         256500 - 257000 : [ 1 0.00 1.00 ]
#...
|                                         300500 - 301000 : [ 1 0.00 1.00 ]
#...
|                                         316000 - 316500 : [ 1 0.00 1.00 ]
#...
|                                         333500 - 334000 : [ 1 0.00 1.00 ]

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


#Found 2391 total values totalling 91818270.0000. <38401.618570 +/- 3704.185314>
#Range: [ 1850 - 81159 ]
#Most likely bin: [ 37000 - 37500 ] 146 counts
#Median bin: [ 38000 - 38500 ] 122 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|                                         1500 - 2000 : [ 1 0.00 0.00 ]
|                                         2000 - 2500 : [ 1 0.00 0.00 ]
#...
|                                         3000 - 3500 : [ 1 0.00 0.00 ]
#...
|                                         23000 - 23500 : [ 1 0.00 0.00 ]
#...
|                                         26500 - 27000 : [ 1 0.00 0.00 ]
|X                                        27000 - 27500 : [ 2 0.00 0.00 ]
|X                                        27500 - 28000 : [ 2 0.00 0.00 ]
|X                                        28000 - 28500 : [ 3 0.00 0.01 ]
|                                         28500 - 29000 : [ 1 0.00 0.01 ]
|X                                        29000 - 29500 : [ 5 0.00 0.01 ]
|X                                        29500 - 30000 : [ 3 0.00 0.01 ]
|X                                        30000 - 30500 : [ 2 0.00 0.01 ]
|XXX                                      30500 - 31000 : [ 12 0.01 0.01 ]
|XXX                                      31000 - 31500 : [ 11 0.00 0.02 ]
|XXXXX                                    31500 - 32000 : [ 18 0.01 0.03 ]
|XXXXX                                    32000 - 32500 : [ 17 0.01 0.03 ]
|XXXXXXX                                  32500 - 33000 : [ 27 0.01 0.05 ]
|XXXXXXXXXX                               33000 - 33500 : [ 38 0.02 0.06 ]
|XXXXXXXXXXXXXX                           33500 - 34000 : [ 50 0.02 0.08 ]
|XXXXXXXXXXXXXXXXXX                       34000 - 34500 : [ 66 0.03 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX                34500 - 35000 : [ 91 0.04 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX              35000 - 35500 : [ 98 0.04 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX         35500 - 36000 : [ 116 0.05 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX        36000 - 36500 : [ 122 0.05 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  36500 - 37000 : [ 144 0.06 0.35 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 146 0.06 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 145 0.06 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX        38000 - 38500 : [ 122 0.05 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX          38500 - 39000 : [ 112 0.05 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX         39000 - 39500 : [ 118 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX         39500 - 40000 : [ 118 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX      40000 - 40500 : [ 128 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX       40500 - 41000 : [ 123 0.05 0.77 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX                41000 - 41500 : [ 92 0.04 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXX                 41500 - 42000 : [ 87 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  42000 - 42500 : [ 85 0.04 0.88 ]
|XXXXXXXXXXXXXXXXXXXX                     42500 - 43000 : [ 72 0.03 0.91 ]
|XXXXXXXXXXXXXXXXXX                       43000 - 43500 : [ 67 0.03 0.94 ]
|XXXXXXXXXXXX                             43500 - 44000 : [ 42 0.02 0.96 ]
|XXXXXXXXXXX                              44000 - 44500 : [ 39 0.02 0.97 ]
|XXXXXXX                                  44500 - 45000 : [ 26 0.01 0.98 ]
|XXXXX                                    45000 - 45500 : [ 17 0.01 0.99 ]
|XXX                                      45500 - 46000 : [ 12 0.01 1.00 ]
|X                                        46000 - 46500 : [ 2 0.00 1.00 ]
|                                         46500 - 47000 : [ 1 0.00 1.00 ]
|                                         47000 - 47500 : [ 1 0.00 1.00 ]
#...
|                                         52500 - 53000 : [ 1 0.00 1.00 ]
#...
|                                         74500 - 75000 : [ 1 0.00 1.00 ]
#...
|                                         81000 - 81500 : [ 1 0.00 1.00 ]



