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

Database: dm6 Primary Table: netDwilCAF1 Row Count: 159,597 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`	8679	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	scf2_1100000004909	`varchar(255)`	values
`qStart`	10595781	`int(10) unsigned`	range
`qEnd`	10596377	`int(10) unsigned`	range
`chainId`	4882	`int(10) unsigned`	range
`ali`	596	`int(10) unsigned`	range
`score`	25291	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	596	`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	qTrf
585	1	chr2L	8679	9275	+	scf2_1100000004909	10595781	10596377	4882	596	25291	-1	-1	596	top	0	0	-1	-1	-1	-1	0
585	1	chr2L	11214	17139	-	scf2_1100000004585	1800214	1808192	901	3471	151398	-1	-1	0	top	150	444	-1	-1	-1	-1	44
585	2	chr2L	11526	11764	-	scf2_1100000004585	1807525	1807871	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0
585	2	chr2L	11905	12086	-	scf2_1100000004585	1807194	1807384	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0
585	2	chr2L	12934	13512	-	scf2_1100000004585	1806295	1806347	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0
585	2	chr2L	13628	13676	-	scf2_1100000004585	1806125	1806176	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0
585	2	chr2L	14875	14935	-	scf2_1100000004585	1804930	1804932	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0
585	2	chr2L	15725	17049	-	scf2_1100000004585	1800304	1804140	0	0	0	-1	-1	-1	gap	93	444	-1	-1	-1	-1	44
585	1	chr2L	22118	24974	-	scf2_1100000004590	4047669	4050075	1236	2327	101449	-1	-1	0	top	249	0	-1	-1	-1	-1	0
585	2	chr2L	24216	24744	-	scf2_1100000004590	4047899	4047955	0	0	0	-1	-1	-1	gap	249	0	-1	-1	-1	-1	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