Tree Position

A0-T-YP2191 > P305[A1] > L413/PF1409/V31 > M168/PF1416[CT] > P143[CF] > M89/PF2746[F] > F1329/M3658[GHI > F929[HIJK] > IJK > IJ > J > J1 > Z2215 > Z2217 > Exact position not yet finalized.

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
7233156-A-G 7365115-A-G CTS1141 YY+
16240481-A-T 14128601-A-T CTS5378 YY+
17539207-T-G 15427327-T-G ZS2835 Y+
17340718-C-T 15228838-C-T CTS7188 YY+
17284207-C-G 15172327-C-G Z1840 CTS7094 YY+
17243839-C-G 15131959-C-G CTS7022 Z1839 YY+
17162788-C-G 15050908-C-G Z1837 CTS6872 Y+
16991572-A-G 14879692-A-G CTS6580 YY+
16922903-G-A 14811023-G-A Y4364Y4372 M12159 YY+
16880722-G-A 14768842-G-A CTS6412 Z1836 YY+
16863934-A-G 14752054-A-G CTS6379 YY+
16681137-T-C 14569257-T-C ZS2831 YY+
16548432-T-G 14436552-T-G Y3497 Z18396 FGC13994 YY+
16252645-C-G 14140765-C-G Z1835 CTS5403 YY+
16055137-C-G 13943257-C-G ZS2828 Y+
17921696-C-A 15809816-C-A ZS2836 YY+
15972355-G-A 13860475-G-A CTS5034 YY+
15691957-G-T 13580077-G-T CTS4520 YY+
15483237-A-C 13371357-A-C Z18428 YY+
15481466-C-G 13369586-C-G CTS4212 YY+
15360352-C-A 13248472-C-A ZS2825 YY+
15217755-T-A 13105841-T-A CTS3835 Y+
15104528-C-A 12992616-C-A YSC0001271 CTS3683 YY+
14869180-G-A 12757250-G-A CTS3367 YY+
14647204-G-A 12535269-G-A CTS3078 YY+
14563608-C-A 12451808-C-A ZS2823 Y+
14270273-C-T 12149567-C-T Y3489 FGC13984 ZS2822 Y+
14137729-C-T 12017023-C-T FGC13990 YY+
14041847-G-A 11921141-G-A Y4414 Z18389 FGC13982 YY+
17796779-C-A 15684899-C-A CTS8016 Y+
17921715-C-A 15809835-C-A ZS2837 YY+
13892807-T-G 11772101-T-G ZS2821 Y+
21984676-A-G 19822790-A-G Y4788 Z18433 FGC13979 YY+
28610813-C-T 26464666-C-T CTS12556 +
23568375-C-T 21406489-C-T Y3514 Z18420 FGC13971 YY+
23417550-A-T 21255664-A-T CTS12012 YSC0001252 YY+
23303571-C-T 21141685-C-T CTS11836 YY+
23129334-C-A 20967448-C-A CTS11479 YY+
22854811-C-A 20692925-C-A Z1844 CTS10957 Y+
22629677-G-A 20467791-G-A ZS2864 Y+
22523323-C-G 20361437-C-G Z1843 Y+
22471606-C-T 20309720-C-T ZS2862 DYZ19 +
22469764-C-T 20307878-C-T ZS2861 DYZ19 +
22218979-C-A 20057093-C-A ZS2860 DYZ19 +
22136047-A-G 19974161-A-G ZS2859 YY+
22043684-C-A 19881798-C-A ZS2858 YY+
21958810-T-C 19796924-T-C ZS2856 Y+
18060253-T-C 15948373-T-C YY+
21849934-G-A 19688048-G-A ZS2855 Y+
21833839-G-A 19671953-G-A ZS2854 Y+
21560242-T-A 19398356-T-A YSC0001071 YY+
21504503-G-A 19342617-G-A ZS2851 YY+
21404829-C-T 19242943-C-T ZS2849 YY+
21328527-G-A 19166641-G-A ZS2847 YY+
21309870-C-T 19147984-C-T Y3505 FGC14001 Z18407 YY+
21234530-G-T 19072644-G-T ZS2845 YY+
21138032-T-C 18976146-T-C Z1842 YY+
20807682-G-A 18645796-G-A YSC0001019 P4_Gap +
19547031-T-C 17435151-T-C Y3503 Z18403 FGC14000 YY+