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

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

# AICI 3172 +- 810 (n=5620)
# AICN 38063 +- 4534 (n=1228)
# AICK 8217 +- 978 (n=5165)


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

extracted from 3634501_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 
AICI    25344     -1    -1     99   785   24713    100   788    100   794
AICK    28416     -1    -1     96   724   26081     99   685    100   697
AICN     9984     -1    -1     82   519    7183     95   685    100   684

        FWD    |----J15---| |----Q20---|  REV    |----J15---| |----Q20---|
LIB    Reads   %pass AvgLen %pass AvgNum  Reads  %pass AvgLen %pass AvgNun
AICI    12363    100   776    100   794   12350    100   800    100   795
AICK    12996     99   696    100   706   13085     99   673    100   688
AICN     3651     95   710    100   693    3532     95   660    100   675


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

extracted from file: 3634501_fasta.screen.r2p  [ from "READ/CLONE COUNT SUMMARY"  to end ]
-------------------------------------------------------------------


plate(s)        reads           clones                  LIBRARY @


]		57977		28371	89.78		cumulative total @@

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 3634501_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------

#Found 57977 total values totalling 41835242.0000. <721.583421 +/- 162.197583>
#Range: [ 13 - 1038 ]
#Most likely bin: [ 800 - 850 ] 15090 counts
#Median bin: [ 750 - 800 ] 14988 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|X                                        0 - 50 : [ 197 0.00 0.00 ]
|X                                        50 - 100 : [ 460 0.01 0.01 ]
|X                                        100 - 150 : [ 443 0.01 0.02 ]
|X                                        150 - 200 : [ 409 0.01 0.03 ]
|X                                        200 - 250 : [ 552 0.01 0.04 ]
|X                                        250 - 300 : [ 555 0.01 0.05 ]
|X                                        300 - 350 : [ 545 0.01 0.05 ]
|XX                                       350 - 400 : [ 610 0.01 0.07 ]
|XX                                       400 - 450 : [ 753 0.01 0.08 ]
|XX                                       450 - 500 : [ 861 0.01 0.09 ]
|XXX                                      500 - 550 : [ 1040 0.02 0.11 ]
|XXXX                                     550 - 600 : [ 1593 0.03 0.14 ]
|XXXXXX                                   600 - 650 : [ 2414 0.04 0.18 ]
|XXXXXXXXXXX                              650 - 700 : [ 4233 0.07 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXX                   700 - 750 : [ 8141 0.14 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 14988 0.26 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 15090 0.26 0.91 ]
|XXXXXXXXXXXX                             850 - 900 : [ 4505 0.08 0.99 ]
|X                                        900 - 950 : [ 486 0.01 1.00 ]
|                                         950 - 1000 : [ 97 0.00 1.00 ]
|                                         1000 - 1050 : [ 5 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for AKYB
trimt JAZZ trim 15 readlength histogram for AICI
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICI 3634501_fasta.screen.trimQ15.SaF > reads.trim15.AICI.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICI.rl 2 50
-------------------------------------------------------------------


