Schema for xenoRefSeqAli
  Database: loxAfr3    Primary Table: xenoRefSeqAli    Row Count: 359,460   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 573int(10) unsigned range Number of bases that match that aren't repeats
misMatches 104int(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 13int(10) unsigned range Number of inserts in query
qBaseInsert 1065int(10) unsigned range Number of bases inserted in query
tNumInsert 11int(10) unsigned range Number of inserts in target
tBaseInsert 754int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001193634varchar(255) values Query sequence name
qSize 1759int(10) unsigned range Query sequence size
qStart 13int(10) unsigned range Alignment start position in query
qEnd 1755int(10) unsigned range Alignment end position in query
tName chrMvarchar(255) values Target sequence name
tSize 16866int(10) unsigned range Target sequence size
tStart 1162int(10) unsigned range Alignment start position in target
tEnd 2593int(10) unsigned range Alignment end position in target
blockCount 14int(10) unsigned range Number of blocks in alignment
blockSizes 27,25,42,24,51,13,27,5,18,1...longblob   Size of each block
qStarts 13,129,162,230,445,545,565,...longblob   Start of each block in query.
tStarts 1162,1276,1308,1376,1596,17...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)
      loxAfr3.all_mrna.qName (via xenoRefSeqAli.qName)
      loxAfr3.refGene.name (via xenoRefSeqAli.qName)
      loxAfr3.refSeqAli.qName (via xenoRefSeqAli.qName)
      loxAfr3.xenoMrna.qName (via xenoRefSeqAli.qName)
      loxAfr3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      loxAfr3.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5855731040013106511754++NM_0011936341759131755chrM16866116225931427,25,42,24,51,13,27,5,18,116,57,21,100,151,13,129,162,230,445,545,565,595,610,642,775,1076,1503,1604,1162,1276,1308,1376,1596,1702,1720,1747,1764,1794,1928,2231,2342,2442,
638127521900121474141751++NR_14891931091393107scaffold_2635828716703254170357861796,256,16,51,172,51,109,93,19,66,44,83,44,11,132,87,164,139,242,533,628,746,1020,1347,1456,2172,2302,2410,2455,2538,2582,2602,2856,2943,7032541,7032643,7032933,7032994,7033105,7033876,7034421,7034533,7034872,7034995,7035094,7035138,7035223,7035268,7035279,7035531, ...
107872224004584712734+-NM_00134826928831061786scaffold_410089347336300926363147568187,142,156,293,139,48,14,117,106,351,493,649,942,1505,1641,1669,64578717,64588109,64588852,64591092,64591391,64592177,64592401,64592430,
79711941680097921111240++NM_00100317025342522406scaffold_98332559027815278278278801239,570,243,72,90,56,36,60,105,9,46,36,252,297,867,1120,1377,1777,1841,1914,2072,2177,2187,2370,27815278,27815329,27826297,27826547,27826804,27827230,27827291,27827366,27827521,27827638,27827650,27827844,
58567185001263611640++NM_0011949671433411433chrM16866117125671354,52,13,30,78,51,8,44,10,24,110,54,228,41,118,177,192,249,464,570,584,629,715,743,1096,1205,1171,1250,1308,1322,1379,1596,1707,1719,1763,1850,1877,2231,2339,
585427660067196720++NM_00119048713951831395chrM1686613132526739,31,57,142,24,13,187,183,295,465,707,1105,1193,1208,1313,1425,1596,1837,2238,2325,2339,
58546463001366714673++NM_00119048914942071401chrM16866137725771621,25,15,13,7,15,45,23,5,33,18,46,30,42,105,84,207,261,368,385,506,519,539,676,700,705,747,765,1055,1161,1206,1317,1377,1431,1539,1555,1686,1700,1718,1850,1873,1879,1922,1941,2231,2339,2385,2493,
585248460028192820++NM_00119364315603171430chrM1686614252539330,66,198,317,809,1232,1425,1918,2341,
8281534200272322609++NM_00136209712581191037scaffold_26358287163189001831892822399,57,39,119,812,998,31890018,31892513,31892783,
58521827000000++NM_001097927151111661411chrM16866233925841245,1166,2339,

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