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 in progress (or initial analysis of completed)
-------------------------------------------------------------------


-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------

Project	Size(KB)	TaxID	GenusSpecies
3634512	6700	NULL	Clostridium beijerincki


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

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




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: 1794510
# phrap: 1013603
# db: 
altered.

6700000
3169371 +/- 2516804

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

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


Number of reads with X's: 2312
Number of reads with percent X's >= 20%:    48 = 0.7%
Number of reads with percent X's >= 50%:    42 = 0.6%
Number of reads with percent X's >= 80%:    22 = 0.3%
Total reads in project: 7173
Total bp X'd : 118147
                                  reads  >= 20% >= 50% >= 80% screened
Nr with L09136                     2312     48     42     22

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

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


Number of reads with X's: 599
Number of reads with percent X's >= 20%:    29 = 1.2%
Number of reads with percent X's >= 50%:    28 = 1.1%
Number of reads with percent X's >= 80%:    19 = 0.8%
Total reads in project: 2494
Total bp X'd : 44703
                                  reads  >= 20% >= 50% >= 80% screened
Nr with L09136                      599     29     28     19


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

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

A = 2327792
C = 1244546
G = 1151544
T = 2195664
N = 68983
X = 118147
GC fraction = 0.34
Total = 7106676

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

Command: /psf/QC/bin/sparc/faCount 3634512_fasta.screen.contigs
-------------------------------------------------------------------


A	740567
C	352024
G	328794
T	765342
N	3519
fraction GC = 0.31
total bases = 2190246



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


#Found 99 total values totalling 256835.0000. <2594.292929 +/- 843.115282>
#Range: [ 881 - 4045 ]
#Most likely bin: [ 2500 - 3000 ] 29 counts
#Median bin: [ 2500 - 3000 ] 29 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXX                                     500 - 1000 : [ 3 0.03 0.03 ]
|XXXXXXXXXXXXXXXXXX                       1000 - 1500 : [ 13 0.13 0.16 ]
|XXXXXXXXXXXXXX                           1500 - 2000 : [ 10 0.10 0.26 ]
|XXXXXXXXXXXXXX                           2000 - 2500 : [ 10 0.10 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 29 0.29 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX            3000 - 3500 : [ 21 0.21 0.87 ]
|XXXXXXXXXXXXXXXXX                        3500 - 4000 : [ 12 0.12 0.99 ]
|X                                        4000 - 4500 : [ 1 0.01 1.00 ]



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

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

# AIFZ 2252 +- 1065 (n=54)


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

extracted from 3634512_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 
AIFZ    79104     88   710     95   729    7173     80   537     86   551

        FWD    |----J15---| |----Q20---|  REV    |----J15---| |----Q20---|
LIB    Reads   %pass AvgLen %pass AvgNum  Reads  %pass AvgLen %pass AvgNun
AIFZ     3783     82   552     87   564    3390     79   518     84   537


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

extracted from file: 3634512_fasta.screen.r2p  [ from "READ/CLONE COUNT SUMMARY"  to end ]
-------------------------------------------------------------------


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

40		7173		3833	 95.83  99.82	AIFZ	@

]		7173		3833	 95.83     	cumulative total@@

LIBRARY PLATE ID COUNT [ AIFZ 40 ] for 40 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 3634512_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------

#Found 7173 total values totalling 3125242.0000. <435.695246 +/- 260.991363>
#Range: [ 0 - 833 ]
#Most likely bin: [ 0 - 50 ] 1174 counts
#Median bin: [ 500 - 550 ] 445 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1174 0.16 0.16 ]
|XXXXXXXX                                 50 - 100 : [ 226 0.03 0.20 ]
|XXXXXXX                                  100 - 150 : [ 193 0.03 0.22 ]
|XXXXXXX                                  150 - 200 : [ 206 0.03 0.25 ]
|XXXXXXX                                  200 - 250 : [ 207 0.03 0.28 ]
|XXXXXXXX                                 250 - 300 : [ 241 0.03 0.31 ]
|XXXXXXXX                                 300 - 350 : [ 234 0.03 0.35 ]
|XXXXXXXX                                 350 - 400 : [ 248 0.03 0.38 ]
|XXXXXXXXXX                               400 - 450 : [ 284 0.04 0.42 ]
|XXXXXXXXXXXXX                            450 - 500 : [ 372 0.05 0.47 ]
|XXXXXXXXXXXXXXX                          500 - 550 : [ 445 0.06 0.53 ]
|XXXXXXXXXXXXXXXXXXXXX                    550 - 600 : [ 613 0.09 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX               600 - 650 : [ 772 0.11 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX          650 - 700 : [ 896 0.12 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX               700 - 750 : [ 764 0.11 0.96 ]
|XXXXXXXXX                                750 - 800 : [ 270 0.04 1.00 ]
|X                                        800 - 850 : [ 28 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for AHYP
trimt JAZZ trim 15 readlength histogram for AHYS
trimt JAZZ trim 15 readlength histogram for AIFZ
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIFZ 3634512_fasta.screen.trimQ15.SaF > reads.trim15.AIFZ.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIFZ.rl 2 50
-------------------------------------------------------------------


