Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > DF49/S474 > Z2980 > Z2976 > DF23 > Z2961 > FGC6540 > FGC30381 > A11223

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
HG02501
Manual
Edits
13723928-A-C 11568252-A-C +
13799230-T-G 11678524-T-G FGC18669 4×AATGG+
13521412-T-A 11365736-T-A +
13529621-G-A 11373945-G-A +
13529634-C-T 11373958-C-T +
13536954-A-T 11381278-A-T +
13569676-G-T 11414000-G-T +
13569677-C-G 11414001-C-G +
13576799-A-G 11421123-A-G +
13616537-A-C 11460861-A-C +
13641354-T-G 11485678-T-G +
13691802-G-GAATGC 11536126-G-GAATGC +
13691811-G-GGAATT 11536135-G-GGAATT +
13691813-A-AATGGC 11536137-A-AATGGC +
13746363-G-C 11590687-G-C +
13847227-T-TGGCAA 11726521-T-TGGCAA +
13510711-T-C 11355035-T-C +
14096636-G-A 11975930-G-A M2455 YY+
14134158-T-G 12013452-T-G Y+
14334340-G-GT 12213635-G-GT +
14430982-A-T 12310255-A-T Y+
14467029-ATCTATCTG-A 12346298-ATCTATCTG-A +
14556176-G-A 12444377-G-A CTS2904 YY+
14556181-T-C 12444382-T-C CTS2905 YY+
14629246-G-A 12517314-G-A YY+
14646872-C-T 12534937-C-T YY+
14888093-T-TTTG 12776159-T-TTTG +
15023585-G-T 12911673-G-T YY+
15066209-GA-G 12954300-GA-G +
15106538-C-T 12994626-C-T YY+
13517094-A-G 11361418-A-G +
13504576-C-G 11348900-C-G +
15223553-G-A 13111639-G-A Y+
13389544-A-G 11233868-A-G +
13289855-G-A 11134179-G-A +
13290104-C-T 11134428-C-T +
13290630-A-C 11134954-A-C +
13290645-G-T 11134969-G-T +
13295933-T-A 11140257-T-A +
13295949-T-A 11140273-T-A +
13309958-C-T 11154282-C-T +
13314327-G-A 11158651-G-A +
13334853-A-G 11179177-A-G +
13384292-A-G 11228616-A-G FGC43581 +
13384789-A-G 11229113-A-G +
13384804-C-T 11229128-C-T +
13385149-C-T 11229473-C-T +
13389962-A-G 11234286-A-G 13×TG+
13504484-C-T 11348808-C-T +
13389990-A-G 11234314-A-G +
13403743-G-A 11248067-G-A +
13414203-C-T 11258527-C-T +
13423471-G-T 11267795-G-T Z11551 +
13437719-G-A 11282043-G-A +
13449890-T-TGTA 11294214-T-TGTA +
13459506-A-G 11303830-A-G A12184 +
13466941-T-C 11311265-T-C +
13494435-C-T 11338759-C-T +
13494558-T-A 11338882-T-A +
13494561-T-A 11338885-T-A +
13500344-C-T 11344668-C-T +
13500539-A-AG 11344863-A-AG +
15137276-T-C 13025363-T-C YY+
15300145-A-G 13188244-A-G Y+
13273282-G-A 11117606-G-A +
28571474-C-T 26425327-C-T +
22260365-A-G 20098479-A-G DYZ19 +
22476041-C-A 20314155-C-A DYZ19 +
22570151-A-G 20408265-A-G YY+
22679866-C-T 20517980-C-T YY+
22687518-G-A 20525632-G-A YY+
22876964-TAA-T 20715078-TAA-T 20×A+
23145384-T-C 20983498-T-C YY+
23206054-G-A 21044168-G-A Y+
23316060-A-ATTTT 21154174-A-ATTTT +
23421018-T-A 21259132-T-A YY+
24884653-G-T 22738506-G-T g1 +
28562093-G-T 26415946-G-T +
28571435-CTT-C 26425288-CTT-C +
28698664-C-T 26552517-C-T +
22091305-T-C 19929419-T-C YY+
28698666-GT-G 26552519-GT-G 9×T+
28698742-G-A 26552595-G-A +
28698745-T-C 26552598-T-C +
28698750-C-T 26552603-C-T +
28726829-C-T 26580682-C-T Y+
28726834-C-T 26580687-C-T Y+
