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
3635488	4200	NULL	Rhodoferex ferrireducens


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

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




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: 4903249
# phrap: 4691387
# db: 
altered.

4200000
4598212 +/- 294562

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

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


Number of reads with X's: 9856
Number of reads with percent X's >= 20%:   213 = 0.4%
Number of reads with percent X's >= 50%:   118 = 0.2%
Number of reads with percent X's >= 80%:    19 = 0.0%
Total reads in project: 50597
Total bp X'd : 498083
                                  reads  >= 20% >= 50% >= 80% screened
Nr with L09136                     8552     41     17      0
Nr with pCC1Fos                    1074      1      0      0
Nr with pMCL200_JGI_XZX+XZK         230    171    101     19

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

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


Number of reads with X's: 18
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: 125
Total bp X'd : 662
                                  reads  >= 20% >= 50% >= 80% screened
Nr with L09136                        6      0      0      0
Nr with pCC1Fos                      12      0      0      0


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

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

A = 9591408
C = 13897775
G = 13841694
T = 9420235
N = 232222
X = 498083
GC fraction = 0.58
Total = 47481417

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

Command: /psf/QC/bin/sparc/faCount 3635488_fasta.screen.contigs
-------------------------------------------------------------------


A	997816
C	1476399
G	1462034
T	990369
N	104
fraction GC = 0.60
total bases = 4926722



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


#Found 9630 total values totalling 35592640.0000. <3696.016615 +/- 6551.075618>
#Range: [ 620 - 499142 ]
#Most likely bin: [ 3000 - 3500 ] 3341 counts
#Median bin: [ 3000 - 3500 ] 3341 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|                                         500 - 1000 : [ 3 0.00 0.00 ]
|                                         1000 - 1500 : [ 12 0.00 0.00 ]
|                                         1500 - 2000 : [ 19 0.00 0.00 ]
|X                                        2000 - 2500 : [ 44 0.00 0.01 ]
|XXXXXXXXXXXXXXXXXX                       2500 - 3000 : [ 1539 0.16 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 3341 0.35 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX          3500 - 4000 : [ 2562 0.27 0.78 ]
|XXXXXXXXXXXXXXXXXXXX                     4000 - 4500 : [ 1697 0.18 0.96 ]
|XXXXX                                    4500 - 5000 : [ 397 0.04 1.00 ]
|                                         5000 - 5500 : [ 4 0.00 1.00 ]
#...
|                                         13500 - 14000 : [ 1 0.00 1.00 ]
#...
|                                         27000 - 27500 : [ 1 0.00 1.00 ]
#...
|                                         30000 - 30500 : [ 1 0.00 1.00 ]
#...
|                                         33500 - 34000 : [ 1 0.00 1.00 ]
#...
|                                         81000 - 81500 : [ 1 0.00 1.00 ]
#...
|                                         111000 - 111500 : [ 1 0.00 1.00 ]
|                                         111500 - 112000 : [ 1 0.00 1.00 ]
#...
|                                         114500 - 115000 : [ 1 0.00 1.00 ]
#...
|                                         126500 - 127000 : [ 1 0.00 1.00 ]
#...
|                                         133500 - 134000 : [ 1 0.00 1.00 ]
#...
|                                         302000 - 302500 : [ 1 0.00 1.00 ]
#...
|                                         499000 - 499500 : [ 1 0.00 1.00 ]

