Schema for Fix Patches - Reference Assembly Fix Patch Sequence Alignments
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Database: mm10 Primary Table: fixSeqLiftOverPsl Row Count: 162   Data last updated: 2021-05-12
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 94 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 429677 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 3 | int(10) unsigned | range | Number of bases that don't match |
repMatches | 255058 | int(10) unsigned | range | Number of bases that match but are part of repeats |
nCount | 0 | int(10) unsigned | range | Number of 'N' bases |
qNumInsert | 3 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 2204 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 4 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 33347 | int(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_fix | varchar(255) | values | Query sequence name |
qSize | 686942 | int(10) unsigned | range | Query sequence size |
qStart | 0 | int(10) unsigned | range | Alignment start position in query |
qEnd | 686942 | int(10) unsigned | range | Alignment end position in query |
tName | chr1 | varchar(255) | values | Target sequence name |
tSize | 195471971 | int(10) unsigned | range | Target sequence size |
tStart | 22159854 | int(10) unsigned | range | Alignment start position in target |
tEnd | 22877939 | int(10) unsigned | range | Alignment end position in target |
blockCount | 6 | int(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. |
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Sample Rows
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bin | matches | misMatches | repMatches | nCount | qNumInsert | qBaseInsert | tNumInsert | tBaseInsert | strand | qName | qSize | qStart | qEnd | tName | tSize | tStart | tEnd | blockCount | blockSizes | qStarts | tStarts |
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94 | 429677 | 3 | 255058 | 0 | 3 | 2204 | 4 | 33347 | + | chr1_KV575234_fix | 686942 | 0 | 686942 | chr1 | 195471971 | 22159854 | 22877939 | 6 | 265013,3059,5,5233,102,411326, | 0,265139,268200,268205,275514,275616, | 22159854,22424967,22428026,22428032,22466510,22466613, |
30 | 91114 | 0 | 108894 | 0 | 0 | 0 | 1 | 1 | + | chr1_KV575232_fix | 200008 | 0 | 200008 | chr1 | 195471971 | 178144750 | 178344759 | 2 | 131753,68255, | 0,131753, | 178144750,178276504, |
31 | 169054 | 35 | 94190 | 0 | 10 | 2737 | 9 | 50434 | + | chr1_KV575233_fix | 266016 | 0 | 266016 | chr1 | 195471971 | 191793212 | 192106925 | 15 | 164025,5,634,8,16,18,1038,3014,171,39383,8,10,2263,5463,47223, | 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 ... |
80 | 167717 | 15 | 186435 | 0 | 7 | 1446 | 6 | 75682 | + | chr10_KZ289071_fix | 355613 | 0 | 355613 | chr10 | 130694993 | 7346540 | 7776389 | 10 | 155336,12,5,9,3308,3543,38,156,913,190847, | 0,156555,156568,156574,156586,159938,163481,163632,163788,164766, | 7346540,7576744,7576756,7576761,7576770,7580178,7583722,7583860,7584017,7585542, |
1029 | 59256 | 0 | 46112 | 0 | 0 | 0 | 0 | 0 | + | chr10_KQ030491_fix | 129865 | 24497 | 129865 | chr10 | 130694993 | 58205865 | 58311233 | 1 | 105368, | 24497, | 58205865, |
137 | 267959 | 58 | 149273 | 0 | 26 | 8096 | 38 | 8067 | + | chr10_KZ289072_fix | 425386 | 0 | 425386 | chr10 | 130694993 | 67228313 | 67653670 | 49 | 142703,8001,15,35,25,10,21,6930,415,581,1550,22,89,1273,911,1599,10918,4123,499,2,3,8,8,296,1432,15,6744,5721,811,1029,20,723,82 ... | 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 ... |
585 | 59256 | 0 | 46112 | 0 | 0 | 0 | 0 | 0 | + | chr10 | 130694993 | 58205865 | 58311233 | chr10_KQ030491_fix | 129865 | 24497 | 129865 | 1 | 105368, | 58205865, | 24497, |
73 | 167717 | 15 | 186435 | 0 | 6 | 75682 | 7 | 1446 | + | chr10 | 130694993 | 7346540 | 7776389 | chr10_KZ289071_fix | 355613 | 0 | 355613 | 10 | 155336,12,5,9,3308,3543,38,156,913,190847, | 7346540,7576744,7576756,7576761,7576770,7580178,7583722,7583860,7584017,7585542, | 0,156555,156568,156574,156586,159938,163481,163632,163788,164766, |
73 | 267959 | 58 | 149273 | 0 | 38 | 8067 | 26 | 8096 | + | chr10 | 130694993 | 67228313 | 67653670 | chr10_KZ289072_fix | 425386 | 0 | 425386 | 49 | 142703,8001,15,35,25,10,21,6930,415,581,1550,22,89,1273,911,1599,10918,4123,499,2,3,8,8,296,1432,15,6744,5721,811,1029,20,723,82 ... | 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, ... |
80 | 132987 | 0 | 173783 | 0 | 1 | 12145 | 1 | 12145 | + | chr11_KZ289076_fix | 318915 | 0 | 318915 | chr11 | 122082543 | 7560597 | 7879512 | 2 | 196716,110054, | 0,208861, | 7560597,7769458, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Fix Patches (fixSeqLiftOverPsl) Track Description
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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.
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