Schema for xenoRefSeqAli
  Database: susScr2    Primary Table: xenoRefSeqAli    Row Count: 471,604   Data last updated: 2020-09-01
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 70int(10) unsigned range Number of bases that match that aren't repeats
misMatches 28int(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 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 39int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001160481varchar(255) values Query sequence name
qSize 1006int(10) unsigned range Query sequence size
qStart 800int(10) unsigned range Alignment start position in query
qEnd 898int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 295529705int(10) unsigned range Target sequence size
tStart 20548int(10) unsigned range Alignment start position in target
tEnd 20685int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 72,26,longblob   Size of each block
qStarts 800,872,longblob   Start of each block in query.
tStarts 20548,20659,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)
      susScr2.all_est.qName (via xenoRefSeqAli.qName)
      susScr2.all_mrna.qName (via xenoRefSeqAli.qName)
      susScr2.xenoMrna.qName (via xenoRefSeqAli.qName)
      susScr2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      susScr2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58570280000139++NM_0011604811006800898chr12955297052054820685272,26,800,872,20548,20659,
58564250000139++NM_0011604811006796885chr12955297052055720685263,26,796,859,20557,20659,
110110818001514+-NR_1457731351132chr151345411036772227567722405296,30,1,102,66818698,66818798,
148913000274342317010+-NR_14581913351571013265chr151345411037913917279456303331,74,16,5710,13174,13249,55084800,55401541,55401915,
76933100112372036+-NR_145822506610711207chr125743134432286723300832462,17,24,21,1071,1133,1150,1186,54130512,54130639,54201729,54202651,
6798520000000+-NR_14573213223128chr125743134412437063124371681105,23,44994176,
586103530000135+-NM_001005428133810961252chr1295529705166208166399244,112,1096,1140,295363306,295363385,
1055616183005206713580++NM_18297862276721677chr17643953396165511361669492878,87,99,72,58,123,134,148,672,804,921,1077,1152,1210,1333,1529,61655113,61662653,61664792,61667993,61668186,61668355,61668630,61669344,
1181022200228823134307++NM_001317990631922435249chr61233051714770040647834837423,32,39,30,2243,2266,5063,5219,47700406,47701634,47761906,47834807,
103335043001070111681++NM_006572624910112105chr3123599780587320295873310312105,53,27,24,6,8,12,31,37,40,25,25,1011,1269,1393,1424,1478,1484,1494,1544,1893,2004,2053,2080,58732029,58732296,58732421,58732451,58732500,58732508,58732517,58732562,58732894,58733004,58733052,58733078,

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