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
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Project Size(KB) TaxID GenusSpecies
3634503 4500 196162 Nocardioides sp.
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Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Nocardioides_sp.
-------------------------------------------------------------------
Actinobacteria, phylum, actinobacteria
Nocardioidaceae, family, high GC Gram+
Propionibacterineae, suborder, high GC Gram+
Actinobacteridae, subclass, high GC Gram+
Nocardioides sp., species, high GC Gram+
Actinomycetales, order, high GC Gram+
Nocardioides, genus, high GC Gram+
Actinobacteria (class) (high G+C Gram-positive bacteria), class, high GC Gram+
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 5272143
# phrap: 5197378
# db:
altered.
4500000
4989840 +/- 347711
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 13271
Number of reads with percent X's >= 20%: 97 = 0.1%
Number of reads with percent X's >= 50%: 31 = 0.0%
Number of reads with percent X's >= 80%: 7 = 0.0%
Total reads in project: 65507
Total bp X'd : 532402
reads >= 20% >= 50% >= 80% screened
Nr with L09136 11754 31 14 5
Nr with LRS 1 0 0 0
Nr with pCC1Fos 1434 13 1 0
Nr with pMCL200_JGI_XZX+XZK 82 53 16 2
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 108
Number of reads with percent X's >= 20%: 8 = 1.6%
Number of reads with percent X's >= 50%: 2 = 0.4%
Number of reads with percent X's >= 80%: 0 = 0.0%
Total reads in project: 498
Total bp X'd : 6887
reads >= 20% >= 50% >= 80% screened
Nr with L09136 46 1 0 0
Nr with pCC1Fos 59 6 1 0
Nr with pMCL200_JGI_XZX+XZK 3 1 1 0
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 9636359
C = 22461087
G = 21401171
T = 10618669
N = 287697
X = 532402
GC fraction = 0.68
Total = 64937385
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634503_fasta.screen.contigs
-------------------------------------------------------------------
A 775518
C 1926619
G 1910429
T 781291
N 201
fraction GC = 0.71
total bases = 5394058
Libraries and Reads
-------------------------------------------------------------------
Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
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-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICT reads.list > grep.reads.list.AICT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICT 4 500
-------------------------------------------------------------------
#Found 12356 total values totalling 39014545.0000. <3157.538443 +/- 1514.622448>
#Range: [ 981 - 122508 ]
#Most likely bin: [ 3000 - 3500 ] 9250 counts
#Median bin: [ 3000 - 3500 ] 9250 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 2 0.00 0.00 ]
| 1000 - 1500 : [ 10 0.00 0.00 ]
| 1500 - 2000 : [ 5 0.00 0.00 ]
| 2000 - 2500 : [ 9 0.00 0.00 ]
|XXXXXXXXXXXX 2500 - 3000 : [ 2859 0.23 0.23 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 9250 0.75 0.98 ]
|X 3500 - 4000 : [ 218 0.02 1.00 ]
#...
| 17000 - 17500 : [ 1 0.00 1.00 ]
#...
| 119000 - 119500 : [ 1 0.00 1.00 ]
#...
| 122500 - 123000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICU reads.list > grep.reads.list.AICU
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICU 4 500
-------------------------------------------------------------------
#Found 12762 total values totalling 88357829.0000. <6923.509560 +/- 826.490872>
#Range: [ 990 - 27088 ]
#Most likely bin: [ 6500 - 7000 ] 3468 counts
#Median bin: [ 6500 - 7000 ] 3468 counts
#Histogram Bins Count Fraction Cum_Fraction
| 500 - 1000 : [ 1 0.00 0.00 ]
| 1000 - 1500 : [ 15 0.00 0.00 ]
| 1500 - 2000 : [ 19 0.00 0.00 ]
| 2000 - 2500 : [ 20 0.00 0.00 ]
| 2500 - 3000 : [ 30 0.00 0.01 ]
| 3000 - 3500 : [ 18 0.00 0.01 ]
| 3500 - 4000 : [ 19 0.00 0.01 ]
| 4000 - 4500 : [ 9 0.00 0.01 ]
| 4500 - 5000 : [ 12 0.00 0.01 ]
| 5000 - 5500 : [ 16 0.00 0.01 ]
|XXXXXXXX 5500 - 6000 : [ 727 0.06 0.07 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 2769 0.22 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 3468 0.27 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 2638 0.21 0.76 ]
|XXXXXXXXXXXXXXXXXXXXXXX 7500 - 8000 : [ 1998 0.16 0.92 ]
|XXXXXXXXXXX 8000 - 8500 : [ 912 0.07 0.99 ]
|X 8500 - 9000 : [ 84 0.01 1.00 ]
| 9000 - 9500 : [ 2 0.00 1.00 ]
| 9500 - 10000 : [ 2 0.00 1.00 ]
| 10000 - 10500 : [ 1 0.00 1.00 ]
#...
