Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	2,411,452	0	T	C	77.3%	25.9 / 4.4	22	S36S (TCT→TCC)	SAUSA300_RS12395	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/5);  new base C (0/17);  total (0/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.52e-01

AAAATATAAAAAAAGAAGAGCTTTAAATCATAACGCATGCCATTTATCTTTAAATGCAATGAGTTATCATTCAAACTCTTCTTATCAACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTGGG  >  NC_007793/2411371‑2411547                                                                                  |                                                                                                aaaatataaaaAAAGAAGAGCTTTAAATCATAACGCATGCCATTTATCTTTAAATGCAATGAGTTATCATTCAAACTCTTCTTATCAACCTACATACAtt                                                                               <  1:148914/100‑1 (MQ=255) aaaatataaaaAAAGAAGAGCTTTAAATCATAACGCATGCCATTTATCTTTAAATGCAATGAGTTATCATTCAAACTCTTCTTATCAACCTACATACAtt                                                                               <  1:6600854/100‑1 (MQ=255) aaaatataaaaAAAGAAGAGCTTTAAATCATAACGCATGCCATTTATCTTTAAATGCAATGAGTTATCATTCAAACTCTTCTTATCAACCTACATACAtt                                                                               <  1:5889612/100‑1 (MQ=255)                                                                     acgtgtgctctTCCGATCTCCCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCa           <  1:1301778/93‑1 (MQ=255)                                                                        tgtgctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGc        <  1:4204510/96‑1 (MQ=255)                                                                        tgtgctctTCCGATCTACCACCATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGc        <  1:2523919/96‑1 (MQ=255)                                                                        cAAACTCTTCTTATCAACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGc        <  1:2944279/100‑1 (MQ=255)                                                                         gtgctctTCCGATCTACCTACATACATAGACATTATACTAACATATGTTGTTTTACATATTCAACAAACATTTCAACGGTAGCACTTTTAATATCATGCa       <  1:3745681/97‑1 (MQ=255)                                                                           gctctTCCGATCTTCCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCAtt     <  1:1605154/99‑1 (MQ=255)                                                                           gctctTCCGATCTGCCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCAtt     <  1:6037563/99‑1 (MQ=255)                                                                           gctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCact     <  1:3933740/99‑3 (MQ=255)                                                                           gctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCAtt     <  1:2649388/99‑1 (MQ=255)                                                                           gctctTCCGATCTACCT‑CATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTg    <  1:3117937/99‑1 (MQ=255)                                                                           gctctTCCGATCTACCCACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCAtt     <  1:2379094/99‑1 (MQ=255)                                                                            ctctTCTTATCAACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTg    <  1:511552/100‑1 (MQ=255)                                                                            ctctTCCGATCTTCCTGCATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTg    <  1:1525911/100‑1 (MQ=255)                                                                            ctctTCCGATCTTCCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTg    <  1:341551/100‑1 (MQ=255)                                                                            ctctTCCGATCTGCCTTCATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTg    <  1:4499346/100‑1 (MQ=255)                                                                            ctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCGCTTTTAATATCATGCATTg    <  1:93516/100‑1 (MQ=255)                                                                            ctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTg    <  1:2631272/100‑1 (MQ=255)                                                                            ctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTg    <  1:4171723/100‑1 (MQ=255)                                                                            ctctTCCGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTg    <  1:6167010/100‑1 (MQ=255)                                                                             tcttccGATCTACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTgc   <  1:2594037/100‑2 (MQ=255)                                                                              cttcttATCAACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTggg  <  1:5274580/100‑1 (MQ=255)                                                                                  |                                                                                                AAAATATAAAAAAAGAAGAGCTTTAAATCATAACGCATGCCATTTATCTTTAAATGCAATGAGTTATCATTCAAACTCTTCTTATCAACCTACATACATTGACATTATACTATCATATGTTGTTTTACATATTCAACAAACATTTCAACGTTAGCACTTTTAATATCATGCATTGGG  >  NC_007793/2411371‑2411547

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