Schema for Fix Patches - Reference Assembly Fix Patch Sequence Alignments
  Database: hg19    Primary Table: fixSeqLiftOverPsl    Row Count: 416   Data last updated: 2018-11-06
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 614smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 13052int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(10) unsigned range Number of bases that don't match
repMatches 8633int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName chr1_jh806574_fixvarchar(255) values Query sequence name
qSize 22982int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 21685int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 249250621int(10) unsigned range Target sequence size
tStart 3823583int(10) unsigned range Alignment start position in target
tEnd 3845268int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 21685,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 3823583,longblob   Start of each block in target.

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
614130520863300000+chr1_jh806574_fix22982021685chr124925062138235833845268121685,0,3823583,
103467044797541077259613+chr1_gl949741_fix1515510151551chr124925062131872758320170631476671,4457,13757,105,15,82,23,13,22,9,3249,371,157,45361,0,76672,81129,94886,94994,95009,95091,95114,95131,95158,95171,98421,106033,106190,31872758,31949429,31953887,31967649,31967754,31967773,31967856,31967880,31967893,31967915,31967924,31971173,31971544,31971702,
23246502147239095039119038214389557+chr1_jh636053_fix167612601676126chr124925062112047104912134635053112643,4401,2974,2778,1,1,2,21239,6419,17278,1158,2818,4207,1892,378,3083,16744,83,2341,3,1103,2876,2,1,2,4097,1708,733,749,2,39 ...0,112643,117045,120020,122803,122805,122807,122810,144056,150481,167759,168917,171751,175960,177853,178231,181315,198059,198142, ...120471049,120583693,120588094,120591068,120593846,120593847,120593848,120593850,120615089,120621508,120638787,120639946,12064276 ...
18810319910886204031761828-chr1_jh636053_fix167612611581671347754chr1249250621120747156120936695504002,22580,11,1,1,1,1,1107,3905,184,257,320,4512,2,11,6,13,8,8,8,42,3922,13545,9586,707,6378,26782,707,10480,3,33971,150,3806,31 ...328372,332374,354961,354973,354975,354977,354979,354981,356088,359994,360178,360435,360758,365271,365274,365286,365293,365307,36 ...120747156,120751159,120773739,120773750,120773751,120773752,120773753,120773754,120774862,120778767,120778952,120779210,12077953 ...
21012434050100358016662332-chr1_jh636052_fix728315017287461953560chr1249250621143871002144095782405235,2,6,2,25743,38204,7168,3133,1649,743,9028,2505,8154,5764,34,3686,3854,3979,9600,14990,43,5544,4645,9,2,8476,5231,25930,3,16 ...5329590,5334826,5334830,5334837,5334841,5360585,5398795,5405963,5409096,5410761,5411504,5420532,5423055,5431209,5436981,5437016, ...143871002,143876237,143876239,143876245,143876247,143901990,143940194,143947363,143950497,143952146,143952890,143961919,14396442 ...
168726325452273430511143655-chr1_jh636052_fix728315059457806000014chr124925062114451242114456659688219,3759,690,2249,861,811,1,1,1,2,16,142,512,1192,258,1830,1,1,1,1,1,3122,1032,1744,16,31,1066,1,12,1506,2,1359,1141,592,804,442 ...1283136,1283355,1287115,1287805,1290055,1290917,1291729,1291731,1291733,1291735,1291739,1291767,1291910,1292423,1293615,1293873, ...144512421,144512643,144516402,144517093,144519342,144520203,144521014,144521015,144521016,144521017,144521019,144521035,14452117 ...
1688125271929981017381631-chr1_jh636052_fix728315059125425935280chr124925062114457735714460008834946,106,505,2293,591,501,1645,2544,257,1574,1990,944,1189,574,686,153,85,443,1,2,3,3,1,1,874,1937,341,204,222,4,1,2,2,2076,1347870,1348816,1348923,1349428,1351722,1352313,1352814,1354459,1357004,1357261,1358835,1360825,1361769,1362958,1363535,1364222, ...144577357,144578304,144578410,144578917,144581210,144581803,144582305,144583953,144586497,144586758,144588333,144590324,14459127 ...
1688876321511242013213057-chr1_jh636052_fix728315058923015912542chr1249250621144600136144620413441488,183,4917,3254,1,20,2001,41,2,420,508,33,1,216,1053,179,771,2,892,33,3,288,2,2,1,1,2,2,1,1,1,1,1,1,3,2,1,1,1,2,1280,2,657,19 ...1370608,1372098,1372282,1377199,1380453,1380454,1380474,1382476,1382517,1382519,1382940,1383450,1383483,1383484,1383702,1384761, ...144600136,144601624,144601807,144606727,144609990,144609992,144610014,144612015,144612058,144612061,144612481,144612989,14461302 ...
16891038531463203338-chr1_jh636052_fix728315058772505892301chr12492506211448107241448257807207,6335,3024,3284,18,24,2156,1390849,1391057,1397393,1400418,1403702,1403720,1403744,144810724,144810931,144817266,144820290,144823576,144823598,144823624,
21111026419481520013322965-chr1_jh636052_fix728315056820725874082chr124925062114482578014501782343893,1,20,4825,2392,4076,11444,11140,3,4,3,3,6,1,1,2,10039,19209,22646,11314,2,2,1,1,37033,3463,2,12,1468,29,11495,1947,2455,9648 ...1409068,1409962,1409964,1409992,1414817,1417209,1421285,1432730,1443870,1443873,1443877,1443880,1443883,1443889,1443890,1443891, ...144825780,144826673,144826674,144826694,144831520,144833914,144837991,144849435,144860577,144860582,144860587,144860591,14486059 ...

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

Fix Patches (fixSeqLiftOverPsl) Track Description
 

Description

This track shows alignments of fix patch sequences to main chromosome sequences in the reference genome assembly. When errors are corrected in the reference genome assembly, the Genome Reference Consortium (GRC) adds fix patch sequences containing the corrected regions. This strikes a balance between providing the most complete and correct genome sequence, while maintaining stable chromosome coordinates for the original assembly sequences.

Fix patches are often associated with incident reports displayed in the GRC Incidents track.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. Mismatching bases are highlighted in red. Several types of alignment gap may also be colored; for more information, see Alignment Insertion/Deletion Display Options.

Credits

The alignments were provided by NCBI as GFF files and translated into the PSL representation for browser display by UCSC.