23andMe
The 23andMe results login screen has 5main menus: Home, Ancestry, Health & Traits, Research and Family & Friends. From these drop down menus there are headings for general introductions to all their areas of interest for 23andMe users.
There is a Search icon (spy glass) at the top right hand side of the menu bar from which a search for "raw data" loads a page with 2 options: Download your Raw Data and Browse Your Raw Data.
Selecting Browse Your Raw Data presents the 22 pairs of chromosomes together with the X and Y (male only) chromosomes plus MT (mitochondria). Select one of these and headed lists are produced. The headings are: Genes, Marker (SNP), Genomic Position (build 37 not the latest build, hg38 - more about that later), Variants and Your Genotype.
Let´s look at one example. I subscribe to https://www.geneticlifehacks.com/ and I have chosen to look at https://www.geneticlifehacks.com/lipoproteina-a-big-genetic-risk-for-heart-disease/ page.
I´ve scrolled down to LPA gene and rs3798220 (because it covers both 23andMe v4 and v5 results). Enter that into the Raw Data browser and chromosome 6 is selected with Genes LPA; Marker(SNP) rs3798220; Genomic Position 160961137; Variants C or T; Your Genotype (is given). Click on rs3798220 and page https://www.ncbi.nlm.nih.gov/snp/rs3798220 is displayed. It´s quite technical. I prefer https://www.snpedia.com/index.php/Rs3798220 from snpedia.com because it gives more detail and at the bottom of the page, in many cases it gives te percentage alleles . The top row of the chart is for UTAH and N & W European ancestry. Note the position for rs3798220 is 160540105 GRCh38, not 160961137 GRCh37.
Click on LPA under genes and about 64 rows of LPA data are shown. 23andMe have genotyped some SNPs. These may also be investigated like the original
rs3798220.
The other option is to Download Your Raw Data where they state the data is not validated for accuracy and could include sensitive information (health issues). Once it is downloaded they cannot ensure its security. I downloaded my raw data via their secure email, December 2019. It is a zipped text file. After unzipping from 5Mb to 15Mb I imported it into a spreadsheet (MS Excel). It had 601873 rows but the file I downloaded in 2017 had 610527 rows meaning that some 8654 rows of data have been removed!
It may be worth downloading the raw data especially if 2 or more family members have subscribed to 23andMe because data from the second and subsequent person may be copied and pasted into the matching rows
#rsid (SNP) Chro Position Family members, 1 to 4
rs11042484 11 1318312 GG GG GG GG
rs5743899 11 1323564 TT CC CT CT
rs117431642 11 1328587 CC CC CC CC
rs5743851 11 1331820 AG AA AG AA
rs2334659 11 1357063 GG GG GG GG
rs4963039 11 1365531 CC CC CC CC
rs2056082 11 1369465 GG GG GG GG
rs10832483 11 1377230 CT TT CT TT
rs6578285 11 1380764 CC CC CC CC
On the first row all 4 people are G/G but on the second the father is TT wheras the mother is CC, the child is CT (50% from mother & 50% from the father. The 4th person, grandchild, has inherited alleles from parents, CT, but could have been CC or TT.
If we look up https://www.snpedia.com/index.php/Rs5743899 , at the bottom of the page, top row gives AA 67%, not TT 67%. The reason A instead of T? At the top of the column it gives Orientation - minus (-) but 23andMe it´s plus (+), so A <-> T and C <-> G (depenting upon direction).
The Ancestry section of 23andMe gives my paternal haplogroup R-M222 where a man about 3200 years ago had a Y chromosome mutation at position hg38 #12790481, Rs20321 from G to A. (FTDNA detect many more recent mutations). Interesting, they give an ancestry composition. For me it givs British & Irish 64%, French & German,15.2%, Scandinavian 4.5%, Broadly NW European 16.5%, Broadly European 0.3% and Unassigned 0.3%. When I look at family surnames from about 200 years ago, 5 generations ago,and look up their surnames in the database, https://www.surnamedb.com/Surname/ I´ve found it was quite accurate! And some surprises such as for James Demaine meaning from Maine south France. Was the family Hugenot? Also Sayer, Sayers, Syer living in Norfolk (Robert Syer b1791) from France or Germany. Also from Norfolk James Tuck (b1809) pre 7th century Scandinavian descent. Many other are Anglo Saxon or Old English.
