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Thread: New mthap tool

  1. #21
    Established Member Member / DNA Hobbyist thetick's Avatar
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    Quote Originally Posted by mr. john View Post
    yahooland

    All your matches were imperfect according to this tool, just like mine.
    Imperfect just means you did not provide FGS information. Get an FTDNA FGS test and that imperfect will go away. 23andme data just provides whatever SNPs were chosen which may or may not include your haplogroup determining mutations.

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  3. #22
    Established Member Letme indoeuropeanize you yahooland's Avatar
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    Quote Originally Posted by thetick View Post
    Imperfect just means you did not provide FGS information. Get an FTDNA FGS test and that imperfect will go away. 23andme data just provides whatever SNPs were chosen which may or may not include your haplogroup determining mutations.
    I tought it was only the case for those written as untested.

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(32): 73G (150T) (215G) 263G 295T 489C 750G 1438G 1850C 2706G 4216C 4769G 7028T 7476T 7789A 8860G 10398G 10499G 11251G 11377A 11719A 12612G 13708A 13722G 14766T 15257A 15326G 15452A 16069T 16126C 16145A 16231C
    Extras(1): 16299G
    No-Calls(2): 14133G 16261T
    Untested(4): 152 195 310.1 319 513

  4. #23
    Established Member Member / DNA Hobbyist thetick's Avatar
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    Quote Originally Posted by yahooland View Post
    I tought it was only the case for those written as untested.
    Exactly! Untested means the data you provided doesn't have any results for those loci which also happen to be haplogroup defining mutations. This is why getting an FGS is so important, so there are no loci untested or reported incorrectly.

    23andme mtDNA has a very high error rate with just blatantly wrong values. In my case my 23andme data incorrectly stats I have 16304G. Also any polymorphisms are not reported correctly with 23andme.

    Below is the known list of bad 23andme results but there are certainly are more for individual results:

    From Dr. Ann Turner:
    These are the false positives that I've encountered when people send me their raw data for analysis. James Lick won't report these with his utility (mthap).

    208A
    300C [another poly-C problem area]
    469G
    5820G
    5877G
    10388T
    14290A
    14422A
    15072T
    16179T
    16180C
    16189C
    16392A

    310C --probably blacklisted
    Last edited by thetick; 2012-04-11 at 15:28.

  5. #24
    Established Member Letme indoeuropeanize you yahooland's Avatar
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    Quote Originally Posted by thetick View Post
    Exactly! Untested means the data you provided doesn't have any results for those loci which also happen to be haplogroup defining mutations. This is why getting an FGS is so important, so there are no loci untested.
    yeah but i have a lot of Imperfect Match(even for my predicted haplogroup on 23andme), what does that mean ? that my mtdna is pretty unique ?

  6. #25
    Established Member Member / DNA Hobbyist thetick's Avatar
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    Quote Originally Posted by yahooland View Post
    yeah but i have a lot of Imperfect Match(even for my predicted haplogroup on 23andme), what does that mean ? that my mtdna is pretty unique ?
    See my modified post above for some gory details. In a nutshell 23andme data has a very high error rate! 23andme has a good product at a great price, but you get what you pay for. 23andme mtDNA data has a high error rate which they will not talk about but will disclose error rates if you ask. Of course 23andme will not call or admit to the error rate being "high".
    Last edited by thetick; 2012-04-11 at 16:03.

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  8. #26
    Established Member Afro-Isleño jibarodepr's Avatar
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    Quote Originally Posted by thetick View Post
    From Dr. Ann Turner:
    These are the false positives that I've encountered when people send me their raw data for analysis. James Lick won't report these with his utility (mthap).

    208A
    300C [another poly-C problem area]
    469G
    5820G
    5877G
    10388T
    14290A
    14422A
    15072T
    16179T
    16180C
    16189C
    16392A

    310C --probably blacklisted
    I have none of those false numbers.
    World9
    1 Atlantic_Baltic 33.46
    2 African 29.01
    3 Southern 17.74
    4 Amerindian 13.15
    5 Caucasus_Gedrosia 5.24
    6 South_Asian 1.41

    ARECIBO 500 years

  9. #27
    Established Member Member / DNA Hobbyist thetick's Avatar
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    Quote Originally Posted by jibarodepr View Post
    I have none of those false numbers.
    Any 23andme marker could be wrong, these were just soon more often.

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  11. #28
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    Quote Originally Posted by thetick View Post
    Any 23andme marker could be wrong, these were just soon more often.
    and the thing is that I have some mismatches and a lot of extras.
    World9
    1 Atlantic_Baltic 33.46
    2 African 29.01
    3 Southern 17.74
    4 Amerindian 13.15
    5 Caucasus_Gedrosia 5.24
    6 South_Asian 1.41

    ARECIBO 500 years

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  13. #29
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    Mine now says (using Fasta from FGS): U5b1b1(T16192C), the two matches on file is from Italy and Algeria (Berber)...
    Last edited by evon; 2012-04-11 at 23:10.
    Women have been exposed to contradictory, dissonant messages and practises, filled with false expectations and aspirations. This has rendered them vulnerable and receptive to an ideology that simplifies reality and promises escape from role conflict and ambiguity
    F Acar On Islamism

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    My haplogroup (H16) didn't change but since it's so rare and geographically specific, it doesn't matter anyway, I guess.

