See help.
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 3746358
# phrap: 2952475
# db:
altered.
9000000
4500000
5049708 +/- 2345426
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 3159
Number of reads with percent X's >= 20%: 229 = 1.6%
Number of reads with percent X's >= 50%: 198 = 1.4%
Number of reads with percent X's >= 80%: 141 = 1.0%
Total reads in project: 14471
Total bp X'd : 276844
reads >= 20% >= 50% >= 80% screened
Nr with L09136 2968 92 76 50
Nr with LRS 20 20 20 20
Nr with pMCL200_JGI_XZX+XZK 171 117 102 71
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 196
Number of reads with percent X's >= 20%: 144 = 14.5%
Number of reads with percent X's >= 50%: 142 = 14.3%
Number of reads with percent X's >= 80%: 122 = 12.2%
Total reads in project: 996
Total bp X'd : 126678
reads >= 20% >= 50% >= 80% screened
Nr with L09136 94 47 46 43
Nr with LRS 20 20 20 20
Nr with pMCL200_JGI_XZX+XZK 82 77 76 59
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 2770381
C = 4204335
G = 4266147
T = 2667507
N = 105566
X = 276844
GC fraction = 0.59
Total = 14290780
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634500_fasta.screen.contigs
-------------------------------------------------------------------
A 744413
C 1227349
G 1220245
T 747729
N 1274
fraction GC = 0.62
total bases = 3941010
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 AICF reads.list > grep.reads.list.AICF
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICF 4 500
-------------------------------------------------------------------
#Found 1130 total values totalling 4152750.0000. <3675.000000 +/- 590.905113>
#Range: [ 949 - 4800 ]
#Most likely bin: [ 3500 - 4000 ] 560 counts
#Median bin: [ 3500 - 4000 ] 560 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
|X 1000 - 1500 : [ 17 0.02 0.02 ]
|X 1500 - 2000 : [ 18 0.02 0.03 ]
|XX 2000 - 2500 : [ 28 0.02 0.06 ]
|XXX 2500 - 3000 : [ 39 0.03 0.09 ]
|XXXXXXXXXXX 3000 - 3500 : [ 153 0.14 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 560 0.50 0.72 ]
|XXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 306 0.27 0.99 ]
| 4500 - 5000 : [ 7 0.01 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICG reads.list > grep.reads.list.AICG
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICG 4 500
-------------------------------------------------------------------
#Found 457 total values totalling 2827877.0000. <6187.914661 +/- 1633.193278>
#Range: [ 974 - 8513 ]
#Most likely bin: [ 6000 - 6500 ] 110 counts
#Median bin: [ 6500 - 7000 ] 85 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
|XXX 1000 - 1500 : [ 9 0.02 0.02 ]
|XXXX 1500 - 2000 : [ 10 0.02 0.04 ]
|XXXX 2000 - 2500 : [ 12 0.03 0.07 ]
|XX 2500 - 3000 : [ 5 0.01 0.08 ]
|XXXX 3000 - 3500 : [ 11 0.02 0.11 ]
|XXX 3500 - 4000 : [ 8 0.02 0.12 ]
|XXXX 4000 - 4500 : [ 12 0.03 0.15 ]
|X 4500 - 5000 : [ 2 0.00 0.15 ]
|XX 5000 - 5500 : [ 5 0.01 0.16 ]
|XXXXXXXXXXXXXX 5500 - 6000 : [ 38 0.08 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 110 0.24 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 85 0.19 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 73 0.16 0.83 ]
|XXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 59 0.13 0.96 ]
|XXXXXX 8000 - 8500 : [ 16 0.04 1.00 ]
| 8500 - 9000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AICF 3560 +- 735 (n=580)
# AICG 5811 +- 1991 (n=240)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634500_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
AICF 30720 -1 -1 97 731 6831 98 776 99 783
