1k Genomes

1kG: NA07048
MDKA Birth: United States
Utahns (CEPH) NW European ancestry

Tree Position

R-U106/S21 > Z2265 > Z381/S263 > Z301/S499 > L48 > Z9 > Z30/S271 > Z349 > Z2 > Z7 > Z8 > ZZ58 > Z11 > Z341 > Z12 > Z8175 > CTS10742 > 16436744-ACA-TC > S3942

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 STR1kG
NA07048		Manual
Edits
28565702-A-G 26419555-A-G CTS12290 +
19328796-G-T 17216916-G-T CTS10214 S3436 Y+
28818197-G-GAATGGAATGTAATGT 26672050-G-GAATGGAATGTAATGT +
7218552-C-A 7350511-C-A CTS1122 YY+
13358325-T-C 11202649-T-C PF511 +
26180029-T-C 24033882-T-C P1_Y1 +
7260177-G-C 7392136-G-C F937 YY+
28622841-C-T 26476694-C-T CTS12579 Y+
13607617-G-A 11451941-G-A +
13240346-C-T 11084670-C-T +
22352681-A-T 20190795-A-T DYZ19 +
22352673-C-A 20190787-C-A DYZ19 +
17143885-G-T 15032005-G-T YY+
13276136-A-C 11120460-A-C +
9384255-A-C 9546646-A-C BY64204FGC33853 Y+
28817653-GGAATGGAATGGAATGGAATGGAAT-G 26671506-GGAATGGAATGGAATGGAATGGAAT-G +
3196582-C-A 3328541-C-A FT316393 +
6445006-T-G 6576965-T-G +
13265038-G-A 11109362-G-A +
3185675-C-A 3317634-C-A +
3205858-C-A 3337817-C-A 15×A+
3389980-C-T 3521939-C-T +
3564277-A-T 3696236-A-T +
3829389-G-C 3961348-G-C +
3888677-T-C 4020636-T-C +
4072018-ACG-A 4203977-ACG-A +
4072019-CGG-C 4203978-CGG-C +
4151920-T-A 4283879-T-A +
4151924-T-A 4283883-T-A +
4167676-G-A 4299635-G-A +
4293797-G-T 4425756-G-T +
4293806-A-G 4425765-A-G +
4375416-A-T 4507375-A-T +
4464639-C-T 4596598-C-T FT158904 +
4510382-A-T 4642341-A-T +
4547920-G-A 4679879-G-A +
4555311-T-C 4687270-T-C FT321016 +
4555316-T-G 4687275-T-G +
4669280-T-TTA 4801239-T-TTA +
4890657-T-C 5022616-T-C +
5204839-G-T 5336798-G-T S9005 +
5220154-G-C 5352113-G-C +
6020686-TTG-T 6152645-TTG-T +
6158441-G-T 6290400-G-T IR3_Dst +
6158454-A-G 6290413-A-G IR3_Dst +
6921866-A-C 7053825-A-C YY+
7103104-C-A 7235063-C-A YY+
7113261-G-T 7245220-G-T YY+
7310413-G-C 7442372-G-C YY+
7545015-G-GC 7676974-G-GC +
8977060-T-G 9139451-T-G Y+
9960332-A-C 10122723-A-C Y+
9960368-T-A 10122759-T-A Y+
10068156-G-C 10230547-G-C +
13137793-A-C 10627279-A-C +
13138222-ATTCC-A 10627708-ATTCC-A +
13194500-C-T 11038824-C-T +
13257526-G-A 11101850-G-A +
13257585-C-T 11101909-C-T +
13292383-CT-C 11136707-CT-C +
13319375-C-G 11163699-C-G S531 +
13319384-T-C 11163708-T-C +
13319386-A-C 11163710-A-C S13768 +
13398996-T-C 11243320-T-C +
13504424-A-G 11348748-A-G +
13504436-G-T 11348760-G-T +
13511050-G-C 11355374-G-C BY184365 +
13616836-A-G 11461160-A-G +
13620868-T-A 11465192-T-A +
13621001-C-T 11465325-C-T +
13686902-GTAATGGACAC-G 11531226-GTAATGGACAC-G +
13924990-AT-A 11804284-AT-A +
13939715-C-T 11819009-C-T Y+
13965291-G-A 11844585-G-A Y+
14128256-A-C 12007550-A-C YY+
14217852-T-C 12097146-T-C CTS2204 YY+
14331122-G-T 12210416-G-T YY+