#Found 7173 total values totalling 3125242.0000. <435.695246 +/- 260.991363>
#Range: [ 0 - 833 ]
#Most likely bin: [ 0 - 50 ] 1174 counts
#Median bin: [ 500 - 550 ] 445 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1174 0.16 0.16 ]
|XXXXXXXX                                 50 - 100 : [ 226 0.03 0.20 ]
|XXXXXXX                                  100 - 150 : [ 193 0.03 0.22 ]
|XXXXXXX                                  150 - 200 : [ 206 0.03 0.25 ]
|XXXXXXX                                  200 - 250 : [ 207 0.03 0.28 ]
|XXXXXXXX                                 250 - 300 : [ 241 0.03 0.31 ]
|XXXXXXXX                                 300 - 350 : [ 234 0.03 0.35 ]
|XXXXXXXX                                 350 - 400 : [ 248 0.03 0.38 ]
|XXXXXXXXXX                               400 - 450 : [ 284 0.04 0.42 ]
|XXXXXXXXXXXXX                            450 - 500 : [ 372 0.05 0.47 ]
|XXXXXXXXXXXXXXX                          500 - 550 : [ 445 0.06 0.53 ]
|XXXXXXXXXXXXXXXXXXXXX                    550 - 600 : [ 613 0.09 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX               600 - 650 : [ 772 0.11 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX          650 - 700 : [ 896 0.12 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX               700 - 750 : [ 764 0.11 0.96 ]
|XXXXXXXXX                                750 - 800 : [ 270 0.04 1.00 ]
|X                                        800 - 850 : [ 28 0.00 1.00 ]

trimt JAZZ trim 15 readlength histogram for AWGG
trimt JAZZ trim 15 readlength histogram for BAOF
trimt JAZZ trim 15 readlength histogram for BAOG
trimt JAZZ trim 15 readlength histogram for BAOH
trimt JAZZ trim 15 readlength histogram for BFTN
trimt JAZZ trim 15 readlength histogram for SCNC
trimt JAZZ trim 15 readlength histogram for SCOU
trimt JAZZ trim 15 readlength histogram for SCOW

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

Command: /home/copeland/scripts/checkScreen.sh 3634512
-------------------------------------------------------------------

AHYP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta 
AIFZ.000001.000100 pUC18.fa pUC18.fa LRS.fasta 
AIFZ.000101.000200 pUC18.fa pUC18.fa LRS.fasta 
AIFZ.000201.000300 pUC18.fa pUC18.fa LRS.fasta 
AIFZ.000301.000400 pUC18.fa pUC18.fa LRS.fasta 
AIFZ.000401.000500 pUC18.fa pUC18.fa LRS.fasta 
AWGG.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta 
BAOF.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta 
BFTN.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta 
AHYP.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta 
AIFZ.000001.000100 pUC18.fa pUC18.fa LRS.fasta 
AIFZ.000101.000200 pUC18.fa pUC18.fa LRS.fasta 
AIFZ.000201.000300 pUC18.fa pUC18.fa LRS.fasta 
AIFZ.000301.000400 pUC18.fa pUC18.fa LRS.fasta 
AIFZ.000401.000500 pUC18.fa pUC18.fa LRS.fasta 
AWGG.000001.000100 pMCL200.fa pMCL200.fa LRS.fasta 
BAOF.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta 
BFTN.000001.000100 pCC1Fos.fa pCC1Fos.fa LRS.fasta 


