Schema for xenoRefSeqAli
  Database: vicPac2    Primary Table: xenoRefSeqAli    Row Count: 343,007   Data last updated: 2020-08-20
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 431int(10) unsigned range Number of bases that match that aren't repeats
misMatches 73int(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 3int(10) unsigned range Number of inserts in query
qBaseInsert 150int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 2272int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001130159varchar(255) values Query sequence name
qSize 1237int(10) unsigned range Query sequence size
qStart 385int(10) unsigned range Alignment start position in query
qEnd 1039int(10) unsigned range Alignment end position in query
tName ABRR02167232varchar(255) values Target sequence name
tSize 31549int(10) unsigned range Target sequence size
tStart 15901int(10) unsigned range Alignment start position in target
tEnd 18677int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 242,72,159,31,longblob   Size of each block
qStarts 385,633,748,1008,longblob   Start of each block in query.
tStarts 15901,16143,18397,18646,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)
      vicPac2.all_est.qName (via xenoRefSeqAli.qName)
      vicPac2.all_mrna.qName (via xenoRefSeqAli.qName)
      vicPac2.refGene.name (via xenoRefSeqAli.qName)
      vicPac2.refSeqAli.qName (via xenoRefSeqAli.qName)
      vicPac2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      vicPac2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5854317300315022272++NM_00113015912373851039ABRR021672323154915901186774242,72,159,31,385,633,748,1008,15901,16143,18397,18646,
5852995400110122423++NM_0011301601037385839ABRR021672323154915901186773163,159,31,385,548,808,15901,18397,18646,
608621000000+-NR_12942363063KB632527675451330512863051349163,0,3703164,
608756000000+-NR_12993686485KB632527675451330515083051589181,4,3702924,
59922862240074571527984++NM_001190946296812968KB63244817131269187592319064171625,246,54,129,391,199,49,969,79,100,63,105,7,12,30,52,1,312,558,661,790,1181,1380,1429,2398,2477,2589,2686,2791,2803,2823,2916,1875923,1889600,1890626,1890726,1891986,1894620,1902034,1902086,1903205,1904101,1906048,1906143,1906249,1906262,1906284,1906365,
585669219009165071645++NM_00119172029372972835ABRR0216723231549159091844210234,72,150,19,96,96,18,96,26,81,297,537,903,1089,1116,1965,2186,2214,2727,2754,15909,16143,16511,16690,16718,17558,17759,17790,18335,18361,
585353126400141229542+-NM_174117598721515987ABRR021676252775714420277572383,124,137,256,243,177,146,91,310,39,127,119,194,187,166,125,309,200,130,171,102,99,260,2151,2234,2358,2495,2751,2994,3171,3317,3408,3759,3798,3925,4044,4238,4425,4591,4716,5025,5225,5355,5526,5628,5727,0,630,845,1079,2821,3156,3415,3809,3993,4344,4991,6913,7194,8161,8630,8882,9400,9796,10321,10546,10995,11204,13077,
585348330800141229542+-NM_001109816598821555987ABRR021676252775714424277572383,124,137,256,243,177,147,90,310,39,127,119,194,187,166,125,309,204,126,171,105,96,256,2155,2238,2362,2499,2755,2998,3175,3322,3412,3763,3802,3929,4048,4242,4429,4595,4720,5029,5233,5359,5530,5635,5731,0,630,845,1079,2821,3156,3415,3810,3993,4344,4991,6913,7194,8161,8630,8882,9400,9796,10325,10546,10995,11207,13077,
585342035500256239558+-NM_001135158603121956026ABRR021676252775714424277572483,124,137,256,243,175,148,91,310,39,127,119,194,187,166,125,309,200,130,171,105,96,153,87,2195,2278,2402,2539,2795,3038,3213,3361,3452,3803,3842,3969,4088,4282,4469,4635,4760,5069,5269,5399,5570,5675,5771,5939,0,630,845,1079,2821,3156,3413,3809,3993,4344,4991,6913,7194,8161,8630,8882,9400,9796,10321,10546,10995,11207,13077,13246,
6001454329001220211814339++NM_00284239231183922KB6326792396302201648420326062032,4,229,120,120,253,80,94,77,135,117,143,136,84,30,14,9,43,18,45,118,150,154,567,1101,2073,2326,2539,2634,2711,2846,2987,3130,3266,3359,3491,3686,3707,3848,3877,2016484,2016543,2016738,2018897,2020932,2021335,2023025,2028885,2029240,2029411,2029911,2030230,2031789,2032027,2032111,2032236, ...

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