23andMe also suggest health traits and suggest family relatives who may be contacted. It predicted my son and granddaughter despite me not using my correct name - impressed.
FTDNA - Family Tree DNA
FTDNA have a number of tests, but only for X and Y chromosomes plus mitochondria. The Y chromosome passes virtually intact from father to son so when linked to the family name ancient lineages may be determined and haplotrees are being developed. With more men being tested these haplotrees are growing. Similarly maternal ancestry research is being carried out although less extensively.I have used FTDNA for Y chromosome paternal ancestry. My first kit was Y-DNA37. That gave me the results from 1 to 37 of the standard short tandem repeats (STR´s) of the Y chromosome. Within the Y chromosome there are many nucleodide repeats such as for DYS458 (DNA Y-chromosome Segment) the repeat is GAAA. This may be repeated from 12 to 21 times. Most Hagan testers had DYS458 16 repeats and a few, myself included, 18 repeats. A further kit, Big-Y700 has taken my number of STR´s tested to 829 spreadsheet columns! STRs mutate relatively quickly so recent ancestral members may be grouped. However, with the modern testing methods analysing SNPs has also managed to allow scientists/geneticists to produce haplotrees that group individuals to recent close relatives.
When 23andMe raw data is uploaded to FTDNA they carry out some family finding, for free. FTDNA encourage their users to join myProjects. I´ve joined a number and perhaps the more useful are Hagan and Ireland yDNA. The Hagan project currently (January 2020) has 108 members. The Excel file may be dowloaded here; I have removed the identifying kit numbers. My paternal ancestor may be identified from Benjamin Hagan 1848. The Y-STR Results may be download from the landing page and clicking on Y-STR. The download icon is a the bottom of the page, Download:CSV. This may be imported into a spreadsheet such as MS Excel for analysis - generally used for comparisons with others or uploading to other user groups.
FTDNA Y700 data may be downloaded from selecting "Results" that opens a page with the option to choose Export(CSV), Download VCF or download Raw Data. I downloaded the zipped raw data at over 656Kb. Once unipped the file may be opened using Google´s BAM archive file (July 24 2011) or download it here. There are 1000 rows per page and about 10200 pages. Further info here The columns are draggable and I find I need to use only 2 columns. They are Position (not Mate Position) and Read Sequence. Rows of data may be copied and pasted into other applications, maybe to compare rows or to print and then find a location of interest.
My current (Jan2020) haplogroup is BY11733. We can search for that in ybrowse.org/gb2/gbrowse/chry/? and insert BY11733 into the Search box
Notice that the hg38 position, at a single location 14002856 is given in the search box. At the bottom left hand sid side of the image there is a red T. This is the ancestral allele for that location. Next move up the screen a little and click on BY11733. This takes us to the next screen of BY11733 details.
BY11733 has the mutation at hg38 position 14002856 from T to C. My mutation may be confirmed from the BAM file:
By moving the pointer over a row it becomes magnified. Row 967 begins at location 14002852 with an A. The sequence is ATTGCAA where the C is at location 14002856 - mutation confirmed, BY11733 proven.
An interesting site is at https://www.genetichomeland.com/ Free registration may be required. The simplest way into the site is enter a surname in the Surname Find box. There is a display of surname locations. Above this image there are menu items, the top one being DNA Pedigree Display. Selecting that should create a 26 row table showing M269 history. Further down the screen there is a Display tree for marker box. Into that enter any haplogroup and the haplotree table is drawn.