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GRCm38 patch release 4, alternate sequences and reference sequence patches   (All Mapping and Sequencing tracks)

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 Haplotypes  New haplotype sequences to GRCm38 Reference Sequence   Schema 
 
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 Alignment  Alignments of the patch 4 sequences to the reference GRCm38   Schema 
 
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Data version: GRCm38 Patch 4 update, Dec. 2015

Description

Patch release 4 is the fourth patch release for the GRCm38 assembly. Patch release 4 includes all contents that were in patch release 3. This is a minor release of GRCm38 that does not disrupt the coordinate system in the reference sequence GRCm38.

Total patch scaffolds in this patch release: 122
Patch scaffolds of type FIX: 29
Patch scaffolds of type NOVEL: 93

Definitions

  • ALT scaffold: A sequence contig/scaffold that is a haplotype sequence to the reference genome indicated location.
  • 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 4 summary table

GRCm38 reference
location
NCBI Entrez
nucleotide record
GRC region
name
sequence
name
patch
type
chr1:60640809-63588262 chr1_JH584320_alt NOD_mouse_Idd5.1 MMCHR1_NOD_IDD5_1alt-scaffold
chr1:60640809-63588262 chr1_KK082441_alt NOD_mouse_Idd5.1 MMCHR1_CHORI29_IDD5_1novel-patch
chr1:65597865-69265254 chr1_JH584321_alt NOD_mouse_Idd5.3 MMCHR1_NOD_IDD5_3alt-scaffold
chr1:78413759-78687489 chr1_GL455993_alt region4 129S6/SVEVTAC_MMCHR1_CTG1alt-scaffold
chr1:130311064-130653047 chr1_JH584322_alt NOD_mouse_Idd5.4 MMCHR1_NOD_IDD5_4alt-scaffold
chr1:133239136-133489442 chr1_GL455991_alt Ren2 129S6/SVEVTAC_MMCHR1_CTG3alt-scaffold
chr1:173701136-174051183 chr1_GL455992v2_alt Ifi_cluster 129S6/SVEVTAC_MMCHR1_CTG4alt-scaffold
chr1:173701136-174051183 chr1_GL456005_alt Ifi_cluster 129X1/SVJ_MMCHR1_CTG2alt-scaffold
chr1:173701136-174051183 chr1_JH584315_alt Ifi_cluster 129X1/SVJ_MMCHR1_CTG1alt-scaffold
chr10:10861646-10927384 chr10_GL456015_alt Grm1 UNKNOWN_MMCHR10_CTG3alt-scaffold
chr10:58205866-58311233 chr10_KQ030491_fix region81 MG4264_PATCHfix-patch
chr11:48799134-49141362 chr11_JH584316_alt region60 CAST/EI_MMCHR11_CTG1alt-scaffold
chr11:58115562-58302084 chr11_JH584317_alt region61 CAST/EI_MMCHR11_CTG3alt-scaffold
chr11:58613181-58787285 chr11_GL455998_alt olfactory_region_1 129S6/SVEVTAC_MMCHR11_CTG1alt-scaffold
chr11:69895472-71298870 chr11_JH584327_alt NOD_mouse_Idd4.1 MMCHR11_NOD_IDD4_1alt-scaffold
chr11:72908911-74370562 chr11_GL456060v2_alt NOD_mouse_Idd4.2 MMCHR11_NOD_IDD4_2alt-scaffold
chr11:86869779-89954755 chr11_JH584265_alt NOD_mouse_Idd4.2Q MMCHR11_CHORI29_IDD4_2Qalt-scaffold
chr11:86869779-89954755 chr11_KB469739_fix NOD_mouse_Idd4.2Q MG3829_PATCHfix-patch
chr11:104203258-104362532 chr11_GL456016_alt Mapt 129X1/SVJ_MMCHR11_CTG3alt-scaffold
chr12:103722705-103922810 chr12_GL456074_alt Serpin_region_1 129S1/SVIMJ_MMCHR12_CTG3alt-scaffold
