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

Database: dm6 Primary Table: netDnavGB1 Row Count: 111,433 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	9	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	11215	`int(10) unsigned`	range
`tEnd`	2044373	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	LSRL01000002	`varchar(255)`	values
`qStart`	2110	`int(10) unsigned`	range
`qEnd`	4034732	`int(10) unsigned`	range
`chainId`	69	`int(10) unsigned`	range
`ali`	61852	`int(10) unsigned`	range
`score`	1519900	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	44217	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	163618	`int(11)`	range
`tR`	88646	`int(11)`	range
`qR`	118710	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	22110	`int(11)`	range
`qTrf`	141149	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
9	1	chr2L	11215	2044373	+	LSRL01000002	2110	4034732	69	61852	1519900	-1	-1	44217	top	163618	88646	118710	-1	-1	-1	-1	22110	141149
585	2	chr2L	11521	11770	+	LSRL01000002	2418	2746	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11941	12077	+	LSRL01000002	2917	3071	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12947	13516	+	LSRL01000002	3940	3971	0	0	0	-1	-1	-1	gap	0	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	14877	14930	+	LSRL01000002	5323	5401	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15725	17049	+	LSRL01000002	6196	7754	0	0	0	-1	-1	-1	gap	0	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17139	93472	+	LSRL01000002	7844	20789	0	0	0	-1	-1	-1	gap	0	7782	0	-1	-1	-1	-1	152	0
585	3	chr2L	22123	24965	+	LSRL01000006	495788	500640	742	2178	91838	-1	-1	0	nonSyn	100	249	1642	-1	-1	-1	-1	0	0
585	4	chr2L	22693	22731	+	LSRL01000006	496361	497720	0	0	0	-1	-1	-1	gap	100	0	695	-1	-1	-1	-1	0	0
585	4	chr2L	23876	23920	+	LSRL01000006	498872	500048	0	0	0	-1	-1	-1	gap	0	0	947	-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