nstd158 (Cleal et al. 2019)

Organism:
Human
Study Type:
Collection
Submitter:
Kez Cleal
Submitter URL:
https://www.cardiff.ac.uk/people/view/122762-baird-duncan
Description:
We performed whole genome sequencing to investigate the impact of a transit through a telomere-driven crisis on the structural integrity of the genome. We find direct evidence of telomere involvement in driving large scale complex structural rearrangement patterns during a telomere crisis. The repair signatures and configuration of these rearrangements were consistent with repair by the break-induced replication pathway. See Variant Summary counts for nstd158 in dbVar Variant Summary.
Project:
PRJNA417592
Publication(s):
Cleal et al. 2019

Detailed Information: Download 1621 Variant Regions, Download 1621 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.11Chr1106106RemappedNC_000001.11
NC_000002.12Chr2126126RemappedNC_000002.12
NC_000003.12Chr3108108RemappedNC_000003.12
NC_000004.12Chr49191RemappedNC_000004.12
NC_000005.10Chr59595RemappedNC_000005.10
NC_000006.12Chr6107107RemappedNC_000006.12
NC_000007.14Chr7164164RemappedNC_000007.14
NC_000008.11Chr8171171RemappedNC_000008.11
NC_000009.12Chr97373RemappedNC_000009.12
NC_000010.11Chr10113113RemappedNC_000010.11
NC_000011.10Chr117878RemappedNC_000011.10
NC_000012.12Chr125454RemappedNC_000012.12
NC_000013.11Chr134242RemappedNC_000013.11
NC_000014.9Chr144141RemappedNC_000014.9
NC_000015.10Chr152424RemappedNC_000015.10
NC_000016.10Chr164848RemappedNC_000016.10
NC_000017.11Chr179292RemappedNC_000017.11
NC_000018.10Chr185858RemappedNC_000018.10
NC_000019.10Chr194949RemappedNC_000019.10
NC_000020.11Chr204848RemappedNC_000020.11
NC_000021.9Chr211313RemappedNC_000021.9
NC_000022.11Chr222323RemappedNC_000022.11
NC_000023.11ChrX5656RemappedNC_000023.11
NC_000024.10ChrY33RemappedNC_000024.10
NT_113889.1Unplaced|NT_113889.144RemappedNT_113889.1
NT_113901.1Unplaced|NT_113901.133RemappedNT_113901.1
NT_167209.1Unplaced|NT_167209.111RemappedNT_167209.1
NT_167211.2Unplaced|NT_167211.222RemappedNT_167211.2
NT_167213.1Unplaced|NT_167213.155RemappedNT_167213.1
NT_167214.1Unplaced|NT_167214.14747RemappedNT_167214.1
NT_167218.1Unplaced|NT_167218.122RemappedNT_167218.1
NT_187361.1Chr1|NT_187361.111RemappedNT_187361.1
NT_187518.1Chr1|NT_187518.122RemappedNT_187518.1
NT_187646.1Chr1|NT_187646.122RemappedNT_187646.1
NW_011332688.1Chr1|NW_011332688.111RemappedNW_011332688.1
NT_187527.1Chr2|NT_187527.111RemappedNT_187527.1
NW_012132915.1Chr2|NW_012132915.122RemappedNW_012132915.1
NW_012132916.1Chr3|NW_012132916.111RemappedNW_012132916.1
NW_013171801.1Chr4|NW_013171801.111RemappedNW_013171801.1
NT_113948.1Chr5|NT_113948.111RemappedNT_113948.1
NW_009646199.1Chr5|NW_009646199.111RemappedNW_009646199.1
NT_167248.2Chr6|NT_167248.211RemappedNT_167248.2
NT_113891.3Chr6|NT_113891.311RemappedNT_113891.3
NW_018654713.1Chr6|NW_018654713.111RemappedNW_018654713.1
NT_187562.1Chr7|NT_187562.122RemappedNT_187562.1
NW_003315922.2Chr7|NW_003315922.211RemappedNW_003315922.2
NW_018654714.1Chr7|NW_018654714.133RemappedNW_018654714.1
NT_187565.1Chr8|NT_187565.111RemappedNT_187565.1
NT_187567.1Chr8|NT_187567.122RemappedNT_187567.1
NT_187576.1Chr8|NT_187576.111RemappedNT_187576.1
NW_018654717.1Chr8|NW_018654717.111RemappedNW_018654717.1
NW_003315934.1Chr10|NW_003315934.111RemappedNW_003315934.1
NW_019805495.1Chr11|NW_019805495.111RemappedNW_019805495.1
NW_003315940.1Chr12|NW_003315940.111RemappedNW_003315940.1