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

Command: 	/bin/nawk '{print $5+$6}' GC.3634512_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------


# GC.3634512_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 6004 total values totalling 1783.9494. <0.297127 +/- 0.051662>
#Range: [ 0.077 - 0.6667 ]
#Most likely bin: [ 0.29 - 0.295 ] 301 counts
#Median bin: [ 0.29 - 0.295 ] 301 counts
|                                         0.075 - 0.08 : [ 1 0.00 0.00 ]
#...
|                                         0.085 - 0.09 : [ 1 0.00 0.00 ]
#...
|                                         0.095 - 0.1 : [ 3 0.00 0.00 ]
|                                         0.1 - 0.105 : [ 1 0.00 0.00 ]
#...
|                                         0.11 - 0.115 : [ 1 0.00 0.00 ]
|                                         0.115 - 0.12 : [ 1 0.00 0.00 ]
#...
|X                                        0.125 - 0.13 : [ 5 0.00 0.00 ]
#...
|                                         0.14 - 0.145 : [ 2 0.00 0.00 ]
|                                         0.145 - 0.15 : [ 3 0.00 0.00 ]
|X                                        0.15 - 0.155 : [ 4 0.00 0.00 ]
|                                         0.155 - 0.16 : [ 1 0.00 0.00 ]
|X                                        0.16 - 0.165 : [ 5 0.00 0.00 ]
|X                                        0.165 - 0.17 : [ 6 0.00 0.01 ]
|X                                        0.17 - 0.175 : [ 8 0.00 0.01 ]
|XX                                       0.175 - 0.18 : [ 16 0.00 0.01 ]
|XX                                       0.18 - 0.185 : [ 12 0.00 0.01 ]
|XX                                       0.185 - 0.19 : [ 13 0.00 0.01 ]
|X                                        0.19 - 0.195 : [ 9 0.00 0.02 ]
|XX                                       0.195 - 0.2 : [ 12 0.00 0.02 ]
|XXXX                                     0.2 - 0.205 : [ 31 0.01 0.02 ]
|XXXX                                     0.205 - 0.21 : [ 33 0.01 0.03 ]
|XXXXXXX                                  0.21 - 0.215 : [ 49 0.01 0.04 ]
|XXXXX                                    0.215 - 0.22 : [ 36 0.01 0.04 ]
|XXXXXXXXX                                0.22 - 0.225 : [ 68 0.01 0.05 ]
|XXXXXXXXXXXX                             0.225 - 0.23 : [ 88 0.01 0.07 ]
|XXXXXXXXXX                               0.23 - 0.235 : [ 79 0.01 0.08 ]
|XXXXXXXXXXXXXXXXXXX                      0.235 - 0.24 : [ 142 0.02 0.10 ]
|XXXXXXXXXXXXXXXXXXX                      0.24 - 0.245 : [ 142 0.02 0.13 ]
|XXXXXXXXXXXXXXXXX                        0.245 - 0.25 : [ 129 0.02 0.15 ]
|XXXXXXXXXXXXXXXXXXXXXXXX                 0.25 - 0.255 : [ 178 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXXX                  0.255 - 0.26 : [ 174 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX            0.26 - 0.265 : [ 218 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX             0.265 - 0.27 : [ 213 0.04 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX        0.27 - 0.275 : [ 247 0.04 0.32 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     0.275 - 0.28 : [ 268 0.04 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     0.28 - 0.285 : [ 274 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX       0.285 - 0.29 : [ 253 0.04 0.45 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.29 - 0.295 : [ 301 0.05 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX         0.295 - 0.3 : [ 241 0.04 0.54 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX   0.3 - 0.305 : [ 283 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     0.305 - 0.31 : [ 268 0.04 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX        0.31 - 0.315 : [ 251 0.04 0.68 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX       0.315 - 0.32 : [ 254 0.04 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX              0.32 - 0.325 : [ 205 0.03 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX                0.325 - 0.33 : [ 191 0.03 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXX                   0.33 - 0.335 : [ 163 0.03 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX                0.335 - 0.34 : [ 188 0.03 0.84 ]