| 17000 - 17500 : [ 1 0.00 1.00 ]
#...
| 27000 - 27500 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICW reads.list > grep.reads.list.AICW
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICW 4 500
-------------------------------------------------------------------
#Found 651 total values totalling 24151932.0000. <37099.741935 +/- 3844.190948>
#Range: [ 17381 - 47949 ]
#Most likely bin: [ 34500 - 35000 ] 39 counts
#Median bin: [ 36500 - 37000 ] 38 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 17000 - 17500 : [ 1 0.00 0.00 ]
#...
|X 22000 - 22500 : [ 1 0.00 0.00 ]
|X 22500 - 23000 : [ 1 0.00 0.00 ]
#...
|X 24500 - 25000 : [ 1 0.00 0.01 ]
#...
|XX 27500 - 28000 : [ 2 0.00 0.01 ]
#...
|X 28500 - 29000 : [ 1 0.00 0.01 ]
|X 29000 - 29500 : [ 1 0.00 0.01 ]
|XXX 29500 - 30000 : [ 3 0.00 0.02 ]
|XX 30000 - 30500 : [ 2 0.00 0.02 ]
|XXXXXXX 30500 - 31000 : [ 7 0.01 0.03 ]
|XXXXXXXXXX 31000 - 31500 : [ 10 0.02 0.05 ]
|XXXXXXXXXX 31500 - 32000 : [ 10 0.02 0.06 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 32000 - 32500 : [ 29 0.04 0.11 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 32500 - 33000 : [ 24 0.04 0.14 ]
|XXXXXXXXXXXXX 33000 - 33500 : [ 13 0.02 0.16 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 31 0.05 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34000 - 34500 : [ 28 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 39 0.06 0.31 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 35 0.05 0.37 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 33 0.05 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 30 0.05 0.46 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 38 0.06 0.52 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 23 0.04 0.56 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 25 0.04 0.60 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 27 0.04 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 34 0.05 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 27 0.04 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 31 0.05 0.78 ]
|XXXXXXXXXXXXXXXXX 40000 - 40500 : [ 17 0.03 0.80 ]
|XXXXXXXXXXXXXXXX 40500 - 41000 : [ 16 0.02 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 23 0.04 0.86 ]
|XXXXXXXXXXXXXXXX 41500 - 42000 : [ 16 0.02 0.89 ]
|XXXXXXXXXXXXXX 42000 - 42500 : [ 14 0.02 0.91 ]
|XXXXXXXXXXXXXXX 42500 - 43000 : [ 15 0.02 0.93 ]
|XXXXXXXXX 43000 - 43500 : [ 9 0.01 0.95 ]
|XXXXXXXX 43500 - 44000 : [ 8 0.01 0.96 ]
|XXXXXXXXX 44000 - 44500 : [ 9 0.01 0.97 ]
|XX 44500 - 45000 : [ 2 0.00 0.98 ]
|XXXXX 45000 - 45500 : [ 5 0.01 0.98 ]
|XXXX 45500 - 46000 : [ 4 0.01 0.99 ]
|XXX 46000 - 46500 : [ 3 0.00 1.00 ]
|XX 46500 - 47000 : [ 2 0.00 1.00 ]
#...