28795287-G-C 26649140-G-C +
28802591-G-T 26656444-G-T +
28805331-T-G 26659184-T-G +
58968006-A-T 56821859-A-T +
58980527-T-TTCCGTTCCATTCCAC 56834380-T-TTCCGTTCCATTCCAC +
58986105-G-C 56839958-G-C +
59017776-A-ATATATATATATAT 56871629-A-ATATATATATATAT +
22256845-AC-A 20094959-AC-A DYZ19 +
21995792-G-A 19833906-G-A YY+
15424418-T-G 13312538-T-G Y+
18211165-C-T 16099285-C-T Y+
15498764-A-G 13386884-A-G YY+
15832214-TTC-T 13720334-TTC-T +
15832215-TC-T 13720335-TC-T +
15865549-C-CTTT 13753669-C-CTTT 22×T+
15956886-T-G 13845006-T-G YY+
16272496-C-T 14160616-C-T Y+
16371266-G-T 14259386-G-T YY+
16809371-GTGAT-G 14697491-GTGAT-G +
17237132-G-A 15125252-G-A YY+
17477546-T-G 15365666-T-G YY+
17828099-G-T 15716219-G-T Y+
18113490-G-A 16001610-G-A YY+
18176281-T-G 16064401-T-G YY+
18230822-G-T 16118942-G-T +
21577826-A-G 19415940-A-G Y+
18540826-A-C 16428946-A-C Y+
18723886-TC-T 16612006-TC-T +
18872278-CTTT-C 16760398-CTTT-C +
18872279-TTTC-T 16760399-TTTC-T +
18916003-TC-T 16804123-TC-T +
18937652-A-G 16825772-A-G M12055 YY+
18952314-T-A 16840434-T-A YY+
19067005-C-T 16955125-C-T YY+
19354307-A-T 17242427-A-T PF5818 Y+
19411986-G-A 17300106-G-A YY+
21153740-C-T 18991854-C-T Y+
21318167-C-T 19156281-C-T YY+
21515862-C-CAAA 19353976-C-CAAA 28×A+
13288294-G-T 11132618-G-T +
13273223-C-G 11117547-C-G +
14612278-C-T 12500484-C-T CTS2999 YY+
22113310-C-T 19951424-C-T BY137728 YY+
16456715-G-T 14344835-G-T YY+
16818570-C-T 14706690-C-T Y52374 YY+
17864515-G-A 15752635-G-A YY+
18758830-C-A 16646950-C-A YY+
19340773-A-G 17228893-A-G YY+
19500657-C-A 17388777-C-A YY+
21118603-G-A 18956717-G-A YY+
21225635-C-A 19063749-C-A YY+
21428948-T-C 19267062-T-C YY+
21472894-C-A 19311008-C-A YY+
21519918-C-T 19358032-C-T PH4831 YY+
21616523-C-T 19454637-C-T YY+
21891846-A-G 19729960-A-G YY+
22114776-T-C 19952890-T-C Z34624 YY+
16379231-G-A 14267351-G-A YY+
22746097-A-T 20584211-A-T YY13×T+
22805626-C-G 20643740-C-G YY+
23250690-C-T 21088804-C-T YY+
23617054-C-A 21455168-C-A YY+
23961713-G-A 21815566-G-A Y+
58877533-T-C 56713338-A-G +
58849671-C-T 56741200-G-A +
58914688-A-G 56676183-T-C +
13258031-A-C 11102355-A-C +
13194516-ATTCC-A 11038840-ATTCC-A +
13504519-G-A 11348843-G-A +
13298174-C-T 11142498-C-T +
16064144-A-C 13952264-A-C Y+
16385564-C-A 14273684-C-A YY+
15898526-C-A 13786646-C-A YY+
2758639-C-T 2890598-C-T YY+
9403543-GC-TT 9565934-GC-TT +
13302042-C-T 11146366-C-T +
21153667-C-A 18991781-C-A S4183 S4067 Y+
28805448-G-T 26659301-G-T +
9722478-T-C 9884869-T-C IR3_Prx +
6447588-A-C 6579547-A-C +
7534406-G-GTT 7666365-G-GTT 19×T+
58917663-N-C 56673208-N-G +
3838601-C-CTTT 3970560-C-CTTT 31×T+
13494543-TAC-T 11338867-TAC-T +
13570257-T-G 11414581-T-G +
13570240-G-A 11414564-G-A +
18804950-C-T 16693070-C-T PF4581 YY+
14866140-C-T 12754206-C-T YY11×GT+
28698742-GCTT-ACTC 26552595-GCTT-ACTC +
15758066-C-G 13646186-C-G YY+