AICG 36480 -1 -1 91 574 7640 87 536 91 565
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AICF 3456 98 768 99 784 3375 98 784 99 782
AICG 3821 84 541 89 559 3819 90 531 93 571
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634500_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
40 6831 3840 96.00 100.00 AICF @
40 7640 3836 95.90 99.90 AICG @
] 14471 7676 95.95 cumulative total@@
LIBRARY PLATE ID COUNT [ AICF 40 AICG 40 ] for 80 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 3634500_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 14471 total values totalling 8770305.0000. <606.060742 +/- 242.098412>
#Range: [ 0 - 943 ]
#Most likely bin: [ 800 - 850 ] 2461 counts
#Median bin: [ 650 - 700 ] 1476 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXX 0 - 50 : [ 970 0.07 0.07 ]
|XXX 50 - 100 : [ 158 0.01 0.08 ]
|XXX 100 - 150 : [ 174 0.01 0.09 ]
|XXX 150 - 200 : [ 179 0.01 0.10 ]
|XXXX 200 - 250 : [ 216 0.01 0.12 ]
|XXXX 250 - 300 : [ 268 0.02 0.14 ]
|XXXXX 300 - 350 : [ 336 0.02 0.16 ]
|XXXXXX 350 - 400 : [ 372 0.03 0.18 ]
|XXXXXX 400 - 450 : [ 390 0.03 0.21 ]
|XXXXXXX 450 - 500 : [ 420 0.03 0.24 ]
|XXXXXXXXX 500 - 550 : [ 546 0.04 0.28 ]
|XXXXXXXXXXXXXX 550 - 600 : [ 850 0.06 0.34 ]
|XXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1266 0.09 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1476 0.10 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1505 0.10 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2359 0.16 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2461 0.17 0.96 ]
|XXXXXXXX 850 - 900 : [ 511 0.04 1.00 ]
| 900 - 950 : [ 14 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICF
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICF 3634500_fasta.screen.trimQ15.SaF > reads.trim15.AICF.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICF.rl 2 50
-------------------------------------------------------------------
#Found 6831 total values totalling 5176602.0000. <757.810277 +/- 143.488993>
#Range: [ 0 - 943 ]
#Most likely bin: [ 800 - 850 ] 2453 counts
#Median bin: [ 750 - 800 ] 2199 counts
#Histogram Bins Count Fraction Cum_Fraction
|XX 0 - 50 : [ 148 0.02 0.02 ]
| 50 - 100 : [ 13 0.00 0.02 ]
| 100 - 150 : [ 11 0.00 0.03 ]
| 150 - 200 : [ 4 0.00 0.03 ]
| 200 - 250 : [ 18 0.00 0.03 ]
| 250 - 300 : [ 24 0.00 0.03 ]
| 300 - 350 : [ 13 0.00 0.03 ]
| 350 - 400 : [ 29 0.00 0.04 ]
| 400 - 450 : [ 10 0.00 0.04 ]
| 450 - 500 : [ 7 0.00 0.04 ]
| 500 - 550 : [ 19 0.00 0.04 ]
|X 550 - 600 : [ 50 0.01 0.05 ]
|XXX 600 - 650 : [ 156 0.02 0.07 ]
|XXXXX 650 - 700 : [ 307 0.04 0.12 ]
|XXXXXXXXXXXXXX 700 - 750 : [ 845 0.12 0.24 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2199 0.32 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2453 0.36 0.92 ]
|XXXXXXXX 850 - 900 : [ 511 0.07 1.00 ]
| 900 - 950 : [ 14 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICG
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICG 3634500_fasta.screen.trimQ15.SaF > reads.trim15.AICG.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICG.rl 2 50
-------------------------------------------------------------------
#Found 7640 total values totalling 3593703.0000. <470.379974 +/- 231.536643>
#Range: [ 0 - 828 ]
#Most likely bin: [ 650 - 700 ] 1169 counts
#Median bin: [ 550 - 600 ] 800 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 822 0.11 0.11 ]
|XXXXX 50 - 100 : [ 145 0.02 0.13 ]
|XXXXXX 100 - 150 : [ 163 0.02 0.15 ]
|XXXXXX 150 - 200 : [ 175 0.02 0.17 ]
|XXXXXXX 200 - 250 : [ 198 0.03 0.20 ]
|XXXXXXXX 250 - 300 : [ 244 0.03 0.23 ]