|X 47500 - 48000 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AICT 3052 +- 278 (n=5965)
# AICW 36817 +- 3521 (n=247)
# AICU 6864 +- 851 (n=5941)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634503_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
AICT 30720 94 673 97 652 30692 94 662 96 659
AICU 36096 91 661 95 619 36096 91 662 95 649
AICW 4608 71 521 81 435 4608 70 522 81 532
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AICT 15349 93 633 96 637 15343 95 690 97 682
AICU 18048 93 676 97 666 18048 90 649 94 633
AICW 2304 69 509 79 517 2304 72 535 84 546
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634503_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
160 28941 14956 93.47 97.37 AICT @
188 33067 17217 91.58 95.40 AICU @
24 3499 1937 80.71 84.07 AICW @
] 65507 34110 91.69 cumulative total@@
LIBRARY PLATE ID COUNT [ AICT 160 AICU 188 AICW 24 ] for 372 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 3634503_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 71396 total values totalling 42624864.0000. <597.020337 +/- 247.184555>
#Range: [ 0 - 941 ]
#Most likely bin: [ 750 - 800 ] 12997 counts
#Median bin: [ 650 - 700 ] 7425 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXX 0 - 50 : [ 5560 0.08 0.08 ]
|XXX 50 - 100 : [ 956 0.01 0.09 ]
|XX 100 - 150 : [ 790 0.01 0.10 ]
|XXX 150 - 200 : [ 891 0.01 0.11 ]
|XXX 200 - 250 : [ 1077 0.02 0.13 ]
|XXXX 250 - 300 : [ 1354 0.02 0.15 ]
|XXXXX 300 - 350 : [ 1655 0.02 0.17 ]
|XXXXX 350 - 400 : [ 1610 0.02 0.19 ]
|XXXXXX 400 - 450 : [ 1807 0.03 0.22 ]
|XXXXXXX 450 - 500 : [ 2224 0.03 0.25 ]
|XXXXXXXX 500 - 550 : [ 2560 0.04 0.29 ]
|XXXXXXXXXXX 550 - 600 : [ 3535 0.05 0.34 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 5013 0.07 0.41 ]
|XXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 7425 0.10 0.51 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 10867 0.15 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 12997 0.18 0.84 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 9167 0.13 0.97 ]
|XXXXXX 850 - 900 : [ 1850 0.03 1.00 ]
| 900 - 950 : [ 58 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICT 3634503_fasta.screen.trimQ15.SaF > reads.trim15.AICT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICT.rl 2 50
-------------------------------------------------------------------
#Found 30692 total values totalling 19070041.0000. <621.335886 +/- 228.762023>
#Range: [ 0 - 941 ]
#Most likely bin: [ 750 - 800 ] 5845 counts
#Median bin: [ 700 - 750 ] 4525 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXX 0 - 50 : [ 1588 0.05 0.05 ]
|XX 50 - 100 : [ 346 0.01 0.06 ]
|XX 100 - 150 : [ 320 0.01 0.07 ]
|XXX 150 - 200 : [ 373 0.01 0.09 ]
|XXX 200 - 250 : [ 477 0.02 0.10 ]
|XXXX 250 - 300 : [ 535 0.02 0.12 ]
|XXXX 300 - 350 : [ 643 0.02 0.14 ]
|XXXXX 350 - 400 : [ 742 0.02 0.16 ]
|XXXXXX 400 - 450 : [ 807 0.03 0.19 ]
|XXXXXXX 450 - 500 : [ 981 0.03 0.22 ]
|XXXXXXXX 500 - 550 : [ 1172 0.04 0.26 ]
|XXXXXXXXXX 550 - 600 : [ 1534 0.05 0.31 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 2127 0.07 0.38 ]
|XXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3086 0.10 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 4525 0.15 0.63 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 5845 0.19 0.82 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4476 0.15 0.96 ]
|XXXXXXX 850 - 900 : [ 1063 0.03 1.00 ]
| 900 - 950 : [ 52 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICU
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICU 3634503_fasta.screen.trimQ15.SaF > reads.trim15.AICU.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICU.rl 2 50
-------------------------------------------------------------------
#Found 36096 total values totalling 21828705.0000. <604.740276 +/- 243.827555>
#Range: [ 0 - 911 ]
#Most likely bin: [ 750 - 800 ] 6927 counts
