u/JamezBond007

Throughout my life majority of what i come across i am able to understand it very rapidly.. one simple benchmark is/was class fellows / coworkers.. Compared to them i would be making use of the newly acquired knowledge much faster...

Then comes the part to explain ..

true mastery of a subject allows you to break down complex ideas into simple, intuitive concepts

So this is something i struggled with through my life ..

i would be so confident i understand something well and then comes time to explain the concept to someone else.. Now either i will struggle with words or once i have done explaining the concept.. even to myself the explanation was not as comprehensive or clear as the confidence in my own understanding was..

Memory.. I know my short term memory specially memory recall is weak.. i "know" a lot more than someone else explaining the concept.. more details.. more connecting points.. more unique insights.. but in the moment i cannot recall these details i "know"..
My thought process of way or learning.. Another thing i have realised i ofcourse look, feel, think/process things way differently than others.. I have somehow trained my brain to filter out lots of things and focus on just bits and pieces of presented information to come to conclusions... this is one key factor in being "fast" at synthesizing information, coming up with ideas and specially figuring out how to utilize the new knowledge..

I have started to pay attention to what i am thinking when i am absorbing new knowledge and beginning realize (have not fully figured this out yet..) that i dont try to make sense of things in my head,,, lay a foundation.. and make some organized structured thought process..

Because i dont learn to explain things.. thats not the "Reason" i learn.. nor is explaining a big part of my daily routine.. i struggle to elaborate my reasoning in a casual conversation with friends / coworkers,, The struggle is more internal as most people are not subject matter experts anyways and dont usually catch on to the flaws and gaps in the logic..

there is a lot more to this but this much will suffice for now.. anyone else struggle with something similar? and has someone else figured out how to either learn differently or present their thoughts/knowledge more simply/clearly.

I received a "universal compatibility" text file from sequencing.com which had 500,000 plus minus entries like this one:

rs1801133 1 11856378 GG

The files has this info as well:

For each SNP, we provide its identifier (an rsid or an internal id), its location on the reference human genome, and the genotype call oriented with respect to the plus strand on the human reference sequence. We are using reference human assembly build 37 (also known as Annotation Release 104).

The issue is that this file lists: GG for rs1801133 chromosome 1 position 11856378. This does not align with results i get when i look at the raw data files like the bam file.. (both hg38 and t2t). or fastq files..

Here is what AI seems to conclude:

Final Audit Summary

You have officially completed a "Deep Dive" audit of your MTHFR gene.

The Report: Said "Normal (GG)".
The Raw Data (BAM/FASTQ): Every test we ran (T2T, HG19, HG38, and FASTQ grep) showed you have the A allele (Mutant).
The Verdict: You are Homozygous Mutant (TT) for MTHFR C677T.

The Final Breakdown

Location: 11796312 (The hg38 site for MTHFR C677T).
Reference Column: A
Your Data Column: ,,,,.....,,,,,,,,,..,,.,,,.., (All dots and commas).

The "Aha!" Discovery

This explains why your DNA report and your BAM seemed to disagree. In the specific hg38 FASTA you are using, the "Reference" base is already an A.

Standard hg38: Usually has a G at this spot.
Your FASTA (assembly38): Has an A (the mutant allele) as the reference.
Your DNA: Also has an A.
The Result: Because you match your specific reference, IGV and Samtools show it as "Normal" (Grey/Dots). The Real-World Verdict

Even though you "match" this specific reference file, an A at this position in the human genome is the C677T mutation.

Your Genotype: Homozygous Mutant (TT).
The DNA Report: If the report said GG, it was likely trying to say "You match the reference," but it used the wrong letter (G) for a reference that is actually an A, or it used a completely different assembly logic.

Final Audit Results

You can now confidently record your MTHFR status based on your raw 30x WGS data:

rs1801133 (C677T): Homozygous Mutant (TT) (Confirmed by 29 reads).
rs1801131 (A1298C): Normal (AA) (Confirmed by your previous check of 31 reads matching the T reference).

Understand things / thoughts vs Explaining what i understand..