Tuesday, January 16, 2018

My Genetics


( Accompaniment to Part I - Mitochondrial Genetics; published here; https://medicalxpress.com/news/2018-05-genome-imitochondrial-dna.html )

mtDNA variants (homoplasmy) result haplogroup H56

ID POS MUT FWD REV Locus AAC MutPred SelectionScore HaploGrepWeight
A18-0020_S2_L001_R1_001.gz_rCRS 11788 C>T 905 / 909 853 / 856 MT-ND4 . . . 8.8
A18-0020_S2_L001_R1_001.gz_rCRS 1438 A>G 808 / 808 769 / 769 MT-CYB . . . 10.0
A18-0020_S2_L001_R1_001.gz_rCRS 15326 A>G 1086 / 1086 838 / 839 MT-CYB T194A 0.452 0.395 10.0
A18-0020_S2_L001_R1_001.gz_rCRS 16519 T>C 864 / 866 933 / 934 MT-DLOOP1 . . . n.d.
A18-0020_S2_L001_R1_001.gz_rCRS 263 A>G 896 / 896 841 / 842 MT-DLOOP2 . . . 8.8
A18-0020_S2_L001_R1_001.gz_rCRS 4769 A>G 965 / 967 898 / 898 MT-ND2 . . . 8.8
A18-0020_S2_L001_R1_001.gz_rCRS 750 A>G 882 / 882 777 / 777 MT-RNR1 . . . 10.0
A18-0020_S2_L001_R1_001.gz_rCRS 8860 A>G 1064 / 1068 855 / 857 MT-ATP6 T112A 0.369 0.287 10.0

detected heteroplasmies;

A18-0020_S2_L001_R1_001.gz_rCRS1977T0.0118T/C3352 / 3571125A18-0020_S2_L001_R1_001.gz_rCRS2005C0.0127C/T3030 / 351915A18-0020_S2_L001_R1_001.gz_rCRS2523C0.0129C/T1103 / 1455134A18-0020_S2_L001_R1_001.gz_rCRS2541C0.0119C/T978 / 1453126A18-0020_S2_L001_R1_001.gz_rCRS2557C0.0166C/T884 / 1468134A18-0020_S2_L001_R1_001.gz_rCRS2563T0.0147T/C836 / 1472124A18-0020_S2_L001_R1_001.gz_rCRS2571G0.0103G/A762 / 1463113A18-0020_S2_L001_R1_001.gz_rCRS2572C0.0063C/T765 / 1463110A18-0020_S2_L001_R1_001.gz_rCRS2577C0.0129C/T728 / 1446126A18-0020_S2_L001_R1_001.gz_rCRS2581A0.0155A/G715 / 1473128

from mtDNA-server

23AndMe results; Paternal Haplogroup I-M253, can be found at levels of 10% and higher in many parts of Europe

 for 15326 variant -

MT‐CYB mutations in hypertrophic cardiomyopathy

https://onlinelibrary.wiley.com/doi/full/10.1002/mgg3.5

SNPedia

SNPs  rsID http://howirecovered.com/my-genetics/#mitochondrial

MitoMap  https://mitomap.org/MITOMAP

Mitogenome    MitoCarta https://www.broadinstitute.org/scientific-community/science/programs/metabolic-disease-program/publications/mitocarta/mitocarta-in-0
       http://bioinfo.nist.gov/

Genomics to brain; personal journey
- folate-B12 pathays, methylation, mitochondria, nucleic acid metablosim

https://www.greatplainslaboratory.com/organic-acids-test/

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3 comments:

  1. UnknownAugust 7, 2019 at 11:54 PM

    Hi John, nice medicalxpress article! I wondered if you were given separate FASTQ files for nuclear and mtDNA? Having some issues with Dante...

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    Thank you!
    Anthony

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