|XXXXXXXXXXXXXXXXXXXXX                    0.34 - 0.345 : [ 161 0.03 0.87 ]
|XXXXXXXXXXXXXXXXX                        0.345 - 0.35 : [ 125 0.02 0.89 ]
|XXXXXXXXXXXXX                            0.35 - 0.355 : [ 99 0.02 0.91 ]
|XXXXXXXXXXXXX                            0.355 - 0.36 : [ 96 0.02 0.92 ]
|XXXXXXX                                  0.36 - 0.365 : [ 53 0.01 0.93 ]
|XXXXXXXX                                 0.365 - 0.37 : [ 62 0.01 0.94 ]
|XXXXXX                                   0.37 - 0.375 : [ 43 0.01 0.95 ]
|XXXXX                                    0.375 - 0.38 : [ 38 0.01 0.96 ]
|XXXX                                     0.38 - 0.385 : [ 32 0.01 0.96 ]
|XXX                                      0.385 - 0.39 : [ 21 0.00 0.97 ]
|XXX                                      0.39 - 0.395 : [ 19 0.00 0.97 ]
|XX                                       0.395 - 0.4 : [ 13 0.00 0.97 ]
|XXX                                      0.4 - 0.405 : [ 20 0.00 0.97 ]
|X                                        0.405 - 0.41 : [ 9 0.00 0.98 ]
|X                                        0.41 - 0.415 : [ 11 0.00 0.98 ]
|X                                        0.415 - 0.42 : [ 6 0.00 0.98 ]
|X                                        0.42 - 0.425 : [ 6 0.00 0.98 ]
|X                                        0.425 - 0.43 : [ 4 0.00 0.98 ]
|X                                        0.43 - 0.435 : [ 4 0.00 0.98 ]
|X                                        0.435 - 0.44 : [ 6 0.00 0.98 ]
|                                         0.44 - 0.445 : [ 3 0.00 0.98 ]
|X                                        0.445 - 0.45 : [ 5 0.00 0.98 ]
|X                                        0.45 - 0.455 : [ 5 0.00 0.98 ]
|                                         0.455 - 0.46 : [ 1 0.00 0.98 ]
|X                                        0.46 - 0.465 : [ 7 0.00 0.99 ]
|X                                        0.465 - 0.47 : [ 5 0.00 0.99 ]
|X                                        0.47 - 0.475 : [ 8 0.00 0.99 ]
|X                                        0.475 - 0.48 : [ 5 0.00 0.99 ]
|X                                        0.48 - 0.485 : [ 6 0.00 0.99 ]
|X                                        0.485 - 0.49 : [ 4 0.00 0.99 ]
|X                                        0.49 - 0.495 : [ 5 0.00 0.99 ]
#...
|X                                        0.5 - 0.505 : [ 6 0.00 0.99 ]
|                                         0.505 - 0.51 : [ 2 0.00 0.99 ]
|                                         0.51 - 0.515 : [ 2 0.00 0.99 ]
|X                                        0.515 - 0.52 : [ 9 0.00 0.99 ]
|X                                        0.52 - 0.525 : [ 7 0.00 1.00 ]
|X                                        0.525 - 0.53 : [ 4 0.00 1.00 ]
|X                                        0.53 - 0.535 : [ 5 0.00 1.00 ]
|X                                        0.535 - 0.54 : [ 4 0.00 1.00 ]
|X                                        0.54 - 0.545 : [ 4 0.00 1.00 ]
|                                         0.545 - 0.55 : [ 2 0.00 1.00 ]
|                                         0.55 - 0.555 : [ 3 0.00 1.00 ]
|                                         0.555 - 0.56 : [ 1 0.00 1.00 ]
|                                         0.56 - 0.565 : [ 1 0.00 1.00 ]
#...
|                                         0.665 - 0.67 : [ 1 0.00 1.00 ]