chr12:105147714-105196166 chr12_GL456349_alt Tcl1_region_1 RIII_MMCHR12_CTG1alt-scaffold
chr12:109373903-109689534 chr12_KB469740_fix Meg3 MG4180_PATCHfix-patch
chr12:113067904-114458697 chr12_GL456017v2_alt Igh 129S1/SVIMJ_MMCHR12_CTG1alt-scaffold
chr12:113067904-114458697 chr12_GL456068_alt Igh BALB/C_MMCHR12_CTG1alt-scaffold
chr12:113067904-114458697 chr12_GL456078_alt Igh 129S7/SVEVBRD-HPRT-B-M2_MMCHR12_CTG2alt-scaffold
chr13:100075065-100330017 chr13_GL455990_alt Naip2_Naip5 A/J_MMCHR13_CTG1alt-scaffold
chr13:100075065-100330017 chr13_JH584305_alt Naip2_Naip5 129S1/SVIMJ_MMCHR13_CTG1alt-scaffold
chr13:106801073-106932896 chr13_GL455999v2_alt Ipo11 129S6/SVEVTAC_MMCHR13_CTG1alt-scaffold
chr14:51863012-51973562 chr14_GL456020_alt region17 129X1/SVJ_MMCHR14_CTG1alt-scaffold
chr14:52352473-54229076 chr14_GL456019_alt Tcra_Tcrd 129S1/SVIMJ_MMCHR14_CTG3alt-scaffold
chr15:3050001-3186530 chr15_KQ030492_fix region82 MG4259_PATCHfix-patch
chr15:38882451-39142852 chr15_KQ030493_fix Baalc MG4261_PATCHfix-patch
chr15:79892564-79986558 chr15_JH584270_alt region65 129S7/SVEVBRD-HPRT-B-M2_MMCHR15_CTG1alt-scaffold
chr15:80502872-80672368 chr15_GL456000_alt region19 129S6/SVEVTAC_MMCHR15_CTG1alt-scaffold
chr16:17742495-19065968 chr16_GL456028v2_alt DiGeorge 129X1/SVJ_MMCHR16_CTG1alt-scaffold
chr16:17742495-19065968 chr16_JH584306_alt DiGeorge 129S1/SVIMJ_MMCHR16_CTG1alt-scaffold
chr16:17742495-19065968 chr16_JH584307_alt DiGeorge 129S1/SVIMJ_MMCHR16_CTG2alt-scaffold
chr16:17742495-19065968 chr16_JH584310_alt DiGeorge 129S6/SVEVTAC_MMCHR16_CTG1alt-scaffold
chr16:17742495-19065968 chr16_JH584311_alt DiGeorge 129S6/SVEVTAC_MMCHR16_CTG2alt-scaffold
chr16:17742495-19065968 chr16_JH584312_alt DiGeorge 129S6/SVEVTAC_MMCHR16_CTG3alt-scaffold
chr16:17742495-19065968 chr16_KB469741_fix DiGeorge MG3833_PATCHfix-patch
chr16:94114272-95747459 chr16_GL456001v2_alt DownSynCrit_region_1 129S6/SVEVTAC_MMCHR16_CTG6alt-scaffold
chr16:95846204-96221063 chr16_JH584313_alt DownSynCrit_region_2 129S6/SVEVTAC_MMCHR16_CTG4alt-scaffold
chr16:97054368-97223607 chr16_JH584314_alt DownSynCrit_region_3 129S6/SVEVTAC_MMCHR16_CTG5alt-scaffold
chr17:12729292-12861171 chr17_GL456069_alt Airn UNKNOWN_MMCHR17_CTG3alt-scaffold
chr17:27313323-29215977 chr17_JH584267_alt NOD_mouse_Idd16.1 MMCHR17_CHORI29_IDD16_1alt-scaffold
chr17:33681276-38548659 chr17_GL456002v2_alt MHC 129S6/SVEVTAC_MMCHR17_CTG2alt-scaffold
chr17:33681276-38548659 chr17_GL456021v2_alt MHC 129S6/SVEVTAC_MMCHR17_CTG1alt-scaffold
chr17:33681276-38548659 chr17_GL456022v2_alt MHC 129X1/SVJ_MMCHR17_CTG2alt-scaffold
chr17:33681276-38548659 chr17_JH584266_alt MHC MMCHR17_CHO_IDD1alt-scaffold
chr17:33681276-38548659 chr17_JH584308_alt MHC 129S1/SVIMJ_MMCHR17_CTG3alt-scaffold
chr17:33681276-38548659 chr17_JH584309_alt MHC 129S1/SVIMJ_MMCHR17_CTG4alt-scaffold
chr17:33681276-38548659 chr17_JH584328_alt MHC MMCHR17_NOD_IDD1alt-scaffold
chr17:33681276-38548659 chr17_JH590470_alt MHC 129S1/SVIMJ_MMCHR17_CTG2alt-scaffold