|XXXXXXXXXXX 300 - 350 : [ 323 0.04 0.27 ]
|XXXXXXXXXXXX 350 - 400 : [ 343 0.04 0.32 ]
|XXXXXXXXXXXXX 400 - 450 : [ 380 0.05 0.37 ]
|XXXXXXXXXXXXXX 450 - 500 : [ 413 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXX 500 - 550 : [ 527 0.07 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 800 0.10 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1110 0.15 0.74 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 1169 0.15 0.89 ]
|XXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 660 0.09 0.98 ]
|XXXXX 750 - 800 : [ 160 0.02 1.00 ]
| 800 - 850 : [ 8 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICH
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634500
-------------------------------------------------------------------
AICF.000001.000100 pUC18.fa LRS.fasta
AICF.000101.000200 pUC18.fa LRS.fasta
AICG.000001.000100 pMCL200.fa LRS.fasta
AICG.000101.000200 pMCL200.fa LRS.fasta
AICH.000001.000100 pCC1Fos.fa LRS.fasta
AICF.000001.000100 pUC18.fa LRS.fasta
AICF.000101.000200 pUC18.fa LRS.fasta
AICG.000001.000100 pMCL200.fa LRS.fasta
AICG.000101.000200 pMCL200.fa LRS.fasta
AICH.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634500_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634500_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 13510 total values totalling 8364.1677. <0.619109 +/- 0.039343>
#Range: [ 0.3871 - 0.7742 ]
#Most likely bin: [ 0.625 - 0.63 ] 861 counts
#Median bin: [ 0.62 - 0.625 ] 828 counts
| 0.385 - 0.39 : [ 1 0.00 0.00 ]
| 0.39 - 0.395 : [ 1 0.00 0.00 ]
| 0.395 - 0.4 : [ 1 0.00 0.00 ]
| 0.4 - 0.405 : [ 1 0.00 0.00 ]
| 0.405 - 0.41 : [ 1 0.00 0.00 ]
| 0.41 - 0.415 : [ 1 0.00 0.00 ]
| 0.415 - 0.42 : [ 3 0.00 0.00 ]
| 0.42 - 0.425 : [ 1 0.00 0.00 ]
| 0.425 - 0.43 : [ 1 0.00 0.00 ]
| 0.43 - 0.435 : [ 3 0.00 0.00 ]
| 0.435 - 0.44 : [ 1 0.00 0.00 ]
| 0.44 - 0.445 : [ 2 0.00 0.00 ]
| 0.445 - 0.45 : [ 4 0.00 0.00 ]
| 0.45 - 0.455 : [ 7 0.00 0.00 ]
| 0.455 - 0.46 : [ 8 0.00 0.00 ]
|X 0.46 - 0.465 : [ 11 0.00 0.00 ]
|X 0.465 - 0.47 : [ 11 0.00 0.00 ]
|X 0.47 - 0.475 : [ 11 0.00 0.01 ]
|X 0.475 - 0.48 : [ 13 0.00 0.01 ]
|X 0.48 - 0.485 : [ 17 0.00 0.01 ]
|X 0.485 - 0.49 : [ 16 0.00 0.01 ]
|X 0.49 - 0.495 : [ 20 0.00 0.01 ]
| 0.495 - 0.5 : [ 9 0.00 0.01 ]
|X 0.5 - 0.505 : [ 32 0.00 0.01 ]
|X 0.505 - 0.51 : [ 25 0.00 0.01 ]
|X 0.51 - 0.515 : [ 20 0.00 0.02 ]
|XX 0.515 - 0.52 : [ 49 0.00 0.02 ]
|XX 0.52 - 0.525 : [ 37 0.00 0.02 ]
|XX 0.525 - 0.53 : [ 44 0.00 0.03 ]
|XXX 0.53 - 0.535 : [ 55 0.00 0.03 ]
|XXX 0.535 - 0.54 : [ 66 0.00 0.03 ]
|XXXX 0.54 - 0.545 : [ 84 0.01 0.04 ]
|XXXX 0.545 - 0.55 : [ 95 0.01 0.05 ]
|XXXXX 0.55 - 0.555 : [ 114 0.01 0.06 ]
|XXXXXXXX 0.555 - 0.56 : [ 162 0.01 0.07 ]
|XXXXXXX 0.56 - 0.565 : [ 157 0.01 0.08 ]
|XXXXXXXXX 0.565 - 0.57 : [ 202 0.01 0.10 ]
|XXXXXXXXXXX 0.57 - 0.575 : [ 234 0.02 0.11 ]
|XXXXXXXXXXXXXX 0.575 - 0.58 : [ 296 0.02 0.13 ]
|XXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 353 0.03 0.16 ]
|XXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 379 0.03 0.19 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 473 0.04 0.22 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.595 - 0.6 : [ 520 0.04 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.6 - 0.605 : [ 633 0.05 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.605 - 0.61 : [ 654 0.05 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.61 - 0.615 : [ 728 0.05 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.615 - 0.62 : [ 777 0.06 0.47 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 828 0.06 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 861 0.06 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 775 0.06 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 759 0.06 0.71 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 689 0.05 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 642 0.05 0.81 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 531 0.04 0.85 ]
|XXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 435 0.03 0.88 ]
|XXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 370 0.03 0.90 ]
|XXXXXXXXXXXXXXX 0.665 - 0.67 : [ 317 0.02 0.93 ]
|XXXXXXXXXXX 0.67 - 0.675 : [ 234 0.02 0.95 ]
|XXXXXXXXXX 0.675 - 0.68 : [ 212 0.02 0.96 ]
|XXXXXX 0.68 - 0.685 : [ 128 0.01 0.97 ]
|XXXX 0.685 - 0.69 : [ 91 0.01 0.98 ]
|XXXX 0.69 - 0.695 : [ 88 0.01 0.98 ]
|XXX 0.695 - 0.7 : [ 67 0.00 0.99 ]
|XX 0.7 - 0.705 : [ 50 0.00 0.99 ]
|X 0.705 - 0.71 : [ 25 0.00 0.99 ]
|X 0.71 - 0.715 : [ 14 0.00 1.00 ]
|X 0.715 - 0.72 : [ 16 0.00 1.00 ]
| 0.72 - 0.725 : [ 8 0.00 1.00 ]
| 0.725 - 0.73 : [ 6 0.00 1.00 ]
| 0.73 - 0.735 : [ 7 0.00 1.00 ]
| 0.735 - 0.74 : [ 6 0.00 1.00 ]
| 0.74 - 0.745 : [ 4 0.00 1.00 ]
| 0.745 - 0.75 : [ 4 0.00 1.00 ]
| 0.75 - 0.755 : [ 1 0.00 1.00 ]
| 0.755 - 0.76 : [ 4 0.00 1.00 ]
| 0.76 - 0.765 : [ 1 0.00 1.00 ]
#...
| 0.77 - 0.775 : [ 4 0.00 1.00 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 1179. 47 reads; 10954 bp (untrimmed), 10954 (trimmed).
Contig 1180. 48 reads; 10138 bp (untrimmed), 10119 (trimmed).
Contig 1181. 48 reads; 10148 bp (untrimmed), 9927 (trimmed).
Contig 1182. 50 reads; 15533 bp (untrimmed), 15527 (trimmed).
Contig 1183. 50 reads; 11543 bp (untrimmed), 11455 (trimmed).
Contig 1184. 51 reads; 9607 bp (untrimmed), 9511 (trimmed).
Contig 1185. 51 reads; 11509 bp (untrimmed), 11486 (trimmed).
Contig 1186. 53 reads; 10888 bp (untrimmed), 10526 (trimmed).
Contig 1187. 53 reads; 11962 bp (untrimmed), 11800 (trimmed).
Contig 1188. 54 reads; 13414 bp (untrimmed), 13209 (trimmed).
Contig 1189. 55 reads; 11809 bp (untrimmed), 11795 (trimmed).
Contig 1190. 56 reads; 11902 bp (untrimmed), 11791 (trimmed).
Contig 1191. 57 reads; 11852 bp (untrimmed), 11755 (trimmed).
Contig 1192. 58 reads; 11485 bp (untrimmed), 11286 (trimmed).
Contig 1193. 59 reads; 13922 bp (untrimmed), 13661 (trimmed).
Contig 1194. 59 reads; 12217 bp (untrimmed), 11946 (trimmed).
Contig 1195. 59 reads; 15765 bp (untrimmed), 15682 (trimmed).
Contig 1196. 60 reads; 16006 bp (untrimmed), 15724 (trimmed).
Contig 1197. 62 reads; 14664 bp (untrimmed), 14663 (trimmed).
Contig 1198. 65 reads; 13012 bp (untrimmed), 12991 (trimmed).
Contig 1199. 68 reads; 12812 bp (untrimmed), 12726 (trimmed).
Contig 1200. 77 reads; 17726 bp (untrimmed), 17658 (trimmed).
Contig 1201. 95 reads; 18200 bp (untrimmed), 18128 (trimmed).
Contig 1202. 96 reads; 21554 bp (untrimmed), 21438 (trimmed).
Contig 1203. 104 reads; 24030 bp (untrimmed), 24009 (trimmed).
Contig 1204. 144 reads; 28507 bp (untrimmed), 28430 (trimmed).
Contig 1205. 193 reads; 42168 bp (untrimmed), 41855 (trimmed).
--------------------------------------------------------------
Totals 13475 reads; 3941010 bp (untrimmed), 3746358 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 3938421 bases Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 92
HQ Discrepant reads = 388
Chimeric reads = 15
Suspect alignments = 45
-------------------------------------------------------------------
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/microbe4/3634500/edit_dir.13May04.QC