`A_MP-coverage.txt`

Reference_Name	Position	Coverage Depth	Consensus	Deletions	Ambiguous	Consensus_Count	Consensus_Average_Quality
A_MP	1	7065	A	0	0	7030	28.51
A_MP	2	7092	T	0	0	7049	30.52
A_MP	3	7114	G	0	0	7073	26.94
A_MP	4	7163	A	0	0	7110	24.92
A_MP	5	7485	G	0	0	7468	25.68
A_MP	6	7644	C	0	0	7617	29.74
A_MP	7	7837	C	0	0	7745	27
A_MP	8	8866	T	0	0	8816	26.82
A_MP	9	8886	T	0	0	8850	30.05
A_MP	10	8904	C	0	0	8858	29.71
A_MP	11	8917	T	0	0	8850	31.26
A_MP	12	9033	A	0	0	8962	24.76
A_MP	13	9062	A	0	0	9001	31.77
A_MP	14	9067	C	0	0	8981	26.89
A_MP	15	9067	C	0	0	9020	27.71
A_MP	16	9079	G	0	0	9034	27.04
A_MP	17	9150	A	0	0	9130	28.38
A_MP	18	9268	G	2	0	9177	22.87
A_MP	19	9405	G	0	0	9329	25.99
A_MP	20	9405	T	0	0	9403	29.7
A_MP	21	9415	C	0	0	9355	30.39
A_MP	22	9463	G	0	0	9376	24.03
A_MP	23	9642	A	0	0	9548	26.84
A_MP	24	9682	A	0	0	9606	26.44
A_MP	25	9738	A	0	0	9735	30.12
A_MP	26	10317	C	0	0	10316	29.87
A_MP	27	10463	G	0	0	10441	27.2
A_MP	28	10532	T	0	0	10452	25.83
A_MP	29	10612	A	0	0	10553	28.68
A_MP	30	10656	T	0	0	10653	30.06
A_MP	31	10859	G	0	0	10795	28
A_MP	32	10874	T	0	0	10818	22.61
A_MP	33	11677	T	1	0	11640	26.19
A_MP	34	12008	C	1	0	11975	30.47
A_MP	35	12047	T	0	0	11951	24.67
A_MP	36	12489	C	0	0	12449	27.18
A_MP	37	12490	T	0	0	12482	26.31
A_MP	38	12973	C	0	0	12912	26.21
A_MP	39	12976	T	0	0	12932	31.9
A_MP	40	13042	A	0	0	13024	28.08

... data truncated ...

Reference_Name - Name of gene segment or genome assembled
Position - Site or position from beginning of the assembled consensus
Coverage Depth - Total coverage depth at position for all alleles (not counting deletions & ambiguous nucleotides)
Consensus - The consensus allele
Deletions - Deleted states, not included in coverage depth
Ambiguous - Number of ambiguous ("N") states in the reads, not included in coverage depth.
Consensus_Count - Coverage depth of the consensus allele.
Consensus_Average_Quality - Average base quality score for the consensus allele.
HMM_Position - Coordinate relative to the profile HMM optionally used for global alignment of the plurality consensus. Insertions use the upstream position.^Optional
Alignment_State - Alignment state relative to the profile HMM coordinate space: M, D, I, P, or X (match state, deletion, insertion, amplicon N-padding, or missing).^Optional

NOTE: The optional HMM_Position and Alignment_State columns are left joined to the variants, allAlleles, insertions, and deletions tables as available.

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