#Found 24713 total values totalling 19420985.0000. <785.861085 +/- 97.970083>
#Range: [ 18 - 1011 ]
#Most likely bin: [ 800 - 850 ] 9564 counts
#Median bin: [ 800 - 850 ] 9564 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|                                         0 - 50 : [ 23 0.00 0.00 ]
|                                         50 - 100 : [ 37 0.00 0.00 ]
|                                         100 - 150 : [ 55 0.00 0.00 ]
|                                         150 - 200 : [ 52 0.00 0.01 ]
|                                         200 - 250 : [ 63 0.00 0.01 ]
|                                         250 - 300 : [ 65 0.00 0.01 ]
|                                         300 - 350 : [ 74 0.00 0.01 ]
|                                         350 - 400 : [ 71 0.00 0.02 ]
|                                         400 - 450 : [ 84 0.00 0.02 ]
|                                         450 - 500 : [ 96 0.00 0.03 ]
|                                         500 - 550 : [ 86 0.00 0.03 ]
|X                                        550 - 600 : [ 135 0.01 0.03 ]
|X                                        600 - 650 : [ 243 0.01 0.04 ]
|XXX                                      650 - 700 : [ 621 0.03 0.07 ]
|XXXXXXXXXX                               700 - 750 : [ 2444 0.10 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX          750 - 800 : [ 7468 0.30 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 9564 0.39 0.86 ]
|XXXXXXXXXXXXXX                           850 - 900 : [ 3287 0.13 0.99 ]
|X                                        900 - 950 : [ 224 0.01 1.00 ]
|                                         950 - 1000 : [ 20 0.00 1.00 ]
|                                         1000 - 1050 : [ 1 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for AICK
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICK 3634501_fasta.screen.trimQ15.SaF > reads.trim15.AICK.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICK.rl 2 50
-------------------------------------------------------------------


#Found 26081 total values totalling 17719366.0000. <679.397492 +/- 171.041037>
#Range: [ 16 - 1038 ]
#Most likely bin: [ 750 - 800 ] 5481 counts
#Median bin: [ 700 - 750 ] 4301 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|                                         0 - 50 : [ 53 0.00 0.00 ]
|X                                        50 - 100 : [ 179 0.01 0.01 ]
|XX                                       100 - 150 : [ 251 0.01 0.02 ]
|XX                                       150 - 200 : [ 250 0.01 0.03 ]
|XX                                       200 - 250 : [ 335 0.01 0.04 ]
|XXX                                      250 - 300 : [ 360 0.01 0.05 ]
|XXX                                      300 - 350 : [ 386 0.01 0.07 ]
|XXX                                      350 - 400 : [ 459 0.02 0.09 ]
|XXXX                                     400 - 450 : [ 566 0.02 0.11 ]
|XXXXX                                    450 - 500 : [ 667 0.03 0.13 ]
|XXXXXX                                   500 - 550 : [ 842 0.03 0.17 ]
|XXXXXXXXX                                550 - 600 : [ 1266 0.05 0.22 ]
|XXXXXXXXXXXXXX                           600 - 650 : [ 1882 0.07 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXX                   650 - 700 : [ 3004 0.12 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX          700 - 750 : [ 4301 0.16 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5481 0.21 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX         800 - 850 : [ 4414 0.17 0.95 ]
|XXXXXXXX                                 850 - 900 : [ 1044 0.04 0.99 ]
|XX                                       900 - 950 : [ 260 0.01 1.00 ]
|X                                        950 - 1000 : [ 77 0.00 1.00 ]
|                                         1000 - 1050 : [ 4 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for AICN
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICN 3634501_fasta.screen.trimQ15.SaF > reads.trim15.AICN.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICN.rl 2 50
-------------------------------------------------------------------


#Found 7183 total values totalling 4694891.0000. <653.611444 +/- 218.634907>
#Range: [ 13 - 920 ]
#Most likely bin: [ 750 - 800 ] 2039 counts
#Median bin: [ 700 - 750 ] 1396 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XX                                       0 - 50 : [ 121 0.02 0.02 ]
|XXXXX                                    50 - 100 : [ 244 0.03 0.05 ]
|XXX                                      100 - 150 : [ 137 0.02 0.07 ]
|XX                                       150 - 200 : [ 107 0.01 0.08 ]
|XXX                                      200 - 250 : [ 154 0.02 0.11 ]
|XXX                                      250 - 300 : [ 130 0.02 0.12 ]
|XX                                       300 - 350 : [ 85 0.01 0.14 ]
|XX                                       350 - 400 : [ 80 0.01 0.15 ]
|XX                                       400 - 450 : [ 103 0.01 0.16 ]
|XX                                       450 - 500 : [ 98 0.01 0.18 ]
|XX                                       500 - 550 : [ 112 0.02 0.19 ]
|XXXX                                     550 - 600 : [ 192 0.03 0.22 ]
|XXXXXX                                   600 - 650 : [ 289 0.04 0.26 ]
|XXXXXXXXXXXX                             650 - 700 : [ 608 0.08 0.34 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX              700 - 750 : [ 1396 0.19 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2039 0.28 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXX                   800 - 850 : [ 1112 0.15 0.98 ]
|XXX                                      850 - 900 : [ 174 0.02 1.00 ]
|                                         900 - 950 : [ 2 0.00 1.00 ]


