Schema for refSeqAli
  Database: rheMac10    Primary Table: refSeqAli    Row Count: 6,455   Data last updated: 2019-07-17
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 2489int(10) unsigned range Number of bases that match that aren't repeats
misMatches 3int(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 1int(10) unsigned range Number of inserts in query
qBaseInsert 1int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 15742int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001258110varchar(255) values Query sequence name
qSize 2493int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2493int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 223616942int(10) unsigned range Target sequence size
tStart 8430int(10) unsigned range Alignment start position in target
tEnd 26664int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 353,1980,64,95,longblob   Size of each block
qStarts 0,354,2334,2398,longblob   Start of each block in query.
tStarts 8430,8783,13490,26569,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via refSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via refSeqAli.qName)
      hgFixed.gbSeq.acc (via refSeqAli.qName)
      hgFixed.gbWarn.acc (via refSeqAli.qName)
      hgFixed.imageClone.acc (via refSeqAli.qName)
      hgFixed.refLink.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqStatus.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqSummary.mrnaAcc (via refSeqAli.qName)
      knownGeneV39.kgXref.refseq (via refSeqAli.qName)
      knownGeneV39.knownToRefSeq.value (via refSeqAli.qName)
      rheMac10.all_est.qName (via refSeqAli.qName)
      rheMac10.all_mrna.qName (via refSeqAli.qName)
      rheMac10.mrnaOrientInfo.name (via refSeqAli.qName)
      rheMac10.refFlat.name (via refSeqAli.qName)
      rheMac10.refGene.name (via refSeqAli.qName)
      rheMac10.xenoRefGene.name (via refSeqAli.qName)
      rheMac10.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
585248930011215742-NM_001258110249302493chr12236169428430266644353,1980,64,95,0,354,2334,2398,8430,8783,13490,26569,
585161400011117282+NM_001261269161501615chr122361694271740806361315,4,186,32,264,49,135,222,78,79,115,100,335,0,15,20,206,238,502,551,686,908,986,1065,1180,1280,71740,72368,72372,72829,73188,74133,74273,74752,75063,75240,76825,80038,80301,
5852568120014611607+NM_001261606259062590chr12236169421036091177968204,63,129,162,174,1737,73,38,6,210,273,402,564,738,2475,2552,103609,111624,111842,113756,115196,115946,117685,117758,
74388280000825868-NM_001114351389003890chr1223616942156286215926209707,171,171,171,171,171,1750,120,458,0,707,878,1049,1220,1391,1562,3312,3432,1562862,1567112,1567802,1575668,1577522,1582203,1585576,1587822,1592162,
915832000011754636+NM_001265933159101585chr12236169422568607332482812241,64,108,58,137,68,103,111,88,175,109,323,0,241,305,413,471,608,676,779,890,978,1153,1262,2568607,2720479,2740828,2746888,2749283,3143974,3145922,3158578,3213050,3218536,3303652,3324505,
615580000000-NR_12836058058chr122361694240618104061868158,0,4061810,
61717233000036976-NM_001257785172601726chr12236169424254576426327841436,64,115,111,0,1436,1500,1615,4254576,4256772,4256989,4263167,
77389360000458910-NM_001257794389903899chr12236169424401239446404853437,142,94,73,153,0,3437,3579,3673,3746,4401239,4418470,4421146,4423811,4463895,
6202390200001241110+NM_001261110240702392chr12236169424663504470700613261,103,69,51,67,108,82,127,155,125,98,150,996,0,261,364,433,484,551,659,741,868,1023,1148,1246,1396,4663504,4677331,4678205,4682693,4690975,4691321,4692470,4695115,4696479,4697642,4699359,4704208,4706010,
62338441002222341-NM_001257892385003847chr1223616942506171450679005570,305,866,1939,165,3,573,879,1746,3685,5061714,5062285,5062590,5063456,5067735,

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