19311920-A-C 17200040-A-C CTS10180 YY+
18900267-G-A 16788387-G-A CTS9446 YY+
14004495-C-T 11883789-C-T Y3488 Z18387 FGC13992 YY+
13660065-T-A 11504389-T-A FGC13972 Z18385 +
16224446-C-A 14112566-C-A CTS5363 YY+
4769767-C-A 4901726-C-A Z1829 +
7233327-A-G 7365286-A-G CTS1142 YY+
7038497-G-A 7170456-G-A ZS2797 YY+
6764073-T-A 6896032-T-A CTS461 YY+
6739448-A-G 6871407-A-G ZS2794 YY+
6658873-A-T 6790832-A-T Y3476 FGC13977 Z18425 YY+
6536772-C-A 6668731-C-A ZS2793 +
6528505-A-T 6660464-A-T ZS2792 +
6511284-T-C 6643243-T-C ZS2791 +
6402483-T-C 6534442-T-C Y4398 ZS2790 FGC13978 +
6090877-G-A 6222836-G-A Y3475 ZS2787 +
6030873-A-G 6162832-A-G ZS2786 +
5638069-T-A 5770028-T-A ZS2784 +
5039284-C-T 5171243-C-T ZS2781 +
4740597-C-A 4872556-C-A ZS2779 +
7334308-A-G 7466267-A-G CTS1318 YSC0001256 YY+
4557332-T-C 4689291-T-C Y3473 ZS2778 +
4244876-G-A 4376835-G-A Y4785 ZS2777 +
4012048-C-T 4144007-C-T ZS2774 +
3888353-A-T 4020312-A-T ZS2772 +
3676778-G-A 3808737-G-A ZS2769 +
3645070-C-A 3777029-C-A ZS2768 +
3634164-A-T 3766123-A-T ZS2767 +
3521680-T-A 3653639-T-A ZS2766 +
3346417-G-T 3478376-G-T ZS2764 +
3129932-C-T 3261891-C-T ZS2762 +
3071336-A-G 3203295-A-G ZS2760 +
2870585-G-T 3002544-G-T YY+
2669716-C-T 2801675-C-T CTS15 Z1828 YY+
7302017-T-G 7433976-T-G CTS1267 YY+
7357038-T-C 7488997-T-C CTS1354 YY+
13351525-G-T 11195849-G-T ZS2818 +
8343894-G-A 8475853-G-A Z1833 YY+
13206218-G-T 11050542-G-T ZS2817 +
9977959-T-C 10140350-T-C ZS2815 Y+
9820427-A-T 9982818-A-T ZS2814 YY+
9380540-C-T 9542931-C-T Y3487 Z18383 FGC13995 Y+
9046036-C-A 9208427-C-A ZS2812 Y+
8982356-A-G 9144747-A-G Y4413 FGC13975 Z18427 Y+
8780597-T-C 8912556-T-C Y3472 Z18381 FGC14005 YY+
8775973-A-T 8907932-A-T ZS2811 YY+
8757939-T-A 8889898-T-A ZS2810 YY+
8734551-C-A 8866510-C-A ZS2809 YY+
8614242-C-T 8746201-C-T BY16430Z1834 YY+
8463365-C-T 8595324-C-T Y3511 Z18379 SK1280 FGC13989 YY+
8378478-A-G 8510437-A-G ZS2806 YY+
8312510-G-A 8444469-G-A Y3510 Z18376 FGC13988 YY+
7416063-C-A 7548022-C-A CTS1460 YY+
8286442-C-T 8418401-C-T YSC0000499 YY+
8279697-G-A 8411656-G-A ZS2805 Y+
8264190-T-C 8396149-T-C Y3484 FGC13976 Z18375 YY+
8170554-G-T 8302513-G-T ZS2804 YY+
8082600-A-C 8214559-A-C Y3483 FGC13985 Z18374 YY+
8029914-G-T 8161873-G-T Y3482 Z18373 FGC13997 YY+
7978315-G-A 8110274-G-A ZS2802 YY+
7960448-T-C 8092407-T-C Z1832 YY+
7887920-T-C 8019879-T-C ZS2801 YY+
7877358-C-T 8009317-C-T Z1831 YY+
7697337-G-A 7829296-G-A Y3481 Z18370 YY+
7600041-C-T 7732000-C-T Y3480 Z18369 FGC13986 YY+
7459849-A-C 7591808-A-C CTS1519 IR1_L +
28647820-G-A 26501673-G-A ZS2869 +

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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