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

Command: /home/copeland/scripts/checkScreen.sh 3634501
-------------------------------------------------------------------

AICI.000001.000100 pUC18.fa.4 LRS.fasta 
AICI.000101.000200 pUC18.fa.4 LRS.fasta 
AICK.000001.000100 pMCL200.fa.4 LRS.fasta 
AICK.000101.000200 pMCL200.fa.4 LRS.fasta 
AICN.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta 
AICI.000001.000100 pUC18.fa.4 LRS.fasta 
AICI.000101.000200 pUC18.fa.4 LRS.fasta 
AICK.000001.000100 pMCL200.fa.4 LRS.fasta 
AICK.000101.000200 pMCL200.fa.4 LRS.fasta 
AICN.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta 


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

Command: 	/bin/nawk '{print $5+$6}' GC.3634501_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------


# GC.3634501_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 57777 total values totalling 34430.4471. <0.595920 +/- 0.042355>
#Range: [ 0 - 0.9091 ]
#Most likely bin: [ 0.605 - 0.61 ] 3672 counts
#Median bin: [ 0.6 - 0.605 ] 3610 counts
|                                         0 - 0.005 : [ 1 0.00 0.00 ]
#...
|                                         0.17 - 0.175 : [ 1 0.00 0.00 ]
#...
|                                         0.265 - 0.27 : [ 1 0.00 0.00 ]
|                                         0.27 - 0.275 : [ 1 0.00 0.00 ]
|                                         0.275 - 0.28 : [ 2 0.00 0.00 ]
|                                         0.28 - 0.285 : [ 1 0.00 0.00 ]
|                                         0.285 - 0.29 : [ 4 0.00 0.00 ]
|                                         0.29 - 0.295 : [ 2 0.00 0.00 ]
|                                         0.295 - 0.3 : [ 2 0.00 0.00 ]
|                                         0.3 - 0.305 : [ 6 0.00 0.00 ]
|                                         0.305 - 0.31 : [ 3 0.00 0.00 ]
|                                         0.31 - 0.315 : [ 4 0.00 0.00 ]
|                                         0.315 - 0.32 : [ 3 0.00 0.00 ]
|                                         0.32 - 0.325 : [ 9 0.00 0.00 ]
|                                         0.325 - 0.33 : [ 9 0.00 0.00 ]
|                                         0.33 - 0.335 : [ 8 0.00 0.00 ]
|                                         0.335 - 0.34 : [ 7 0.00 0.00 ]
|                                         0.34 - 0.345 : [ 12 0.00 0.00 ]
|                                         0.345 - 0.35 : [ 20 0.00 0.00 ]
|                                         0.35 - 0.355 : [ 18 0.00 0.00 ]
|                                         0.355 - 0.36 : [ 15 0.00 0.00 ]
|                                         0.36 - 0.365 : [ 20 0.00 0.00 ]
|                                         0.365 - 0.37 : [ 14 0.00 0.00 ]
|                                         0.37 - 0.375 : [ 17 0.00 0.00 ]
|                                         0.375 - 0.38 : [ 32 0.00 0.00 ]
|                                         0.38 - 0.385 : [ 19 0.00 0.00 ]
|                                         0.385 - 0.39 : [ 22 0.00 0.00 ]
|                                         0.39 - 0.395 : [ 27 0.00 0.00 ]
|                                         0.395 - 0.4 : [ 17 0.00 0.01 ]
|                                         0.4 - 0.405 : [ 19 0.00 0.01 ]
|                                         0.405 - 0.41 : [ 26 0.00 0.01 ]
|                                         0.41 - 0.415 : [ 26 0.00 0.01 ]
|                                         0.415 - 0.42 : [ 40 0.00 0.01 ]
|                                         0.42 - 0.425 : [ 27 0.00 0.01 ]
|                                         0.425 - 0.43 : [ 27 0.00 0.01 ]
|                                         0.43 - 0.435 : [ 29 0.00 0.01 ]
|                                         0.435 - 0.44 : [ 34 0.00 0.01 ]
|                                         0.44 - 0.445 : [ 27 0.00 0.01 ]
|                                         0.445 - 0.45 : [ 38 0.00 0.01 ]
|                                         0.45 - 0.455 : [ 32 0.00 0.01 ]
|X                                        0.455 - 0.46 : [ 46 0.00 0.01 ]
|X                                        0.46 - 0.465 : [ 57 0.00 0.01 ]
|                                         0.465 - 0.47 : [ 37 0.00 0.01 ]
|X                                        0.47 - 0.475 : [ 49 0.00 0.01 ]
|X                                        0.475 - 0.48 : [ 87 0.00 0.02 ]
|X                                        0.48 - 0.485 : [ 92 0.00 0.02 ]
|X                                        0.485 - 0.49 : [ 130 0.00 0.02 ]
|XX                                       0.49 - 0.495 : [ 153 0.00 0.02 ]
|XX                                       0.495 - 0.5 : [ 152 0.00 0.02 ]
