`A_MP-variants.txt`

Reference_Name	Position	Total	Consensus_Allele	Minority_Allele	Consensus_Count	Minority_Count	Consensus_Frequency	Minority_Frequency	Consensus_Average_Quality	Minority_Average_Quality	ConfidenceNotMacErr	PairedUB	QualityUB	Phase
A_MP	89	16457	A	C	16250	187	0.987421765813939	0.011362945858905	36.9733538461538	35.2727272727273	0.973864167670226	0.00300579333125917	0.000945028060441746	2
A_MP	97	16609	G	T	16528	73	0.995123126016015	0.00439520741766512	37.667412875121	35.9452054794521	0.942123790899509	0.00299911875994572	0.000869703813724233	3
A_MP	145	18059	A	G	17929	121	0.992801373276483	0.00670026025804308	37.4800602376039	34.2396694214876	0.943773456597157	0.00294018560306109	0.00103136016001577	4
A_MP	278	22330	T	G	22181	130	0.99332736229288	0.0058217644424541	37.5011045489383	33.3	0.91965749457736	0.00280443275721211	0.00107989618019399	5
A_MP	561	22914	G	A	22313	591	0.973771493410142	0.0257920921707253	37.3027383139874	37.2470389170897	0.992691814939746	0.00278916159432848	0.000637407095637786	1
A_MP	693	19781	T	C	19212	548	0.971235023507406	0.0277033517011273	37.2342286071205	37.4580291970803	0.993518660591569	0.00287963759070433	0.00067177826901097	1
A_MP	763	21062	G	T	20423	624	0.96966100085462	0.0296268160668503	36.658179503501	36.5224358974359	0.992482534753728	0.00283996776414694	0.000723004897268827	1
A_MP	840	20706	T	C	20102	583	0.970829711194823	0.0281560900222158	37.1336682917123	37.21269296741	0.993252259721596	0.00285058539986555	0.000673714439603282	1
A_MP	841	20749	C	T	20166	566	0.971902260349896	0.0272784230565328	36.3534662302886	36.3975265017668	0.991597121396618	0.00284928699675475	0.000739122927039003	1

Reference_Name - Name of gene segment or genome assembled
Position - Position of the called single nucleotide variant
Total - Total coverage depth at that position for all alleles not counting ambiguous nucleotides
Consensus_Allele - Plurality consensus allele at that position
Minority_Allele - Variant allele at that position
Consensus_Count - Plurality consensus observation count at that position
Minority_Count - Variant observation count at that position
Consensus_Frequency - Plurality consensus frequency at that position
Minority_Frequency - Variant frequency at that position
Consensus_Average_Quality - Plurality consensus average quality score
Minority_Average_Quality - Variant average quality score
ConfidenceNotMacErr - Confidence not machine/sequence error, see formula
PairedUB - Assembly-specific interval upperbound for significance testing based on paired-end end error estimates (uses error rate of 0 for single-end).
QualityUB - Allele-specific interval upperbound for significance testing based on quality error estimates
Phase - A phase number where minor variants with the same number co-occur on the same gene.

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