Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > DF49/S474 > Z2980 > FGC9595

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
117897
6801766-T-C 6933725-T-C YY+
9726023-T-C 9888414-T-C L277 S334 IR3_Prx +
22440791-C-T 20278905-C-T DYZ19 +
17275835-G-GAAGCA 15163955-G-GAAGCA 6×AAGCA+
6154481-A-G 6286440-A-G IR3_Dst +
14926489-G-A 12814554-G-A L18 YY+
8109592-G-C 8241551-G-C BY23545 YY+
8210611-AC-A 8342570-AC-A +
9393231-A-G 9555622-A-G BY23651 YY+
21732450-C-G 19570564-C-G YY+
23135573-G-C 20973687-G-C BY24726 YY+
19529505-G-A 17417625-G-A BY24244 YY+
19524034-G-A 17412154-G-A BY24242 YY+
13675577-AG-A 11519901-AG-A +
19165998-T-A 17054118-T-A ZP83 Y+
17679647-C-A 15567767-C-A ZP82 YY+
16910836-A-T 14798956-A-T YY+
16455153-A-G 14343273-A-G ZP81 YY+
7235379-G-T 7367338-G-T **
16492411-C-A 14380531-C-A **
22950334-C-A 20788448-C-A **
15530359-T-C 13418479-T-C PR5566 **
24296171-CTT-C 22150024-CTT-C P3_t1 31×T***
28811970-T-G 26665823-T-G ***
22247022-C-A 20085136-C-A DYZ19 ***
22233720-T-A 20071834-T-A DYZ19 ***
22227774-A-C 20065888-A-C DYZ19 ***
28809001-T-A 26662854-T-A ***
21175749-C-CA 19013863-C-CA 27×A***
20645842-TC-T 18483956-TC-T P4_Prx ***
20084461-T-TTTC 17972581-T-TTTC P5_Dst ***
20036025-C-G 17924145-C-G P5_Prx ***
19985642-G-A 17873762-G-A P5_Prx ***
19948179-C-CTTCT 17836299-C-CTTCT P5_Prx ***
19868139-TTG-T 17756259-TTG-T P5_Prx ***
28811914-T-C 26665767-T-C ***
19492290-C-CAA 17380410-C-CAA 37×A***
22268046-G-C 20106160-G-C DYZ19 ***
58978536-CCTTTG-C 56832389-CCTTTG-C ***
19202962-G-A 17091082-G-A ***
19202958-G-A 17091078-G-A ***
19202954-G-A 17091074-G-A ***
19202928-C-CAA 17091048-C-CAA 25×A***
59004524-G-T 56858377-G-T ***
18325701-ATT-A 16213821-ATT-A P6_Prx 27×T***
13821246-C-A,G 11700540-C-A,G ***
28793488-ATGG-A 26647341-ATGG-A ***
16757043-A-ATTT 14645163-A-ATTT 27×T***
13842641-A-C,T 11721935-A-C,T ***
13140128-C-CTCCAT,T 10629614-C-CTCCAT,T ***
22265413-G-A 20103527-G-A DYZ19 ***
22280400-G-C 20118514-G-C DYZ19 ***
24262223-C-G 22116076-C-G P3_b1 ***
25899791-CAAA-C 23753644-CAAA-C P1_Y1 15×A***
24117760-C-A 21971613-C-A P3_b1 ***
23899401-CGTGTGT-C 21737515-CGTGTGT-C 17×GT***
23728039-G-A 21566153-G-A ***
24945853-G-T 22799706-G-T g1 ***
25206657-C-T 23060510-C-T g1 ***
22508106-T-G 20346220-T-G DYZ19 ***
22489867-T-A 20327981-T-A DYZ19 ***
22486909-T-C 20325023-T-C DYZ19 ***
22486876-C-T 20324990-C-T DYZ19 ***
22449357-C-G 20287471-C-G DYZ19 ***
22448673-T-G 20286787-T-G DYZ19 ***
22447442-A-T 20285556-A-T DYZ19 ***
22420181-C-T 20258295-C-T DYZ19 ***
22283304-C-A 20121418-C-A DYZ19 ***
26117886-G-A 23971739-G-A P1_Y1 ***
22363261-TG-T 20201375-TG-T DYZ19 ***
26251138-GA-G 24104991-GA-G P1_Y1 ***
26914079-A-T 24767932-A-T P1_r3 ***
22357553-G-A 20195667-G-A DYZ19 ***
28784396-GAGTGGAATGT-G 26638249-GAGTGGAATGT-G ***
22339299-G-C 20177413-G-C DYZ19 ***
22321521-C-A 20159635-C-A DYZ19 ***