#Median bin: [ 700 - 750 ] 5916 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXX 0 - 50 : [ 2841 0.08 0.08 ]
|XX 50 - 100 : [ 376 0.01 0.09 ]
|XX 100 - 150 : [ 372 0.01 0.10 ]
|XX 150 - 200 : [ 404 0.01 0.11 ]
|XXX 200 - 250 : [ 475 0.01 0.12 ]
|XXXX 250 - 300 : [ 617 0.02 0.14 ]
|XXXX 300 - 350 : [ 727 0.02 0.16 ]
|XXXX 350 - 400 : [ 686 0.02 0.18 ]
|XXXXX 400 - 450 : [ 840 0.02 0.20 ]
|XXXXXX 450 - 500 : [ 1045 0.03 0.23 ]
|XXXXXXX 500 - 550 : [ 1212 0.03 0.27 ]
|XXXXXXXXXX 550 - 600 : [ 1760 0.05 0.31 ]
|XXXXXXXXXXXXXXX 600 - 650 : [ 2559 0.07 0.39 ]
|XXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 3937 0.11 0.49 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5916 0.16 0.66 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 6927 0.19 0.85 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4614 0.13 0.98 ]
|XXXXX 850 - 900 : [ 784 0.02 1.00 ]
| 900 - 950 : [ 4 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AICW
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AICW 3634503_fasta.screen.trimQ15.SaF > reads.trim15.AICW.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICW.rl 2 50
-------------------------------------------------------------------
#Found 4608 total values totalling 1726118.0000. <374.591580 +/- 280.238576>
#Range: [ 0 - 909 ]
#Most likely bin: [ 0 - 50 ] 1131 counts
#Median bin: [ 350 - 400 ] 182 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 50 : [ 1131 0.25 0.25 ]
|XXXXXXXX 50 - 100 : [ 234 0.05 0.30 ]
|XXX 100 - 150 : [ 98 0.02 0.32 ]
|XXXX 150 - 200 : [ 114 0.02 0.34 ]
|XXXX 200 - 250 : [ 125 0.03 0.37 ]
|XXXXXXX 250 - 300 : [ 202 0.04 0.41 ]
|XXXXXXXXXX 300 - 350 : [ 285 0.06 0.48 ]
|XXXXXX 350 - 400 : [ 182 0.04 0.51 ]
|XXXXXX 400 - 450 : [ 160 0.03 0.55 ]
|XXXXXXX 450 - 500 : [ 198 0.04 0.59 ]
|XXXXXX 500 - 550 : [ 176 0.04 0.63 ]
|XXXXXXXXX 550 - 600 : [ 241 0.05 0.68 ]
|XXXXXXXXXXXX 600 - 650 : [ 327 0.07 0.75 ]
|XXXXXXXXXXXXXX 650 - 700 : [ 402 0.09 0.84 ]
|XXXXXXXXXXXXXXX 700 - 750 : [ 426 0.09 0.93 ]
|XXXXXXXX 750 - 800 : [ 225 0.05 0.98 ]
|XXX 800 - 850 : [ 77 0.02 1.00 ]
| 850 - 900 : [ 3 0.00 1.00 ]
| 900 - 950 : [ 2 0.00 1.00 ]
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634503
-------------------------------------------------------------------
AICT.000001.000100 pUC18.fa LRS.fasta
AICT.000101.000200 pUC18.fa LRS.fasta
AICU.000001.000100 pMCL200.fa LRS.fasta
AICU.000101.000200 pMCL200.fa LRS.fasta
AICW.000001.000100 pCC1Fos.fa LRS.fasta
AICT.000001.000100 pUC18.fa LRS.fasta
AICT.000101.000200 pUC18.fa LRS.fasta
AICU.000001.000100 pMCL200.fa LRS.fasta
AICU.000101.000200 pMCL200.fa LRS.fasta
AICW.000001.000100 pCC1Fos.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634503_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634503_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 65332 total values totalling 46302.0268. <0.708719 +/- 0.040544>
#Range: [ 0.0286 - 1 ]
#Most likely bin: [ 0.72 - 0.725 ] 3637 counts
#Median bin: [ 0.71 - 0.715 ] 3550 counts
| 0.025 - 0.03 : [ 1 0.00 0.00 ]
#...
| 0.205 - 0.21 : [ 1 0.00 0.00 ]
#...
| 0.275 - 0.28 : [ 1 0.00 0.00 ]
#...
| 0.31 - 0.315 : [ 1 0.00 0.00 ]
#...
| 0.33 - 0.335 : [ 2 0.00 0.00 ]
#...
| 0.35 - 0.355 : [ 1 0.00 0.00 ]
| 0.355 - 0.36 : [ 1 0.00 0.00 ]
#...
| 0.365 - 0.37 : [ 2 0.00 0.00 ]
#...
| 0.38 - 0.385 : [ 2 0.00 0.00 ]
#...
| 0.39 - 0.395 : [ 2 0.00 0.00 ]
| 0.395 - 0.4 : [ 1 0.00 0.00 ]
| 0.4 - 0.405 : [ 3 0.00 0.00 ]
#...
| 0.41 - 0.415 : [ 3 0.00 0.00 ]
| 0.415 - 0.42 : [ 2 0.00 0.00 ]
| 0.42 - 0.425 : [ 1 0.00 0.00 ]
#...
| 0.43 - 0.435 : [ 3 0.00 0.00 ]
| 0.435 - 0.44 : [ 4 0.00 0.00 ]
| 0.44 - 0.445 : [ 4 0.00 0.00 ]
| 0.445 - 0.45 : [ 1 0.00 0.00 ]
| 0.45 - 0.455 : [ 3 0.00 0.00 ]
| 0.455 - 0.46 : [ 3 0.00 0.00 ]
#...
| 0.465 - 0.47 : [ 3 0.00 0.00 ]
| 0.47 - 0.475 : [ 3 0.00 0.00 ]
#...
