Schema for RefSeq Drosophila Chain/Net - RefSeq Drosophila Genomes, Chain and Net Alignments
  Database: dm6    Primary Table: netDsimRefSeq3    Row Count: 169,728   Data last updated: 2022-08-20
fieldexampleSQL type info
bin 1smallint(5) unsigned range
level 1int(10) unsigned range
tName chr2Lvarchar(255) values
tStart 4992int(10) unsigned range
tEnd 23512345int(10) unsigned range
strand +char(1) values
qName NC_052520varchar(255) values
qStart 60468int(10) unsigned range
qEnd 23749786int(10) unsigned range
chainId 2int(10) unsigned range
ali 20432154int(10) unsigned range
score 1696072952double range
qOver -1int(11) range
qFar -1int(11) range
qDup 2940870int(11) range
type topvarchar(255) values
tN 200int(11) range
qN 0int(11) range
tR 2270178int(11) range
qR 2477267int(11) range
tNewR -1int(11) range
qNewR -1int(11) range
tOldR -1int(11) range
qOldR -1int(11) range
tTrf 328752int(11) range
qTrf 283548int(11) range

Sample Rows
 
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
11chr2L499223512345+NC_05252060468237497862204321541696072952-1-12940870top200022701782477267-1-1-1-1328752283548
5852chr2L52045216+NC_0525206067561725000-1-1-1gap000891-1-1-1-1121050
5852chr2L53935489+NC_0525206189762883000-1-1-1gap000887-1-1-1-10986
5853chr2L53935478-NC_0525232813222128132306188364855133-1-185nonSyn0000-1-1-1-100
5852chr2L60056553+NC_0525206431765256000-1-1-1gap0010897-1-1-1-10939
5853chr2L60056072-NC_0525232813183128131898142691673840-1-145nonSyn00107-1-1-1-100
5852chr2L66809673+NC_0525206537878303000-1-1-1gap0008841-1-1-1-101903
5853chr2L67766858-NC_0525232813185328131935130586824494-1-182nonSyn00044-1-1-1-100
5853chr2L74299643-NC_0525251866588118668458521532136126069-1-12120nonSyn0000-1-1-1-1081
5854chr2L77907802-NC_0525251866810218668102000-1-1-1gap0000-1-1-1-100

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.