Schema for RefSeq Drosophila Chain/Net - RefSeq Drosophila Genomes, Chain and Net Alignments
  Database: dm6    Primary Table: netDalbRefSeq1    Row Count: 143,056   Data last updated: 2022-08-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
level 1int(10) unsigned range
tName chr2Lvarchar(255) values
tStart 8679int(10) unsigned range
tEnd 9275int(10) unsigned range
strand +char(1) values
qName NC_047627varchar(255) values
qStart 32527761int(10) unsigned range
qEnd 32528357int(10) unsigned range
chainId 46708int(10) unsigned range
ali 596int(10) unsigned range
score 26961double range
qOver -1int(11) range
qFar -1int(11) range
qDup 596int(11) range
type topvarchar(255) values
tN 0int(11) range
qN 0int(11) range
tR 0int(11) range
qR 0int(11) range
tNewR -1int(11) range
qNewR -1int(11) range
tOldR -1int(11) range
qOldR -1int(11) range
tTrf 0int(11) range
qTrf 0int(11) range

Sample Rows
 
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
5851chr2L86799275+NC_04762732527761325283574670859626961-1-1596top0000-1-1-1-100
731chr2L11255152903-NC_047628305805393071861137318072767182-1-10top0087272917-1-1-1-1532381
5852chr2L1137111402-NC_0476283071847430718495000-1-1-1gap0000-1-1-1-100
5852chr2L1152011770-NC_0476283071799530718356000-1-1-1gap0000-1-1-1-1031
5852chr2L1195412074-NC_0476283071767930717811000-1-1-1gap0000-1-1-1-100
5852chr2L1222712280-NC_0476283071746830717526000-1-1-1gap0000-1-1-1-100
5852chr2L1293513515-NC_0476283071675330716813000-1-1-1gap00570-1-1-1-100
5852chr2L1488014928-NC_0476283071535730715401000-1-1-1gap0000-1-1-1-100
5852chr2L1572217050-NC_0476283071327430714563000-1-1-1gap00930-1-1-1-100
5852chr2L17141104473-NC_0476283063055030713183000-1-1-1gap0077822275-1-1-1-1466292

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.