GRC Patch Release Track Settings
GRCh38 patch release 9, alternate sequences and reference sequence patches   (All Mapping and Sequencing tracks)

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 Haplotypes  New haplotype sequences to GRCh38 Reference Sequence   schema 
 Patches  Patches to GRCh38 Reference Sequence   schema 
 Alignment  Alignments of the patch 9 sequences to the reference GRCh38   schema 
 Chain  GRCh38 patch 9 Sequence Chained Alignments   schema 
 Net  GRCh38 patch 9 Sequence Alignment Net   schema 
Data version: GRCh38 Patch 9 update, Sep. 2016


Patch release 9 is the ninth patch release for the GRCh38 assembly. Patch release 9 includes all contents that were in patch release 8. This is a minor release of GRCh38 that does not disrupt the coordinate system in the reference sequence GRCh38.

Total patch scaffolds in this patch release: 96
Patch scaffolds of type FIX: 48
Patch scaffolds of type NOVEL: 48


Items in the Haplotype track show sequence variation present in the population for certain sections of the genome. Items in this track were either designated as alternate loci or novel patches by the GRC. To view the alternate sequence, click on the "Fetch alternate sequence" link that appears on the sequence details pages. Data points in this track are always displayed in blue.


Items in the Patch track indicate areas of the sequence that have been corrected by the GRC and will be updated to new sequence in the next full human assembly release. To view the new, corrected sequence, click on the "Fetch alternate sequence" link that appears on the sequence details pages. Data points in this track are always displayed in red.


The Alignment track is the PSL representation of the Chain track. This PSL representation allows the side-by-side alignment to be viewed. It was created from the Chain track data using the chainToPsl kent source utility. This track follows the display conventions for PSL alignment tracks. Alignments are displayed in black and, depending on the track configuration settings, may be interspersed with vertical orange lines.

Chain Track

The chain track shows the alignment of human genome alternate sequence to the human Dec. 2013 (GRCh38/hg38) genome sequence using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and the alternate sequence simultaneously.

Net Track

The net track shows the best human/alternate chain for every part of the alternate sequence. It is useful for finding orthologous regions and for studying genome rearrangement. The human sequence used in this annotation is from the Dec. 2013 (GRCh38/hg38) assembly.

In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases, gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth.

In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement.

Individual items in the display are categorized as one of four types (other than gap):

  • Top - The best, longest match. Displayed on level 1.
  • Syn - Line-ups on the same chromosome as the gap in the level above it.
  • Inv - A line-up on the same chromosome as the gap above it, but in the opposite orientation.
  • NonSyn - A match to a chromosome different from the gap in the level above.

Data points in this track are displayed according to the chromosome color key that appears just below the Browser display (e.g., data points on chromosome 21 appear in pink).

The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the alternate sequence. Double lines represent more complex gaps that involve substantial sequence in both sequences.


  • Genome Patch: A sequence contig/scaffold that corrects sequence in a major release of the genome, or adds sequence to it.
  • FIX patch: A patch that corrects sequence or reduces an assembly gap in a given major release. FIX patch sequences are meant to be incorporated into the primary or existing alt-loci assembly units at the next major release, and their accessions will then be deprecated.
  • NOVEL patch: A patch that adds sequence to a major release. Typically, NOVEL patch sequences are meant to be incorporated into the assembly as new alternate loci at the next major release, and their accessions will not be deprecated (UCSC term: "new haplotype sequence").