| 0.48 - 0.485 : [ 2 0.00 0.00 ]
| 0.485 - 0.49 : [ 4 0.00 0.00 ]
| 0.49 - 0.495 : [ 6 0.00 0.00 ]
#...
| 0.5 - 0.505 : [ 5 0.00 0.00 ]
| 0.505 - 0.51 : [ 3 0.00 0.00 ]
| 0.51 - 0.515 : [ 1 0.00 0.00 ]
| 0.515 - 0.52 : [ 4 0.00 0.00 ]
| 0.52 - 0.525 : [ 5 0.00 0.00 ]
| 0.525 - 0.53 : [ 9 0.00 0.00 ]
| 0.53 - 0.535 : [ 8 0.00 0.00 ]
| 0.535 - 0.54 : [ 17 0.00 0.00 ]
| 0.54 - 0.545 : [ 16 0.00 0.00 ]
| 0.545 - 0.55 : [ 25 0.00 0.00 ]
| 0.55 - 0.555 : [ 34 0.00 0.00 ]
| 0.555 - 0.56 : [ 26 0.00 0.00 ]
| 0.56 - 0.565 : [ 23 0.00 0.00 ]
| 0.565 - 0.57 : [ 25 0.00 0.00 ]
| 0.57 - 0.575 : [ 26 0.00 0.00 ]
| 0.575 - 0.58 : [ 40 0.00 0.01 ]
| 0.58 - 0.585 : [ 39 0.00 0.01 ]
| 0.585 - 0.59 : [ 31 0.00 0.01 ]
|X 0.59 - 0.595 : [ 65 0.00 0.01 ]
|X 0.595 - 0.6 : [ 91 0.00 0.01 ]
|X 0.6 - 0.605 : [ 103 0.00 0.01 ]
|XX 0.605 - 0.61 : [ 159 0.00 0.01 ]
|XX 0.61 - 0.615 : [ 205 0.00 0.02 ]
|XXX 0.615 - 0.62 : [ 274 0.00 0.02 ]
|XXXX 0.62 - 0.625 : [ 390 0.01 0.03 ]
|XXXXXX 0.625 - 0.63 : [ 525 0.01 0.03 ]
|XXXXXX 0.63 - 0.635 : [ 585 0.01 0.04 ]
|XXXXXXX 0.635 - 0.64 : [ 671 0.01 0.05 ]
|XXXXXXXX 0.64 - 0.645 : [ 756 0.01 0.06 ]
|XXXXXXXXX 0.645 - 0.65 : [ 804 0.01 0.08 ]
|XXXXXXXXXXX 0.65 - 0.655 : [ 957 0.01 0.09 ]
|XXXXXXXXXXXX 0.655 - 0.66 : [ 1125 0.02 0.11 ]
|XXXXXXXXXXXXXX 0.66 - 0.665 : [ 1275 0.02 0.13 ]
|XXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 1645 0.03 0.15 ]
|XXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 1811 0.03 0.18 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 2010 0.03 0.21 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 2381 0.04 0.25 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 2525 0.04 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 2742 0.04 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 3160 0.05 0.38 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 3152 0.05 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 3352 0.05 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 3550 0.05 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 3574 0.05 0.59 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 3637 0.06 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.725 - 0.73 : [ 3506 0.05 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.73 - 0.735 : [ 3393 0.05 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.735 - 0.74 : [ 3027 0.05 0.79 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.74 - 0.745 : [ 2682 0.04 0.83 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.745 - 0.75 : [ 2235 0.03 0.87 ]
|XXXXXXXXXXXXXXXXXXXXXX 0.75 - 0.755 : [ 2030 0.03 0.90 ]
|XXXXXXXXXXXXXXXXX 0.755 - 0.76 : [ 1528 0.02 0.92 ]
|XXXXXXXXXXXXX 0.76 - 0.765 : [ 1221 0.02 0.94 ]
|XXXXXXXXXXX 0.765 - 0.77 : [ 998 0.02 0.96 ]
|XXXXXXXX 0.77 - 0.775 : [ 724 0.01 0.97 ]
|XXXXXX 0.775 - 0.78 : [ 583 0.01 0.98 ]
