Schema for xenoRefSeqAli
  Database: neoSch1    Primary Table: xenoRefSeqAli    Row Count: 446,526   Data last updated: 2020-08-19
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 230int(10) unsigned range Number of bases that match that aren't repeats
misMatches 70int(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 2int(10) unsigned range Number of inserts in target
tBaseInsert 6678int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001006460varchar(255) values Query sequence name
qSize 2005int(10) unsigned range Query sequence size
qStart 300int(10) unsigned range Alignment start position in query
qEnd 600int(10) unsigned range Alignment end position in query
tName NW_018726556v1varchar(255) values Target sequence name
tSize 10277int(10) unsigned range Target sequence size
tStart 3140int(10) unsigned range Alignment start position in target
tEnd 10118int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 35,115,150,longblob   Size of each block
qStarts 300,335,450,longblob   Start of each block in query.
tStarts 3140,8875,9968,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)
      neoSch1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      neoSch1.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58523070000026678++NM_0010064602005300600NW_018726556v110277314010118335,115,150,300,335,450,3140,8875,9968,
58522872000026678++NM_001085698803267567NW_018726556v110277314010118336,114,150,267,303,417,3140,8876,9968,
58522278000026678++NM_001102769879307607NW_018726556v110277314010118336,114,150,307,343,457,3140,8876,9968,
58522773000026678++NM_001245818971196496NW_018726556v110277314010118336,114,150,196,232,346,3140,8876,9968,
58528931000026678++NM_0010762561084307627NW_018726556v110277314010138335,115,170,307,342,457,3140,8875,9968,
58528832000026678++NM_0013085701021301621NW_018726556v110277314010138335,115,170,301,336,451,3140,8875,9968,
58528040000026678++NM_0107531194296616NW_018726556v110277314010138335,115,170,296,331,446,3140,8875,9968,
5851921331000075144++NM_19805526662792531NW_018734339v173861239284466808438,185,4,66,121,245,395,798,279,717,902,906,972,1093,1338,1733,39284,40165,40551,41042,41223,45227,45478,45882,
58522176000026678++NM_001090987934413710NW_018726556v110277314310118333,114,150,413,446,560,3143,8876,9968,
5852413800001978++NM_0011083641185289568NW_018726556v1102778873101302117,162,289,406,8873,9968,

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