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


#Found 9359 total values totalling 65226821.0000. <6969.422054 +/- 9372.365611>
#Range: [ 961 - 466848 ]
#Most likely bin: [ 6000 - 6500 ] 2317 counts
#Median bin: [ 6500 - 7000 ] 2134 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|                                         500 - 1000 : [ 3 0.00 0.00 ]
|X                                        1000 - 1500 : [ 41 0.00 0.00 ]
|X                                        1500 - 2000 : [ 52 0.01 0.01 ]
|X                                        2000 - 2500 : [ 38 0.00 0.01 ]
|X                                        2500 - 3000 : [ 59 0.01 0.02 ]
|X                                        3000 - 3500 : [ 49 0.01 0.03 ]
|X                                        3500 - 4000 : [ 52 0.01 0.03 ]
|X                                        4000 - 4500 : [ 56 0.01 0.04 ]
|X                                        4500 - 5000 : [ 60 0.01 0.04 ]
|XX                                       5000 - 5500 : [ 116 0.01 0.06 ]
|XXXXXXXXXXXXXXXXXX                       5500 - 6000 : [ 1060 0.11 0.17 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2317 0.25 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    6500 - 7000 : [ 2134 0.23 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX           7000 - 7500 : [ 1751 0.19 0.83 ]
|XXXXXXXXXXXXXXXXXX                       7500 - 8000 : [ 1018 0.11 0.94 ]
|XXXXXXXX                                 8000 - 8500 : [ 482 0.05 0.99 ]
|X                                        8500 - 9000 : [ 40 0.00 1.00 ]
|                                         9000 - 9500 : [ 4 0.00 1.00 ]
|                                         9500 - 10000 : [ 1 0.00 1.00 ]
#...
|                                         13000 - 13500 : [ 1 0.00 1.00 ]
|                                         13500 - 14000 : [ 1 0.00 1.00 ]
#...
|                                         14500 - 15000 : [ 1 0.00 1.00 ]
#...
|                                         19000 - 19500 : [ 1 0.00 1.00 ]
#...
|                                         20500 - 21000 : [ 1 0.00 1.00 ]
#...
|                                         23500 - 24000 : [ 1 0.00 1.00 ]
#...
|                                         28000 - 28500 : [ 1 0.00 1.00 ]
#...
|                                         37000 - 37500 : [ 1 0.00 1.00 ]
#...
|                                         56500 - 57000 : [ 1 0.00 1.00 ]
#...
|                                         59000 - 59500 : [ 1 0.00 1.00 ]
#...
|                                         60500 - 61000 : [ 1 0.00 1.00 ]
#...
|                                         64000 - 64500 : [ 1 0.00 1.00 ]
#...
|                                         67500 - 68000 : [ 1 0.00 1.00 ]
#...
|                                         101500 - 102000 : [ 1 0.00 1.00 ]
#...
|                                         136000 - 136500 : [ 1 0.00 1.00 ]
#...
|                                         137500 - 138000 : [ 1 0.00 1.00 ]
#...
|                                         142500 - 143000 : [ 1 0.00 1.00 ]
#...
|                                         146500 - 147000 : [ 1 0.00 1.00 ]
#...
|                                         156500 - 157000 : [ 1 0.00 1.00 ]
#...
|                                         163500 - 164000 : [ 1 0.00 1.00 ]
#...
|                                         204000 - 204500 : [ 1 0.00 1.00 ]
#...
|                                         275500 - 276000 : [ 1 0.00 1.00 ]
#...
|                                         287500 - 288000 : [ 1 0.00 1.00 ]
#...
|                                         293500 - 294000 : [ 1 0.00 1.00 ]
#...
|                                         433000 - 433500 : [ 1 0.00 1.00 ]
#...
|                                         466500 - 467000 : [ 1 0.00 1.00 ]

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


#Found 805 total values totalling 29818911.0000. <37042.125466 +/- 4644.799254>
#Range: [ 4910 - 45969 ]
#Most likely bin: [ 37500 - 38000 ] 46 counts
#Median bin: [ 37000 - 37500 ] 44 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|X                                        4500 - 5000 : [ 1 0.00 0.00 ]
#...
|X                                        8500 - 9000 : [ 1 0.00 0.00 ]
|X                                        9000 - 9500 : [ 1 0.00 0.00 ]
#...
|XX                                       10000 - 10500 : [ 2 0.00 0.01 ]
|XX                                       10500 - 11000 : [ 2 0.00 0.01 ]
#...
|X                                        13000 - 13500 : [ 1 0.00 0.01 ]
#...
|X                                        16500 - 17000 : [ 1 0.00 0.01 ]
#...
|X                                        21000 - 21500 : [ 1 0.00 0.01 ]
#...
|X                                        26500 - 27000 : [ 1 0.00 0.01 ]
|X                                        27000 - 27500 : [ 1 0.00 0.01 ]
|X                                        27500 - 28000 : [ 1 0.00 0.02 ]
|XX                                       28000 - 28500 : [ 2 0.00 0.02 ]
|X                                        28500 - 29000 : [ 1 0.00 0.02 ]
|XXX                                      29000 - 29500 : [ 3 0.00 0.02 ]
|XXXXXX                                   29500 - 30000 : [ 7 0.01 0.03 ]
|XXXX                                     30000 - 30500 : [ 5 0.01 0.04 ]
|XXXXXXXX                                 30500 - 31000 : [ 9 0.01 0.05 ]
|XXXXXXXXXXXXXXX                          31000 - 31500 : [ 17 0.02 0.07 ]
|XXXXXXXXXXXXXXX                          31500 - 32000 : [ 17 0.02 0.09 ]
|XXXXXXXXXXXXXXX                          32000 - 32500 : [ 17 0.02 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX                32500 - 33000 : [ 29 0.04 0.15 ]
|XXXXXXXXXXXXXXXXXXXXX                    33000 - 33500 : [ 24 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXX                      33500 - 34000 : [ 22 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  34000 - 34500 : [ 27 0.03 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXX                   34500 - 35000 : [ 25 0.03 0.27 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  35000 - 35500 : [ 26 0.03 0.30 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX   35500 - 36000 : [ 44 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX      36000 - 36500 : [ 40 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     36500 - 37000 : [ 41 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX   37000 - 37500 : [ 44 0.05 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 46 0.06 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX         38000 - 38500 : [ 37 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  38500 - 39000 : [ 45 0.06 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX       39000 - 39500 : [ 39 0.05 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX             39500 - 40000 : [ 32 0.04 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX          40000 - 40500 : [ 36 0.04 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     40500 - 41000 : [ 41 0.05 0.86 ]
|XXXXXXXXXXXX                             41000 - 41500 : [ 14 0.02 0.87 ]
|XXXXXXXXXX                               41500 - 42000 : [ 11 0.01 0.89 ]
|XXXXXXXXXXXXXXXXX                        42000 - 42500 : [ 20 0.02 0.91 ]
|XXXXXXXXXXX                              42500 - 43000 : [ 13 0.02 0.93 ]
|XXXXXXXXXXXX                             43000 - 43500 : [ 14 0.02 0.95 ]
|XXXXXXXXXXXX                             43500 - 44000 : [ 14 0.02 0.96 ]
|XXXXXXXXXXX                              44000 - 44500 : [ 13 0.02 0.98 ]
|XXXXXXXX                                 44500 - 45000 : [ 9 0.01 0.99 ]
|XXX                                      45000 - 45500 : [ 4 0.00 1.00 ]
|XXX                                      45500 - 46000 : [ 4 0.00 1.00 ]