NW_003315941.1Chr12|NW_003315941.111RemappedNW_003315941.1
NW_011332696.1Chr12|NW_011332696.111RemappedNW_011332696.1
NW_018654718.1Chr12|NW_018654718.111RemappedNW_018654718.1
NW_011332699.1Chr13|NW_011332699.122RemappedNW_011332699.1
NT_167219.1Chr14|NT_167219.11616RemappedNT_167219.1
NT_187600.1Chr14|NT_187600.133RemappedNT_187600.1
NW_018654722.1Chr14|NW_018654722.122RemappedNW_018654722.1
NT_187603.1Chr15|NT_187603.111RemappedNT_187603.1
NW_003315944.2Chr15|NW_003315944.211RemappedNW_003315944.2
NW_019805500.1Chr16|NW_019805500.111RemappedNW_019805500.1
NT_113930.2Chr17|NT_113930.288RemappedNT_113930.2
NT_187614.1Chr17|NT_187614.122RemappedNT_187614.1
NT_187665.1Chr18|NT_187665.111RemappedNT_187665.1
NW_003315958.1Chr18|NW_003315958.111RemappedNW_003315958.1
NT_187693.1Chr19|NT_187693.111RemappedNT_187693.1
NW_003571061.2Chr19|NW_003571061.211RemappedNW_003571061.2
NW_003571057.2Chr19|NW_003571057.211RemappedNW_003571057.2
NW_003571058.2Chr19|NW_003571058.211RemappedNW_003571058.2
NW_003571059.2Chr19|NW_003571059.211RemappedNW_003571059.2
NW_003571060.1Chr19|NW_003571060.111RemappedNW_003571060.1
NW_003571056.2Chr19|NW_003571056.211RemappedNW_003571056.2
NW_003571055.2Chr19|NW_003571055.211RemappedNW_003571055.2
NW_003315962.1Chr19|NW_003315962.133RemappedNW_003315962.1
NW_003571054.1Chr19|NW_003571054.111RemappedNW_003571054.1
NT_187632.1Chr22|NT_187632.111RemappedNT_187632.1
NT_187635.1ChrX|NT_187635.111RemappedNT_187635.1
NW_009646209.1ChrY|NW_009646209.133RemappedNW_009646209.1
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr1107107SubmittedNC_000001.10
NC_000002.11Chr2126126SubmittedNC_000002.11
NC_000003.11Chr3108108SubmittedNC_000003.11
NC_000004.11Chr49191SubmittedNC_000004.11
NC_000005.9Chr59595SubmittedNC_000005.9
NC_000006.11Chr6107107SubmittedNC_000006.11
NC_000007.13Chr7164164SubmittedNC_000007.13
NC_000008.10Chr8171171SubmittedNC_000008.10
NC_000009.11Chr97373SubmittedNC_000009.11
NC_000010.10Chr10113113SubmittedNC_000010.10
NC_000011.9Chr117878SubmittedNC_000011.9
NC_000012.11Chr125454SubmittedNC_000012.11
NC_000013.10Chr134040SubmittedNC_000013.10
NC_000014.8Chr144141SubmittedNC_000014.8
NC_000015.9Chr152424SubmittedNC_000015.9
NC_000016.9Chr164848SubmittedNC_000016.9
NC_000017.10Chr179393SubmittedNC_000017.10
NC_000018.9Chr185858SubmittedNC_000018.9
NC_000019.9Chr194949SubmittedNC_000019.9
NC_000020.10Chr204848SubmittedNC_000020.10
NC_000021.8Chr211313SubmittedNC_000021.8
NC_000022.10Chr222020SubmittedNC_000022.10
NC_000023.10ChrX5656SubmittedNC_000023.10
NC_000024.9ChrY33SubmittedNC_000024.9
NT_113889.1Unplaced|NT_113889.144SubmittedNT_113889.1
NT_167211.1Unplaced|NT_167211.122SubmittedNT_167211.1
NT_167212.1Unplaced|NT_167212.111SubmittedNT_167212.1
NT_167213.1Unplaced|NT_167213.155SubmittedNT_167213.1
NT_167214.1Unplaced|NT_167214.14747SubmittedNT_167214.1
NT_167218.1Unplaced|NT_167218.122SubmittedNT_167218.1
NT_167219.1Unplaced|NT_167219.11616SubmittedNT_167219.1
NT_167229.1Unplaced|NT_167229.111SubmittedNT_167229.1
NT_167235.1Unplaced|NT_167235.111SubmittedNT_167235.1
NT_113923.1Unplaced|NT_113923.122SubmittedNT_113923.1
NT_167209.1Unplaced|NT_167209.111SubmittedNT_167209.1
NT_113891.2Chr6|NT_113891.211SubmittedNT_113891.2
NT_167248.1Chr6|NT_167248.111SubmittedNT_167248.1
NT_113901.1Chr7|NT_113901.133SubmittedNT_113901.1
NT_113930.1Chr17|NT_113930.188SubmittedNT_113930.1
NT_113948.1Chr19|NT_113948.111SubmittedNT_113948.1