22296865-T-A 20134979-T-A DYZ19 ***
28786701-G-GTGGAA 26640554-G-GTGGAA ***
28790608-GTGGAA-G 26644461-GTGGAA-G 4×TGGAA***
28808530-T-G 26662383-T-G ***
13196180-A-T 11040504-A-T ***
13832506-A-ATGGAAT,T 11711800-A-ATGGAAT,T 12×GGAAT***
13865779-C-CGAATGGAATG 11745073-C-CGAATGGAATG 10×GAATG***
24108394-A-T 21962247-A-T FGC7515 ZS1243 P3_b1 ***
15336049-AGT-A 13224167-AGT-A ***
19839616-G-A,GAA 17727736-G-A,GAA P5_Prx 26×A***
24811219-CAA-C 22665072-CAA-C P3_b2 18×A***
28808033-C-G 26661886-C-G ***
28808875-T-A 26662728-T-A BY27891 ***
13452389-T-C 11296713-T-C ***
13455782-T-G 11300106-T-G ***
6244485-CCA-C 6376444-CCA-C IR3_Dst 9×CA***
13838223-AATCAG-A 11717517-AATCAG-A ***
13141921-T-TATTCC 10631407-T-TATTCC 4×ATTCC***
28787600-T-A 26641453-T-A ***
20045274-A-AAAG 17933394-A-AAAG P5_Prx 14×AAAG***
24302840-AG-A 22156693-AG-A P3_t1 ***
28807064-G-A 26660917-G-A ***
13722149-T-G 11566473-T-G ***
25998834-AAG-A 23852687-AAG-A P1_Y1 8×AG***
13853165-T-A 11732459-T-A ***
13455019-A-T 11299343-A-T ***
13457776-CACTCGGATTG-C 11302100-CACTCGGATTG-C ***
13818177-C-G 11697471-C-G ***
13853170-C-A 11732464-C-A ***
28807543-C-G 26661396-C-G ***
28811945-T-G 26665798-T-G ***
10012224-CT-C 10174615-CT-C ***
13691277-A-T 11535601-A-T ***
13138465-G-T 10627951-G-T ***
13691283-A-G 11535607-A-G 4×GAATG***
13850358-C-A 11729652-C-A ***
13853563-C-A 11732857-C-A ***
13866452-A-T 11745746-A-T ***
19394059-C-T 17282179-C-T 37×T***
19668782-TAA-T 17556902-TAA-T P5_Prx 33×A***
28808502-G-A 26662355-G-A F14076 ***
3131457-ATCTCT-A,G 3263416-ATCTCT-A,G 14×TCTCT***
13860217-A-C 11739511-A-C ***
13692467-A-C 11536791-A-C ***
13458788-T-A 11303112-T-A ***
13480209-A-T 11324533-A-T ***
13648138-A-G 11492462-A-G ***
13664688-CGAACA-G 11509012-CGAACA-G ***
13684782-GAATAT-G 11529106-GAATAT-G ***
13686875-A-T 11531199-A-T ***
13740144-C-G 11584468-C-G ***
13454203-A-T 11298527-A-T ***
13815562-GGAATA-G 11694856-GGAATA-G ***
13821222-T-A 11700516-T-A ***
13831668-G-A 11710962-G-A ***
13430263-C-CAT 11274587-C-CAT ***
13855597-A-T 11734891-A-T ***
13856302-G-C 11735596-G-C ***
13454295-G-T 11298619-G-T ***
13453592-T-A 11297916-T-A ***
6188408-A-G 6320367-A-G IR3_Dst ***
10018585-A-ATTCTTTCTTTCTTCTTTCT 10180976-A-ATTCTTTCTTTCTTCTTTCT 4×TTCT***
7414310-T-A 7546269-T-A ***
8125051-A-G 8257010-A-G ***
8125052-G-A 8257011-G-A ***
8125053-A-G 8257012-A-G ***
9982750-G-C 10145141-G-C ***
9982755-A-AG 10145146-A-AG ***
13137855-A-T 10627341-A-T ***
13448312-C-G 11292636-C-G ***
13138475-T-C 10627961-T-C ***
13141722-G-GCCATT 10631208-G-GCCATT ***
13195019-C-T 11039343-C-T ***
13204013-A-G 11048337-A-G ***
13430256-C-T 11274580-C-T ***
13445513-C-T 11289837-C-T ***
13856303-A-AAATGGAATGGAATGG,G 11735597-A-AAATGGAATGGAATGG,G 15×AATGG***

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.

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