Schema for refSeqAli
  Database: bosTau2    Primary Table: refSeqAli    Row Count: 17,810   Data last updated: 2020-08-20
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 817smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1858int(10) unsigned range Number of bases that match that aren't repeats
misMatches 1int(10) unsigned range Number of bases that don't match
repMatches 67int(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 5int(10) unsigned range Number of inserts in target
tBaseInsert 16852int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001034507varchar(255) values Query sequence name
qSize 1943int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1926int(10) unsigned range Alignment end position in query
tName chr15varchar(255) values Target sequence name
tSize 53815408int(10) unsigned range Target sequence size
tStart 30476330int(10) unsigned range Alignment start position in target
tEnd 30495108int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 1291,135,109,92,230,69,longblob   Size of each block
qStarts 17,1308,1443,1552,1644,1874,longblob   Start of each block in query.
tStarts 30476330,30482047,30484320,...longblob   Start of each block in target.

Connected Tables and Joining Fields
        bosTau2.all_est.qName (via refSeqAli.qName)
      bosTau2.all_mrna.qName (via refSeqAli.qName)
      bosTau2.refFlat.name (via refSeqAli.qName)
      bosTau2.refGene.name (via refSeqAli.qName)
      bosTau2.xenoMrna.qName (via refSeqAli.qName)
      bosTau2.xenoRefGene.name (via refSeqAli.qName)
      bosTau2.xenoRefSeqAli.qName (via refSeqAli.qName)
      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)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
8171858167000516852-NM_001034507194301926chr1553815408304763303049510861291,135,109,92,230,69,17,1308,1443,1552,1644,1874,30476330,30482047,30484320,30490799,30494317,30495039,
587128720400610333-NM_001046407131001293chr11028340293138193254457303,96,132,159,68,168,367,17,320,416,548,707,775,943,313819,314411,316030,317469,320866,322633,325078,
7339510330003182355-NM_174468398403984chr11028340293341644205033278,24,233,109,40,31,39,39,144,210,163,79,216,118,157,159,193,141,85,192,24,157,153,82,170,97,62,84,226,268,87,124,0,78,102,335,444,484,515,554,593,737,947,1110,1189,1405,1523,1680,1839,2032,2173,2258,2450,2474,2631,2784,2866,3036,3133,3195,32 ...334164,337044,341095,341591,344907,344948,345111,348269,348869,350161,354077,356354,359395,359710,360416,361716,362112,363327,36 ...
5933110111600131525251+NM_174552328403284chr1102834029106781610963481634,83,136,121,182,158,142,115,200,158,151,146,929,4,527,195,0,34,117,253,374,556,714,856,971,1171,1329,1480,1626,2555,2559,3089,1067816,1067851,1067938,1073951,1081542,1083989,1084253,1085932,1088865,1089173,1092671,1093313,1094686,1095616,1095621,1096153,
59436830320002222284-NM_001040473378803715chr1102834029126444512904442388,694,116,142,131,138,207,153,252,199,110,95,232,169,86,88,126,69,112,175,96,186,51,73,161,855,971,1113,1244,1382,1589,1742,1994,2193,2303,2398,2630,2799,2885,2973,3099,3168,3280,3455,3551,3737,1264445,1264534,1265310,1266083,1266466,1267590,1268813,1270736,1271181,1272475,1273016,1273420,1275394,1278598,1278931,1279505, ...
746125010860001223645+NM_001083694721307211chr11028340291291424132228013126,167,1802,3144,162,147,189,111,117,148,72,116,910,0,126,293,2095,5239,5401,5548,5737,5848,5965,6113,6185,6301,1291424,1294548,1296470,1299229,1303670,1305734,1306074,1313361,1314482,1318631,1320562,1320735,1321370,
59521090820112097763-NM_001083445231202311chr11028340291322539133249310772,213,199,105,82,179,179,204,82,176,1,773,986,1185,1290,1372,1551,1730,1934,2136,1322539,1324486,1325878,1326923,1327136,1327841,1329233,1330314,1331203,1332317,
94422070000054694-NM_001080233222702207chr769141744471012474710814861453,108,89,170,177,210,20,1473,1581,1670,1840,2017,47101247,47103715,47104996,47105894,47106960,47107938,
5977364000066619-NM_17424477939779chr1102834029169653917038987182,87,113,130,111,51,66,0,182,269,382,512,623,674,1696539,1696998,1698310,1699105,1701388,1702445,1703832,
5991509220411132726766-NM_001076975184801848chr1102834029184048318689658566,307,158,148,167,158,124,88,0,698,1005,1163,1311,1478,1636,1760,1840483,1841099,1847342,1854931,1860095,1861758,1866394,1868877,

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