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

Database: dm6 Primary Table: chainDalbRefSeq1 Row Count: 20,853 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	26961	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8679	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	NC_047627	`varchar(255)`	values
`qSize`	33427555	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	32527761	`int(10) unsigned`	range
`qEnd`	32528357	`int(10) unsigned`	range
`id`	46708	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	26961	chr2L	23513712	8679	9275	NC_047627	33427555	+	32527761	32528357	46708
585	8658	chr2L	23513712	9105	9275	NC_047631	32236572	-	28965216	28965386	165912
73	767182	chr2L	23513712	11255	152903	NC_047628	30772581	-	53970	192042	373
585	91501	chr2L	23513712	22122	24968	NC_047627	33427555	-	14630907	14634604	8844
585	701673	chr2L	23513712	26520	102006	NC_047628	30772581	+	30634974	30708320	429
585	7915	chr2L	23513712	77159	77546	NC_047628	30772581	+	30679772	30680159	200179
585	42273	chr2L	23513712	102610	103763	NC_047628	30772581	+	11018185	11019315	27317
585	8384	chr2L	23513712	118561	118874	NC_047628	30772581	-	161963	162273	178162
585	12475	chr2L	23513712	118605	119543	NC_047628	30772581	+	30424293	30425072	99066
585	9684	chr2L	23513712	118712	126216	NC_047629	55557198	-	35039557	35041003	131437

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