Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,267,454	C→T	R20C (CGC→TGC)	soxR →	redox‑sensitive transcriptional activator SoxR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,267,454	0	C	T	100.0%	165.7 / NA	42	R20C (CGC→TGC)	soxR	redox‑sensitive transcriptional activator SoxR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (23/19);  total (23/19)

TCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC  >  NZ_CP009273/4267370‑4267538                                                                                     |                                                                                     tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 >  2:274606/1‑90 (MQ=255) tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 <  2:435057/90‑1 (MQ=255) tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 >  2:268609/1‑90 (MQ=255) tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 >  2:1229221/1‑90 (MQ=255)               ggTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATc                                                                   >  2:356730/1‑90 (MQ=255)                    aGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgcgc                                                              <  1:137023/90‑1 (MQ=255)                       gATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgc                                                                <  1:852857/85‑1 (MQ=255)                       gATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgc                                                                >  2:852857/1‑85 (MQ=255)                              ggAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTa                                                    >  2:1102886/1‑90 (MQ=255)                                  aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCAtt                                                        <  1:1321864/82‑1 (MQ=255)                                  aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa                                                <  2:213478/90‑1 (MQ=255)                                  aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa                                                <  1:407385/90‑1 (MQ=255)                                  aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGGGCTGCAtt                                                        >  2:1321864/1‑82 (MQ=255)                                             ccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGtt                                     >  2:399993/1‑90 (MQ=255)                                              cGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTg                                    >  2:192116/1‑90 (MQ=255)                                               gCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGa                                   >  2:888757/1‑90 (MQ=255)                                               gCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCTGCATTTCTATGGAAGTAAAGGGGTGa                                   >  2:640793/1‑90 (MQ=255)                                                cATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGAt                                  <  1:399993/90‑1 (MQ=255)                                                cATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGAt                                  >  2:487819/1‑90 (MQ=255)                                                      aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg                            <  1:799289/90‑1 (MQ=255)                                                      aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg                            <  2:1243901/90‑1 (MQ=255)                                                      aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg                            <  1:1229221/90‑1 (MQ=255)                                                        cgcTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTa                          <  1:426522/90‑1 (MQ=255)                                                        cgcTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTa                          <  1:411337/90‑1 (MQ=255)                                                        cgcTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTa                          <  1:356730/90‑1 (MQ=255)                                                         gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGa                                                 <  1:211337/66‑1 (MQ=255)                                                         gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGa                                                 >  2:211337/1‑66 (MQ=255)                                                         gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg                            <  1:1096922/87‑1 (MQ=255)                                                         gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg                            >  2:1096922/1‑87 (MQ=255)                                                         gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAAGAAAGGGGTGATTACCAGTAt                         >  1:974633/1‑90 (MQ=255)                                                          ctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCTGCATTTTTATGAAAGTAAAGGGGTGGTTACCAGTATc                        >  1:828886/1‑90 (MQ=255)                                                           tgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATcc                       <  1:917269/90‑1 (MQ=255)                                                            gctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCCGCCTTTCTATGAAAGGAAAAGGGTGATTACCAGTATCCg                      >  1:1233243/1‑90 (MQ=255)                                                                    ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCg              >  2:240562/1‑90 (MQ=255)                                                                    ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGATTACCAGTATCCGTAACAGCg              >  2:772367/1‑90 (MQ=255)                                                                    ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCTGCATTTCTATGGAAGAAAAGGGGTGATTACCAGGATCCGTAAAAGCg              >  1:1192921/1‑90 (MQ=255)                                                                     cGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCgg             <  2:712432/90‑1 (MQ=255)                                                                      ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt                                      <  2:301448/64‑1 (MQ=255)                                                                      ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt                                      >  1:301448/1‑64 (MQ=255)                                                                      ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCTGCCTTTTTATGAAAGGAAAGGGTTGATTACCAGTATCCGTAACAGCGGc            >  1:997093/1‑90 (MQ=255)                                                                           aGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGGAAAGGGTTGATTACCAGTATCCGTAAAAGCGGCAATCa       >  2:995453/1‑90 (MQ=255)                                                                                cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc  <  1:121771/90‑1 (MQ=255)                                                                                     |                                                                                     TCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC  >  NZ_CP009273/4267370‑4267538

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