==============================================================================
This file is from:

  http://hgdownloads.cse.ucsc.edu/goldenPath/mm10/mm10Patch4/README.txt

GRCm38.p4 data is from:

ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCA_000001635.6_GRCm38.p4/

Files in this directory:

mm10Patch4.fa.gz - GRCm38.p4 fasta sequences
mm10Patch4.2bit - GRCm38.p4 sequences in 2bit format
mm10Patch4.agp - GRCm38.p4 AGP structure definitions
md5sum.txt - MD5 sums to verify downloads of these files


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

==============================================================================
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"


Total patch scaffolds in this patch release: 130
   92 patch scaffolds of type ALT scaffold (== haplotype)
   29 patch scaffolds of type FIX
    1 patch scaffolds of type NOVEL
    8 alternate strain sequences (no placement on reference GRCm38)

==============================================================================

GRCm38 reference         NCBI Entrez            GRC region    sequence   patch
location                 nucleotide record      name          name       type

chr1:60640809-63588262   KK082441.1 NOD_mouse_Idd5.1 MMCHR1_CHORI29_IDD5_1 novel-patch
chr3:15760691-15949398   KQ030484.1 region80 MG4248_PATCH fix-patch
chr4:143214657-143582942 JH792826.1 region71 MG4136_PATCH fix-patch
chr4:60250666-61586638   KQ030485.1 Mup_region_4 MG3561_PATCH fix-patch
chr4:60250666-61586638   KQ030486.1 Mup_region_4 MG3562_PATCH fix-patch
chr4:122217500-122473817 KQ030487.1 region79 MG3609_PATCH fix-patch
chr4:128397119-131686709 KQ030488.1 NOD_mouse_Idd9.1 MG4265_PATCH fix-patch
chr4:128397119-131686709 KQ030489.1 NOD_mouse_Idd9.1 MG4266_PATCH fix-patch
chr5:15457667-15635395   JH792827.1 region75 MG4212_PATCH fix-patch
chr6:72296717-72451483   KK082442.1 Sftpb MG184_PATCH fix-patch
chr7:3000001-3475222     JH792828.1 region72 MG4151_PATCH fix-patch
chr9:124268539-124479149 KB469738.3 Nlrp4g MG132_PATCH fix-patch
chr9:108784955-108953239 KQ030490.1 Slc26a6 MG117_PATCH fix-patch
chr10:58205866-58311233  KQ030491.1 region81 MG4264_PATCH fix-patch
chr11:86869779-89954755  KB469739.1 NOD_mouse_Idd4.2Q MG3829_PATCH fix-patch
chr12:109373903-109689534 KB469740.1 Meg3 MG4180_PATCH fix-patch
chr15:3050001-3186530    KQ030492.1 region82 MG4259_PATCH fix-patch
chr15:38882451-39142852  KQ030493.1 Baalc MG4261_PATCH fix-patch
chr16:17742495-19065968  KB469741.1 DiGeorge MG3833_PATCH fix-patch
chr17:54687402-55747384  KB469742.1 region78 MG4222_MG3908_PATCH fix-patch
chr18:11238883-11458280  JH792829.1 Impact MG3835_PATCH fix-patch
chr19:4013986-4260737    JH792830.1 Tmem134 MG153_PATCH fix-patch
chr19:6183084-6688105    KQ030494.1 region83 MG4249_PATCH fix-patch
chrX:37804742-37986547   JH792831.1 region77 MG4214_PATCH fix-patch
chrX:60271962-60763715   KQ030495.1 region84 MG3231_PATCH fix-patch
chrX:29000987-29562451   KQ030496.1 region85 MG4254_PATCH fix-patch
chrX:29000987-29562451   KQ030497.1 region85 MG4255_PATCH fix-patch
chrY:45842743-46337667   JH792832.1 region73 MG4209_PATCH fix-patch
chrY:66019703-66188541   JH792833.1 region74 MG4211_PATCH fix-patch
chrY:49216909-49556418   JH792834.1 region76 MG4213_PATCH fix-patch
chr19:5679043-5707799    GL456079.1 region28 129P2/OLAHSD_MMCHR19_CTG1 alt-scaffold
chr2:102983310-103388989 GL456024.2 region29 129S1/SVIMJ_MMCHR2_CTG2 alt-scaffold
chr3:36806723-37563603   GL456006.1 NOD_mouse_Idd3.1 129S1/SVIMJ_MMCHR3_CTG3 alt-scaffold
chr3:36806723-37563603   GL456007.1 NOD_mouse_Idd3.1 129S1/SVIMJ_MMCHR3_CTG2 alt-scaffold
chr3:93583858-93685263   GL456008.1 Tdpoz_cluster 129S1/SVIMJ_MMCHR3_CTG4 alt-scaffold
