Schema for xenoRefSeqAli
  Database: panPan2    Primary Table: xenoRefSeqAli    Row Count: 240,975   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 590smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 651int(10) unsigned range Number of bases that match that aren't repeats
misMatches 9int(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 4int(10) unsigned range Number of inserts in query
qBaseInsert 1046int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 5720int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NR_027055varchar(255) values Query sequence name
qSize 1779int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1706int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 229774977int(10) unsigned range Target sequence size
tStart 770925int(10) unsigned range Alignment start position in target
tEnd 777305int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 60,72,62,44,389,33,longblob   Size of each block
qStarts 0,1099,1172,1235,1279,1673,longblob   Start of each block in query.
tStarts 228997672,229003451,2290035...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)
      panPan2.all_mrna.qName (via xenoRefSeqAli.qName)
      panPan2.refGene.name (via xenoRefSeqAli.qName)
      panPan2.refSeqAli.qName (via xenoRefSeqAli.qName)
      panPan2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      panPan2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5906519004104625720+-NR_027055177901706chr1229774977770925777305660,72,62,44,389,33,0,1099,1172,1235,1279,1673,228997672,229003451,229003523,229003585,229003630,229004019,
591146338003561425+-NR_026874150601506chr12297749778158298187551058,159,103,37,91,154,452,56,14,377,0,58,217,321,358,449,603,1055,1114,1129,228956222,228956322,228956485,228956588,228957046,228957786,228958241,228958701,228958757,228958771,
591140437003561485+-NR_122045144601446chr12297749778158298187551058,159,103,37,91,94,452,56,14,377,0,58,217,321,358,449,543,995,1054,1069,228956222,228956322,228956485,228956588,228957046,228957846,228958241,228958701,228958757,228958771,
591873210005615108237++NM_0013054462116241722chr122977497783368884300811121,29,130,164,108,159,27,99,105,87,54,24,145,243,373,945,1053,1218,1269,1368,1473,1668,833688,836804,837053,839962,841603,841714,841876,842139,842555,842759,842954,
11858806290081555094970+-NM_001165989666626666chr1113418326247252273473537525387,94,194,207,172,133,101,114,105,90,165,127,201,96,112,93,186,89,64,126,140,175,114,129,195,136,89,126,150,204,136,194,168,175, ...2,89,183,377,584,756,889,990,1104,1209,1299,1464,1592,1793,1889,2001,2094,2280,2369,2433,2559,2699,2874,2988,3117,3312,3448,3537 ...86829510,86853951,86856844,86858929,86864146,86865501,86865875,86867227,86874088,86877215,86877418,86878446,86879597,86884755,86 ...
59122921230052702414745+-NR_0028262747372722chr12297749778423808595402615,65,79,16,38,57,121,91,79,111,114,189,6,128,112,112,98,150,114,136,27,169,97,273,4,14,37,52,117,383,401,439,496,617,708,787,898,1012,1201,1207,1335,1447,1559,1657,1807,1921,2057,2134,2311,2431,2704,2708,228915437,228917598,228917675,228919023,228919039,228919080,228919825,228920026,228921957,228922147,228922751,228923439,22892381 ...
4116957702112304371153218+-NM_00523512097012097chr2B2478699752171072652182722764625,81,85,153,165,135,66,119,142,114,127,74,91,200,133,94,155,75,133,123,99,186,156,76,147,98,171,48,298,458,296,510,763,102,1465 ...0,186,269,354,528,693,828,894,1013,1155,1269,1396,1470,1561,1761,1894,1988,2143,2218,2351,2474,2573,2759,2915,2991,3138,3236,340 ...29597699,29597885,29597966,30009814,30196257,30351150,30388696,30414127,30416778,30425621,30427097,30433839,30435031,30437061,30 ...
59116223330042951511906+-NM_0010343262535392289chr122977497784351785737817153,28,53,121,91,75,115,114,189,142,110,114,102,147,110,138,153,39,402,433,486,607,698,773,888,1002,1191,1333,1443,1557,1659,1807,1917,2136,228917599,228919056,228919084,228919825,228920026,228921957,228922143,228922751,228923439,228923900,228924842,228927509,22892788 ...
59113573200066401512163+-NM_0010338972485412358chr12297749778435418573811678,45,115,87,68,114,114,189,142,110,116,151,114,138,18,78,41,543,597,712,799,879,993,1107,1296,1438,1548,1757,1908,2022,2248,2280,228917596,228919089,228919831,228920026,228921953,228922144,228922751,228923439,228923900,228924842,228927509,228929566,22892983 ...
59114073450054911512090+-NM_0213032785482291chr122977497784354785738916101,27,122,91,61,114,107,196,140,112,114,94,152,111,138,72,48,455,535,657,748,821,935,1042,1238,1378,1490,1604,1698,1853,1964,2219,228917588,228919059,228919824,228920026,228921960,228922144,228922751,228923432,228923900,228924840,228927509,228927880,22892956 ...

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