|XXXX 0.78 - 0.785 : [ 404 0.01 0.98 ]
|XXX 0.785 - 0.79 : [ 306 0.00 0.99 ]
|XX 0.79 - 0.795 : [ 195 0.00 0.99 ]
|X 0.795 - 0.8 : [ 122 0.00 0.99 ]
|X 0.8 - 0.805 : [ 90 0.00 0.99 ]
|X 0.805 - 0.81 : [ 72 0.00 1.00 ]
|X 0.81 - 0.815 : [ 55 0.00 1.00 ]
| 0.815 - 0.82 : [ 36 0.00 1.00 ]
| 0.82 - 0.825 : [ 34 0.00 1.00 ]
| 0.825 - 0.83 : [ 25 0.00 1.00 ]
| 0.83 - 0.835 : [ 18 0.00 1.00 ]
| 0.835 - 0.84 : [ 19 0.00 1.00 ]
| 0.84 - 0.845 : [ 19 0.00 1.00 ]
| 0.845 - 0.85 : [ 14 0.00 1.00 ]
| 0.85 - 0.855 : [ 14 0.00 1.00 ]
| 0.855 - 0.86 : [ 8 0.00 1.00 ]
| 0.86 - 0.865 : [ 7 0.00 1.00 ]
| 0.865 - 0.87 : [ 11 0.00 1.00 ]
| 0.87 - 0.875 : [ 2 0.00 1.00 ]
| 0.875 - 0.88 : [ 3 0.00 1.00 ]
| 0.88 - 0.885 : [ 7 0.00 1.00 ]
| 0.885 - 0.89 : [ 4 0.00 1.00 ]
| 0.89 - 0.895 : [ 2 0.00 1.00 ]
| 0.895 - 0.9 : [ 1 0.00 1.00 ]
| 0.9 - 0.905 : [ 2 0.00 1.00 ]
| 0.905 - 0.91 : [ 3 0.00 1.00 ]
| 0.91 - 0.915 : [ 1 0.00 1.00 ]
| 0.915 - 0.92 : [ 2 0.00 1.00 ]
| 0.92 - 0.925 : [ 4 0.00 1.00 ]
| 0.925 - 0.93 : [ 2 0.00 1.00 ]
#...
| 0.96 - 0.965 : [ 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 206. 652 reads; 57526 bp (untrimmed), 56152 (trimmed).
Contig 207. 654 reads; 48283 bp (untrimmed), 47862 (trimmed).
Contig 208. 667 reads; 49723 bp (untrimmed), 48726 (trimmed).
Contig 209. 678 reads; 52515 bp (untrimmed), 52064 (trimmed).
Contig 210. 688 reads; 53244 bp (untrimmed), 53220 (trimmed).
Contig 211. 709 reads; 70906 bp (untrimmed), 70277 (trimmed).
Contig 212. 731 reads; 62051 bp (untrimmed), 62000 (trimmed).
Contig 213. 734 reads; 52447 bp (untrimmed), 51843 (trimmed).
Contig 214. 768 reads; 72217 bp (untrimmed), 71869 (trimmed).
Contig 215. 796 reads; 78300 bp (untrimmed), 77257 (trimmed).
Contig 216. 819 reads; 79884 bp (untrimmed), 79632 (trimmed).
Contig 217. 866 reads; 60297 bp (untrimmed), 59523 (trimmed).
Contig 218. 877 reads; 81431 bp (untrimmed), 81061 (trimmed).
Contig 219. 885 reads; 62441 bp (untrimmed), 62131 (trimmed).
Contig 220. 888 reads; 68474 bp (untrimmed), 68184 (trimmed).
Contig 221. 888 reads; 82229 bp (untrimmed), 81730 (trimmed).
Contig 222. 894 reads; 75391 bp (untrimmed), 75213 (trimmed).
Contig 223. 908 reads; 68174 bp (untrimmed), 67828 (trimmed).
Contig 224. 919 reads; 66674 bp (untrimmed), 66447 (trimmed).
Contig 225. 1101 reads; 87861 bp (untrimmed), 87614 (trimmed).
Contig 226. 1140 reads; 104422 bp (untrimmed), 104278 (trimmed).
Contig 227. 1262 reads; 102481 bp (untrimmed), 102095 (trimmed).
Contig 228. 1642 reads; 139711 bp (untrimmed), 139578 (trimmed).
Contig 229. 1663 reads; 122090 bp (untrimmed), 121383 (trimmed).
Contig 230. 2112 reads; 165533 bp (untrimmed), 165274 (trimmed).
Contig 231. 2575 reads; 207576 bp (untrimmed), 206470 (trimmed).
Contig 232. 7151 reads; 307941 bp (untrimmed), 307870 (trimmed).