Patch release 9 summary table

GRCh38 reference
NCBI Entrez
nucleotide record
GRC region
chr1:12818488-13312803 chr1_KQ031383v1_fix PRAME_REGION_1 HG1342_HG2282_PATCHfix-patch
chr1:12818488-13312803 chr1_KQ983255v1_alt PRAME_REGION_1 HSCHR1_5_CTG3novel-patch
chr1:17157487-17460319 chr1_KN538361v1_fix REGION200 HG2095_PATCHfix-patch
chr1:23237486-23579959 chr1_KQ458383v1_alt REGION228 HSCHR1_4_CTG3novel-patch
chr1:26512383-26678582 chr1_KN196473v1_fix REGION189 HG2058_PATCHfix-patch
chr1:41250328-41436604 chr1_KN196472v1_fix FOXO6 HG986_PATCHfix-patch
chr1:103909381-104045121 chr1_KQ458382v1_alt REGION229 HSCHR1_3_CTG3novel-patch
chr1:112909422-113029606 chr1_KN196474v1_fix REGION190 HG2104_PATCHfix-patch
chr1:210220259-210677001 chr1_KN538360v1_fix REGION199 HG1832_PATCHfix-patch
chr1:235360200-235568613 chr1_KQ458384v1_alt TBCE HSCHR1_5_CTG32_1novel-patch
chr10:38918270-39338430 chr10_KN538367v1_fix REGION205 HG2244_HG2245_PATCHfix-patch
chr10:65503225-65684914 chr10_KQ090020v1_alt REGION216 HSCHR10_1_CTG6novel-patch
chr10:74797382-75073121 chr10_KN196480v1_fix REGION195 HG2191_PATCHfix-patch
chr10:87784179-88048756 chr10_KQ090021v1_fix PTEN HG2334_PATCHfix-patch
chr10:124109957-124195365 chr10_KN538366v1_fix REGION204 HG2242_HG2243_PATCHfix-patch
chr10:131588434-131607480 chr10_KN538365v1_fix REGION203 HG2241_PATCHfix-patch
chr11:937258-1207515 chr11_KQ759759v1_fix MUCIN_REGION_1 HG107_PATCHfix-patch
chr11:7779133-7972558 chr11_KN538368v1_alt OLFACTORY_REGION_2 HSCHR11_1_CTG1_2novel-patch
chr11:49958373-50099251 chr11_KV766195v1_fix OLFACTORY_REGION_4 HG1708_PATCHfix-patch
chr11:92232311-92410192 chr11_KQ090022v1_fix REGION215 HG2116_PATCHfix-patch
chr11:118978401-119087276 chr11_KN196481v1_fix SLC37A4 HG2217_PATCHfix-patch
chr12:1033530-1135924 chr12_KQ090023v1_alt REGION217 HSCHR12_2_CTG1novel-patch
chr12:12031003-12572035 chr12_KN538369v1_fix REGION206 HG1362_PATCHfix-patch
chr12:17717409-17928910 chr12_KN196482v1_fix REGION196 HG23_PATCHfix-patch
chr12:86768210-87083988 chr12_KQ759760v1_fix REGION232 HG2063_PATCHfix-patch
chr12:122057735-122145576 chr12_KN538370v1_fix REGION207 HG2247_PATCHfix-patch
chr13:18171249-18358106 chr13_KN538372v1_fix BAGE5 HG2291_PATCHfix-patch
chr13:84294441-84452423 chr13_KQ090024v1_alt REGION218 HSCHR13_1_CTG7novel-patch
chr13:86269523-86292877 chr13_KN196483v1_fix REGION197 HG2216_PATCHfix-patch
chr13:100900735-101049613 chr13_KN538373v1_fix REGION208 HG2249_PATCHfix-patch
chr13:108604134-108722945 chr13_KQ090025v1_alt REGION219 HSCHR13_1_CTG8novel-patch
chr13:113936976-114147229 chr13_KN538371v1_fix REGION209 HG2288_HG2289_PATCHfix-patch
chr15:27865714-32946929 chr15_KQ031389v1_alt REGION25 HSCHR15_6_CTG8novel-patch
chr15_KI270905v1_alt:1-5161414 chr15_KN538374v1_fix REGION1A HG2139_PATCHfix-patch
chr16:2820536-2873621 chr16_KQ090026v1_alt REGION221 HSCHR16_5_CTG1novel-patch
chr16:71137292-71399966 chr16_KQ090027v1_alt REGION220 HSCHR16_4_CTG3_1novel-patch
chr16:75930096-76091406 chr16_KQ031390v1_alt REGION213 HSCHR16_3_CTG3_1novel-patch
chr17:402638-722442 chr17_KV766196v1_fix RFLNB HG2285_HG106_HG2252_PATCHfix-patch
chr17:7379544-7534268 chr17_KV575245v1_fix POLR2A HG2046_PATCHfix-patch
chr17:18239627-18506313 chr17_KV766198v1_alt REGION238 HSCHR17_3_CTG1novel-patch
chr17:52434177-52673566 chr17_KV766197v1_alt REGION237 HSCHR17_11_CTG4novel-patch
chr18:22388680-22588100 chr18_KQ458385v1_alt REGION230 HSCHR18_5_CTG1_1novel-patch
chr18:48514982-48918117 chr18_KQ090028v1_fix CTIF HG2213_PATCHfix-patch
chr19:38590365-38995717 chr19_KQ458386v1_fix REGION231 HG26_PATCHfix-patch
chr19:39740125-40095774 chr19_KN196484v1_fix FCGBP HG2021_PATCHfix-patch
