Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > ZZ10 > Z253 > BY39781 > BY39770 > BY39769

Unique Mutations

The mutations unique to this man are summarized in the table below. Those with a '+' or '*' confidence level are considered by FamilyTreeDNA or FullGenomesCorp to be high quality SNPs/INDELs. For completeness, all other mutations of lesser confidence are included as well. These additional mutations may be useful for distinguishing between very closely related men.

Occasionally, some of the mutations listed here will be thought to be shared with other men in which case they might appear in upstream blocks on the tree. When this happens, the 'Blocks' field will indicate what block they appear in. Such a situation might arise with BigY men if the BED data suggests another man may be positive for a SNP, even though it doesn't appear in his VCF data. It might also happen if Chromo2 testing or Sanger sequencing of other men not on the tree show the SNP to be shared.

POS-REF-ALT (hg19) POS-REF-ALT (hg38) Blocks Names Region McDonald BED combBED STRFTDNA
86086
6653849-A-T 6785808-A-T YP4709 YY+
6909829-G-A 7041788-G-A BY62140 YY+
8422355-C-T 8554314-C-T Y63710 YY+
8452179-T-C 8584138-T-C FT259959 YY+
16230319-C-G 14118439-C-G BY106146 YY+
17094451-T-C 14982571-T-C BY112255 YY+
17186868-A-T 15074988-A-T BY112901 YY+
21172465-C-G 19010579-C-G BY130858 YY+
21330280-G-A 19168394-G-A BY55237 YY+
22478967-C-T 20317081-C-T BY224134 DYZ19 +
24470190-C-G 22324043-C-G BY150181 Y+
18968388-C-A 16856508-C-A CTS9572 **
28580457-T-C 26434310-T-C CTS12347 **
28732065-C-T 26585918-C-T M954L1315 **
15566748-C-T 13454868-C-T **
18875676-C-A 16763796-C-A **
9186918-G-A 9349309-G-A 13×A***
9994857-A-T 10157248-A-T ***
13697389-T-A 11541713-T-A ***
13713655-AGGAAT-A 11557979-AGGAAT-A ***
13869155-G-A 11748449-G-A ***
22435481-A-C 20273595-A-C A4236 DYZ19 ***
26953138-T-A 24806991-T-A P1_r3 ***
13648921-C-A 11493245-C-A ***
13690802-GGAATT-G 11535126-GGAATT-G ***
13691277-A-T 11535601-A-T ***
13691283-A-G 11535607-A-G 4×GAATG***
13697738-AAATGG-A 11542062-AAATGG-A 7×AATGG***
13704276-G-C 11548600-G-C ***
13704277-T-A 11548601-T-A ***
13866452-A-T 11745746-A-T ***
18982611-C-A 16870731-C-A ***
18982612-C-A 16870732-C-A ***
20645811-C-T 18483925-C-T P4_Prx ***
26902324-ATAG-A 24756177-ATAG-A P1_r3 ***
28805251-AT-A 26659104-AT-A ***
28808484-A-G 26662337-A-G ***
28808494-T-G 26662347-T-G ***
28808495-T-G 26662348-T-G ***
58975050-C-T 56828903-C-T ***
9403543-G-T 9565934-G-T ***
13832601-C-T 11711895-C-T FT104823 ***
10020493-G-A 10182884-G-A ***
13451866-C-CCCATTCCATT 11296190-C-CCCATTCCATT ***
13687043-A-AAGTCG 11531367-A-AAGTCG ***
19682204-AG-A 17570324-AG-A P5_Prx ***
22360800-T-A 20198914-T-A DYZ19 ***
22962414-G-T 20800528-G-T 20×T***
24998151-A-AT 22852004-A-AT g1 20×T***
26117892-C-A 23971745-C-A P1_Y1 ***
26228676-TC-T 24082529-TC-T P1_Y1 ***
13477311-G-A 11321635-G-A ***
18378989-C-T 16267109-C-T P6_Prx ***
9994862-T-A 10157253-T-A ***
13705314-TGAAATGGCATGTAATGGAA-T 11549638-TGAAATGGCATGTAATGGAA-T ***
13825036-A-C 11704330-A-C ***
15309789-C-A 13197894-C-A ***
19892868-G-T 17780988-G-T P5_Prx 31×T***
22359993-G-T 20198107-G-T DYZ19 ***
22438513-A-AG 20276627-A-AG DYZ19 ***
28808480-T-G 26662333-T-G Z43363 ***
28808502-G-A 26662355-G-A F14076 ***
6126093-TGACTGAAAAAA-T 6258052-TGACTGAAAAAA-T ***
13446527-C-CTCCAT,T 11290851-C-CTCCAT,T 16×TCCAT***
13452364-T-G 11296688-T-G ***
13452367-C-A 11296691-C-A ***
13452369-T-A 11296693-T-A ***
13452374-T-C 11296698-T-C ***
20045238-A-G 17933358-A-G P5_Prx ***
24830466-C-A 22684319-C-A P3_b2 ***
10020396-G-T 10182787-G-T ***
13453538-T-C 11297862-T-C ***
19492290-C-CAA 17380410-C-CAA 37×A***
23899401-CGTGTGT-C 21737515-CGTGTGT-C 17×GT***
26117886-G-A 23971739-G-A P1_Y1 ***
13720755-CTCCAATGGAATGGAG-C 11565079-CTCCAATGGAATGGAG-C ***
25176845-A-T 23030698-A-T g1 ***
26184646-C-CT 24038499-C-CT P1_Y1 19×T***
20757348-A-T 18595462-A-T P4_Prx ***
13737178-C-G 11581502-C-G ***
14637667-T-A 12525736-T-A FT335687 ***