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

Contig 1489.    8 reads;   2720 bp (untrimmed),   2662 (trimmed).
Contig 1490.    8 reads;   3516 bp (untrimmed),   3444 (trimmed).
Contig 1491.    8 reads;   2115 bp (untrimmed),   1527 (trimmed).
Contig 1492.    8 reads;   2473 bp (untrimmed),   2020 (trimmed).
Contig 1493.    9 reads;   3418 bp (untrimmed),   2908 (trimmed).
Contig 1494.    9 reads;   3922 bp (untrimmed),   3550 (trimmed).
Contig 1495.    9 reads;   3394 bp (untrimmed),   3196 (trimmed).
Contig 1496.    9 reads;   3870 bp (untrimmed),   3509 (trimmed).
Contig 1497.    9 reads;   3819 bp (untrimmed),   3746 (trimmed).
Contig 1498.   10 reads;   3206 bp (untrimmed),   3136 (trimmed).
Contig 1499.   10 reads;   3325 bp (untrimmed),   3253 (trimmed).
Contig 1500.   10 reads;   3104 bp (untrimmed),   3055 (trimmed).
Contig 1501.   10 reads;   3932 bp (untrimmed),   3443 (trimmed).
Contig 1502.   10 reads;   3340 bp (untrimmed),   3176 (trimmed).
Contig 1503.   11 reads;   3199 bp (untrimmed),   2802 (trimmed).
Contig 1504.   11 reads;   3621 bp (untrimmed),   3421 (trimmed).
Contig 1505.   12 reads;   2869 bp (untrimmed),   2815 (trimmed).
Contig 1506.   12 reads;   3583 bp (untrimmed),   3546 (trimmed).
Contig 1507.   12 reads;   4045 bp (untrimmed),   3911 (trimmed).
Contig 1508.   12 reads;   3652 bp (untrimmed),   3577 (trimmed).
Contig 1509.   13 reads;   4028 bp (untrimmed),   4027 (trimmed).
Contig 1510.   14 reads;   5069 bp (untrimmed),   5009 (trimmed).
Contig 1511.   15 reads;   5461 bp (untrimmed),   4992 (trimmed).
Contig 1512.   15 reads;   4380 bp (untrimmed),   4333 (trimmed).
Contig 1513.   16 reads;   1784 bp (untrimmed),   1783 (trimmed).
Contig 1514.   25 reads;   3576 bp (untrimmed),   3461 (trimmed).
Contig 1515.   58 reads;   6296 bp (untrimmed),   6292 (trimmed).
--------------------------------------------------------------
Totals      4679 reads; 2190246 bp (untrimmed), 1794510 (trimmed).


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

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

depth.out contains 2170204 bases  = 1.74 +- 0.94   = 0.72 +- 1.12  


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

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


#Found 1492 total values totalling 2541.8600. <1.703660 +/- 0.462865>
#Range: [ 1.05 - 7.30 ]
#Most likely bin: [ 1.5 - 2 ] 632 counts
#Median bin: [ 1.5 - 2 ] 632 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX      1 - 1.5 : [ 552 0.37 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 632 0.42 0.79 ]
|XXXXXXXXXXXXXX                           2 - 2.5 : [ 224 0.15 0.94 ]
|XXXX                                     2.5 - 3 : [ 68 0.05 0.99 ]
|X                                        3 - 3.5 : [ 10 0.01 1.00 ]
|                                         3.5 - 4 : [ 4 0.00 1.00 ]
#...
|                                         4.5 - 5 : [ 1 0.00 1.00 ]
#...
|                                         7 - 7.5 : [ 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 17 total values totalling 49.1800. <2.892941 +/- 1.268620>
#Range: [ 1.93 - 7.30 ]
#Most likely bin: [ 2 - 2.5 ] 7 counts
#Median bin: [ 2.5 - 3 ] 6 counts
#Histogram                                Bins      Count Fraction Cum_Fraction
|XXXXXX                                   1.5 - 2 : [ 1 0.06 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 7 0.41 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX       2.5 - 3 : [ 6 0.35 0.82 ]
#...
|XXXXXX                                   3.5 - 4 : [ 1 0.06 0.88 ]
#...
|XXXXXX                                   4.5 - 5 : [ 1 0.06 0.94 ]
#...
|XXXXXX                                   7 - 7.5 : [ 1 0.06 1.00 ]