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

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

# AOTY 3401 +- 716 (n=4865)
# AOUA 36725 +- 4890 (n=415)
# AOTZ 6559 +- 1330 (n=4734)


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

extracted from 3635488_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 
AOTY    24192     -1    -1     97   630   24093     93   590     96   598
AOTZ    30720     -1    -1     93   675   30720     81   743     93   725
AOUA     4608     62   450     80   381    3744     68   507     82   494

        FWD    |----J15---| |----Q20---|  REV    |----J15---| |----Q20---|
LIB    Reads   %pass AvgLen %pass AvgNum  Reads  %pass AvgLen %pass AvgNun
AOTY    11853     92   579     95   587   12240     94   602     96   608
AOTZ    15360     81   740     93   723   15360     81   746     93   728
AOUA     1824     66   520     79   497    1920     69   496     84   492


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

extracted from file: 3635488_fasta.screen.r2p  [ from "READ/CLONE COUNT SUMMARY"  to end ]
-------------------------------------------------------------------


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

124		22709		11548	 93.13  97.01	AOTY	@
160		25087		12742	 79.64  82.96	AOTZ	@
20		2801		1551	 77.55  80.78	AOUA	@

]		50597		25841	 85.00     	cumulative total@@

LIBRARY PLATE ID COUNT [ AOTY 124 AOTZ 160 AOUA 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 3635488_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------

#Found 58557 total values totalling 33203392.0000. <567.026863 +/- 273.739113>
#Range: [ 0 - 964 ]
#Most likely bin: [ 750 - 800 ] 11140 counts
#Median bin: [ 650 - 700 ] 6752 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX             0 - 50 : [ 7858 0.13 0.13 ]
|XXX                                      50 - 100 : [ 754 0.01 0.15 ]
|XX                                       100 - 150 : [ 625 0.01 0.16 ]
|XX                                       150 - 200 : [ 634 0.01 0.17 ]
|XX                                       200 - 250 : [ 621 0.01 0.18 ]
|XXX                                      250 - 300 : [ 804 0.01 0.19 ]
|XXX                                      300 - 350 : [ 878 0.01 0.21 ]
|XXX                                      350 - 400 : [ 971 0.02 0.22 ]
|XXXX                                     400 - 450 : [ 1143 0.02 0.24 ]
|XXXXX                                    450 - 500 : [ 1413 0.02 0.27 ]
|XXXXXXX                                  500 - 550 : [ 1838 0.03 0.30 ]
|XXXXXXXXXX                               550 - 600 : [ 2774 0.05 0.35 ]
|XXXXXXXXXXXXXXX                          600 - 650 : [ 4292 0.07 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXX                 650 - 700 : [ 6752 0.12 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX       700 - 750 : [ 9565 0.16 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 11140 0.19 0.89 ]
|XXXXXXXXXXXXXXXXXXXXX                    800 - 850 : [ 5817 0.10 0.99 ]
|XX                                       850 - 900 : [ 643 0.01 1.00 ]
|                                         900 - 950 : [ 34 0.00 1.00 ]
|                                         950 - 1000 : [ 1 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for AOTY
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTY 3635488_fasta.screen.trimQ15.SaF > reads.trim15.AOTY.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOTY.rl 2 50
-------------------------------------------------------------------