|XX                                       0.5 - 0.505 : [ 225 0.00 0.03 ]
|XXX                                      0.505 - 0.51 : [ 250 0.00 0.03 ]
|XXXX                                     0.51 - 0.515 : [ 331 0.01 0.04 ]
|XXXX                                     0.515 - 0.52 : [ 361 0.01 0.04 ]
|XXXX                                     0.52 - 0.525 : [ 402 0.01 0.05 ]
|XXXXX                                    0.525 - 0.53 : [ 420 0.01 0.06 ]
|XXXXXX                                   0.53 - 0.535 : [ 520 0.01 0.07 ]
|XXXXXXX                                  0.535 - 0.54 : [ 621 0.01 0.08 ]
|XXXXXXXX                                 0.54 - 0.545 : [ 707 0.01 0.09 ]
|XXXXXXXXX                                0.545 - 0.55 : [ 829 0.01 0.11 ]
|XXXXXXXXXXX                              0.55 - 0.555 : [ 986 0.02 0.12 ]
|XXXXXXXXXXXXX                            0.555 - 0.56 : [ 1212 0.02 0.14 ]
|XXXXXXXXXXXXXXXX                         0.56 - 0.565 : [ 1460 0.03 0.17 ]
|XXXXXXXXXXXXXXXXXXX                      0.565 - 0.57 : [ 1743 0.03 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  0.57 - 0.575 : [ 2069 0.04 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX               0.575 - 0.58 : [ 2370 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX           0.58 - 0.585 : [ 2769 0.05 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX        0.585 - 0.59 : [ 3001 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     0.59 - 0.595 : [ 3269 0.06 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX      0.595 - 0.6 : [ 3224 0.06 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  0.6 - 0.605 : [ 3610 0.06 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 3672 0.06 0.61 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    0.61 - 0.615 : [ 3438 0.06 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     0.615 - 0.62 : [ 3271 0.06 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX         0.62 - 0.625 : [ 2935 0.05 0.78 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX             0.625 - 0.63 : [ 2589 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXX                 0.63 - 0.635 : [ 2223 0.04 0.86 ]
|XXXXXXXXXXXXXXXXXXXX                     0.635 - 0.64 : [ 1817 0.03 0.90 ]
|XXXXXXXXXXXXXXXX                         0.64 - 0.645 : [ 1467 0.03 0.92 ]
|XXXXXXXXXXXXX                            0.645 - 0.65 : [ 1224 0.02 0.94 ]
|XXXXXXXXXX                               0.65 - 0.655 : [ 938 0.02 0.96 ]
|XXXXXXXX                                 0.655 - 0.66 : [ 697 0.01 0.97 ]
|XXXXX                                    0.66 - 0.665 : [ 469 0.01 0.98 ]
|XXXX                                     0.665 - 0.67 : [ 405 0.01 0.99 ]
|XXX                                      0.67 - 0.675 : [ 238 0.00 0.99 ]
|XX                                       0.675 - 0.68 : [ 201 0.00 0.99 ]
|X                                        0.68 - 0.685 : [ 116 0.00 1.00 ]
|X                                        0.685 - 0.69 : [ 85 0.00 1.00 ]
|X                                        0.69 - 0.695 : [ 54 0.00 1.00 ]
|                                         0.695 - 0.7 : [ 36 0.00 1.00 ]
|                                         0.7 - 0.705 : [ 28 0.00 1.00 ]
|                                         0.705 - 0.71 : [ 16 0.00 1.00 ]
|                                         0.71 - 0.715 : [ 11 0.00 1.00 ]
|                                         0.715 - 0.72 : [ 14 0.00 1.00 ]
|                                         0.72 - 0.725 : [ 3 0.00 1.00 ]
|                                         0.725 - 0.73 : [ 1 0.00 1.00 ]
|                                         0.73 - 0.735 : [ 3 0.00 1.00 ]
|                                         0.735 - 0.74 : [ 3 0.00 1.00 ]
|                                         0.74 - 0.745 : [ 1 0.00 1.00 ]
|                                         0.745 - 0.75 : [ 1 0.00 1.00 ]
|                                         0.75 - 0.755 : [ 3 0.00 1.00 ]
|                                         0.755 - 0.76 : [ 2 0.00 1.00 ]
|                                         0.76 - 0.765 : [ 1 0.00 1.00 ]
|                                         0.765 - 0.77 : [ 4 0.00 1.00 ]
|                                         0.77 - 0.775 : [ 1 0.00 1.00 ]
#...
|                                         0.78 - 0.785 : [ 2 0.00 1.00 ]
|                                         0.785 - 0.79 : [ 1 0.00 1.00 ]
#...
|                                         0.8 - 0.805 : [ 1 0.00 1.00 ]
#...
|                                         0.825 - 0.83 : [ 1 0.00 1.00 ]
#...
|                                         0.905 - 0.91 : [ 1 0.00 1.00 ]