--------------------------------------------------------------
Totals 65009 reads; 5394058 bp (untrimmed), 5272143 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 5382468 bases = 9.65 +- 4.85 = 0.22 +- 3.26
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 220 total values totalling 1672.0300. <7.600136 +/- 2.701256>
#Range: [ 1.09 - 20.34 ]
#Most likely bin: [ 8 - 8.5 ] 27 counts
#Median bin: [ 7.5 - 8 ] 24 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 1 - 1.5 : [ 6 0.03 0.03 ]
|XXXX 1.5 - 2 : [ 3 0.01 0.04 ]
|XXXXXXX 2 - 2.5 : [ 5 0.02 0.06 ]
|XXX 2.5 - 3 : [ 2 0.01 0.07 ]
|X 3 - 3.5 : [ 1 0.00 0.08 ]
|XXXXXX 3.5 - 4 : [ 4 0.02 0.10 ]
|XXXXXXXXX 4 - 4.5 : [ 6 0.03 0.12 ]
|XXXXXXXXXX 4.5 - 5 : [ 7 0.03 0.15 ]
|XXXX 5 - 5.5 : [ 3 0.01 0.17 ]
|XXXXXXXXXXXXXXX 5.5 - 6 : [ 10 0.05 0.21 ]
|XXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 12 0.05 0.27 ]
|XXXXXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 14 0.06 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 20 0.09 0.42 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 24 0.11 0.53 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 27 0.12 0.65 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 22 0.10 0.75 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 17 0.08 0.83 ]
|XXXXXXXXXXXXXXX 9.5 - 10 : [ 10 0.05 0.88 ]
|XXXXXXXXXXXX 10 - 10.5 : [ 8 0.04 0.91 ]
|XXXXXXXXX 10.5 - 11 : [ 6 0.03 0.94 ]
|XXXX 11 - 11.5 : [ 3 0.01 0.95 ]
|XXXX 11.5 - 12 : [ 3 0.01 0.97 ]
|X 12 - 12.5 : [ 1 0.00 0.97 ]
#...
|X 13 - 13.5 : [ 1 0.00 0.98 ]
|XXX 13.5 - 14 : [ 2 0.01 0.99 ]
#...
|XXX 16 - 16.5 : [ 2 0.01 1.00 ]
#...
|X 20 - 20.5 : [ 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 195 total values totalling 1581.5200. <8.110359 +/- 2.201569>
#Range: [ 2.66 - 20.34 ]
#Most likely bin: [ 8 - 8.5 ] 27 counts
#Median bin: [ 8 - 8.5 ] 27 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 2.5 - 3 : [ 1 0.01 0.01 ]
#...
|XXX 3.5 - 4 : [ 2 0.01 0.02 ]
|XXXXXXXXX 4 - 4.5 : [ 6 0.03 0.05 ]
|XXXXXXXXX 4.5 - 5 : [ 6 0.03 0.08 ]
|XXXX 5 - 5.5 : [ 3 0.02 0.09 ]
|XXXXXXXXXXXXXXX 5.5 - 6 : [ 10 0.05 0.14 ]
|XXXXXXXXXXXXXXX 6 - 6.5 : [ 10 0.05 0.19 ]
|XXXXXXXXXXXXXXXXXX 6.5 - 7 : [ 12 0.06 0.26 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7 - 7.5 : [ 20 0.10 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 7.5 - 8 : [ 24 0.12 0.48 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 - 8.5 : [ 27 0.14 0.62 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8.5 - 9 : [ 21 0.11 0.73 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 9 - 9.5 : [ 17 0.09 0.82 ]
|XXXXXXXXXXXXXXX 9.5 - 10 : [ 10 0.05 0.87 ]
|XXXXXXXXXXXX 10 - 10.5 : [ 8 0.04 0.91 ]
|XXXXXXXXX 10.5 - 11 : [ 6 0.03 0.94 ]
|XXXX 11 - 11.5 : [ 3 0.02 0.95 ]
|XXXX 11.5 - 12 : [ 3 0.02 0.97 ]
|X 12 - 12.5 : [ 1 0.01 0.97 ]
#...
|X 13 - 13.5 : [ 1 0.01 0.98 ]
|X 13.5 - 14 : [ 1 0.01 0.98 ]
#...
|XXX 16 - 16.5 : [ 2 0.01 0.99 ]
#...