chr17:54687402-55747384 chr17_KB469742_fix region78 MG4222_MG3908_PATCHfix-patch
chr18:11238883-11458280 chr18_GL456070_alt Impact RIII_MMCHR18_CTG1alt-scaffold
chr18:11238883-11458280 chr18_JH792829_fix Impact MG3835_PATCHfix-patch
chr18:60125920-60496981 chr18_JH584318_alt region70 CAST/EI_MMCHR18_CTG1alt-scaffold
chr19:4013986-4260737 chr19_JH792830_fix Tmem134 MG153_PATCHfix-patch
chr19:5679043-5707799 chr19_GL456079_alt region28 129P2/OLAHSD_MMCHR19_CTG1alt-scaffold
chr19:6183084-6688105 chr19_KQ030494_fix region83 MG4249_PATCHfix-patch
chr19:28892559-28918752 chr19_JH584319_alt Slc1a1 UNKNOWN_MMCHR19_CTG2alt-scaffold
chr2:102983310-103388989 chr2_GL456024v2_alt region29 129S1/SVIMJ_MMCHR2_CTG2alt-scaffold
chr3:15760691-15949398 chr3_KQ030484_fix region80 MG4248_PATCHfix-patch
chr3:36806723-37563603 chr3_GL456006_alt NOD_mouse_Idd3.1 129S1/SVIMJ_MMCHR3_CTG3alt-scaffold
chr3:36806723-37563603 chr3_GL456007_alt NOD_mouse_Idd3.1 129S1/SVIMJ_MMCHR3_CTG2alt-scaffold
chr3:36806723-37563603 chr3_GL456045v2_alt NOD_mouse_Idd3.1 MMCHR3_NODMRKTAC_CTG1alt-scaffold
chr3:36806723-37563603 chr3_GL456048_alt NOD_mouse_Idd3.1 MMCHR3_NOD_IDD3_1alt-scaffold
chr3:47447005-47679964 chr3_GL456049v2_alt region31 MMCHR3_NODMRKTAC_CTG2alt-scaffold
chr3:93583858-93685263 chr3_GL456008_alt Tdpoz_cluster 129S1/SVIMJ_MMCHR3_CTG4alt-scaffold
chr3:99953865-101307585 chr3_JH584323_alt NOD_mouse_Idd10.1 MMCHR3_NOD_IDD10_1alt-scaffold
chr3:103590378-104055839 chr3_GL456044v2_alt NOD_mouse_Idd18.2 MMCHR3_NOD_IDD18_2alt-scaffold
chr3:109116720-109807685 chr3_GL456042v2_alt NOD_mouse_Idd18.1 MMCHR3_NOD_IDD18_1alt-scaffold
chr4:43762692-43857014 chr4_GL456010_alt olfactory_region_2 129X1/SVJ_MMCHR4_CTG2alt-scaffold
chr4:59870283-60154907 chr4_JH584269_alt Mup_region_3 129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG6alt-scaffold
chr4:60250666-61586638 chr4_GL456077_alt Mup_region_4 129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG4alt-scaffold
chr4:60250666-61586638 chr4_JH584268_alt Mup_region_4 129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG5alt-scaffold
chr4:60250666-61586638 chr4_KQ030485_fix Mup_region_4 MG3561_PATCHfix-patch
chr4:60250666-61586638 chr4_KQ030486_fix Mup_region_4 MG3562_PATCHfix-patch
chr4:61778759-62041201 chr4_GL456075_alt Mup_region_1 129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG2alt-scaffold
chr4:62045255-62237529 chr4_GL456076_alt Mup_region_2 129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG3alt-scaffold
chr4:67057602-67195172 chr4_GL456064_alt region40 UNKNOWN_MMCHR4_CTG1alt-scaffold
chr4:122217500-122473817 chr4_KQ030487_fix region79 MG3609_PATCHfix-patch
chr4:128397119-131686709 chr4_JH584324_alt NOD_mouse_Idd9.1 MMCHR4_NOD_IDD9_1alt-scaffold
chr4:128397119-131686709 chr4_KQ030488_fix NOD_mouse_Idd9.1 MG4265_PATCHfix-patch
chr4:128397119-131686709 chr4_KQ030489_fix NOD_mouse_Idd9.1 MG4266_PATCHfix-patch
chr4:135021547-135237421 chr4_JH584325_alt NOD_mouse_Idd9.1M MMCHR4_NOD_IDD9_1Malt-scaffold