#Found 24093 total values totalling 13271599.0000. <550.848753 +/- 213.054542>
#Range: [ 0 - 964 ]
#Most likely bin: [ 650 - 700 ] 4260 counts
#Median bin: [ 600 - 650 ] 3274 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXX                             0 - 50 : [ 1278 0.05 0.05 ]
|XXXX                                     50 - 100 : [ 411 0.02 0.07 ]
|XXXX                                     100 - 150 : [ 436 0.02 0.09 ]
|XXXX                                     150 - 200 : [ 425 0.02 0.11 ]
|XXXX                                     200 - 250 : [ 448 0.02 0.12 ]
|XXXXX                                    250 - 300 : [ 518 0.02 0.15 ]
|XXXXXX                                   300 - 350 : [ 603 0.03 0.17 ]
|XXXXXXX                                  350 - 400 : [ 727 0.03 0.20 ]
|XXXXXXXX                                 400 - 450 : [ 892 0.04 0.24 ]
|XXXXXXXXXX                               450 - 500 : [ 1099 0.05 0.28 ]
|XXXXXXXXXXXXX                            500 - 550 : [ 1407 0.06 0.34 ]
|XXXXXXXXXXXXXXXXXXXX                     550 - 600 : [ 2181 0.09 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX          600 - 650 : [ 3274 0.14 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 4260 0.18 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    700 - 750 : [ 3935 0.16 0.91 ]
|XXXXXXXXXXXXXXXXX                        750 - 800 : [ 1805 0.07 0.98 ]
|XXX                                      800 - 850 : [ 283 0.01 1.00 ]
|X                                        850 - 900 : [ 79 0.00 1.00 ]
|                                         900 - 950 : [ 31 0.00 1.00 ]
|                                         950 - 1000 : [ 1 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for AOTZ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOTZ 3635488_fasta.screen.trimQ15.SaF > reads.trim15.AOTZ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOTZ.rl 2 50
-------------------------------------------------------------------


#Found 30720 total values totalling 18618628.0000. <606.075130 +/- 300.764436>
#Range: [ 0 - 918 ]
#Most likely bin: [ 750 - 800 ] 9220 counts
#Median bin: [ 700 - 750 ] 5353 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXX                 0 - 50 : [ 5571 0.18 0.18 ]
|X                                        50 - 100 : [ 141 0.00 0.19 ]
|                                         100 - 150 : [ 81 0.00 0.19 ]
|                                         150 - 200 : [ 81 0.00 0.19 ]
|                                         200 - 250 : [ 83 0.00 0.19 ]
|                                         250 - 300 : [ 100 0.00 0.20 ]
|X                                        300 - 350 : [ 119 0.00 0.20 ]
|X                                        350 - 400 : [ 119 0.00 0.20 ]
|X                                        400 - 450 : [ 146 0.00 0.21 ]
|X                                        450 - 500 : [ 170 0.01 0.22 ]
|X                                        500 - 550 : [ 264 0.01 0.22 ]
|X                                        550 - 600 : [ 335 0.01 0.23 ]
|XXX                                      600 - 650 : [ 748 0.02 0.26 ]
|XXXXXXXXX                                650 - 700 : [ 2104 0.07 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  700 - 750 : [ 5353 0.17 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 9220 0.30 0.80 ]
|XXXXXXXXXXXXXXXXXXXXXXXX                 800 - 850 : [ 5519 0.18 0.98 ]
|XX                                       850 - 900 : [ 563 0.02 1.00 ]
|                                         900 - 950 : [ 3 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for AOUA
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AOUA 3635488_fasta.screen.trimQ15.SaF > reads.trim15.AOUA.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOUA.rl 2 50
-------------------------------------------------------------------


#Found 3744 total values totalling 1313165.0000. <350.738515 +/- 276.878272>
#Range: [ 0 - 882 ]
#Most likely bin: [ 0 - 50 ] 1009 counts
#Median bin: [ 300 - 350 ] 156 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1009 0.27 0.27 ]
|XXXXXXXX                                 50 - 100 : [ 202 0.05 0.32 ]
|XXXX                                     100 - 150 : [ 108 0.03 0.35 ]
|XXXXX                                    150 - 200 : [ 128 0.03 0.39 ]
|XXXX                                     200 - 250 : [ 90 0.02 0.41 ]
|XXXXXXX                                  250 - 300 : [ 186 0.05 0.46 ]
|XXXXXX                                   300 - 350 : [ 156 0.04 0.50 ]
|XXXXX                                    350 - 400 : [ 125 0.03 0.54 ]
|XXXX                                     400 - 450 : [ 105 0.03 0.56 ]
|XXXXXX                                   450 - 500 : [ 144 0.04 0.60 ]
|XXXXXXX                                  500 - 550 : [ 167 0.04 0.65 ]
|XXXXXXXXXX                               550 - 600 : [ 258 0.07 0.72 ]
|XXXXXXXXXXX                              600 - 650 : [ 270 0.07 0.79 ]
|XXXXXXXXXXXXXXX                          650 - 700 : [ 388 0.10 0.89 ]
|XXXXXXXXXXX                              700 - 750 : [ 277 0.07 0.97 ]
|XXXXX                                    750 - 800 : [ 115 0.03 1.00 ]
|X                                        800 - 850 : [ 15 0.00 1.00 ]
|                                         850 - 900 : [ 1 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for ATUA

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

Command: /home/copeland/scripts/checkScreen.sh 3635488
-------------------------------------------------------------------

AOTY.000001.000100 pUC18.fa LRS.fasta 
AOTY.000101.000200 pUC18.fa LRS.fasta 
AOTZ.000001.000100 pMCL200.fa LRS.fasta 
AOTZ.000101.000200 pMCL200.fa LRS.fasta 
AOUA.000001.000100 pCC1Fos.fa LRS.fasta 
AOTY.000001.000100 pUC18.fa LRS.fasta 
AOTY.000101.000200 pUC18.fa LRS.fasta 
AOTZ.000001.000100 pMCL200.fa LRS.fasta 
AOTZ.000101.000200 pMCL200.fa LRS.fasta 
AOUA.000001.000100 pCC1Fos.fa LRS.fasta 


