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Validation experiments:

Run	Assay Type	Release Date	Published consensus	Differences	Acceptable?
SRR11177792	RNA-Seq	2020-02-25	MT072688	sam2conseq reports extra GGTTTATAC at 5' end, and extra AGTGC (run of ?) poly-A at 3' end - all else identical
SRR10903401	RNA-Seq	2020-01-18	MN988669.1	sam2conseq reports extra A at 5' end, and poly-A tail
SRR10903402	RNA-Seq	2020-01-18	MN988668.1	sam2conseq reports poly-A tail (21 nt + ?)
SRR10971381	RNA-Seq	2020-01-27	MN908947	published sequence has 7 nt reported as ? by sam2conseq (6193 A, 6592 A, 7030 T, 29864 G, 29867 T, 29868 G, 29870 C) and an extra 3' ?
SRR11241254	RNA-Seq	2020-03-04	MT163716.1 or EPI_ISL_413025	MT163716: 3 nt diff, poly-A tail absent (see #7); EPI_ISL_413025: same issues as MT163716, plus a large deletion	Y
SRR11241255	RNA-Seq	2020-03-04	MT163717.1	3 nt differences (29861 A->T, 29862 A->G, 29864 A->C), extra ? on 3' end.	Y
SRR11247075	RNA-Seq	2020-03-05	MT163721.1	Stretches of N’s and covid seqs between 0-578; Poly-A tail differences 29851 A->N 29852 A->N 29855 A->T 29856 A->G 29858 A->C; Generically low coverage throughout (n<50) except positions 29870-29903; otherwise same
SRR11247076	RNA-Seq	2020-03-05	MT163720.1	“TGAC” at position 29870-29874 present in sam2conseq and published sequence; published sequence missing nucleotides at positions 0-174; otherwise all same. Published consensus sequences for SRR11247075, SRR11247076 aren't reporting nucleotides with low (n<10) coverage
SRR11247077	RNA-Seq	2020-03-05	MT163719.1	Published consensus seq missing characters 0-578 Sam2conseq start of Poly-A-Tail has “GAATGA”, similar to reference (NC_045512) 29864 A->G 29867 A->T 29868 A->G 29870 A->C
SRR11247078	RNA-Seq	2020-03-05	MT163718.1	5’ end some differences; T -> A (1), T -> G (3), A -> G (4), T -> A (5), T -> A (6), S -> C (20); Depth <10, but no ambiguity. Grep for sequence preceding position 20 does show any ambiguity in raw fast file
SRR11278090	RNA-Seq	2020-03-09	WA13-UW9	Can't find the published consensus sequence
SRR11278091	RNA-Seq	2020-03-09	EPI_ISL_413563	Exact match except 3' end has extra "?"	Y
SRR11278092	RNA-Seq	2020-03-09	WA11-UW7	Lots of sporadic "N's" in the sam2conseq. The highest frequency base for N's (in sam2conseq generated frequency csv) is the base called in the reported consensus sequence. Sam2conseq also reports more bases on the 5' end where the published consensus sequence has "?".
SRR11278164	RNA-Seq	2020-03-09	WA18-UW14	T->A (1), T->A (6); otherwise same
SRR11278165	RNA-Seq	2020-03-09	WA17-UW13	5' end discrepancies, same as SRR11278092; 29860 A->G, 29863 G->A, 29866 A -> T, 29867 A ->G, 29869 A->C
SRR11278166	RNA-Seq	2020-03-09	WA16-UW12	No differences
SRR11278167	RNA-Seq	2020-03-09	WA15-UW11	sam2conseq missing an A at position 1; reported gap
SRR11278168	RNA-Seq	2020-03-09	WA14-UW10	sam2conseq has 85 additional NT's at 5' end, more A's at 3' end. Differences at 3' end 29861 A->G, 29864 C->G, 29868 C->G
SRR11140744	WGS	2020-02-21	EPI_ISL_408670 (2019-nCoV/USA-WI1/2020)	Conseq has longer polyA tail on 3' end
SRR11140746	WGS	2020-02-21	EPI_ISL_408670 (2019-nCoV/USA-WI1/2020)	Published has extra 3 A's at 3' end
SRR11140748	WGS	2020-02-21	EPI_ISL_408670 (2019-nCoV/USA-WI1/2020)	Same sample as above
SRR11140750	WGS	2020-02-21	EPI_ISL_408670 (2019-nCoV/USA-WI1/2020)	Same sample as above
SRR11092057	RNA-Seq	2020-02-15	MN996528.1	failure to map, BLASTed sequences, found human/eukaryotic sequences
SRR11092058	RNA-Seq	2020-02-15	MN996527.1	mix of human and synthetic DNA, failure to map
SRR11092064	RNA-Seq	2020-02-15	MN996531.1	mix of human and synthetic DNA, failure to map
SRR11085733	RNA-Seq	2020-02-13	MN611525	non-human, failure to map
SRR11085736	RNA-Seq	2020-02-13	MN611522	non-human, failure to map
SRR11085737	RNA-Seq	2020-02-13	MN611521	non-human, failure to map
SRR11085738	RNA-Seq	2020-02-13	MN611520	non-human, failure to map
SRR11085740	RNA-Seq	2020-02-13	MN611518	non-human, failure to map
SRR11085741	RNA-Seq	2020-02-13	MN611517	non-human, failure to map
SRR11085797	RNA-Seq	2020-02-13	MN996532.1	non-human, failure to map
SRR11314339	RNA-Seq	2020-03-17	MT192765	3' tail has several has several N's
SRR11092056	RNA-Seq	2020-02-15	MN996530	Low coverage, sample is mostly human DNA (known issue)	Y