chr4:140721097-140961448 chr4_GL456009_alt Padi_cluster UNKNOWN_MMCHR4_CTG7alt-scaffold
chr4:143214657-143582942 chr4_JH792826_fix region71 MG4136_PATCHfix-patch
chr4:144179444-144348902 chr4_GL455994_alt Prame_region_1 129S6/SVEVTAC_MMCHR4_CTG1alt-scaffold
chr4:146068508-151320022 chr4_GL456053v2_alt NOD_mouse_Idd9.2_Idd9.3 MMCHR4_NOD_IDD9_2alt-scaffold
chr4:146068508-151320022 chr4_JH584326_alt NOD_mouse_Idd9.2_Idd9.3 MMCHR4_NOD_IDD9_3alt-scaffold
chr5:15457667-15635395 chr5_JH792827_fix region75 MG4212_PATCHfix-patch
chr5:90653128-90826761 chr5_GL456011_alt region44 129S1/SVIMJ_MMCHR5_CTG5alt-scaffold
chr5:150872255-151123781 chr5_GL455995_alt region45 129S6/SVEVTAC_MMCHR5_CTG1alt-scaffold
chr6:50779502-50919227 chr6_GL456025_alt region46 129S1/SVIMJ_MMCHR6_CTG1alt-scaffold
chr6:72296717-72451483 chr6_KK082442_fix Sftpb MG184_PATCHfix-patch
chr6:82734575-83039841 chr6_GL456012v2_alt region47 129X1/SVJ_MMCHR6_CTG1alt-scaffold
chr6:89851149-90290463 chr6_GL456065_alt vomeronasal_region_1 129X1/SVJ_MMCHR6_CTG3alt-scaffold
chr6:120377222-121015201 chr6_GL456026v2_alt region49 129S1/SVIMJ_MMCHR6_CTG5alt-scaffold
chr6:129636567-130656471 chr6_JH584264_alt NOD_mouse_Idd6.3 MMCHR6_CHORI29_IDD6_3alt-scaffold
chr6:143536594-149568188 chr6_GL456054v2_alt NOD_mouse_Idd6.1+2 MMCHR6_CHORI29_IDD6_1+2alt-scaffold
chr7:3000001-3475222 chr7_JH792828_fix region72 MG4151_PATCHfix-patch
chr7:27743215-27826849 chr7_GL456014_alt region51 129S1/SVIMJ_MMCHR7_CTG1alt-scaffold
chr7:103811478-103860690 chr7_GL455989_alt Hbb_cluster BALB/C_MMCHR7_CTG1alt-scaffold
chr7:106888710-106927250 chr7_GL456013_alt olfactory_region_3 129S2/SVPAS_MMCHR7_CTG1alt-scaffold
chr8:41292834-41482533 chr8_GL455996_alt region54 129S6/SVEVTAC_MMCHR8_CTG1alt-scaffold
chr8:73065642-73319050 chr8_GL455997_alt Large 129S6/SVEVTAC_MMCHR8_CTG2alt-scaffold
chr9:108784955-108953239 chr9_KQ030490_fix Slc26a6 MG117_PATCHfix-patch
chr9:124268539-124479149 chr9_KB469738v3_fix Nlrp4g MG132_PATCHfix-patch
chrX:29000987-29562451 chrX_KQ030496_fix region85 MG4254_PATCHfix-patch
chrX:29000987-29562451 chrX_KQ030497_fix region85 MG4255_PATCHfix-patch
chrX:37804742-37986547 chrX_JH792831_fix region77 MG4214_PATCHfix-patch
chrX:42891057-43298842 chrX_GL456003v2_alt Odz1 129S6/SVEVTAC_MMCHRX_CTG2alt-scaffold
chrX:60271962-60763715 chrX_KQ030495_fix region84 MG3231_PATCHfix-patch
chrX:72166181-72363206 chrX_GL456032_alt region57 129S1/SVIMJ_MMCHRX_CTG3alt-scaffold
chrX:73003651-73121964 chrX_GL456004_alt Xlr_region_1 129S6/SVEVTAC_MMCHRX_CTG6alt-scaffold
chrX:73185425-73263090 chrX_GL456033v2_alt Xlr_region_2 129S1/SVIMJ_MMCHRX_CTG7alt-scaffold
chrX:103589284-103841870 chrX_GL456031_alt Xic 129S1/SVIMJ_MMCHRX_CTG10alt-scaffold
chrY:45842743-46337667 chrY_JH792832_fix region73 MG4209_PATCHfix-patch
chrY:49216909-49556418 chrY_JH792834_fix region76 MG4213_PATCHfix-patch
chrY:66019703-66188541 chrY_JH792833_fix region74 MG4211_PATCHfix-patch

References

Data obtained from the FTP site of the Genome Reference Consortium.