Schema for RefSeq Drosophila Chain/Net - RefSeq Drosophila Genomes, Chain and Net Alignments

Database: dm6 Primary Table: netDkikRefSeq2 Row Count: 267,502 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	7570	`int(10) unsigned`	range
`tEnd`	9281	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NW_024571405	`varchar(255)`	values
`qStart`	22392778	`int(10) unsigned`	range
`qEnd`	22394903	`int(10) unsigned`	range
`chainId`	99884	`int(10) unsigned`	range
`ali`	875	`int(10) unsigned`	range
`score`	38071	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	885	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	0	`int(11)`	range
`qR`	0	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	0	`int(11)`	range
`qTrf`	0	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7570	9281	-	NW_024571405	22392778	22394903	99884	875	38071	-1	-1	885	top	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	7779	7862	-	NW_024571405	22394545	22394685	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	7926	8679	-	NW_024571405	22393380	22394481	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
1	1	chr2L	11205	23461797	-	NW_024571435	638243	28706607	3	2059083	102989904	-1	-1	900901	top	200	2219747	2535877	-1	-1	-1	-1	327898	623398
585	2	chr2L	11536	11772	-	NW_024571435	28705980	28706268	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12934	13500	-	NW_024571435	28704680	28704815	0	0	0	-1	-1	-1	gap	0	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	13628	13675	-	NW_024571435	28704485	28704552	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15734	16318	-	NW_024571435	28701959	28702407	0	0	0	-1	-1	-1	gap	0	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	16430	17046	-	NW_024571435	28701201	28701847	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	17136	22113	-	NW_024571435	28069821	28701111	0	0	0	-1	-1	-1	gap	0	0	77279	-1	-1	-1	-1	0	90239

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

RefSeq Drosophila Chain/Net (refseqDrosChainNet) Track Description


	Description Genomic scaffolds from each Drosophila species are aligned against the D. melanogaster genome assembly (dm6) using LAST with default parameters. The alignments are then processed using the UCSC whole genome alignment protocol (i.e. chaining and netting). References Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93. doi: 10.1101/gr.113985.110. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. doi: 10.1073/pnas.1932072100.

Description