13477316-C-A 11321640-C-A ***
25376536-CTT-C 23230389-CTT-C P2_r2 24×T***
27127602-ATTTCTTTCTTTC-A 24981455-ATTTCTTTCTTTC-A P1_g3 14×TTTC***
7053357-T-A 7185316-T-A ***
13836369-GACTCC-G 11715663-GACTCC-G ***
13138450-A-C,T 10627936-A-C,T ***
13662017-C-A 11506341-C-A FT447548 ***
28791633-A-G 26645486-A-G ***
9959863-T-A 10122254-T-A 7×TAA***
18378987-TG-T 16267107-TG-T P6_Prx ***
20045233-A-G 17933353-A-G P5_Prx ***
26991333-T-TAAAAA 24845186-T-TAAAAA P1_r4 33×A***
13735116-G-GAAAA 11579440-G-GAAAA ***
13735125-T-C 11579449-T-C ***
25472735-C-A 23326588-C-A P2_r2 23×A***
13648207-C-A 11492531-C-A ***
13860245-G-A 11739539-G-A ***
18982615-T-A 16870735-T-A ***
13455544-G-A 11299868-G-A ***
58975047-A-T 56828900-A-T ***
58975056-C-A 56828909-C-A ***
58975066-C-T 56828919-C-T ***
58975087-A-T 56828940-A-T ***
24182564-A-AT 22036417-A-AT P3_b1 15×T***
13866941-A-G 11746235-A-G ***
19949608-GT-G 17837728-GT-G P5_Prx 16×T***
13467780-C-A 11312104-C-A ***
24235387-G-GTTT 22089240-G-GTTT P3_b1 29×T***
13717240-G-T 11561564-G-T ***
18369802-C-CAA 16257922-C-CAA P6_Prx 25×A***
22723386-C-CAA 20561500-C-CAA 17×A***
13856262-G-A 11735556-G-A ***
20757361-C-T 18595475-C-T P4_Prx ***
13459516-G-A,GTTCCA 11303840-G-A,GTTCCA 11×TTCCA***
20045234-A-G 17933354-A-G P5_Prx ***
6234012-C-T 6365971-C-T IR3_Dst ***
13658765-T-A 11503089-T-A ***
13658769-ATGAAGTGTAATGGAAAGAAT-A 11503093-ATGAAGTGTAATGGAAAGAAT-A ***
13690437-TGTAA-G 11534761-TGTAA-G ***
13706482-C-G 11550806-C-G FT310221 ***
13743145-G-A 11587469-G-A ***
13803108-G-GAATGC 11682402-G-GAATGC ***
15358760-G-A 13246879-G-A ***
19651599-A-G 17539719-A-G P5_Prx ***
19972999-G-A 17861119-G-A P5_Prx ***
20213071-C-CTTCT 18051185-C-CTTCT P5_Dst ***
20213078-T-A 18051192-T-A P5_Dst ***
22221563-C-A 20059677-C-A DYZ19 ***
22229570-T-G 20067684-T-G DYZ19 ***
22260556-A-C 20098670-A-C DYZ19 ***
22283007-T-G 20121121-T-G DYZ19 ***
22283027-G-T 20121141-G-T DYZ19 ***
22312905-A-C 20151019-A-C BY25063 DYZ19 ***
22360649-G-T 20198763-G-T DYZ19 ***
22430020-A-C 20268134-A-C DYZ19 ***
22449144-G-T 20287258-G-T DYZ19 ***
22475800-C-G 20313914-C-G BY196887 DYZ19 ***
22485797-T-G 20323911-T-G DYZ19 ***
23127414-C-A 20965528-C-A 24×A***
24073865-G-A 21927718-G-A P3_b1 ***
24952649-C-G 22806502-C-G g1 ***
28030722-T-C 25884575-T-C P1_Y2 ***
28030728-C-T 25884581-C-T P1_Y2 ***
28030732-C-T 25884585-C-T P1_Y2 ***
58975041-C-T 56828894-C-T ***
58975116-C-G 56828969-C-G ***
58983765-G-T 56837618-G-T ***
5785700-AC-A,AA 5917659-AC-A,AA ***
13464965-CT-C,CC 11309289-CT-C,CC ***

In the table above, the meaning of the confidence field depends on whether the data comes from an FTDNA kit or an FGC kit. For FTDNA kits, + implies a "PASS" result with just one possible variant, * indicates a "PASS" but with multiple variants, ** indicates "REJECTED" with just a single variant, and *** indicates "REJECTED" with multiple possible variants. 'A*' are heterozygous variants not called by FTDNA, but still pulled from the VCF file. For FGC kits, + indicates over 99% likely genuine (95% for INDELs); * over 95% likely genuine (90% for INDELs); ** about 40% likely genuine; *** about 10% likely genuine. Manual entries read directly from a BAM file will be either + indicating positive, or * indicating that the data show a mixture of possible variants.

For the FTDNA kits, the BED data is encoded in the background color of the cells. Those cells with a white background have coverage, those with a grey background indicate no coverage in the BED file, and those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the vcf file.

The combBED column indicates whether or not the mutation is a SNP and falls in the combBED region defined in Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data by Dmitry Adamov, Vladimir Guryanov, Sergey Karzhavin, Vladimir Tagankin, Vadim Urasin.

The McDonald BED column indicates whether or not the mutation is a SNP and falls in the BED region used by Dr. Iain McDonald in the age analysis he does for R-U106 men.