14737352-C-T 12625420-C-T Y+
19500154-A-G 17388274-A-G BY1545 PH4556 YY+
7429912-G-C 7561871-G-C YY+
7632556-C-T 7764515-C-T Y+
7987260-T-C 8119219-T-C YY+
8159650-T-C 8291609-T-C Z3966 YY+
8411740-C-A 8543699-C-A Y39497 YY+
8627357-A-C 8759316-A-C YY+
9009248-C-T 9171639-C-T Y+
9410448-G-A 9572839-G-A Y+
14191430-C-A 12070724-C-A YY+
15178383-C-T 13066469-C-T Y+
15388611-C-A 13276731-C-A YY+
14664252-G-GA 12552317-G-GA +
2810389-T-TTTG 2942348-T-TTTG +
13273100-A-G 11117424-A-G +
8818289-G-A 8950248-G-A YY+
6768761-AG-A 6900720-AG-A +
6810165-C-A 6942124-C-A YY+
6866004-C-T 6997963-C-T YY+
7133635-G-A 7265594-G-A YY+
7199179-A-C 7331138-A-C YY+
7401154-TG-T 7533113-TG-T +
7428503-C-T 7560462-C-T CTS1473 YY+
7508384-T-TTCCA 7640343-T-TTCCA +
8237408-T-G 8369367-T-G YY+
8403170-GTTTGT-G 8535129-GTTTGT-G 5×TTTGT+
8532125-C-T 8664084-C-T YY+
8535223-TG-T 8667182-TG-T +
8754663-G-C 8886622-G-C YY+
9075188-C-CTTT 9237579-C-CTTT 20×T+
6445370-A-C 6577329-A-C +
9094402-G-C 9256793-G-C Y+
9310538-TCA-T 9472929-TCA-T +
9722448-T-C 9884839-T-C IR3_Prx +
9777524-AG-A 9939915-AG-A +
9788994-C-T 9951385-C-T Y+
9944613-T-G 10107004-T-G Y+
9944642-G-A 10107033-G-A Y+
9992247-A-T 10154638-A-T Y+
9997100-A-G 10159491-A-G Y+
10055774-C-A 10218165-C-A 15×A+
13242235-A-G 11086559-A-G +
13243793-T-C 11088117-T-C +
13264852-T-TG 11109176-T-TG +
6586037-T-C 6717996-T-C +
6402493-G-A 6534452-G-A Z36464 +
3196576-T-C 3328535-T-C +
4256150-G-A 4388109-G-A +
3271615-TG-T 3403574-TG-T +
3403258-ATCC-A 3535217-ATCC-A +
3412067-T-C 3544026-T-C +
3444239-G-C 3576198-G-C +
3489789-C-A 3621748-C-A +
3588034-C-T 3719993-C-T +
3637683-C-T 3769642-C-T +
3640982-C-T 3772941-C-T +
3641088-TC-T 3773047-TC-T +
3662605-CTA-C 3794564-CTA-C 8×TA+
3820295-G-T 3952254-G-T +
3856326-T-C 3988285-T-C +
4185004-G-A 4316963-G-A +
4282216-A-G 4414175-A-G +
6150000-G-T 6281959-G-T IR3_Dst +
4293676-T-A 4425635-T-A +
4317897-T-C 4449856-T-C +
4325774-G-C 4457733-G-C +
4370594-T-TAC 4502553-T-TAC 19×AC+
4375325-T-G 4507284-T-G +
4503344-T-C 4635303-T-C +
4715693-C-G 4847652-C-G +
4940950-C-G 5072909-C-G +
5193881-A-G 5325840-A-G +
5422921-C-T 5554880-C-T FGC69174 +
5847133-G-C 5979092-G-C +
6010663-C-A 6142622-C-A +
6149989-G-A 6281948-G-A IR3_Dst +
59030666-A-C 56884519-A-C +

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
Manual13745750-A-T11590074-A-T2T 1A
Manual6140004-TTTTG-T6271963-TTTTG-TJust one read.
Manual7829918-C-G7961877-C-G4G
Manual8138930-C-T8270889-C-T1T
Manual22257064-T-G20095178-T-G1T 1G
Manual22438611-C-T20276725-C-T4T 2C
Manual22446921-T-A20285035-T-A1A 5T
Manual22505603-A-G20343717-A-G1G
Manual24006637-G-C21860490-G-C3C
Manual4439911-TGCAGCTTCACTCCTGAGG-T4571870-TGCAGCTTCACTCCTGAGG-T2 reads, both positive.
Manual22487093-TG-T20325207-TG-TBoth reads show the deletion.



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