14981888-TCCTTCCTC-T 12869956-TCCTTCCTC-T +
15318439-A-G 13206545-A-G YY+
15512640-G-A 13400760-G-A YY+
16247952-T-C 14136072-T-C YY+
16314126-A-C 14202246-A-C YY+
17136924-A-T 15025044-A-T YY+
17136930-TC-T 15025050-TC-T +
17172142-T-C 15060262-T-C YY+
17361085-T-G 15249205-T-G YY+
17784121-C-A 15672241-C-A M12018 Y15×A+
18630907-T-C 16519027-T-C YY+
18948677-C-A 16836797-C-A M5755 YY+
21227374-TC-T 19065488-TC-T +
22245749-C-T 20083863-C-T DYZ19 +
22253017-C-A 20091131-C-A DYZ19 +
22253036-C-A 20091150-C-A S5961 DYZ19 +
22282035-C-T 20120149-C-T DYZ19 +
22294753-G-C 20132867-G-C DYZ19 +
23322005-T-A 21160119-T-A YY+
28565749-G-A 26419602-G-A +
28601212-T-C 26455065-T-C Y+
28601227-G-A 26455080-G-A CTS12521 Y+
28680603-G-A 26534456-G-A +
28680607-T-G 26534460-T-G +
28761439-C-T 26615292-C-T +
28814566-A-T 26668419-A-T +
2735430-T-G 2867389-T-G M12000 YY+
3572277-T-C 3704236-T-C +
3653403-G-A 3785362-G-A +
4499575-G-A 4631534-G-A +
5022475-G-T 5154434-G-T +
5096711-G-A 5228670-G-A FGC37897 +
5622917-A-G 5754876-A-G +
5680402-G-A 5812361-G-A +
5736940-GTA-G 5868899-GTA-G BY39087 +
5784590-GAAA-G 5916549-GAAA-G 13×A+
6091970-T-G 6223929-T-G +
6648610-ATT-A 6780569-ATT-A +
6784475-CGAAA-C 6916434-CGAAA-C +
6881815-G-A 7013774-G-A FT327070 Y+
6887620-T-A 7019579-T-A S3433 CTS604 YY+
7056495-G-C 7188454-G-C CTS867 S3944 YY+
8549669-C-A 8681628-C-A YY+
8703677-TG-T 8835636-TG-T +
8746749-G-A 8878708-G-A Z459 FGC3288 YY+
8773390-C-T 8905349-C-T M12006 YY+
9992788-C-CA 10155179-C-CA +
10033953-C-T 10196344-C-T Y+
13212797-T-A 11057121-T-A +
13240556-T-C 11084880-T-C +
13285917-A-C 11130241-A-C +
13319344-A-G 11163668-A-G BY85177 10×TG+
13388454-C-T 11232778-C-T +
13465647-G-A 11309971-G-A +
13502151-G-T 11346475-G-T +
13502167-C-T 11346491-C-T +
13718632-AT-A 11562956-AT-A +
14208587-C-G 12087881-C-G CTS2178 YY+
14778628-A-T 12666698-A-T M12009 YY+
15049917-TC-T 12938008-TC-T +
15117153-T-C 13005240-T-C Y+
16739066-T-TA 14627186-T-TA +
16819159-C-T 14707279-C-T CTS6322 S3949 YY+
17374938-C-T 15263058-C-T FT330374 Y+
17387317-TAA-T 15275437-TAA-T +
18245477-T-C 16133597-T-C M12020 Y+
18825052-G-T 16713172-G-T Z14953 YY+
19008632-T-C 16896752-T-C Z9495 YY+
21109850-C-T 18947964-C-T Z27638 YY+
21227373-TTC-T 19065487-TTC-T +
23160049-T-G 20998163-T-G CTS11555 S3437 Y+
23206208-C-T 21044322-C-T FTA13375 Y+
23505518-AC-A 21343632-AC-A +
23547950-C-G 21386064-C-G M12024 YY+
23741385-A-T 21579499-A-T +
25803115-CAT-C 23656968-CAT-C P1_b3 +

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.

Mutation Notes:

Kit POSITION-REF-ALT (hg19) POSITION-REF-ALT (hg38) Note
Manual24248789-G-GA22102642-G-GA2 reads match the reference sequence and 3 show the insertion.
Manual23301667-A-G21139781-A-G1G