    It didn't change for my paternal grandmother either - the best match is U4b3, just like in the previous tool (though 23andme has it as U4):
    Best mtDNA Haplogroup Matches: 1) U4b3
    Defining Markers for haplogroup U4b3:
    HVR2: 73G 195C 215G 263G 499A
    CR: 750G 1438G 1811G 2706G 4646C 4769G 5999C 6047G 7028T 7705C 8860G 11332T 11467G 11719A 12308G 12372A 14620T 14766T 15326G 15693C
    HVR1: 16356C

    Marker path from rCRS to haplogroup U4b3 (plus extra markers):
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 11467G 12308G 12372A ⇨ U ⇨ 1811G ⇨ U2'3'4'7'8'9 ⇨ 195C 499A 5999C ⇨ U4'9 ⇨ 4646C 6047G 11332T 14620T 15693C 16356C ⇨ U4 ⇨ 7705C ⇨ U4b ⇨ 215G ⇨ U4b3 ⇨ (16519C)

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(23): 73G 215G 263G 499A 750G 1438G 1811G 2706G 4646C 4769G 5999C 6047G 7028T 8860G 11467G 11719A 12308G 12372A 14620T 14766T 15326G 15693C 16356C
    Extras(0): (16519C)
    No-Calls(1): 11332T
    Untested(2): 195 7705
    However, it did change for my grandfathers.

    The best match for paternal grandfather is now:
    Quote Originally Posted by The New Version
    1) U5b1e1
    Defining Markers for haplogroup U5b1e1:
    HVR2: 73G 150T 152C 263G
    CR: 750G 1438G 2706G 2757G 3197C 4769G 5656G 7028T 7768G 8860G 9477A 10283G 11467G 11719A 12308G 12372A 12616C 13617C 14182C 14766T 15326G
    HVR1: 16189C 16270T 16465T

    Marker path from rCRS to haplogroup U5b1e1 (plus extra markers):
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 11467G 12308G 12372A ⇨ U ⇨ 3197C 9477A 13617C 16192T 16270T ⇨ U5 ⇨ 150T 7768G 14182C ⇨ U5b ⇨ 5656G ⇨ U5b1 ⇨ 16189C ⇨ U5b1(T16189C) ⇨ 16192C ⇨ U5b1(T16189C T16192C) ⇨ 152C 2757G 10283G 12616C ⇨ U5b1e ⇨ 16465T ⇨ U5b1e1 ⇨ 10235C 16086C

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(24): 73G 150T 263G 750G 1438G 2706G 3197C 4769G 5656G 7028T 7768G 8860G 9477A 10283G 11467G 11719A 12308G 12372A 13617C 14182C 14766T 15326G 16270T 16465T
    Extras(2): 10235C 16086C
    Untested(5): 152 2757 12616 16189 16192

    The best match with the previous tool was (23andme has him listed as U5b1e too):
    Quote Originally Posted by The Old Version
    1) U5b1e
    Defining Markers for haplogroup U5b1e:
    HVR2: 73G 150T 152C 263G
    CR: 750G 1438G 2706G 2757G 3197C 4769G 5656G 7028T 7768G 8860G 9477A 10283G 11467G 11719A 12308G 12372A 12616C 13617C 14182C 14766T 15326G
    HVR1: 16189C 16270T

    Marker path from rCRS to haplogroup U5b1e (plus extra markers):
    H2a2a(rCRS) ⇨ 263G 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 11467G 12308G 12372A ⇨ U ⇨ 3197C 9477A 13617C 16192T 16270T ⇨ U5 ⇨ 150T 7768G 14182C ⇨ U5b ⇨ 5656G ⇨ U5b1 ⇨ 16189C ⇨ U5b1(16189) ⇨ 16192C ⇨ U5b1(16189 16192!) ⇨ 152C 2757G 10283G 12616C ⇨ U5b1e ⇨ 10235C 16086C 16465T

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(23): 73G 150T 263G 750G 1438G 2706G 3197C 4769G 5656G 7028T 7768G 8860G 9477A 10283G 11467G 11719A 12308G 12372A 13617C 14182C 14766T 15326G 16270T
    Extras(3): 10235C 16086C 16465T
    Untested(5): 152 2757 12616 16189 16192


    The best match for maternal grandfather:
    Quote Originally Posted by The New Version
    1) J1c3f
    Defining Markers for haplogroup J1c3f:
    HVR2: 73G 228A 263G 295T 462T 489C
    CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12477C 12612G 13708A 13934T 14766T 14798C 15326G 15452A
    HVR1: 16063C 16069T 16126C

    Marker path from rCRS to haplogroup J1c3f:
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 4216C ⇨ R2'JT ⇨ 11251G 15452A 16126C ⇨ JT ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ 185A 228A 14798C ⇨ J1c ⇨ 13934T ⇨ J1c3 ⇨ 185G 12477C 16063C ⇨ J1c3f

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(27): 73G 185G 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12477C 12612G 13708A 13934T 14766T 14798C 15326G 15452A 16063C 16069T 16126C
    Mismatches(1): 228G
    No-Calls(1): 462T
    From the previous tool (23andMe has him listed as J1c3):
    Quote Originally Posted by The Old Version
    1) J1c3
    Defining Markers for haplogroup J1c3:
    HVR2: 73G (185A) (228A) 263G 295T 462T 489C
    CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A
    HVR1: 16069T 16126C

    Marker path from rCRS to haplogroup J1c3 (plus extra markers):
    H2a2a(rCRS) ⇨ 263G 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 4216C ⇨ R2'JT ⇨ 11251G 15452A 16126C ⇨ JT ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 13934T ⇨ J1c3 ⇨ 12477C 16063C

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(24): 73G 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A 16069T 16126C
    Mismatches(0): (185G) (228G)
    Extras(2): 12477C 16063C
    No-Calls(1): 462T

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