chr5:90653128-90826761   GL456011.1 region44 129S1/SVIMJ_MMCHR5_CTG5 alt-scaffold
chr6:50779502-50919227   GL456025.1 region46 129S1/SVIMJ_MMCHR6_CTG1 alt-scaffold
chr6:120377222-121015201 GL456026.2 region49 129S1/SVIMJ_MMCHR6_CTG5 alt-scaffold
chr7:27743215-27826849   GL456014.1 region51 129S1/SVIMJ_MMCHR7_CTG1 alt-scaffold
chr12:113067904-114458697 GL456017.2 Igh 129S1/SVIMJ_MMCHR12_CTG1 alt-scaffold
chr12:103722705-103922810 GL456074.1 Serpin_region_1 129S1/SVIMJ_MMCHR12_CTG3 alt-scaffold
chr13:100075065-100330017 JH584305.1 Naip2_Naip5 129S1/SVIMJ_MMCHR13_CTG1 alt-scaffold
chr14:52352473-54229076  GL456019.1 Tcra_Tcrd 129S1/SVIMJ_MMCHR14_CTG3 alt-scaffold
chr16:17742495-19065968  JH584306.1 DiGeorge 129S1/SVIMJ_MMCHR16_CTG1 alt-scaffold
chr16:17742495-19065968  JH584307.1 DiGeorge 129S1/SVIMJ_MMCHR16_CTG2 alt-scaffold
chr17:33681276-38548659  JH584308.1 MHC 129S1/SVIMJ_MMCHR17_CTG3 alt-scaffold
chr17:33681276-38548659  JH584309.1 MHC 129S1/SVIMJ_MMCHR17_CTG4 alt-scaffold
chr17:33681276-38548659  JH590470.1 MHC 129S1/SVIMJ_MMCHR17_CTG2 alt-scaffold
chrX:103589284-103841870 GL456031.1 Xic 129S1/SVIMJ_MMCHRX_CTG10 alt-scaffold
chrX:72166181-72363206   GL456032.1 region57 129S1/SVIMJ_MMCHRX_CTG3 alt-scaffold
chrX:73185425-73263090   GL456033.2 Xlr_region_2 129S1/SVIMJ_MMCHRX_CTG7 alt-scaffold
chr7:106888710-106927250 GL456013.1 olfactory_region_3 129S2/SVPAS_MMCHR7_CTG1 alt-scaffold
chr1:133239136-133489442 GL455991.1 Ren2 129S6/SVEVTAC_MMCHR1_CTG3 alt-scaffold
chr1:173701136-174051183 GL455992.2 Ifi_cluster 129S6/SVEVTAC_MMCHR1_CTG4 alt-scaffold
chr1:78413759-78687489   GL455993.1 region4 129S6/SVEVTAC_MMCHR1_CTG1 alt-scaffold
chr4:144179444-144348902 GL455994.1 Prame_region_1 129S6/SVEVTAC_MMCHR4_CTG1 alt-scaffold
chr5:150872255-151123781 GL455995.1 region45 129S6/SVEVTAC_MMCHR5_CTG1 alt-scaffold
chr8:41292834-41482533   GL455996.1 region54 129S6/SVEVTAC_MMCHR8_CTG1 alt-scaffold
chr8:73065642-73319050   GL455997.1 Large 129S6/SVEVTAC_MMCHR8_CTG2 alt-scaffold
chr11:58613181-58787285  GL455998.1 olfactory_region_1 129S6/SVEVTAC_MMCHR11_CTG1 alt-scaffold
chr13:106801073-106932896 GL455999.2 Ipo11 129S6/SVEVTAC_MMCHR13_CTG1 alt-scaffold
chr15:80502872-80672368  GL456000.1 region19 129S6/SVEVTAC_MMCHR15_CTG1 alt-scaffold
chr16:94114272-95747459  GL456001.2 DownSynCrit_region_1 129S6/SVEVTAC_MMCHR16_CTG6 alt-scaffold
chr16:17742495-19065968  JH584310.1 DiGeorge 129S6/SVEVTAC_MMCHR16_CTG1 alt-scaffold
chr16:17742495-19065968  JH584311.1 DiGeorge 129S6/SVEVTAC_MMCHR16_CTG2 alt-scaffold
chr16:17742495-19065968  JH584312.1 DiGeorge 129S6/SVEVTAC_MMCHR16_CTG3 alt-scaffold
chr16:95846204-96221063  JH584313.1 DownSynCrit_region_2 129S6/SVEVTAC_MMCHR16_CTG4 alt-scaffold
chr16:97054368-97223607  JH584314.1 DownSynCrit_region_3 129S6/SVEVTAC_MMCHR16_CTG5 alt-scaffold
chr17:33681276-38548659  GL456002.2 MHC 129S6/SVEVTAC_MMCHR17_CTG2 alt-scaffold
chr17:33681276-38548659  GL456021.2 MHC 129S6/SVEVTAC_MMCHR17_CTG1 alt-scaffold
chrX:42891057-43298842   GL456003.2 Odz1 129S6/SVEVTAC_MMCHRX_CTG2 alt-scaffold
chrX:73003651-73121964   GL456004.1 Xlr_region_1 129S6/SVEVTAC_MMCHRX_CTG6 alt-scaffold
chr1:173701136-174051183 GL456005.1 Ifi_cluster 129X1/SVJ_MMCHR1_CTG2 alt-scaffold
chr1:173701136-174051183 JH584315.1 Ifi_cluster 129X1/SVJ_MMCHR1_CTG1 alt-scaffold
chr4:43762692-43857014   GL456010.1 olfactory_region_2 129X1/SVJ_MMCHR4_CTG2 alt-scaffold
chr6:82734575-83039841   GL456012.2 region47 129X1/SVJ_MMCHR6_CTG1 alt-scaffold
chr6:89851149-90290463   GL456065.1 vomeronasal_region_1 129X1/SVJ_MMCHR6_CTG3 alt-scaffold
chr11:104203258-104362532 GL456016.1 Mapt 129X1/SVJ_MMCHR11_CTG3 alt-scaffold
chr14:51863012-51973562  GL456020.1 region17 129X1/SVJ_MMCHR14_CTG1 alt-scaffold
