Schema for xenoRefSeqAli
  Database: calMil1    Primary Table: xenoRefSeqAli    Row Count: 409,319   Data last updated: 2020-08-18
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 110int(10) unsigned range Number of bases that match that aren't repeats
misMatches 55int(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 2595int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 6014int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_132824varchar(255) values Query sequence name
qSize 3692int(10) unsigned range Query sequence size
qStart 635int(10) unsigned range Alignment start position in query
qEnd 3395int(10) unsigned range Alignment end position in query
tName AAVX02039917varchar(255) values Target sequence name
tSize 81585int(10) unsigned range Target sequence size
tStart 13668int(10) unsigned range Alignment start position in target
tEnd 19847int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 30,99,36,longblob   Size of each block
qStarts 635,3260,3359,longblob   Start of each block in query.
tStarts 13668,19692,19811,longblob   Start of each block in target.

Connected Tables and Joining Fields
        calMil1.all_est.qName (via xenoRefSeqAli.qName)
      calMil1.all_mrna.qName (via xenoRefSeqAli.qName)
      calMil1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      calMil1.xenoRefGene.name (via xenoRefSeqAli.qName)
      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)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58511055001259526014++NM_13282436926353395AAVX02039917815851366819847330,99,36,635,3260,3359,13668,19692,19811,
58514193990055011623518++NM_001300813484613163635AAVX020404876340722605479411760,48,15,99,3,124,110,113,115,51,200,122,159,174,111,176,138,1316,1616,1720,1922,2021,2024,2148,2258,2371,2495,2555,2755,2877,3036,3210,3321,3497,22605,27462,27557,29993,30144,32511,33342,33634,34478,36027,38663,41184,43654,44675,45951,46994,47803,
58514193990055011623518++NM_001318085475312233542AAVX020404876340722605479411760,48,15,99,3,124,110,113,115,51,200,122,159,174,111,176,138,1223,1523,1627,1829,1928,1931,2055,2165,2278,2402,2462,2662,2784,2943,3117,3228,3404,22605,27462,27557,29993,30144,32511,33342,33634,34478,36027,38663,41184,43654,44675,45951,46994,47803,
5976219000000++NM_004675204911491230KI635918432622616189981619079181,1149,1618998,
5984521610014741350++NM_0014922579326986KI6359184326226176893017708935165,3,178,119,148,326,491,494,672,838,1768930,1769139,1769698,1770208,1770745,
58513723860042641518721++NM_001042734465114183440AAVX020404876340727462479411648,15,99,3,124,110,113,115,51,200,122,159,174,111,176,138,1418,1522,1727,1826,1829,1953,2063,2176,2300,2360,2560,2682,2841,3015,3126,3302,27462,27557,29993,30144,32511,33342,33634,34478,36027,38663,41184,43654,44675,45951,46994,47803,
58513723860042611518721++NM_001318086464814183437AAVX020404876340727462479411648,15,99,3,124,110,113,115,51,200,122,159,174,111,176,138,1418,1522,1724,1823,1826,1950,2060,2173,2297,2357,2557,2679,2838,3012,3123,3299,27462,27557,29993,30144,32511,33342,33634,34478,36027,38663,41184,43654,44675,45951,46994,47803,
58514074560045641525103++NM_001106474500114573884AAVX020404876340727462544281654,99,3,124,110,113,115,51,200,122,159,174,111,176,138,114,1457,1754,1853,1856,1980,2090,2203,2327,2387,2587,2709,2868,3042,3153,3329,3770,27462,29993,30144,32511,33342,33634,34478,36027,38663,41184,43654,44675,45951,46994,47803,54314,
58513445370042491722557++NM_001101849643614303560AAVX020404876340729990544281899,6,124,110,109,4,118,207,6,117,157,174,111,89,141,90,95,124,1430,1529,1535,1659,1769,1878,1882,2057,2264,2270,2387,2544,2718,2829,3002,3161,3341,3436,29990,30289,32511,33342,33634,33770,34478,38654,39564,41191,43656,44675,45951,46994,47800,50404,53721,54304,
58513845780031681722476++NM_001105780468518724002AAVX020404876340729990544281898,7,124,110,111,2,115,207,6,117,157,174,111,176,138,90,95,124,1872,1970,1977,2101,2211,2322,2324,2499,2706,2712,2829,2986,3160,3271,3447,3603,3783,3878,29990,30148,32511,33342,33634,33924,34478,38654,39988,41191,43656,44675,45951,46994,47803,50404,53721,54304,

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