Schema for Fix Patches - Reference Assembly Fix Patch Sequence Alignments
  Database: mm10    Primary Table: fixSeqLiftOverPsl    Row Count: 162   Data last updated: 2021-05-12
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 94smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 429677int(10) unsigned range Number of bases that match that aren't repeats
misMatches 3int(10) unsigned range Number of bases that don't match
repMatches 255058int(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 2204int(10) unsigned range Number of bases inserted in query
tNumInsert 4int(10) unsigned range Number of inserts in target
tBaseInsert 33347int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName chr1_KV575234_fixvarchar(255) values Query sequence name
qSize 686942int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 686942int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 195471971int(10) unsigned range Target sequence size
tStart 22159854int(10) unsigned range Alignment start position in target
tEnd 22877939int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 265013,3059,5,5233,102,411326,longblob   Size of each block
qStarts 0,265139,268200,268205,2755...longblob   Start of each block in query.
tStarts 22159854,22424967,22428026,...longblob   Start of each block in target.

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
944296773255058032204433347+chr1_KV575234_fix6869420686942chr119547197122159854228779396265013,3059,5,5233,102,411326,0,265139,268200,268205,275514,275616,22159854,22424967,22428026,22428032,22466510,22466613,
3091114010889400011+chr1_KV575232_fix2000080200008chr11954719711781447501783447592131753,68255,0,131753,178144750,178276504,
3116905435941900102737950434+chr1_KV575233_fix2660160266016chr119547197119179321219210692515164025,5,634,8,16,18,1038,3014,171,39383,8,10,2263,5463,47223,0,164025,164063,164697,164706,164722,164743,165781,168839,169011,208395,208404,210804,213230,218793,191793212,191957238,191957361,191957997,191958005,191958023,191958041,191959081,191962203,191962374,192001757,192001765,19205177 ...
8016771715186435071446675682+chr10_KZ289071_fix3556130355613chr101306949937346540777638910155336,12,5,9,3308,3543,38,156,913,190847,0,156555,156568,156574,156586,159938,163481,163632,163788,164766,7346540,7576744,7576756,7576761,7576770,7580178,7583722,7583860,7584017,7585542,
10295925604611200000+chr10_KQ030491_fix12986524497129865chr1013069499358205865583112331105368,24497,58205865,
137267959581492730268096388067+chr10_KZ289072_fix4253860425386chr10130694993672283136765367049142703,8001,15,35,25,10,21,6930,415,581,1550,22,89,1273,911,1599,10918,4123,499,2,3,8,8,296,1432,15,6744,5721,811,1029,20,723,82 ...0,142717,150719,150735,150771,150797,150808,150891,157822,158237,158856,160407,160430,160971,162315,163226,166503,180797,185259, ...67228313,67371117,67379118,67379133,67379168,67379193,67379203,67379324,67386254,67386672,67387418,67388968,67388990,67389179,67 ...
5855925604611200000+chr101306949935820586558311233chr10_KQ030491_fix129865244971298651105368,58205865,24497,
7316771715186435067568271446+chr1013069499373465407776389chr10_KZ289071_fix355613035561310155336,12,5,9,3308,3543,38,156,913,190847,7346540,7576744,7576756,7576761,7576770,7580178,7583722,7583860,7584017,7585542,0,156555,156568,156574,156586,159938,163481,163632,163788,164766,
73267959581492730388067268096+chr101306949936722831367653670chr10_KZ289072_fix425386042538649142703,8001,15,35,25,10,21,6930,415,581,1550,22,89,1273,911,1599,10918,4123,499,2,3,8,8,296,1432,15,6744,5721,811,1029,20,723,82 ...67228313,67371117,67379118,67379133,67379168,67379193,67379203,67379324,67386254,67386672,67387418,67388968,67388990,67389179,67 ...0,142717,150719,150735,150771,150797,150808,150891,157822,158237,158856,160407,160430,160971,162315,163226,166503,180797,185259, ...
8013298701737830112145112145+chr11_KZ289076_fix3189150318915chr11122082543756059778795122196716,110054,0,208861,7560597,7769458,

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.