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

Contig  30.   15 reads;    890 bp (untrimmed),    475 (trimmed).
Contig  31.   17 reads;    949 bp (untrimmed),    421 (trimmed).
Contig  32.   18 reads;   5176 bp (untrimmed),   2989 (trimmed).
Contig  33.   18 reads;    961 bp (untrimmed),    434 (trimmed).
Contig  34.   20 reads;    230 bp (untrimmed),    230 (trimmed).
Contig  35.   30 reads;    975 bp (untrimmed),    494 (trimmed).
Contig  36.   32 reads;    972 bp (untrimmed),    459 (trimmed).
Contig  37.   56 reads;    876 bp (untrimmed),    811 (trimmed).
Contig  38.   67 reads;    308 bp (untrimmed),    308 (trimmed).
Contig  39.  245 reads;  18413 bp (untrimmed),  18407 (trimmed).
Contig  40.  326 reads;  26114 bp (untrimmed),  25009 (trimmed).
Contig  41.  380 reads;  28954 bp (untrimmed),  28902 (trimmed).
Contig  42.  647 reads;  50784 bp (untrimmed),  49909 (trimmed).
Contig  43.  872 reads;  62108 bp (untrimmed),  62085 (trimmed).
Contig  44. 1394 reads; 111405 bp (untrimmed), 111404 (trimmed).
Contig  45. 1734 reads; 125225 bp (untrimmed), 125224 (trimmed).
Contig  46. 2118 reads; 156150 bp (untrimmed), 156125 (trimmed).
Contig  47. 2196 reads; 160110 bp (untrimmed), 160092 (trimmed).
Contig  48. 3312 reads; 249415 bp (untrimmed), 249415 (trimmed).
Contig  49. 3507 reads; 270982 bp (untrimmed), 270768 (trimmed).
Contig  50. 3610 reads; 131131 bp (untrimmed), 130925 (trimmed).
Contig  51. 3864 reads; 299799 bp (untrimmed), 299797 (trimmed).
Contig  52. 5225 reads; 400577 bp (untrimmed), 398809 (trimmed).
Contig  53. 5319 reads; 370475 bp (untrimmed), 370189 (trimmed).
Contig  54. 6094 reads; 464027 bp (untrimmed), 463953 (trimmed).
Contig  55. 7209 reads; 553087 bp (untrimmed), 553087 (trimmed).
Contig  56. 8991 reads; 663817 bp (untrimmed), 663814 (trimmed).
--------------------------------------------------------------
Totals      57429 reads; 4198271 bp (untrimmed), 4176047 (trimmed).


