`A_MP-allAlleles.txt`

Reference_Name	Position	Allele	Count	Total	Frequency	Average_Quality	ConfidenceNotMacErr	PairedUB	QualityUB	Allele_Type
A_MP	1	A	7065	7065	1	37.0837933474876	0.999804286553343	0.00383989976733253	0.00130396576194621	Consensus
A_MP	2	T	7092	7092	1	37.0159334461365	0.999801204451458	0.00383490965230615	0.00130688430983112	Consensus
A_MP	3	G	7114	7114	1	36.3427045262862	0.999767870921491	0.00383086782774475	0.00137166258639983	Consensus
A_MP	4	A	7150	7163	0.998185117967332	37.2932867132867	0.999813164138875	0.00382194267761465	0.00127261385795681	Consensus
A_MP	4	T	2	7163	0.000279212620410443	39	0.549115863765919	0.00382194267761465	0.00114305544413727	Minority
A_MP	4	G	11	7163	0.00153566941225743	32.9090909090909	0.666732337744004	0.00382194267761465	0.00188193812925811	Minority
A_MP	5	A	3	7485	0.000400801603206413	31	0	0.00376581013932197	0.00230618280247349	Minority
A_MP	5	T	1	7485	0.000133600534402138	21	0	0.00376581013932197	0.0115718556222517	Minority
A_MP	5	C	1	7485	0.000133600534402138	16	0	0.00376581013932197	0.0311411370908471	Minority
A_MP	5	G	7480	7485	0.999331997327989	36.3413101604278	0.999767641164772	0.00376581013932197	0.00132678163840589	Consensus
A_MP	6	A	9	7644	0.00117739403453689	20.5555555555556	0	0.00373960122470029	0.012546493326044	Minority
A_MP	6	T	1	7644	0.000130821559392988	33	0	0.00373960122470029	0.00180095073354187	Minority
A_MP	6	C	7633	7644	0.998560962846677	36.6973666972357	0.999785765827535	0.00373960122470029	0.00127239912684235	Consensus
A_MP	6	G	1	7644	0.000130821559392988	15	0	0.00373960122470029	0.0382245249426021	Minority
A_MP	7	A	2	7837	0.000255199693760367	16	0	0.00370902133144235	0.0309945701615491	Minority
A_MP	7	T	2	7837	0.000255199693760367	20.5	0	0.00370902133144235	0.0126282152375825	Minority
A_MP	7	C	7832	7837	0.999362000765599	36.9384576098059	0.999797497025414	0.00370902133144235	0.00122845888630678	Consensus
A_MP	7	G	1	7837	0.000127599846880184	15	0	0.00370902133144235	0.0381375623976758	Minority
A_MP	8	A	3	8866	0.000338371306113242	17.6666666666667	0	0.0035655066325283	0.0217427927158127	Minority
A_MP	8	T	8856	8866	0.998872095646289	36.6994128274616	0.999785933436925	0.0035655066325283	0.00115524035447687	Consensus
A_MP	8	C	7	8866	0.000789533047597564	34.1428571428571	0.512085221542203	0.0035655066325283	0.00147133155051775	Minority
A_MP	9	A	1	8886	0.000112536574386676	16	0	0.00356300086682597	0.0306128718920438	Minority
A_MP	9	T	8882	8886	0.999549853702453	37.0024769196127	0.999800497727007	0.00356300086682597	0.00112527550299364	Consensus
A_MP	9	C	3	8886	0.000337609723160027	35.6666666666667	0.196624862001853	0.00356300086682597	0.00126320442003306	Minority
A_MP	10	A	2	8904	0.000224618149146451	27	0	0.0035607539034893	0.0038600297757552	Minority
A_MP	10	C	8902	8904	0.999775381850854	37.0768366659178	0.999803928760288	0.0035607539034893	0.00111710092619444	Consensus
A_MP	11	T	8915	8917	0.999775709319278	37.1771172181716	0.999808404326747	0.00355913591765995	0.00110715793644471	Consensus
A_MP	11	G	2	8917	0.000224290680722216	22	0	0.00355913591765995	0.00928707592919	Minority
A_MP	12	A	9030	9033	0.99966788442378	37.3042081949059	0.999813909826658	0.00354487484044728	0.00108684424878405	Consensus
A_MP	12	T	1	9033	0.000110705192073508	16	0	0.00354487484044728	0.03056498855948	Minority
A_MP	12	C	2	9033	0.000221410384147017	26.5	0	0.00354487484044728	0.00417103794981313	Minority
A_MP	13	A	9052	9062	0.998896490840874	37.7338709677419	0.999831308804602	0.00354135832886955	0.00104932493056915	Consensus
A_MP	13	C	6	9062	0.000662105495475612	19.6666666666667	0	0.00354135832886955	0.014525221459046	Minority
A_MP	13	G	4	9062	0.000441403663650408	37.5	0.597130799655682	0.00354135832886955	0.00106814352741159	Minority
A_MP	14	A	4	9067	0.000441160251461343	18	0	0.00354075397500493	0.0202681647715053	Minority
A_MP	14	T	1	9067	0.000110290062865336	39	0	0.00354075397500493	0.000960463588871021	Minority
A_MP	14	C	9062	9067	0.999448549685673	37.4500110350916	0.999820014112292	0.00354075397500493	0.00107188370952337	Consensus
A_MP	15	A	8	9067	0.000882320502922687	19.25	0	0.00354075397500493	0.0157727891223844	Minority
A_MP	15	T	5	9067	0.000551450314326679	29.8	0	0.00354075397500493	0.00250409603794814	Minority
A_MP	15	C	9054	9067	0.998566229182751	37.4046830130329	0.999817965030958	0.00354075397500493	0.00107566444276477	Consensus

... data truncated ...

Reference_Name - Name of gene segment or genome assembled
Position - Site or position from beginning of the assembled consensus
Allele - Nucleotide allele at position
Count - Count of allele at position
Total - Total coverage depth at position for all alleles not counting ambiguous nucleotides
Frequency - Frequency of allele at position
Average_Quality - Average quality score of allele at position
ConfidenceNotMacErr - Confidence not machine/sequence error, see formula
PairedUB - Assembly-specific interval upperbound for significance testing based on paired-end end error estimates
QualityUB - Allele-specific interval upperbound for significance testing based on quality error estimates
Allele_Type - Allele is either a plurality consensus allele or a minority allele

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