Schema for xenoRefSeqAli
  Database: aplCal1    Primary Table: xenoRefSeqAli    Row Count: 246,163   Data last updated: 2020-08-17
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 496int(10) unsigned range Number of bases that match that aren't repeats
misMatches 179int(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 2int(10) unsigned range Number of inserts in query
qBaseInsert 78int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 75int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001097928varchar(255) values Query sequence name
qSize 2989int(10) unsigned range Query sequence size
qStart 1984int(10) unsigned range Alignment start position in query
qEnd 2737int(10) unsigned range Alignment end position in query
tName chrMvarchar(255) values Target sequence name
tSize 14117int(10) unsigned range Target sequence size
tStart 724int(10) unsigned range Alignment start position in target
tEnd 1474int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 96,168,411,longblob   Size of each block
qStarts 1984,2110,2326,longblob   Start of each block in query.
tStarts 724,847,1063,longblob   Start of each block in target.

Connected Tables and Joining Fields
        aplCal1.all_est.qName (via xenoRefSeqAli.qName)
      aplCal1.all_mrna.qName (via xenoRefSeqAli.qName)
      aplCal1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      aplCal1.xenoRefGene.name (via xenoRefSeqAli.qName)
      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)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58549617900278275++NM_001097928298919842737chrM141177241474396,168,411,1984,2110,2326,724,847,1063,
5857434000000++NM_001190732334117225chrM14117216922771108,117,2169,
5861788000111423050+-NM_1451092256609981scaffold_923209538161600164908354,129,75,609,777,906,44630,47153,47863,
585108510011719215432++NM_00009054904352313scaffold_7112757752423839829360,30,69,435,495,2244,24238,25374,39760,
585197360063447220++NM_00119496714338261403chrM14117216926228106,4,9,16,16,18,15,49,826,945,949,1010,1104,1223,1281,1354,2169,2286,2291,2350,2384,2464,2502,2573,
5887035000000+-NM_000061257516871792scaffold_713160034065864066911105,1687,909312,
5851727400121624885+-NM_01838764519861448scaffold_9212215361588121012393,87,66,986,1079,1382,200524,201747,205589,
58588290022002278490+-NM_001136233517915903709scaffold_148516001350354128961360,18,39,1590,3651,3670,31052,109577,109620,
58642919200361855856+-NM_00119907764652721511scaffold_7492529321637561702336162,201,3,72,60,123,272,446,647,650,752,1388,82699,84359,84672,85095,85880,89053,
590741600128347783+-NM_001374703442233923510scaffold_101149529737266785139429,7,21,33,3392,3421,3428,3477,364390,365606,366174,412230,

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