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%	152.8 / NA	39	R20C (CGC→TGC)	soxR	redox‑sensitive transcriptional activator SoxR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (25/14);  total (25/14)

CCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCG  >  NZ_CP009273/4267368‑4267536                                                                                       |                                                                                   ccTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCa                                                                                 >  2:47189/1‑90 (MQ=255) ccTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCa                                                                                 >  1:451071/1‑90 (MQ=255) ccTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCa                                                                                 >  2:44428/1‑90 (MQ=255)   tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                               >  1:323657/1‑90 (MQ=255)   tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                               <  1:352814/90‑1 (MQ=255)   tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                               >  2:306266/1‑90 (MQ=255)     aaGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCgg                                                                             <  1:327208/90‑1 (MQ=255)       gTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGgtg                                                                           <  2:149226/90‑1 (MQ=255)                aGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTAt                                                                  >  1:257320/1‑90 (MQ=255)                aGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTAt                                                                  >  2:711238/1‑90 (MQ=255)                         gATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGc                                                         >  1:4325/1‑90 (MQ=255)                                    aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa                                              <  1:686113/90‑1 (MQ=255)                                        aaTTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTa                                          >  1:61805/1‑90 (MQ=255)                                         aTTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTaa                                         <  1:671652/90‑1 (MQ=255)                                          ttACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTaaa                                        <  2:526082/90‑1 (MQ=255)                                                cGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgcgc                                                            >  1:599778/1‑64 (MQ=255)                                                cGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgcgc                                                            <  2:599778/64‑1 (MQ=255)                                                cGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTg                                  >  1:603315/1‑90 (MQ=255)                                                      aaaGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTAcc                            <  2:829326/90‑1 (MQ=255)                                                        aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg                          <  2:887081/90‑1 (MQ=255)                                                           gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAgggg                                    >  1:677805/1‑76 (MQ=255)                                                           gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt                                    <  2:677805/77‑1 (MQ=255)                                                           gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTAt                       >  2:654588/1‑90 (MQ=255)                                                            ctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATc                      >  1:421639/1‑90 (MQ=255)                                                              gctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgc                                                              >  1:800031/1‑48 (MQ=255)                                                              gctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgc                                                              <  2:800031/48‑1 (MQ=255)                                                              gctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCCTTTCTTTGAAAGGAAAGGGGTGGTTACCAGTATCCg                    >  1:820426/1‑90 (MQ=255)                                                                      ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTTTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCg            >  2:752344/1‑90 (MQ=255)                                                                      ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa                                              >  1:83707/1‑56 (MQ=255)                                                                      ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa                                              <  2:83707/56‑1 (MQ=255)                                                                      ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCg            >  1:623328/1‑90 (MQ=255)                                                                        ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAgg                                      >  2:474967/1‑62 (MQ=255)                                                                        ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAgg                                      <  1:474967/62‑1 (MQ=255)                                                                        ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGc          >  2:383848/1‑90 (MQ=255)                                                                        ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAAGAAAGGGGTGGTTACCAGTATCCGTAACAGCGGc          >  1:608572/1‑90 (MQ=255)                                                                        ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCTGCATTTTTATGAAAGAAAAAGGGTGATTACCAGGATCCGTAACAGCGGc          >  1:548775/1‑90 (MQ=255)                                                                             aGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCa     >  2:98972/1‑90 (MQ=255)                                                                             aGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTCCATTTCTATGAAAATAAAGGGGTGATTACCAGTATCCGTAACAGCGGCAATCa     >  1:537863/1‑90 (MQ=255)                                                                                ggCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcg  <  2:61805/90‑1 (MQ=255)                                                                                       |                                                                                   CCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCG  >  NZ_CP009273/4267368‑4267536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