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

Command: 	/bin/nawk '{print $5+$6}' GC.3635488_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------


# GC.3635488_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 50437 total values totalling 30177.5776. <0.598322 +/- 0.047155>
#Range: [ 0.2 - 1 ]
#Most likely bin: [ 0.605 - 0.61 ] 2391 counts
#Median bin: [ 0.6 - 0.605 ] 2295 counts
|                                         0.2 - 0.205 : [ 1 0.00 0.00 ]
#...
|                                         0.25 - 0.255 : [ 1 0.00 0.00 ]
#...
|                                         0.3 - 0.305 : [ 1 0.00 0.00 ]
#...
|                                         0.31 - 0.315 : [ 1 0.00 0.00 ]
#...
|                                         0.32 - 0.325 : [ 1 0.00 0.00 ]
|                                         0.325 - 0.33 : [ 1 0.00 0.00 ]
|                                         0.33 - 0.335 : [ 3 0.00 0.00 ]
|                                         0.335 - 0.34 : [ 1 0.00 0.00 ]
|                                         0.34 - 0.345 : [ 1 0.00 0.00 ]
|                                         0.345 - 0.35 : [ 5 0.00 0.00 ]
|                                         0.35 - 0.355 : [ 5 0.00 0.00 ]
|                                         0.355 - 0.36 : [ 5 0.00 0.00 ]
|                                         0.36 - 0.365 : [ 9 0.00 0.00 ]
|                                         0.365 - 0.37 : [ 5 0.00 0.00 ]
|                                         0.37 - 0.375 : [ 6 0.00 0.00 ]
|                                         0.375 - 0.38 : [ 4 0.00 0.00 ]
|                                         0.38 - 0.385 : [ 5 0.00 0.00 ]
|                                         0.385 - 0.39 : [ 5 0.00 0.00 ]
|                                         0.39 - 0.395 : [ 10 0.00 0.00 ]
|                                         0.395 - 0.4 : [ 7 0.00 0.00 ]
|                                         0.4 - 0.405 : [ 12 0.00 0.00 ]
|                                         0.405 - 0.41 : [ 20 0.00 0.00 ]
|                                         0.41 - 0.415 : [ 12 0.00 0.00 ]
|                                         0.415 - 0.42 : [ 15 0.00 0.00 ]
|                                         0.42 - 0.425 : [ 21 0.00 0.00 ]
|                                         0.425 - 0.43 : [ 21 0.00 0.00 ]
|                                         0.43 - 0.435 : [ 24 0.00 0.00 ]
|X                                        0.435 - 0.44 : [ 30 0.00 0.00 ]
|X                                        0.44 - 0.445 : [ 33 0.00 0.01 ]
|                                         0.445 - 0.45 : [ 24 0.00 0.01 ]
|X                                        0.45 - 0.455 : [ 42 0.00 0.01 ]
|X                                        0.455 - 0.46 : [ 52 0.00 0.01 ]
|X                                        0.46 - 0.465 : [ 67 0.00 0.01 ]
|X                                        0.465 - 0.47 : [ 67 0.00 0.01 ]
|X                                        0.47 - 0.475 : [ 67 0.00 0.01 ]
|X                                        0.475 - 0.48 : [ 86 0.00 0.01 ]
|XX                                       0.48 - 0.485 : [ 144 0.00 0.02 ]
|XX                                       0.485 - 0.49 : [ 122 0.00 0.02 ]
|XXX                                      0.49 - 0.495 : [ 171 0.00 0.02 ]
|XXX                                      0.495 - 0.5 : [ 183 0.00 0.03 ]
|XXXXXX                                   0.5 - 0.505 : [ 345 0.01 0.03 ]
|XXXXXX                                   0.505 - 0.51 : [ 345 0.01 0.04 ]
|XXXXXX                                   0.51 - 0.515 : [ 383 0.01 0.05 ]
|XXXXXXX                                  0.515 - 0.52 : [ 401 0.01 0.05 ]
|XXXXXXXXX                                0.52 - 0.525 : [ 545 0.01 0.07 ]
|XXXXXXXXX                                0.525 - 0.53 : [ 517 0.01 0.08 ]
|XXXXXXXXXXX                              0.53 - 0.535 : [ 669 0.01 0.09 ]
|XXXXXXXXXXXXX                            0.535 - 0.54 : [ 771 0.02 0.10 ]
|XXXXXXXXXXXXXXX                          0.54 - 0.545 : [ 900 0.02 0.12 ]
|XXXXXXXXXXXXXXXX                         0.545 - 0.55 : [ 943 0.02 0.14 ]