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

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

Contig 491         2 reads      1556 bases  =   1.05 +- 0.21     =   0.17 +-  0.96
Contig 226         2 reads      1803 bases  =   1.06 +- 0.25     =  -0.06 +-  0.97
Contig 238         2 reads      1906 bases  =   1.06 +- 0.24     =   0.14 +-  0.96
Contig 448         2 reads      1927 bases  =   1.06 +- 0.24     =   0.02 +-  0.97
Contig 514         2 reads      1369 bases  =   1.06 +- 0.24     =   0.12 +-  0.96
Contig 198         2 reads      1751 bases  =   1.07 +- 0.26     =  -0.06 +-  0.96
Contig 241         2 reads      1051 bases  =   1.07 +- 0.26     =  -0.93 +-  0.26
Contig 373         2 reads      1803 bases  =   1.07 +- 0.26     =  -0.04 +-  0.96
Contig 374         2 reads      1751 bases  =   1.07 +- 0.26     =   1.07 +-  0.26
Contig 399         2 reads      1489 bases  =   1.07 +- 0.25     =   1.07 +-  0.25
Contig 586         2 reads      1435 bases  =   1.07 +- 0.26     =   0.12 +-  0.96
Contig 164         2 reads      1098 bases  =   1.08 +- 0.27     =  -0.92 +-  0.27
Contig 170         2 reads      1629 bases  =   1.08 +- 0.27     =   1.08 +-  0.27
Contig 254         2 reads      1729 bases  =   1.08 +- 0.26     =   1.08 +-  0.26
Contig 395         2 reads      1466 bases  =   1.08 +- 0.28     =   0.24 +-  0.93
Contig 152         2 reads      1486 bases  =   1.09 +- 0.29     =   1.09 +-  0.29
Contig 336         2 reads      1396 bases  =   1.09 +- 0.29     =  -0.04 +-  0.95
Contig 338         2 reads      1222 bases  =   1.09 +- 0.28     =  -0.22 +-  0.93
Contig 445         2 reads       725 bases  =   1.09 +- 0.29     =  -0.91 +-  0.29
Contig 453         2 reads      1742 bases  =   1.09 +- 0.28     =   0.11 +-  0.95

Contig 1152        4 reads       932 bases  =   2.95 +- 0.96     =   1.44 +-  0.60
Contig 1383        5 reads      1510 bases  =   2.95 +- 1.62     =   0.57 +-  1.68
Contig 1480        7 reads      1799 bases  =   2.96 +- 1.79     =   1.83 +-  0.91
Contig 1330        5 reads      1128 bases  =   2.98 +- 1.08     =   0.12 +-  1.17
Contig 1326        5 reads      1399 bases  =   3.02 +- 1.63     =   0.59 +-  0.99
Contig 1422        6 reads      1529 bases  =   3.05 +- 1.34     =  -0.62 +-  0.91
Contig 1467        7 reads      1785 bases  =   3.06 +- 1.38     =   2.14 +-  0.82
Contig 1448        6 reads      1562 bases  =   3.17 +- 1.33     =   2.13 +-  0.80
Contig 1465        7 reads      1753 bases  =   3.17 +- 1.75     =   2.53 +-  1.41
Contig 1255        4 reads       754 bases  =   3.26 +- 0.94     =   0.37 +-  0.97
Contig 1277        4 reads      1031 bases  =   3.27 +- 1.05     =   1.35 +-  1.00
Contig 1235        4 reads       901 bases  =   3.28 +- 0.94     =   1.89 +-  0.71
Contig 1478        7 reads      1738 bases  =   3.31 +- 1.62     =   3.31 +-  1.62
Contig 1234        4 reads      1084 bases  =   3.34 +- 0.95     =   1.94 +-  0.75
Contig 1505       12 reads      2869 bases  =   3.53 +- 2.54     =   1.86 +-  1.46
Contig 1486        8 reads      1857 bases  =   3.54 +- 2.28     =   0.30 +-  1.33
Contig 1392        5 reads      1185 bases  =   3.69 +- 1.53     =   0.71 +-  0.48
Contig 1374        5 reads      1017 bases  =   3.96 +- 1.21     =   0.32 +-  0.70
Contig 1514       25 reads      3576 bases  =   4.70 +- 3.83     =   0.35 +-  1.81
Contig 1515       58 reads      6296 bases  =   7.30 +- 4.55     =   0.32 +-  2.66


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

Small Inserts = 44

HQ Discrepant reads = 214

Chimeric reads = 26

Suspect alignments = 15


-------------------------------------------------------------------
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/microbe4/3634512/edit_dir.15Jun04.QC