Schema for xenoRefSeqAli
  Database: danRer4    Primary Table: xenoRefSeqAli    Row Count: 290,059   Data last updated: 2020-08-21
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 998smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 145int(10) unsigned range Number of bases that match that aren't repeats
misMatches 32int(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 201int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 1125int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001160517varchar(255) values Query sequence name
qSize 1076int(10) unsigned range Query sequence size
qStart 21int(10) unsigned range Alignment start position in query
qEnd 399int(10) unsigned range Alignment end position in query
tName chr15varchar(255) values Target sequence name
tSize 57214918int(10) unsigned range Target sequence size
tStart 54221476int(10) unsigned range Alignment start position in target
tEnd 54222778int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 123,54,longblob   Size of each block
qStarts 21,345,longblob   Start of each block in query.
tStarts 2992140,2993388,longblob   Start of each block in target.

Connected Tables and Joining Fields
        danRer4.all_est.qName (via xenoRefSeqAli.qName)
      danRer4.all_mrna.qName (via xenoRefSeqAli.qName)
      danRer4.refGene.name (via xenoRefSeqAli.qName)
      danRer4.refSeqAli.qName (via xenoRefSeqAli.qName)
      danRer4.xenoMrna.qName (via xenoRefSeqAli.qName)
      danRer4.xenoRefGene.name (via xenoRefSeqAli.qName)
      hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
      hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
9981453200120111125+-NM_001160517107621399chr155721491854221476542227782123,54,21,345,2992140,2993388,
642347910022147173++NM_0011651171155278737chr166548954775303627537973566,42,148,113,69,278,350,392,540,668,7530362,7530544,7532552,7534497,7537904,
731189413008117118132051+-NM_0011072874564582831chr170589895715314080619131,4,99,46,56,97,153,101,4,152,72,22,84,48,126,69,90,102,146,58,189,193,297,364,420,628,781,882,886,1038,1110,1633,1858,2182,2308,2377,2548,2685,70449089,70449674,70522183,70522607,70524703,70528009,70530567,70532396,70532822,70533125,70533555,70535403,70556112,70562003,70 ...
731165387007121717132100+-NM_13408248574113180chr170589895715414080618131,4,99,46,56,97,153,102,3,152,72,22,84,126,69,90,102,144,411,542,546,650,717,773,981,1134,1236,1239,1391,1463,1983,2532,2658,2727,2898,3036,70449089,70449674,70522183,70522607,70524703,70528009,70530567,70532396,70532823,70533125,70533555,70535403,70556112,70578036,70 ...
731161387008121817132110+-NM_00113229347751292895chr170589895715414081218137,4,81,21,56,97,154,96,155,70,21,87,126,69,90,81,59,144,129,266,270,373,441,497,704,858,963,1118,1188,1701,2247,2373,2442,2532,2621,2751,70449083,70449674,70522183,70522606,70524703,70528009,70530566,70532396,70533125,70533558,70535404,70556112,70578036,70578248,70 ...
1184952010061380617071++NM_02277839373462422chr16654895474809418948111956787,69,135,135,57,108,105,346,664,1153,1483,2035,2149,2317,48094189,48094519,48097368,48099091,48109186,48109306,48111851,
95282930800161014448++NM_001199179492818793022chr1665489547481427564815834111176,94,51,165,2,69,117,146,98,142,77,1879,2055,2155,2206,2371,2373,2442,2559,2705,2803,2945,48142756,48144583,48148575,48148707,48148910,48148956,48151238,48151474,48155315,48156006,48158264,
71856324100518093444+-NM_00240226462591243chr447249802174435011744774910147,78,78,57,33,69,92,64,60,126,259,412,490,715,772,808,886,978,1057,1117,29802053,29802288,29802443,29802845,29803010,29803120,29804487,29804652,29805157,29806175,
5854852140041233749611+-NM_14551939295172449chr1705898951157861888881,153,87,150,3,72,84,69,517,727,880,985,1135,1138,1711,2380,70528007,70530567,70532396,70533125,70533284,70533556,70556118,70578248,
58532612100221955147+-NM_00109646024367061372chr1705898955629461888636,126,87,150,2,46,706,943,1069,1174,1324,1326,70528007,70530594,70532396,70533125,70533281,70533555,

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