chr16:17742495-19065968  GL456028.2 DiGeorge 129X1/SVJ_MMCHR16_CTG1 alt-scaffold
chr17:33681276-38548659  GL456022.2 MHC 129X1/SVJ_MMCHR17_CTG2 alt-scaffold
chr13:100075065-100330017 GL455990.1 Naip2_Naip5 A/J_MMCHR13_CTG1 alt-scaffold
chr7:103811478-103860690 GL455989.1 Hbb_cluster BALB/C_MMCHR7_CTG1 alt-scaffold
chr12:113067904-114458697 GL456068.1 Igh BALB/C_MMCHR12_CTG1 alt-scaffold
chr11:48799134-49141362  JH584316.1 region60 CAST/EI_MMCHR11_CTG1 alt-scaffold
chr11:58115562-58302084  JH584317.1 region61 CAST/EI_MMCHR11_CTG3 alt-scaffold
chr18:60125920-60496981  JH584318.1 region70 CAST/EI_MMCHR18_CTG1 alt-scaffold
chr1:60640809-63588262   JH584320.1 NOD_mouse_Idd5.1 MMCHR1_NOD_IDD5_1 alt-scaffold
chr1:65597865-69265254   JH584321.1 NOD_mouse_Idd5.3 MMCHR1_NOD_IDD5_3 alt-scaffold
chr1:130311064-130653047 JH584322.1 NOD_mouse_Idd5.4 MMCHR1_NOD_IDD5_4 alt-scaffold
chr3:109116720-109807685 GL456042.2 NOD_mouse_Idd18.1 MMCHR3_NOD_IDD18_1 alt-scaffold
chr3:103590378-104055839 GL456044.2 NOD_mouse_Idd18.2 MMCHR3_NOD_IDD18_2 alt-scaffold
chr3:36806723-37563603   GL456045.2 NOD_mouse_Idd3.1 MMCHR3_NODMRKTAC_CTG1 alt-scaffold
chr3:36806723-37563603   GL456048.1 NOD_mouse_Idd3.1 MMCHR3_NOD_IDD3_1 alt-scaffold
chr3:47447005-47679964   GL456049.2 region31 MMCHR3_NODMRKTAC_CTG2 alt-scaffold
chr3:99953865-101307585  JH584323.1 NOD_mouse_Idd10.1 MMCHR3_NOD_IDD10_1 alt-scaffold
chr4:146068508-151320022 GL456053.2 NOD_mouse_Idd9.2_Idd9.3 MMCHR4_NOD_IDD9_2 alt-scaffold
chr4:128397119-131686709 JH584324.1 NOD_mouse_Idd9.1 MMCHR4_NOD_IDD9_1 alt-scaffold
chr4:135021547-135237421 JH584325.1 NOD_mouse_Idd9.1M MMCHR4_NOD_IDD9_1M alt-scaffold
chr4:146068508-151320022 JH584326.1 NOD_mouse_Idd9.2_Idd9.3 MMCHR4_NOD_IDD9_3 alt-scaffold
chr11:72908911-74370562  GL456060.2 NOD_mouse_Idd4.2 MMCHR11_NOD_IDD4_2 alt-scaffold
chr11:69895472-71298870  JH584327.1 NOD_mouse_Idd4.1 MMCHR11_NOD_IDD4_1 alt-scaffold
chr17:33681276-38548659  JH584328.1 MHC MMCHR17_NOD_IDD1 alt-scaffold
chr6:143536594-149568188 GL456054.2 NOD_mouse_Idd6.1+2 MMCHR6_CHORI29_IDD6_1+2 alt-scaffold
chr6:129636567-130656471 JH584264.1 NOD_mouse_Idd6.3 MMCHR6_CHORI29_IDD6_3 alt-scaffold
chr11:86869779-89954755  JH584265.1 NOD_mouse_Idd4.2Q MMCHR11_CHORI29_IDD4_2Q alt-scaffold
chr17:33681276-38548659  JH584266.1 MHC MMCHR17_CHO_IDD1 alt-scaffold
chr17:27313323-29215977  JH584267.1 NOD_mouse_Idd16.1 MMCHR17_CHORI29_IDD16_1 alt-scaffold
chr12:105147714-105196166 GL456349.1 Tcl1_region_1 RIII_MMCHR12_CTG1 alt-scaffold
chr18:11238883-11458280  GL456070.1 Impact RIII_MMCHR18_CTG1 alt-scaffold
chr4:140721097-140961448 GL456009.1 Padi_cluster UNKNOWN_MMCHR4_CTG7 alt-scaffold
chr4:67057602-67195172   GL456064.1 region40 UNKNOWN_MMCHR4_CTG1 alt-scaffold
chr10:10861646-10927384  GL456015.1 Grm1 UNKNOWN_MMCHR10_CTG3 alt-scaffold
chr17:12729292-12861171  GL456069.1 Airn UNKNOWN_MMCHR17_CTG3 alt-scaffold
chr19:28892559-28918752  JH584319.1 Slc1a1 UNKNOWN_MMCHR19_CTG2 alt-scaffold
chr4:61778759-62041201   GL456075.1 Mup_region_1 129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG2 alt-scaffold
chr4:62045255-62237529   GL456076.1 Mup_region_2 129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG3 alt-scaffold
chr4:60250666-61586638   GL456077.1 Mup_region_4 129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG4 alt-scaffold
chr4:60250666-61586638   JH584268.1 Mup_region_4 129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG5 alt-scaffold
chr4:59870283-60154907   JH584269.1 Mup_region_3 129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG6 alt-scaffold
chr12:113067904-114458697 GL456078.1 Igh 129S7/SVEVBRD-HPRT-B-M2_MMCHR12_CTG2 alt-scaffold
chr15:79892564-79986558  JH584270.1 region65 129S7/SVEVBRD-HPRT-B-M2_MMCHR15_CTG1 alt-scaffold

