Schema for xenoRefSeqAli
  Database: micMur2    Primary Table: xenoRefSeqAli    Row Count: 347,000   Data last updated: 2020-08-22
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 207int(10) unsigned range Number of bases that match that aren't repeats
misMatches 47int(10) unsigned range Number of bases that don't match
repMatches 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 3int(10) unsigned range Number of inserts in query
qBaseInsert 60int(10) unsigned range Number of bases inserted in query
tNumInsert 3int(10) unsigned range Number of inserts in target
tBaseInsert 47int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001265952varchar(255) values Query sequence name
qSize 1345int(10) unsigned range Query sequence size
qStart 930int(10) unsigned range Alignment start position in query
qEnd 1244int(10) unsigned range Alignment end position in query
tName ABDC02000615v1varchar(255) values Target sequence name
tSize 1794int(10) unsigned range Target sequence size
tStart 0int(10) unsigned range Alignment start position in target
tEnd 301int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 100,70,54,30,longblob   Size of each block
qStarts 930,1042,1137,1214,longblob   Start of each block in query.
tStarts 0,116,211,271,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)
      micMur2.all_mrna.qName (via xenoRefSeqAli.qName)
      micMur2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      micMur2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5852074700360347++NM_00126595213459301244ABDC02000615v1179403014100,70,54,30,930,1042,1137,1214,0,116,211,271,
5854659802392339560++NM_01608018639641783ABDC02000615v117940114610100,69,54,18,11,31,24,60,81,138,964,1076,1171,1248,1282,1315,1417,1442,1537,1645,0,116,211,271,307,339,443,822,909,1008,
5853955800217322++NM_001303105228177547ABDC02000617v12474164621214105,42,30,276,77,198,241,271,1646,1766,1812,1845,
5853905800217427++NM_001303106241577542ABDC02000617v12474164621215105,42,30,68,203,77,198,241,271,339,1646,1766,1812,1845,1918,
58539558003137322++NR_130121240177667ABDC02000617v12474164621215105,42,30,67,209,77,198,241,271,458,1646,1766,1812,1845,1912,
5851938000011265++NM_00119357351948249ABDC02000622v12514104825142108,93,48,156,1048,2421,
5851929000011265++NM_00128310355160261ABDC02000622v12514104825142108,93,60,168,1048,2421,
58517317000021271++NM_00110156159244234ABDC02000622v12514105325143103,47,40,44,147,194,1053,2421,2474,
58517917000011265++NM_01322656448244ABDC02000622v12514105325142103,93,48,151,1053,2421,
58518214000011265++NM_17208650444240ABDC02000622v12514105325142103,93,44,147,1053,2421,

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