Schema for xenoRefSeqAli
  Database: gorGor5    Primary Table: xenoRefSeqAli    Row Count: 338,535   Data last updated: 2020-08-22
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 3271int(10) unsigned range Number of bases that match that aren't repeats
misMatches 472int(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 46int(10) unsigned range Number of 'N' bases
qNumInsert 7int(10) unsigned range Number of inserts in query
qBaseInsert 344int(10) unsigned range Number of bases inserted in query
tNumInsert 28int(10) unsigned range Number of inserts in target
tBaseInsert 10814int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_009208varchar(255) values Query sequence name
qSize 4441int(10) unsigned range Query sequence size
qStart 11int(10) unsigned range Alignment start position in query
qEnd 4144int(10) unsigned range Alignment end position in query
tName CYUI01000001v1varchar(255) values Target sequence name
tSize 36219563int(10) unsigned range Target sequence size
tStart 4129int(10) unsigned range Alignment start position in target
tEnd 18732int(10) unsigned range Alignment end position in target
blockCount 31int(10) unsigned range Number of blocks in alignment
blockSizes 72,73,166,161,39,123,121,76...longblob   Size of each block
qStarts 11,194,267,433,657,704,827,...longblob   Start of each block in query.
tStarts 36200831,36201404,36201838,...longblob   Start of each block in target.

Connected Tables and Joining Fields
        gorGor5.all_mrna.qName (via xenoRefSeqAli.qName)
      gorGor5.refGene.name (via xenoRefSeqAli.qName)
      gorGor5.refSeqAli.qName (via xenoRefSeqAli.qName)
      gorGor5.xenoRefFlat.name (via xenoRefSeqAli.qName)
      gorGor5.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
585327147204673442810814+-NM_0092084441114144CYUI01000001v1362195634129187323172,73,166,161,39,123,121,76,149,179,138,184,100,185,85,140,211,6,151,195,36,48,123,90,167,254,170,174,81,25,67,11,194,267,433,657,704,827,948,1024,1173,1352,1490,1674,1774,1959,2045,2185,2396,2402,2553,2748,2795,2844,2967,3057,3224,3478,36 ...36200831,36201404,36201838,36202577,36202801,36203005,36203582,36203706,36205394,36205688,36206297,36206699,36207305,36207845,36 ...
5852782321046599197507+-NM_00128943533931443392CYUI01000001v13621956341511480723127,149,179,138,184,100,185,86,139,212,150,195,32,21,30,134,86,171,254,170,174,144,89,144,271,420,599,737,921,1021,1206,1293,1432,1650,1800,1995,2028,2049,2080,2214,2300,2471,2725,2895,3069,3303,36204756,36205394,36205688,36206297,36206699,36207305,36207845,36208696,36208782,36209097,36209724,36210131,36211032,36211064,36 ...
585335838404671752510202+-NM_0012894333995313994CYUI01000001v1362195634151181412955,41,122,162,26,131,229,149,179,138,184,100,185,86,139,212,150,195,32,21,30,134,86,171,254,170,174,144,89,31,86,127,249,476,502,644,873,1022,1201,1339,1523,1623,1808,1895,2034,2252,2402,2597,2630,2651,2682,2816,2902,3073,3327,3497,367 ...36201422,36201838,36201882,36202577,36202801,36202984,36203553,36205394,36205688,36206297,36206699,36207305,36207845,36208696,36 ...
585333638004671742510228+-NM_0012894343968313967CYUI01000001v1362195634151181412955,41,122,162,26,131,203,149,179,138,184,100,185,86,139,212,150,195,32,21,30,134,86,171,254,170,174,144,89,31,86,127,249,476,502,643,846,995,1174,1312,1496,1596,1781,1868,2007,2225,2375,2570,2603,2624,2655,2789,2875,3046,3300,3470,3644 ...36201422,36201838,36201882,36202577,36202801,36202984,36203579,36205394,36205688,36206297,36206699,36207305,36207845,36208696,36 ...
5854105460466702310159+-NM_0013265594315344301CYUI01000001v13621956341691852528142,144,166,162,23,32,116,281,149,181,136,184,100,185,86,139,212,150,195,32,63,134,90,167,254,170,174,330,34,176,320,486,708,732,764,880,1161,1310,1491,1627,1811,1911,2096,2183,2322,2540,2690,2885,2918,2982,3116,3206,3373,3627,3797,39 ...36201038,36201333,36201838,36202577,36202799,36202822,36203012,36203501,36205394,36205688,36206299,36206699,36207305,36207845,36 ...
59316393500720172443+-NM_0011460691717171711CYUI01015591v11535335111796211220792240,192,97,31,70,88,71,162,99,25,87,109,91,48,90,13,114,21,48,69,54,55,17,57,249,346,378,449,538,609,771,880,905,992,1101,1192,1240,1330,1345,1460,1481,1529,1602,1656,413256,414028,414307,414762,414793,415189,415277,415435,415794,416010,416036,416284,416482,416673,416796,416991,417005,417119,41 ...
5854052390466702310219+-NM_2015744255344241CYUI01000001v13621956341691852528142,84,166,162,23,32,116,281,149,181,136,184,100,185,86,139,212,150,195,32,63,134,90,167,254,170,174,330,34,176,260,426,648,672,704,820,1101,1250,1431,1567,1751,1851,2036,2123,2262,2480,2630,2825,2858,2922,3056,3146,3313,3567,3737,39 ...36201038,36201393,36201838,36202577,36202799,36202822,36203012,36203501,36205394,36205688,36206299,36206699,36207305,36207845,36 ...
5854049460466702310215+-NR_0485514245344245CYUI01000001v13621956341691852528142,144,166,162,23,32,116,200,149,181,136,184,125,185,86,139,212,150,195,32,63,134,90,167,254,170,174,330,34,176,320,486,708,732,764,880,1080,1229,1410,1546,1730,1855,2040,2127,2266,2484,2634,2829,2862,2926,3060,3150,3317,3571,3741,39 ...36201038,36201333,36201838,36202577,36202799,36202822,36203012,36203582,36205394,36205688,36206299,36206699,36207280,36207845,36 ...
5853910710468722510244+-NM_001132203410914100CYUI01000001v1362195634178184493171,111,27,166,162,23,32,116,200,149,181,136,184,100,185,86,139,212,150,195,32,74,123,90,167,254,170,174,130,170,18,1,72,184,211,377,599,623,655,771,971,1120,1301,1437,1621,1721,1906,1993,2132,2350,2500,2695,2728,2803,2926,3016,3183,3437,3607,3 ...36201114,36201339,36201450,36201838,36202577,36202799,36202822,36203012,36203582,36205394,36205688,36206299,36206699,36207305,36 ...
5853882610466702410301+-NM_001135466407714060CYUI01000001v1362195634178184682985,84,166,162,23,32,116,200,149,181,136,184,100,185,86,139,212,150,195,32,74,123,90,167,254,170,174,130,190,1,86,170,336,558,582,614,730,930,1079,1260,1396,1580,1680,1865,1952,2091,2309,2459,2654,2687,2762,2885,2975,3142,3396,3566,3740, ...36201095,36201393,36201838,36202577,36202799,36202822,36203012,36203582,36205394,36205688,36206299,36206699,36207305,36207845,36 ...

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