Schema for xenoRefSeqAli
  Database: rn3    Primary Table: xenoRefSeqAli    Row Count: 428,843   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 1700int(10) unsigned range Number of bases that match that aren't repeats
misMatches 276int(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 3int(10) unsigned range Number of 'N' bases
qNumInsert 2int(10) unsigned range Number of inserts in query
qBaseInsert 138int(10) unsigned range Number of bases inserted in query
tNumInsert 3int(10) unsigned range Number of inserts in target
tBaseInsert 9439int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NR_038052varchar(255) values Query sequence name
qSize 2581int(10) unsigned range Query sequence size
qStart 55int(10) unsigned range Alignment start position in query
qEnd 2172int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 268121971int(10) unsigned range Target sequence size
tStart 5501int(10) unsigned range Alignment start position in target
tEnd 16919int(10) unsigned range Alignment end position in target
blockCount 5int(10) unsigned range Number of blocks in alignment
blockSizes 89,809,130,763,188,longblob   Size of each block
qStarts 55,280,1089,1219,1984,longblob   Start of each block in query.
tStarts 5501,8986,14677,15968,16731,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)
      rn3.all_est.qName (via xenoRefSeqAli.qName)
      rn3.all_mrna.qName (via xenoRefSeqAli.qName)
      rn3.refGene.name (via xenoRefSeqAli.qName)
      rn3.refSeqAli.qName (via xenoRefSeqAli.qName)
      rn3.xenoMrna.qName (via xenoRefSeqAli.qName)
      rn3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      rn3.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
585170027603213839439++NR_0380522581552172chr1268121971550116919589,809,130,763,188,55,280,1089,1219,1984,5501,8986,14677,15968,16731,
585159325403213829566++NR_1043842457582046chr1268121971550316919487,809,766,188,58,281,1090,1858,5503,8986,15965,16731,
585198727800427469073++NM_001104620254712540chr1268121971552616864963,90,62,600,204,223,124,766,133,1,198,423,485,1088,1292,1515,1639,2407,5526,8276,8507,8993,9593,10770,12217,15965,16731,
585193427600415666378++NM_00110462625681952561chr1268121971827616864890,78,804,2,213,124,766,133,195,423,510,1314,1316,1536,1660,2428,8276,8507,8994,9803,10773,14683,15965,16731,
912295550051139161067435+-NM_00116621839704143337chr12681219718702107792117188,5,82,100,18,61,195,201,191,247,97,71,73,24,168,41,22,414,602,607,689,804,822,883,1078,1279,1470,1717,1821,1892,1986,2010,3237,3315,267044050,267044409,267044498,267044664,267044863,267255808,267255953,267508186,267509056,267509331,267509662,267509849,26755212 ...
7362728900210044310123++NM_00109957223403932313chr126812197190963201355119,20,345,64,368,393,512,1494,1881,1945,9096,9916,16027,16414,319767,
736822840039213669735++NM_00109959326106242511chr126812197191056798064126,105,357,378,624,1554,1725,2133,9105,317984,679020,679428,
7358323300210682669882++NM_00109956423674052289chr12681219719108679806381,357,378,405,1503,1911,9108,319319,679428,
91322266007451181048846+-NR_0154912131922131chr126812197130112108054619129,61,39,79,210,22,48,205,129,156,98,68,35,9,35,10,81,126,48,92,221,282,321,735,977,999,1047,1252,1381,1537,1635,1704,1739,1773,1859,1869,1955,2083,267041425,267041745,267042940,267043398,267185843,267405547,267715321,267759807,267936329,267937900,267938058,267938169,26805235 ...
9276086400131093261029051+-NM_00124238850111244841chr126812197147870108054527130,861,45,38,328,514,274,47,162,54,150,66,38,72,126,31,33,24,213,79,46,5,100,33,46,42,67,124,334,1195,1240,1278,1606,2120,2394,2441,2753,2918,3087,3291,3451,3598,3772,3803,3836,4079,4317,4396,4442,4449,4635,4686,4732, ...267041426,267043548,267255672,267255801,267256007,267256416,267287117,267508321,267508369,267508689,267508854,267550889,26755213 ...

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