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

Database: dm6 Primary Table: netDbiaGB2 Row Count: 211,213

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	7557	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	KB462640	`varchar(255)`	values
`qStart`	5376	`int(10) unsigned`	range
`qEnd`	7431	`int(10) unsigned`	range
`chainId`	1354	`int(10) unsigned`	range
`ali`	1499	`int(10) unsigned`	range
`score`	63418	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	1438	`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	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7557	9275	+	KB462640	5376	7431	1354	1499	63418	-1	-1	1438	top	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8072	8215	+	KB462640	5906	6337	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8347	8403	+	KB462640	6469	6570	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11214	102039	+	KB462393	16253	110590	144	53147	2925235	-1	-1	204	top	7932	3256	-1	-1	-1	-1	466	85
585	2	chr2L	11375	11385	+	KB462393	16416	16416	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11757	11767	+	KB462393	16807	16807	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12941	13517	+	KB462393	17970	18661	0	0	0	-1	-1	-1	gap	57	251	-1	-1	-1	-1	0	0
585	2	chr2L	15721	17049	+	KB462393	20861	23526	0	0	0	-1	-1	-1	gap	93	1343	-1	-1	-1	-1	0	0
585	2	chr2L	17229	20804	+	KB462393	23707	24358	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	3	chr2L	17999	18196	+	KB462393	24358	24562	17707	196	8530	0	0	204	syn	0	0	-1	-1	-1	-1	0	0

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

Drosophila Chain/Net (drosophilaChainNet) 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 Chain/Net Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 2003 100(20): 11484-11489. LAST Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93.

Description