Schema for xenoRefSeqAli
  Database: calJac4    Primary Table: xenoRefSeqAli    Row Count: 256,337   Data last updated: 2020-09-21
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 587smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 157int(10) unsigned range Number of bases that match that aren't repeats
misMatches 6int(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 1int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 2778int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NR_126383varchar(255) values Query sequence name
qSize 631int(10) unsigned range Query sequence size
qStart 467int(10) unsigned range Alignment start position in query
qEnd 631int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 217961735int(10) unsigned range Target sequence size
tStart 305304int(10) unsigned range Alignment start position in target
tEnd 308245int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 33,130,longblob   Size of each block
qStarts 467,501,longblob   Start of each block in query.
tStarts 217653490,217656301,longblob   Start of each block in target.

Connected Tables and Joining Fields
        calJac4.all_est.qName (via xenoRefSeqAli.qName)
      calJac4.all_mrna.qName (via xenoRefSeqAli.qName)
      calJac4.refGene.name (via xenoRefSeqAli.qName)
      calJac4.refSeqAli.qName (via xenoRefSeqAli.qName)
      calJac4.xenoMrna.qName (via xenoRefSeqAli.qName)
      calJac4.xenoRefFlat.name (via xenoRefSeqAli.qName)
      calJac4.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
5871576001112778+-NR_126383631467631chr1217961735305304308245233,130,467,501,217653490,217656301,
5873532170023332359+-NM_00117607318826781581chr12179617353823543832833399,126,45,678,1185,1536,217578452,217578988,217579336,
591280350012216232++NR_0469891001491808chr1217961735868811885358419,109,88,99,491,512,621,709,868811,868830,882389,885259,
5914821600034083216++NR_15554615871161166chr12179617358708268716844540,63,21,18,116,1016,1096,1148,870826,871558,871635,871666,
59339861890033172538+-NM_032229424904206chr12179617351147788115450110302,116,79,1792,883,108,373,76,279,167,0,302,420,499,2294,3203,3311,3684,3760,4039,216807234,216807537,216807653,216810234,216812026,216812933,216813044,216813418,216813497,216813780,
59329305460014719163239+-NM_175499424304195chr12179617351147788115450318155,51,88,884,913,832,75,57,9,27,12,11,13,14,86,85,140,24,0,159,215,511,1395,2319,3227,3307,3364,3413,3444,3553,3764,3808,3825,3944,4029,4171,216807232,216807389,216807443,216810230,216811117,216812038,216812952,216813033,216813091,216813142,216813174,216813287,21681351 ...
59330375890019583213090+-NM_001106057424804209chr1217961735114778811545042377,54,52,84,68,20,879,914,829,11,13,7,138,10,12,10,69,11,12,18,173,141,24,0,83,161,218,343,424,517,1396,2323,3152,3168,3182,3228,3366,3445,3474,3489,3560,3662,3749,3837,4042,4185,216807231,216807312,216807389,216807444,216807565,216807638,216810235,216811117,216812041,216812872,216812889,216812902,21681295 ...
5932242281000000+-NM_001257070252302523chr12179617351148947115147012523,0,216810265,
59394147200696351023+-NM_00130555338902542630chr121796173511489501151386766,540,357,90,114,102,144,254,434,1358,1928,2021,2357,2486,216810349,216810529,216811501,216812074,216812164,216812512,216812641,
601180230019128443++NR_1323713049221chr121796173521436722172318252,151,9,70,2143672,2172167,

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