==============================================================================
No corresponding GRCm38 reference sequence location has been established:

NCBI Entrez                 sequence              patch
nucleotide record           name                  type

KK082443.1/NW_006763130.1   MG4237_PATCH          fix-patch
GL456050.1/NT_080256.1      NOD/MrkTac            alt-scaffold
GL456071.1/NT_166396.1      CAST/EI_MMCHRY_CTG1   alt-scaffold    
GL456072.1/NT_166398.1      CAST/EI_MMCHRY_CTG2   alt-scaffold
GL456073.1/NT_166399.1      CAST/EI_MMCHRY_CTG3   alt-scaffold
GL456080.1/NT_166394.1      AKR/J_MMCHRY_CTG1     alt-scaffold
GL456081.1/NT_166397.1      AKR/J_MMCHRY_CTG2     alt-scaffold
GL456082.1/NT_166400.1      AKR/J_MMCHRY_CTG3     alt-scaffold

==============================================================================
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt17-May-2016 15:55 12K 
[TXT]md5sum.txt17-May-2016 14:38 150  
[   ]mm10Patch4.2bit16-May-2016 09:25 20M 
[   ]mm10Patch4.agp16-May-2016 13:54 41K 
[   ]mm10Patch4.fa.gz08-Mar-2016 11:34 22M 

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