|XXXXXXXXXXXXXXXXXXX                      0.55 - 0.555 : [ 1141 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXXXXX                    0.555 - 0.56 : [ 1277 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXX                   0.56 - 0.565 : [ 1327 0.03 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX               0.565 - 0.57 : [ 1577 0.03 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX            0.57 - 0.575 : [ 1708 0.03 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX          0.575 - 0.58 : [ 1865 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX         0.58 - 0.585 : [ 1924 0.04 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX       0.585 - 0.59 : [ 2004 0.04 0.40 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     0.59 - 0.595 : [ 2152 0.04 0.44 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    0.595 - 0.6 : [ 2205 0.04 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX   0.6 - 0.605 : [ 2295 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 2391 0.05 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  0.61 - 0.615 : [ 2307 0.05 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX   0.615 - 0.62 : [ 2300 0.05 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    0.62 - 0.625 : [ 2189 0.04 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     0.625 - 0.63 : [ 2149 0.04 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX        0.63 - 0.635 : [ 1976 0.04 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX           0.635 - 0.64 : [ 1823 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX                0.64 - 0.645 : [ 1504 0.03 0.86 ]
|XXXXXXXXXXXXXXXXXXXXXX                   0.645 - 0.65 : [ 1334 0.03 0.88 ]
|XXXXXXXXXXXXXXXXXXXX                     0.65 - 0.655 : [ 1187 0.02 0.91 ]
|XXXXXXXXXXXXXXXX                         0.655 - 0.66 : [ 927 0.02 0.93 ]
|XXXXXXXXXXXXX                            0.66 - 0.665 : [ 791 0.02 0.94 ]
|XXXXXXXXXXX                              0.665 - 0.67 : [ 667 0.01 0.95 ]
|XXXXXXXXX                                0.67 - 0.675 : [ 548 0.01 0.97 ]
|XXXXXXX                                  0.675 - 0.68 : [ 440 0.01 0.97 ]
|XXXXXX                                   0.68 - 0.685 : [ 334 0.01 0.98 ]
|XXXX                                     0.685 - 0.69 : [ 232 0.00 0.99 ]
|XXX                                      0.69 - 0.695 : [ 152 0.00 0.99 ]
|XX                                       0.695 - 0.7 : [ 134 0.00 0.99 ]
|XX                                       0.7 - 0.705 : [ 123 0.00 0.99 ]
|X                                        0.705 - 0.71 : [ 88 0.00 0.99 ]
|X                                        0.71 - 0.715 : [ 62 0.00 1.00 ]
|X                                        0.715 - 0.72 : [ 34 0.00 1.00 ]
|X                                        0.72 - 0.725 : [ 32 0.00 1.00 ]
|                                         0.725 - 0.73 : [ 23 0.00 1.00 ]
|                                         0.73 - 0.735 : [ 20 0.00 1.00 ]
|                                         0.735 - 0.74 : [ 7 0.00 1.00 ]
|                                         0.74 - 0.745 : [ 7 0.00 1.00 ]
|                                         0.745 - 0.75 : [ 6 0.00 1.00 ]
|                                         0.75 - 0.755 : [ 10 0.00 1.00 ]
|                                         0.755 - 0.76 : [ 12 0.00 1.00 ]
|                                         0.76 - 0.765 : [ 8 0.00 1.00 ]
|                                         0.765 - 0.77 : [ 5 0.00 1.00 ]
|                                         0.77 - 0.775 : [ 7 0.00 1.00 ]
|                                         0.775 - 0.78 : [ 1 0.00 1.00 ]
|                                         0.78 - 0.785 : [ 5 0.00 1.00 ]
|                                         0.785 - 0.79 : [ 3 0.00 1.00 ]
|                                         0.79 - 0.795 : [ 2 0.00 1.00 ]
#...
|                                         0.8 - 0.805 : [ 3 0.00 1.00 ]
|                                         0.805 - 0.81 : [ 1 0.00 1.00 ]
|                                         0.81 - 0.815 : [ 2 0.00 1.00 ]
|                                         0.815 - 0.82 : [ 2 0.00 1.00 ]
#...
|                                         0.825 - 0.83 : [ 1 0.00 1.00 ]
#...
|                                         0.845 - 0.85 : [ 1 0.00 1.00 ]
#...
|                                         0.875 - 0.88 : [ 1 0.00 1.00 ]
#...
|                                         0.9 - 0.905 : [ 1 0.00 1.00 ]
#...
|                                         1 - 1.005 : [ 1 0.00 1.00 ]