chr19:54025634-55084318 chr19_KV575246v1_alt LRC_KIR HSCHR19KIR_0019-4656-A_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575247v1_alt LRC_KIR HSCHR19KIR_CA01-TA01_1_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575248v1_alt LRC_KIR HSCHR19KIR_CA01-TA01_2_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575249v1_alt LRC_KIR HSCHR19KIR_CA01-TB04_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575250v1_alt LRC_KIR HSCHR19KIR_CA01-TB01_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575251v1_alt LRC_KIR HSCHR19KIR_HG2394_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575252v1_alt LRC_KIR HSCHR19KIR_502960008-2_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575253v1_alt LRC_KIR HSCHR19KIR_502960008-1_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575254v1_alt LRC_KIR HSCHR19KIR_0010-5217-AB_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575255v1_alt LRC_KIR HSCHR19KIR_7191059-1_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575256v1_alt LRC_KIR HSCHR19KIR_0019-4656-B_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575257v1_alt LRC_KIR HSCHR19KIR_CA04_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575258v1_alt LRC_KIR HSCHR19KIR_HG2393_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575259v1_alt LRC_KIR HSCHR19KIR_7191059-2_CTG3_1novel-patch
chr19:54025634-55084318 chr19_KV575260v1_alt LRC_KIR HSCHR19KIR_HG2396_CTG3_1novel-patch
chr2:88891175-89330679 chr2_KQ031384v1_fix IGK HG2290_PATCHfix-patch
chr2:205890983-206421450 chr2_KQ983256v1_alt REGION233 HSCHR2_6_CTG7_2novel-patch
chr2:233054663-233420161 chr2_KN538363v1_fix REGION201 HG2232_PATCHfix-patch
chr2:239696904-239905046 chr2_KN538362v1_fix REGION202 HG2233_PATCHfix-patch
chr22:42077656-42253758 chr22_KN196485v1_alt CYP2D6 HSCHR22_4_CTG1novel-patch
chr22:42077656-42253758 chr22_KN196486v1_alt CYP2D6 HSCHR22_5_CTG1novel-patch
chr22:42077656-42253758 chr22_KQ458387v1_alt CYP2D6 HSCHR22_6_CTG1novel-patch
chr22:42077656-42253758 chr22_KQ458388v1_alt CYP2D6 HSCHR22_7_CTG1novel-patch
chr22:42077656-42253758 chr22_KQ759761v1_alt CYP2D6 HSCHR22_8_CTG1novel-patch
chr22:50663907-50764925 chr22_KQ759762v1_fix SHANK3 HG1311_PATCHfix-patch
chr3:16687511-17099186 chr3_KV766192v1_fix REGION235 HG2236_PATCHfix-patch
chr3:44474647-44925818 chr3_KN196475v1_fix REGION192 HG2066_PATCHfix-patch
chr3:66023201-66396803 chr3_KQ031385v1_fix SLC25A26 HG2235_PATCHfix-patch
chr3:72325441-72740399 chr3_KN538364v1_fix RYBP HG126_PATCHfix-patch
chr3:90528825-90699772 chr3_KQ031386v1_fix REGION210 HG2237_PATCHfix-patch
chr3:91247723-91553319 chr3_KN196476v1_fix REGION191 HG2022_PATCHfix-patch
chr4:14931450-15019028 chr4_KQ090013v1_alt REGION222 HSCHR4_2_CTG4novel-patch
chr4:65880454-66040277 chr4_KQ090014v1_alt REGION223 HSCHR4_8_CTG12novel-patch
chr4:69959865-70191926 chr4_KQ090015v1_alt REGION224 HSCHR4_9_CTG12novel-patch
chr4:154079465-154493046 chr4_KV766193v1_alt REGION236 HSCHR4_12_CTG12novel-patch
chr4:189361858-190204555 chr4_KQ983257v1_fix REGION134 HG2023_PATCHfix-patch
chr4:189361858-190204555 chr4_KQ983258v1_alt REGION134 HSCHR4_11_CTG12novel-patch
chr5:21098347-21230960 chr5_KN196477v1_alt REGION193 HSCHR5_7_CTG1novel-patch
chr5:21481419-21713081 chr5_KV575243v1_alt GUSBP1 HSCHR5_8_CTG1novel-patch
chr5:179235294-179907499 chr5_KV575244v1_fix REGION234 HG30_PATCHfix-patch
chr6:13101650-13179113 chr6_KQ090017v1_alt REGION225 HSCHR6_1_CTG10novel-patch
chr6:61123605-61470683 chr6_KQ031387v1_fix REGION211 HG1651_PATCHfix-patch
chr6:67533466-67796090 chr6_KN196478v1_fix REGION194 HG2128_PATCHfix-patch
chr6:82140389-82375901 chr6_KQ090016v1_fix REGION214 HG2072_PATCHfix-patch
chr6:89804656-89941739 chr6_KV766194v1_fix CASP8AP2 HG2121_PATCHfix-patch
chr7:154422352-154602937 chr7_KQ031388v1_fix REGION212 HG2239_PATCHfix-patch
chr9:8983671-9142737 chr9_KQ090018v1_alt REGION226 HSCHR9_1_CTG6novel-patch
chr9:24949709-25079413 chr9_KQ090019v1_alt REGION227 HSCHR9_1_CTG7novel-patch
chr9:133174055-133504070 chr9_KN196479v1_fix ABO HG2030_PATCHfix-patch
chrX:4950957-5129468 chrX_KV766199v1_alt REGION239 HSCHRX_3_CTG7novel-patch
chrY:56821510-56887902 chrY_KN196487v1_fix REGION198 HG2062_PATCHfix-patch


Data obtained from the Genome Reference Consortium:   FTP.