Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	2,411,452	0	T	C	73.3%	13.6 / 3.8	15	S36S (TCT→TCC)	SAUSA300_RS12395	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (2/2);  new base C (0/11);  total (2/13)
Fisher's exact test for biased strand distribution p-value = 5.71e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.93e-01

TAAAATATAAAAAAAGAAGAGCTTTAAATCATAACGCATGCCATTTATCTTTAAATGCAATGAGTTATCATTCAAACTCTTCTTATCAACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTGGG  >  NC_007793/2411370‑2411547                                                                                   |                                                                                                taaaatataaaaAAAGAAGAGCTTTAAATCATAACGCATGCCATTTATCTTTAAATGCAATGAGTTATCATTCAAACTCTTCTTATCAACCTacatacat                                                                                <  1:3618396/100‑1 (MQ=255)  aaaatataaaaAAAGAAGAGCTTTAAATCATAACGCATGCCATTTATCTTTAAATGCAATGAGTTATCATTCAAACTCTTCTTATCAACCTACATACAtt                                                                               >  1:3109238/1‑100 (MQ=255)                                                                      acgtgtgctctTCCGATCTACCCACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCa           <  1:4330127/93‑1 (MQ=255)                                                                         tgtgctctTCCGATCTACCTATATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGc        <  1:5751738/96‑1 (MQ=255)                                                                         tgtgctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGc        <  1:3285264/96‑1 (MQ=255)                                                                         tgtgctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGc        <  1:828512/96‑1 (MQ=255)                                                                         tgtgctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGc        <  1:949124/96‑1 (MQ=255)                                                                         cAAACTCTTCTTATCAACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGc        >  1:1677903/1‑100 (MQ=255)                                                                            gctctTCCGATCTTCCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCAtt     <  1:2644425/99‑1 (MQ=255)                                                                            gctctTCCGATCTCCCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCAtt     <  1:5646107/99‑1 (MQ=255)                                                                            gctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCAtt     <  1:2172052/99‑1 (MQ=255)                                                                            gctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCAtt     <  1:5532784/99‑1 (MQ=255)                                                                             ctctTCTTATCAACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTg    <  1:2419498/100‑1 (MQ=255)                                                                             ctctTCCGATCTACCTCCATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCaagg    <  1:5577542/100‑4 (MQ=255)                                                                             ctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTg    <  1:4767736/100‑1 (MQ=255)                                                                               cttcttATCAACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTgaa  <  1:4555717/100‑3 (MQ=255)                                                                                   |                                                                                                TAAAATATAAAAAAAGAAGAGCTTTAAATCATAACGCATGCCATTTATCTTTAAATGCAATGAGTTATCATTCAAACTCTTCTTATCAACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTGGG  >  NC_007793/2411370‑2411547

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