Schema for xenoRefSeqAli
  Database: ochPri2    Primary Table: xenoRefSeqAli    Row Count: 666,260   Data last updated: 2020-08-22
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 94int(10) unsigned Number of bases that match that aren't repeats
misMatches 2int(10) unsigned Number of bases that don't match
repMatches 0int(10) unsigned Number of bases that match but are part of repeats
nCount 0int(10) unsigned Number of 'N' bases
qNumInsert 0int(10) unsigned Number of inserts in query
qBaseInsert 0int(10) unsigned Number of bases inserted in query
tNumInsert 0int(10) unsigned Number of inserts in target
tBaseInsert 0int(10) unsigned Number of bases inserted in target
strand +-char(2) + or - for strand. First character query, second target (optional)
qName NM_001132992varchar(255) Query sequence name
qSize 2040int(10) unsigned Query sequence size
qStart 1685int(10) unsigned Alignment start position in query
qEnd 1781int(10) unsigned Alignment end position in query
tName scaffold_0varchar(255) Target sequence name
tSize 1977105int(10) unsigned Target sequence size
tStart 689int(10) unsigned Alignment start position in target
tEnd 785int(10) unsigned Alignment end position in target
blockCount 1int(10) unsigned Number of blocks in alignment
blockSizes 96,longblob Size of each block
qStarts 1685,longblob Start of each block in query.
tStarts 1976320,longblob Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
      hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
      hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
      hgFixed.imageClone.acc (via xenoRefSeqAli.qName)
      ochPri2.all_mrna.qName (via xenoRefSeqAli.qName)
      ochPri2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      ochPri2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
585942000000+-NM_001132992204016851781scaffold_01977105689785196,1685,1976320,
585104130012741113010+-NM_00108729811386621053scaffold_01977105694113821224,93,662,960,1863284,1976318,
58531878000033718++NM_20134316889141310scaffold_326051000628096923471,196,90,39,914,985,1181,1271,2809,3079,5402,6884,
585317800042579437797++NM_0023893402192995scaffold_019771054049678690548,112,13,197,27,19,265,600,647,2968,40496,49921,51816,52316,78663,
5859411000000+-NM_0013235123703461566scaffold_572739409338834931105,461,5916,
5851979400258721274++NM_00129761023352891167scaffold_57281397445137352938330,219,42,289,705,1125,51373,52644,52896,
5853498700322325+-NM_001256400259919462404scaffold_572644452643743442044243,79,57,57,1946,2196,2284,2347,322,570,662,726,
5853498700322325+-NM_001256398267020172475scaffold_572644452643743442044243,79,57,57,2017,2267,2355,2418,322,570,662,726,
58521915000000+-NM_05290012545255489scaffold_572246311129915331234,255,4778,
5853498700322325+-NM_001037290280421512609scaffold_572644452643743442044243,79,57,57,2151,2401,2489,2552,322,570,662,726,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.