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

Contig 116.  439 reads;  46692 bp (untrimmed),  46420 (trimmed).
Contig 117.  463 reads;  43700 bp (untrimmed),  43643 (trimmed).
Contig 118.  606 reads;  55230 bp (untrimmed),  55104 (trimmed).
Contig 119.  678 reads;  73590 bp (untrimmed),  73559 (trimmed).
Contig 120.  691 reads;  66437 bp (untrimmed),  66367 (trimmed).
Contig 121.  693 reads;  62641 bp (untrimmed),  62579 (trimmed).
Contig 122.  712 reads;  72917 bp (untrimmed),  72789 (trimmed).
Contig 123.  749 reads;  85309 bp (untrimmed),  85158 (trimmed).
Contig 124.  786 reads;  87129 bp (untrimmed),  86973 (trimmed).
Contig 125.  889 reads;  84721 bp (untrimmed),  84633 (trimmed).
Contig 126.  899 reads;  78076 bp (untrimmed),  77775 (trimmed).
Contig 127. 1022 reads;  91928 bp (untrimmed),  91891 (trimmed).
Contig 128. 1033 reads;  98843 bp (untrimmed),  98742 (trimmed).
Contig 129. 1073 reads; 100490 bp (untrimmed), 100450 (trimmed).
Contig 130. 1093 reads; 103404 bp (untrimmed), 103385 (trimmed).
Contig 131. 1214 reads; 117735 bp (untrimmed), 117735 (trimmed).
Contig 132. 1237 reads; 132676 bp (untrimmed), 132652 (trimmed).
Contig 133. 1355 reads; 125697 bp (untrimmed), 125495 (trimmed).
Contig 134. 1434 reads; 117688 bp (untrimmed), 117661 (trimmed).
Contig 135. 1633 reads; 167329 bp (untrimmed), 167309 (trimmed).
Contig 136. 1980 reads; 173080 bp (untrimmed), 172675 (trimmed).
Contig 137. 2024 reads; 195394 bp (untrimmed), 195083 (trimmed).
Contig 138. 2369 reads; 200194 bp (untrimmed), 200172 (trimmed).
Contig 139. 2632 reads; 255694 bp (untrimmed), 255665 (trimmed).
Contig 140. 4805 reads; 403089 bp (untrimmed), 403067 (trimmed).
Contig 141. 5175 reads; 431186 bp (untrimmed), 431175 (trimmed).
Contig 142. 6179 reads; 575359 bp (untrimmed), 575302 (trimmed).
--------------------------------------------------------------
Totals      50472 reads; 4926722 bp (untrimmed), 4903249 (trimmed).


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

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

depth.out contains 4925102 bases  = 8.81 +- 3.64   = 0.17 +- 3.24  


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

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


#Found 138 total values totalling 685.1600. <4.964928 +/- 2.867002>
#Range: [ 1.21 - 10.58 ]
#Most likely bin: [ 2.5 - 3 ] 21 counts
#Median bin: [ 3.5 - 4 ] 13 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXX                               1 - 1.5 : [ 5 0.04 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  1.5 - 2 : [ 12 0.09 0.12 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX                2 - 2.5 : [ 13 0.09 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 21 0.15 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  3 - 3.5 : [ 12 0.09 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX                3.5 - 4 : [ 13 0.09 0.55 ]
|XXXXXX                                   4 - 4.5 : [ 3 0.02 0.57 ]
|XXXXXXXX                                 4.5 - 5 : [ 4 0.03 0.60 ]
|XXXXXX                                   5 - 5.5 : [ 3 0.02 0.62 ]
|XX                                       5.5 - 6 : [ 1 0.01 0.63 ]
|XXXXXX                                   6 - 6.5 : [ 3 0.02 0.65 ]
|XXXXXX                                   6.5 - 7 : [ 3 0.02 0.67 ]
|XX                                       7 - 7.5 : [ 1 0.01 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  7.5 - 8 : [ 12 0.09 0.77 ]
|XXXXXXXXXXXXX                            8 - 8.5 : [ 7 0.05 0.82 ]
|XXXXXXXXXXXXXXX                          8.5 - 9 : [ 8 0.06 0.88 ]
|XXXXXXXXXXXXX                            9 - 9.5 : [ 7 0.05 0.93 ]
|XXXXXXXXXX                               9.5 - 10 : [ 5 0.04 0.96 ]
|XXXXXXXX                                 10 - 10.5 : [ 4 0.03 0.99 ]
|XX                                       10.5 - 11 : [ 1 0.01 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 92 total values totalling 577.8400. <6.280870 +/- 2.628361>
#Range: [ 2.27 - 10.58 ]
#Most likely bin: [ 7.5 - 8 ] 12 counts
#Median bin: [ 6.5 - 7 ] 3 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXX                               2 - 2.5 : [ 3 0.03 0.03 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    2.5 - 3 : [ 11 0.12 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  3 - 3.5 : [ 7 0.08 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX           3.5 - 4 : [ 9 0.10 0.33 ]
|XXXXXXXXXX                               4 - 4.5 : [ 3 0.03 0.36 ]
|XXXXXXXXXXXXX                            4.5 - 5 : [ 4 0.04 0.40 ]
|XXXXXXXXXX                               5 - 5.5 : [ 3 0.03 0.43 ]
|XXX                                      5.5 - 6 : [ 1 0.01 0.45 ]
|XXXXXXXXXX                               6 - 6.5 : [ 3 0.03 0.48 ]
|XXXXXXXXXX                               6.5 - 7 : [ 3 0.03 0.51 ]
|XXX                                      7 - 7.5 : [ 1 0.01 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 12 0.13 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  8 - 8.5 : [ 7 0.08 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX              8.5 - 9 : [ 8 0.09 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  9 - 9.5 : [ 7 0.08 0.89 ]
|XXXXXXXXXXXXXXXXX                        9.5 - 10 : [ 5 0.05 0.95 ]
|XXXXXXXXXXXXX                            10 - 10.5 : [ 4 0.04 0.99 ]
|XXX                                      10.5 - 11 : [ 1 0.01 1.00 ]


