platemap_fields
	platewell	(1a01)
	dilution_id	(z7987a01a02)
	accessionname	(z001e0001)
	source_id	(eb04p1367a51a)
	conc_ng/u	(10)
	volume	(73.6666)
	column	(1)
	plate_boxid	(NAM Plate 1 Cleaned 10ng/ul)
	wellnum	(a01)
	date	(11-Aug-10)
	preparer	(Wenyan Zhu)

run description fields
	flowcell	(42A87AAXX)
	plex	(4)
	run description	(first test of 4-plex)
	order	(1)
	machine	(HWI-EAS339)
	NAM families	(z1,z2)
	nRILs	(92,93)
	notes	(85bp)
	lane 1 cv	(35.89%)
	.
	.
	lane 8
	timept	(1)

flowcell_key fields
	flowcell (628p9aaxx)
	lane	(1)
	barcode	(CTCC)
	sample	(z011e0100)
	plate	(22)
	row	(E)
	column	(1)
	platename	(NAM22B)
	well	(E01)
	platewell	(22E01)

QC1 Fields
	Lane	(1)
	Pass_Count	(34750651)
	read_count	(44764030)
	pass_rate	(.77)
	pass_filter_count	(31043339)
	pass_filter_rate	(.69)
	adapter_dimers	(174414)
	rev_adapter_first_24_bases	(869)
	n_samples	(40)
	mean_count	(868766)
	sd_count	(311815)
	cv_count	(35.89%)

qc_stats Fields
	Flowcell	628P9AAXX
	Run Descrip:	"NAM22b,28,29,30"
	Machine	HWI-EAS339
	Run	16
	n_Lanes_used	7
	Tot_n_DNAs	308
	Tot_n_reads	"307,362,588"
	n_reads_pass_filter	"222,187,717"
	Adapter_dimers	1281813
	n_reads_with_barcode_etc	"250,561,109"
	%reads_with_barcode_etc	81.52%
	CV_over_DNAs	33.20%
	n_reads_sampled_for_BLAST	7000
	%reads_with_1+_hits	93.53
	%avg_hit_len (including zeros)	56.22
	Avg_hit_len_hits	60.11
	Median_hit_len	64
	Estimated # good reads	"234,346,226"
	Estimated # good reads/lane	"33,478,032"
	Estimated # good reads/DNA	"760,864"

WIKILIMS Fields
1 	NAM22B/Elshire, Robert 
2 	NAM28A/Elshire, Robert 
3 	NAM28B/Elshire, Robert 
4 	NAM29A/Elshire, Robert 
5 	NAM29B/Elshire, Robert 
6 	NAM30A/Elshire, Robert 
7 	NAM30B/Elshire, Robert 
8 	PhiX/Tom Stelick 
Paired End 	no 
Indexing 	no 
Run Length 	86 
Cluster Station 	CBot600560 
Loaded on 	HWI-EAS339 
Disk 	Disk5 
Status 	distributed 
Created: 	
Runs: 	100910 HWI-EAS339 0016 628P9AAXX


allele assay annotations	(need table for GBS annotation types)
	int primary key
	text global key
	int annotation type foreign key
	int allele assay foreign key
	text annotation value

allele assay conditions
	int primary key	required
	text global key
	int marker foreign key
	int assay foreign key
	int polymorphism type foreign key	required
	int scoring technology type foreign key
	text comments
	date assay date	required
	varchar assay name (marker name, scoring technology, "assay")	required
	varchar assay producer's lab's name
	int marker length
	varchar marker position
	text marker reference sequence	required
	int marker stock ID
	blob binary position	
	blob binary annotation
	blob binary id
	
generations
	int primary key	required
	text global key
	text comments
	text icis id
	int selfing number	required
	int sibbing number	required
		
locations
	int primary key 	required
	text global key (authority: table name:object id)
	int collection site elevation
	varchar city
	varchar country (3-letter code)
	varchar country of origin
	double collection latitude
	double collection longitude
	varchar locality name
	varchar province
	varchar Gazetteer Ontology Term ID

passport
	int primary key	required
	text global key (authority:table name:object id)
	int taxonomy foreign key
	int accession collecting id foreign key
	int cdv source foreign key
	varchar accession name	required
	text comments
	varchar germplasm type
	varchar source 	required (contact information goes into cdv_source)
	varchar accession number
	varchar sampstat code
	
allele assay technology
	int primary key	required
	text global key
	varchar technology group (e.g. SNP or RFLP)	required
	varchar technology type (e.g. GBS)	required
		
stock number
	int primary key	required
	text global key 
	int generation id foreign key
	int passport foreign id	required
	varchar seedlot number	required
	varchar stock source	required
	text comments

stock number parents
	int primary key	required
	text global key 
	int stock id 	required
	int parent stock id	required
	int number of times backcrossed	required
	varchar role (self, male, female)

passport synonyms
	int primary key 	required
	text global key 
	int passport foreign key	required
	varchar synonym	required
	text comments

taxonomy
	int primary key	required
	text global key 	
	varchar genus
	varchar species	required
	varchar subspecies
	varchar subtaxa
	varchar race
	varchar population
	varchar common name
	varchar Gramene Taxonomy Ontology term ID