Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,661,508	T→G	T250P (ACC→CCC)	hcaR ←	DNA‑binding transcriptional regulator HcaR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,661,508	0	T	G	88.9%	22.7 / ‑3.0	9	T250P (ACC→CCC)	hcaR	DNA‑binding transcriptional regulator HcaR
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base G (3/5);  total (3/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.99e-01

ATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTG  >  NZ_CP009273/2661429‑2661591                                                                                |                                                                                    aTCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAatta                                                                           <  1:22737/90‑1 (MQ=255)   ctcCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAattatt                                                                         <  1:11330/90‑1 (MQ=255)                      aTCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCaaa                                                      >  2:226472/1‑90 (MQ=255)                          gTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGa                                                  <  1:168894/90‑1 (MQ=255)                            aaaGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACg                                                >  1:326421/1‑90 (MQ=255)                                            caTTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATCAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCcca                                >  2:138336/1‑90 (MQ=255)                                                tCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAg                            <  1:226472/90‑1 (MQ=255)                                                        tGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATgg                    <  1:383352/90‑1 (MQ=255)                                                                          gTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTg  <  1:250723/90‑1 (MQ=255)                                                                                |                                                                                    ATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTG  >  NZ_CP009273/2661429‑2661591

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