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

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

Contig 4           2 reads      1294 bases  =   1.21 +- 0.41     =   1.21 +-  0.41
Contig 14          3 reads      1509 bases  =   1.32 +- 0.49     =   0.48 +-  1.19
Contig 6           3 reads      2233 bases  =   1.32 +- 0.47     =   0.48 +-  0.94
Contig 12          3 reads      1908 bases  =   1.45 +- 0.50     =   0.38 +-  0.64
Contig 10          3 reads      2019 bases  =   1.46 +- 0.50     =   0.47 +-  0.56
Contig 7           3 reads      1065 bases  =   1.54 +- 0.85     =   0.94 +-  0.24
Contig 24          4 reads      2115 bases  =   1.57 +- 0.72     =  -0.05 +-  0.83
Contig 5           3 reads      1816 bases  =   1.64 +- 0.74     =   0.42 +-  1.04
Contig 30          5 reads      2524 bases  =   1.67 +- 0.79     =   1.18 +-  0.49
Contig 15          3 reads      1360 bases  =   1.70 +- 0.71     =   0.27 +-  0.72
Contig 32          5 reads      2357 bases  =   1.74 +- 0.78     =   0.29 +-  0.94
Contig 17          4 reads      1813 bases  =   1.76 +- 0.64     =   0.77 +-  0.69
Contig 28          5 reads      2501 bases  =   1.78 +- 0.98     =   0.32 +-  1.16
Contig 8           3 reads      1597 bases  =   1.84 +- 0.70     =   1.84 +-  0.70
Contig 13          3 reads      1270 bases  =   1.87 +- 0.91     =   1.13 +-  0.37
Contig 11          3 reads      1172 bases  =   1.90 +- 0.69     =   0.51 +-  1.16
Contig 37          6 reads      2399 bases  =   1.96 +- 0.68     =   0.79 +-  1.84
Contig 49          9 reads      3627 bases  =   2.05 +- 0.70     =   1.62 +-  0.71
Contig 23          4 reads      1382 bases  =   2.11 +- 0.91     =   0.77 +-  0.77
Contig 18          4 reads      1632 bases  =   2.15 +- 0.91     =   2.15 +-  0.91

Contig 131      1214 reads    117735 bases  =   8.89 +- 3.16     =   0.13 +-  3.21
Contig 128      1033 reads     98843 bases  =   8.96 +- 3.23     =  -0.00 +-  3.02
Contig 120       691 reads     66437 bases  =   8.97 +- 3.35     =   0.04 +-  3.19
Contig 117       463 reads     43700 bases  =   9.01 +- 3.58     =   0.85 +-  3.50
Contig 130      1093 reads    103404 bases  =   9.07 +- 3.23     =   0.14 +-  3.41
Contig 125       889 reads     84721 bases  =   9.09 +- 3.30     =   0.04 +-  3.33
Contig 129      1073 reads    100490 bases  =   9.18 +- 3.04     =   0.06 +-  3.22
Contig 133      1355 reads    125697 bases  =   9.25 +- 3.04     =   0.06 +-  3.36
Contig 142      6179 reads    575359 bases  =   9.25 +- 3.15     =   0.00 +-  3.13
Contig 118       606 reads     55230 bases  =   9.43 +- 3.75     =   0.17 +-  3.48
Contig 127      1022 reads     91928 bases  =   9.50 +- 3.25     =   0.16 +-  3.71
Contig 121       693 reads     62641 bases  =   9.52 +- 3.47     =   0.41 +-  3.55
Contig 109       318 reads     28714 bases  =   9.63 +- 4.05     =   0.62 +-  3.43
Contig 136      1980 reads    173080 bases  =   9.75 +- 3.35     =   0.05 +-  3.61
Contig 126       899 reads     78076 bases  =   9.89 +- 3.83     =   0.10 +-  3.43
Contig 115       414 reads     35139 bases  =  10.09 +- 4.14     =   0.08 +-  3.58
Contig 138      2369 reads    200194 bases  =  10.21 +- 3.38     =   0.05 +-  3.90
Contig 140      4805 reads    403089 bases  =  10.28 +- 3.64     =   0.07 +-  3.38
Contig 141      5175 reads    431186 bases  =  10.37 +- 3.50     =  -0.02 +-  3.51
Contig 134      1434 reads    117688 bases  =  10.58 +- 3.72     =   0.19 +-  3.25


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

Small Inserts = 1246

HQ Discrepant reads = 67

Chimeric reads = 136

Suspect alignments = 334


-------------------------------------------------------------------
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/microbe3/3635488/edit_dir.08Sep04.QD