Schema for xenoRefSeqAli
  Database: galVar1    Primary Table: xenoRefSeqAli    Row Count: 568,133   Data last updated: 2020-08-19
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 73smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 78int(10) unsigned Number of bases that match that aren't repeats
misMatches 12int(10) unsigned Number of bases that don't match
repMatches 0int(10) unsigned Number of bases that match but are part of repeats
nCount 0int(10) unsigned Number of 'N' bases
qNumInsert 1int(10) unsigned Number of inserts in query
qBaseInsert 199int(10) unsigned Number of bases inserted in query
tNumInsert 2int(10) unsigned Number of inserts in target
tBaseInsert 594887int(10) unsigned Number of bases inserted in target
strand +-char(2) + or - for strand. First character query, second target (optional)
qName NM_001083353varchar(255) Query sequence name
qSize 3897int(10) unsigned Query sequence size
qStart 3438int(10) unsigned Alignment start position in query
qEnd 3727int(10) unsigned Alignment end position in query
tName NW_007726111v1varchar(255) Target sequence name
tSize 3276566int(10) unsigned Target sequence size
tStart 313542int(10) unsigned Alignment start position in target
tEnd 908519int(10) unsigned Alignment end position in target
blockCount 3int(10) unsigned Number of blocks in alignment
blockSizes 19,29,42,longblob Size of each block
qStarts 3438,3457,3685,longblob Start of each block in query.
tStarts 2368047,2581625,2962982,longblob Start of each block in target.

Connected Tables and Joining Fields
        galVar1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      galVar1.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
7378120011992594887+-NM_001083353389734383727NW_007726111v13276566313542908519319,29,42,3438,3457,3685,2368047,2581625,2962982,
734157300343450926+-NR_1100805461532NW_007726111v13276566345817397231669,51,109,101,125,33,1,81,132,268,369,499,2879335,2879426,2895966,2917950,2930591,2930716,
736281030071232839231+-NR_110079410411964NW_007726111v13276566357269397231969,51,109,102,63,36,144,72,85,1,81,132,268,532,633,999,1197,1879,2879335,2879426,2895966,2917950,2918191,2918295,2918529,2918730,2919212,
7338234810022180144205363++NM_009152685006105NW_007726111v132765666906329002994833,105,40,100,37,36,276,158,63,120,94,118,145,115,68,145,220,92,42,159,67,143,534,57,86,43,93,21,42,14,27,135,25,39,66,65,10,18, ...0,33,183,229,347,449,485,761,919,982,1102,1196,1314,1459,1576,1644,1789,2009,2101,2143,2302,2369,2512,3046,3103,3222,3265,3360,3 ...690632,690666,690830,690870,690976,691051,691090,746737,751485,771426,813918,822287,854497,857296,857506,860567,864245,867355,87 ...
58519818008310131781++NM_000612558027563282NW_007732789v112473710468124651524,15,10,9,21,16,20,15,15,8,9,13,7,18,16,2756,2819,2835,2845,2869,2934,2950,2970,3013,3069,3077,3090,3103,3248,3266,10468,10905,10920,10986,11070,11177,11204,11912,11942,11974,11988,12000,12018,12347,12449,
585183450087709913+-NM_0122131305424663464NW_007732789v112473710929120701078,12,14,8,12,12,11,7,25,49,2466,2705,2747,2782,2792,3222,3281,3359,3390,3415,112667,112788,112870,112929,112941,113153,113184,113344,113405,113759,
5859124000041424++NM_015246393035033618NW_007732789v11247371106612605518,22,36,21,18,3503,3521,3543,3579,3600,11066,11118,12269,12356,12587,
7334224520018166739205256++NM_00124307265822965837NW_007726111v1327656669116990029942197,158,63,120,94,118,145,115,68,145,220,92,42,159,67,143,534,57,86,43,93,21,42,14,27,135,25,39,66,65,10,18,90,38,21,18,27,84,32 ...296,493,651,714,834,928,1046,1191,1308,1376,1521,1741,1833,1875,2034,2101,2244,2778,2835,2954,2997,3092,3114,3180,3199,3228,3396 ...691169,746737,751485,771426,813918,822287,854497,857296,857506,860567,864245,867355,875927,879559,883100,895099,896640,897176,89 ...
7334194520018166739205256++NM_00124307364221395677NW_007726111v1327656669117290029942194,158,63,120,94,118,145,115,68,145,220,92,42,159,67,143,534,57,86,43,93,21,42,14,27,135,25,39,66,65,10,18,90,38,21,18,27,84,32 ...139,333,491,554,674,768,886,1031,1148,1216,1361,1581,1673,1715,1874,1941,2084,2618,2675,2794,2837,2932,2954,3020,3039,3068,3236, ...691172,746737,751485,771426,813918,822287,854497,857296,857506,860567,864245,867355,875927,879559,883100,895099,896640,897176,89 ...
73207843600552421204014++NM_20497732631603198NW_007726111v1327656669124789777522119,158,63,2,118,94,120,143,113,4,68,145,220,94,161,68,127,505,24,24,12,132,160,279,437,500,502,620,714,834,977,1090,1094,1162,1307,1527,1658,1819,1887,2030,2549,2573,2957,3066,691247,746737,751485,751672,771428,813918,822287,854499,857296,857432,857506,860567,864245,867355,879556,883099,895099,896640,89 ...

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