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

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

depth.out contains 4192585 bases  = 13.97 +- 5.49   = 0.13 +- 4.34  


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

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


#Found 45 total values totalling 383.9900. <8.533111 +/- 7.969913>
#Range: [ 1.05 - 39.06 ]
#Most likely bin: [ 1 - 1.5 ] 12 counts
#Median bin: [ 8 - 8.5 ] 1 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 12 0.27 0.27 ]
|XXXXXXXXXXXXX                            1.5 - 2 : [ 4 0.09 0.36 ]
|XXXXXXX                                  2 - 2.5 : [ 2 0.04 0.40 ]
|XXX                                      2.5 - 3 : [ 1 0.02 0.42 ]
|XXX                                      3 - 3.5 : [ 1 0.02 0.44 ]
|XXX                                      3.5 - 4 : [ 1 0.02 0.47 ]
|XXX                                      4 - 4.5 : [ 1 0.02 0.49 ]
#...
|XXX                                      8 - 8.5 : [ 1 0.02 0.51 ]
#...
|XXX                                      9 - 9.5 : [ 1 0.02 0.53 ]
#...
|XXXXXXXXXXXXX                            12.5 - 13 : [ 4 0.09 0.62 ]
|XXXXXXXXXXXXXXXXXXXX                     13 - 13.5 : [ 6 0.13 0.76 ]
|XXXXXXXXXXXXX                            13.5 - 14 : [ 4 0.09 0.84 ]
|XXXXXXXXXX                               14 - 14.5 : [ 3 0.07 0.91 ]
|XXX                                      14.5 - 15 : [ 1 0.02 0.93 ]
#...
|XXX                                      16 - 16.5 : [ 1 0.02 0.96 ]
#...
|XXX                                      28.5 - 29 : [ 1 0.02 0.98 ]
#...
|XXX                                      39 - 39.5 : [ 1 0.02 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 20 total values totalling 263.7400. <13.187000 +/- 4.835566>
#Range: [ 2.18 - 28.55 ]
#Most likely bin: [ 13 - 13.5 ] 6 counts
#Median bin: [ 13 - 13.5 ] 6 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXX                                  2 - 2.5 : [ 1 0.05 0.05 ]
#...
|XXXXXXX                                  3 - 3.5 : [ 1 0.05 0.10 ]
#...
|XXXXXXXXXXXXXXXXXXXX                     12.5 - 13 : [ 3 0.15 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 6 0.30 0.55 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX              13.5 - 14 : [ 4 0.20 0.75 ]
|XXXXXXXXXXXXXXXXXXXX                     14 - 14.5 : [ 3 0.15 0.90 ]
|XXXXXXX                                  14.5 - 15 : [ 1 0.05 0.95 ]
#...
|XXXXXXX                                  28.5 - 29 : [ 1 0.05 1.00 ]