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.10Chr110785200371078520037
NC_000002.11Chr21267623005112676230051
NC_000003.11Chr310885400371088540037
NC_000004.11Chr4917030036917030036
NC_000005.9Chr5956300063956300063
NC_000006.11Chr61076514005610765140056
NC_000007.13Chr71649227208216492272082
NC_000008.10Chr817110311001091711031100109
NC_000009.11Chr9735160032735160032
NC_000010.10Chr101137511005311375110053
NC_000011.9Chr11785130048785130048
NC_000012.11Chr12543260031543260031
NC_000013.10Chr13403320010403320010
NC_000014.8Chr14412610026412610026
NC_000015.9Chr15241320017241320017
NC_000016.9Chr16483110031483110031
NC_000017.10Chr17934820085934820085
NC_000018.9Chr18583740033583740033
NC_000019.9Chr19492950026492950026
NC_000020.10Chr20483030030483030030
NC_000021.8Chr211353001013530010
NC_000022.10Chr22201200016201200016
NC_000023.10ChrX563960021563960021
NC_000024.9ChrY300004300004
NT_113889.1Unplaced|NT_113889.1420004420004
NT_113891.2Chr6|NT_113891.2100002100002
NT_113901.1Chr7|NT_113901.1320002320002
NT_113923.1Unplaced|NT_113923.1200004200004
NT_113930.1Chr17|NT_113930.1870002870002
NT_113948.1Chr19|NT_113948.1110000110000
NT_167209.1Unplaced|NT_167209.1100002100002
NT_167211.1Unplaced|NT_167211.1220000220000
NT_167212.1Unplaced|NT_167212.1100002100002
NT_167213.1Unplaced|NT_167213.1540002540002
NT_167214.1Unplaced|NT_167214.14760008247600082
NT_167218.1Unplaced|NT_167218.1220000220000
NT_167219.1Unplaced|NT_167219.11616000016160000
NT_167229.1Unplaced|NT_167229.1100002100002
NT_167235.1Unplaced|NT_167235.1100002100002
NT_167248.1Chr6|NT_167248.1100002100002

Samplesets

Number of Samplesets: 1

Name:
SUB3205485 derivatives
Description:
All samples were derived from original BioSample SUB3205485.
Size:
66
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported
  • Download Samples as CSV file
  • Samples for sampleset 1
    Sample IDCell TypeSubject ID Subject Phenotype
    DB98HCT116DB98Not reported
    DB85HCT116DB85Not reported
    DB108HCT116DB108Not reported
    DB99HCT116DB99Not reported
    DB116HCT116DB116Not reported
    DB95HCT116DB95Not reported
    DB105HCT116DB105Not reported
    DB49HCT116DB49Not reported
    DB70HCT116DB70Not reported
    DB53HCT116DB53Not reported
    DB87HCT116DB87Not reported
    DB50HCT116DB50Not reported
    DB80HCT116DB80Not reported
    DB48HCT116DB48Not reported
    DB57HCT116DB57Not reported
    DB106HCT116DB106Not reported
    DB79HCT116DB79Not reported
    DB68HCT116DB68Not reported
    DB101HCT116DB101Not reported
    DB46HCT116DB46Not reported
    DB103HCT116DB103Not reported
    DB45HCT116DB45Not reported
    DB47HCT116DB47Not reported
    DB56HCT116DB56Not reported
    DB100HCT116DB100Not reported
    DB86HCT116DB86Not reported
    DB83HCT116DB83Not reported
    DB78HCT116DB78Not reported
    DB81HCT116DB81Not reported
    DB104HCT116DB104Not reported
    DB92HCT116DB92Not reported
    DB73HCT116DB73Not reported
    DB94HCT116DB94Not reported
    DB38HCT116DB38Not reported
    DB90HCT116DB90Not reported
    DB55HCT116DB55Not reported
    DB115HCT116DB115Not reported
    DB54HCT116DB54Not reported
    DB96HCT116DB96Not reported
    DB107HCT116DB107Not reported
    DB97HCT116DB97Not reported
    DB114HCT116DB114Not reported
    DB77HCT116DB77Not reported
    DB88HCT116DB88Not reported
    DB52HCT116DB52Not reported
    DB39HCT116DB39Not reported
    DB76HCT116DB76Not reported
    DB69HCT116DB69Not reported
    DB82HCT116DB82Not reported
    DB111HCT116DB111Not reported
    DB71HCT116DB71Not reported
    DB37HCT116DB37Not reported
    DB102HCT116DB102Not reported
    DB67HCT116DB67Not reported
    DB91HCT116DB91Not reported
    DB75HCT116DB75Not reported
    DB40HCT116DB40Not reported
    DB93HCT116DB93Not reported
    DB112HCT116DB112Not reported
    DB109HCT116DB109Not reported
    DB89HCT116DB89Not reported
    DB51HCT116DB51Not reported
    DB41HCT116DB41Not reported
    DB84HCT116DB84Not reported
    DB110HCT116DB110Not reported
    DB113HCT116DB113Not reported

    Experimental Details

    Experiment IDTypeMethodAnalysisPlatformsNumber of Variant Calls
    1DiscoverySequencingPaired-end mappingIllumina1,621

    Validations

    No validation data were submitted for this study.

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