Schema for xenoRefSeqAli
  Database: cavPor3    Primary Table: xenoRefSeqAli    Row Count: 337,367   Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 754smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 10250int(10) unsigned range Number of bases that match that aren't repeats
misMatches 2425int(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 28int(10) unsigned range Number of inserts in query
qBaseInsert 1107int(10) unsigned range Number of bases inserted in query
tNumInsert 60int(10) unsigned range Number of inserts in target
tBaseInsert 34558int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001009944varchar(255) values Query sequence name
qSize 14140int(10) unsigned range Query sequence size
qStart 156int(10) unsigned range Alignment start position in query
qEnd 13938int(10) unsigned range Alignment end position in query
tName scaffold_4varchar(255) values Target sequence name
tSize 61496919int(10) unsigned range Target sequence size
tStart 22182587int(10) unsigned range Alignment start position in target
tEnd 22229820int(10) unsigned range Alignment end position in target
blockCount 63int(10) unsigned range Number of blocks in alignment
blockSizes 109,107,73,69,170,221,136,2...longblob   Size of each block
qStarts 156,317,424,497,568,738,962...longblob   Start of each block in query.
tStarts 39267099,39267260,39282386,...longblob   Start of each block in target.

Connected Tables and Joining Fields
        cavPor3.all_est.qName (via xenoRefSeqAli.qName)
      cavPor3.all_mrna.qName (via xenoRefSeqAli.qName)
      cavPor3.refGene.name (via xenoRefSeqAli.qName)
      cavPor3.refSeqAli.qName (via xenoRefSeqAli.qName)
      cavPor3.xenoMrna.qName (via xenoRefSeqAli.qName)
      cavPor3.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
754102502425002811076034558+-NM_0010099441414015613938scaffold_461496919221825872222982063109,107,73,69,170,221,136,284,189,223,135,210,90,401,207,131,177,134,1620,611,1386,150,144,280,214,12,117,153,139,492,96,156,245 ...156,317,424,497,568,738,962,1121,1405,1594,1931,2096,2306,2433,2855,3062,3193,3370,3504,5124,5738,7124,7274,7418,7698,7912,7955, ...39267099,39267260,39282386,39282593,39282858,39283285,39283506,39283668,39284076,39285276,39286962,39287419,39288126,39288253,39 ...
58522743000000++NM_00119073233448318chrM16801186121311270,48,1861,
58567619300001826++NM_001097928298919672836chrM1680151606855218,851,1967,1985,5160,6004,
836481920034207278897++NM_21279317631741434scaffold_37555112610933268112130058138,143,112,81,96,87,81,102,174,381,524,636,1053,1149,1251,1332,10933268,11127581,11150102,11176508,11211426,11212258,11212354,11212903,
739361850032613228+-NM_0013085787171708scaffold_322564124220265967202666414117,150,36,143,1,358,518,565,5374601,5374931,5375088,5375132,
882609157002233568+-NM_0013085979039777scaffold_15417620413894853438952868472,250,282,162,9,82,333,615,2809173,2812211,2812854,2813345,
58513349002349218408+-NM_14649395712543scaffold_0886756662338941979399,38,45,12,351,498,88633687,88634021,88652232,
625149670011231331++NM_0011947231421351690scaffold_421595134852488045249351278,138,351,552,5248804,5249213,
585737169000000+-NM_0010003699390906scaffold_08867566646602475081906,0,88628158,
585740166000000+-NM_1464009390906scaffold_08867566646602475081906,0,88628158,

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