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

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

Contig 7           2 reads      1986 bases  =   1.05 +- 0.22     =   1.05 +-  0.22
Contig 20          3 reads      2578 bases  =   1.07 +- 0.34     =   0.09 +-  0.99
Contig 12          3 reads      1233 bases  =   1.09 +- 0.42     =  -0.91 +-  0.42
Contig 8           2 reads      1705 bases  =   1.12 +- 0.33     =   1.12 +-  0.33
Contig 21          4 reads      2258 bases  =   1.25 +- 0.52     =   0.28 +-  1.09
Contig 18          3 reads      1677 bases  =   1.28 +- 0.60     =   0.27 +-  0.90
Contig 22          5 reads      3452 bases  =   1.28 +- 0.56     =  -0.01 +-  1.33
Contig 4           2 reads      1559 bases  =   1.28 +- 0.45     =   1.28 +-  0.45
Contig 15          3 reads      2028 bases  =   1.31 +- 0.66     =   0.15 +-  1.04
Contig 11          3 reads      1729 bases  =   1.32 +- 0.68     =   0.32 +-  1.07
Contig 27          7 reads      2367 bases  =   1.35 +- 0.60     =   0.88 +-  0.72
Contig 23          5 reads      3461 bases  =   1.38 +- 0.50     =   1.21 +-  0.56
Contig 5           2 reads       912 bases  =   1.54 +- 0.50     =   1.54 +-  0.50
Contig 31         17 reads       949 bases  =   1.60 +- 0.68     =  -1.57 +-  0.71
Contig 14          3 reads      1548 bases  =   1.65 +- 0.93     =   0.56 +-  0.82
Contig 26          6 reads      2744 bases  =   1.95 +- 1.17     =   1.02 +-  0.66
Contig 17          3 reads      1036 bases  =   2.14 +- 0.79     =   2.14 +-  0.79
Contig 29         14 reads      3705 bases  =   2.18 +- 2.14     =   0.36 +-  1.01
Contig 33         18 reads       961 bases  =   2.69 +- 1.46     =  -2.66 +-  1.49
Contig 32         18 reads      5176 bases  =   3.01 +- 2.78     =   0.08 +-  1.24

Contig 35         30 reads       975 bases  =  12.78 +- 9.22     =  12.77 +-  9.22
Contig 42        647 reads     50784 bases  =  12.86 +- 4.26     =   0.28 +-  4.02
Contig 40        326 reads     26114 bases  =  12.89 +- 4.59     =   1.84 +-  4.78
Contig 39        245 reads     18413 bases  =  13.19 +- 3.77     =   0.65 +-  4.36
Contig 51       3864 reads    299799 bases  =  13.19 +- 4.17     =   0.13 +-  3.88
Contig 41        380 reads     28954 bases  =  13.23 +- 3.55     =   0.31 +-  2.97
Contig 49       3507 reads    270982 bases  =  13.24 +- 4.45     =   0.04 +-  3.88
Contig 55       7209 reads    553087 bases  =  13.27 +- 3.91     =   0.02 +-  4.16
Contig 52       5225 reads    400577 bases  =  13.42 +- 4.17     =   0.01 +-  4.08
Contig 54       6094 reads    464027 bases  =  13.50 +- 4.26     =   0.19 +-  4.14
Contig 48       3312 reads    249415 bases  =  13.56 +- 4.33     =   0.00 +-  4.30
Contig 56       8991 reads    663817 bases  =  13.87 +- 5.00     =   0.00 +-  4.70
Contig 46       2118 reads    156150 bases  =  13.89 +- 3.97     =   0.19 +-  4.15
Contig 47       2196 reads    160110 bases  =  14.01 +- 4.17     =   0.15 +-  4.05
Contig 45       1734 reads    125225 bases  =  14.15 +- 4.10     =   0.03 +-  4.06
Contig 43        872 reads     62108 bases  =  14.27 +- 4.18     =   0.23 +-  4.44
Contig 53       5319 reads    370475 bases  =  14.75 +- 5.23     =   0.19 +-  4.29
Contig 36         32 reads       972 bases  =  16.38 +- 10.81    =  16.37 +-  10.81
Contig 50       3610 reads    131131 bases  =  28.55 +- 9.27     =   0.29 +-  6.37
Contig 37         56 reads       876 bases  =  39.06 +- 16.96    =  39.06 +-  16.96


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

Small Inserts = 560

HQ Discrepant reads = 69

Chimeric reads = 89

Suspect alignments = 393


-------------------------------------------------------------------
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/microbe3/3634501/edit_dir.12Feb04.QD