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

Database: dm6 Primary Table: netDanaCAF1 Row Count: 244,890 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`	8706	`int(10) unsigned`	range
`tEnd`	9281	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	scaffold_12903	`varchar(255)`	values
`qStart`	632684	`int(10) unsigned`	range
`qEnd`	633259	`int(10) unsigned`	range
`chainId`	3511	`int(10) unsigned`	range
`ali`	575	`int(10) unsigned`	range
`score`	28227	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	575	`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	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	8706	9281	+	scaffold_12903	632684	633259	3511	575	28227	-1	-1	575	top	0	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11263	94386	+	scaffold_12916	1772617	2083924	223	25959	1119348	-1	-1	493	top	1525	7932	10569	-1	-1	-1	-1	186	10559
585	2	chr2L	11349	11407	+	scaffold_12916	1772703	1772776	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11523	11772	+	scaffold_12916	1772892	1773853	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11905	12076	+	scaffold_12916	1773986	1774154	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12935	13517	+	scaffold_12916	1775006	1775053	0	0	0	-1	-1	-1	gap	0	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15723	17050	+	scaffold_12916	1777259	1778728	0	0	0	-1	-1	-1	gap	0	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17136	21958	+	scaffold_12916	1778814	2006446	0	0	0	-1	-1	-1	gap	1500	0	9186	-1	-1	-1	-1	0	9106
585	2	chr2L	22037	22114	+	scaffold_12916	2006525	2006596	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	22939	22988	+	scaffold_12916	2007428	2007494	0	0	0	-1	-1	-1	gap	0	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