|X 20 - 20.5 : [ 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 13 2 reads 1234 bases = 1.09 +- 0.29 = 1.09 +- 0.29
Contig 14 2 reads 969 bases = 1.27 +- 0.44 = 0.73 +- 0.44
Contig 16 3 reads 1278 bases = 1.31 +- 0.46 = 1.31 +- 0.46
Contig 19 3 reads 1011 bases = 1.33 +- 0.70 = 1.33 +- 0.70
Contig 17 3 reads 1005 bases = 1.38 +- 0.54 = -0.62 +- 0.54
Contig 23 5 reads 1896 bases = 1.40 +- 0.72 = 0.17 +- 1.11
Contig 15 3 reads 739 bases = 1.77 +- 0.88 = 1.77 +- 0.88
Contig 24 5 reads 2261 bases = 1.82 +- 1.02 = 1.82 +- 1.02
Contig 22 5 reads 1661 bases = 1.94 +- 1.06 = 1.22 +- 0.60
Contig 20 4 reads 1574 bases = 2.05 +- 1.14 = 1.20 +- 0.52
Contig 26 6 reads 1909 bases = 2.15 +- 1.61 = 0.40 +- 1.33
Contig 30 9 reads 2660 bases = 2.15 +- 1.09 = 0.84 +- 1.52
Contig 21 4 reads 1394 bases = 2.23 +- 1.22 = 1.16 +- 0.46
Contig 25 5 reads 1047 bases = 2.31 +- 1.55 = 0.60 +- 1.57
Contig 36 12 reads 3340 bases = 2.66 +- 1.77 = 0.69 +- 1.22
Contig 18 3 reads 635 bases = 2.76 +- 0.47 = 0.76 +- 0.47
Contig 31 9 reads 1818 bases = 3.11 +- 2.63 = 1.24 +- 1.82
Contig 41 17 reads 2559 bases = 3.51 +- 2.01 = 0.52 +- 1.25
Contig 29 9 reads 1529 bases = 3.82 +- 2.80 = 0.84 +- 0.96
Contig 28 7 reads 1240 bases = 3.84 +- 2.38 = 1.45 +- 1.00
Contig 229 1663 reads 122090 bases = 10.46 +- 3.68 = 0.14 +- 3.59
Contig 225 1101 reads 87861 bases = 10.50 +- 3.22 = -0.09 +- 3.52
Contig 230 2112 reads 165533 bases = 10.53 +- 4.38 = -0.07 +- 3.37
Contig 210 688 reads 53244 bases = 10.70 +- 4.34 = 0.37 +- 3.25
Contig 219 885 reads 62441 bases = 10.73 +- 4.18 = 0.33 +- 3.75
Contig 183 374 reads 26830 bases = 10.75 +- 3.70 = 0.06 +- 3.23
Contig 227 1262 reads 102481 bases = 10.82 +- 3.53 = 0.14 +- 3.14
Contig 105 112 reads 7671 bases = 11.04 +- 4.27 = 1.37 +- 2.96
Contig 224 919 reads 66674 bases = 11.25 +- 4.03 = 0.04 +- 3.37
Contig 135 173 reads 12503 bases = 11.28 +- 4.88 = -0.06 +- 3.67
Contig 201 587 reads 43212 bases = 11.57 +- 3.57 = 0.20 +- 3.96
Contig 213 734 reads 52447 bases = 11.88 +- 4.29 = 0.13 +- 3.62
Contig 207 654 reads 48283 bases = 11.91 +- 5.15 = -0.04 +- 3.80
Contig 217 866 reads 60297 bases = 12.19 +- 3.75 = 0.08 +- 3.72
Contig 147 207 reads 13879 bases = 13.22 +- 2.98 = 0.34 +- 3.64
Contig 205 646 reads 41847 bases = 13.60 +- 4.12 = 0.08 +- 3.95
Contig 50 23 reads 1405 bases = 13.66 +- 9.22 = 13.66 +- 9.22
Contig 155 226 reads 12486 bases = 16.34 +- 4.08 = 0.37 +- 3.57
Contig 100 103 reads 4996 bases = 16.49 +- 11.10 = -0.05 +- 6.11
Contig 232 7151 reads 307941 bases = 20.34 +- 5.59 = 0.11 +- 4.73
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 576
HQ Discrepant reads = 59
Chimeric reads = 34
Suspect alignments = 693
-------------------------------------------------------------------
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: -8)
A C G T N X
A 1 -8 -8 -8 0 -9
C -8 1 -8 -8 0 -9
G -8 -8 1 -8 0 -9
T -8 -8 -8 1 0 -9
N 0 0 0 0 0 0
X -9 -9 -9 -9 0 -9
gap_init: -10
gap_ext: -9
ins_gap_ext: -9
del_gap_ext: -9
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: 55
maxmatch: 80
max_group_size: 20
minscore: 75
bandwidth: 14
indexwordsize: 10
vector_bound: 50
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 20
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -8
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
max_subclone_size: 50000
File generated in /psf/project/microbe2/3634503/edit_dir.20Oct04.QD