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%	144.2 / NA	37	R20C (CGC→TGC)	soxR	redox‑sensitive transcriptional activator SoxR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (18/19);  total (18/19)

CCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC  >  NZ_CP009273/4267368‑4267538                                                                                       |                                                                                     ccTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCa                                                                                   >  2:99007/1‑90 (MQ=255)   tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 >  2:1088922/1‑90 (MQ=255)     aaGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCgg                                                                               <  1:127532/90‑1 (MQ=255)               gAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTa                                                                     >  1:667023/1‑90 (MQ=255)                aGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTAt                                                                    >  1:538497/1‑90 (MQ=255)                 ggTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATc                                                                   <  1:734815/90‑1 (MQ=255)                            ttATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCAtt                                                        <  2:284050/90‑1 (MQ=255)                            ttATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCAtt                                                        <  2:633714/90‑1 (MQ=255)                                   aaaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGa                                                 <  1:1099580/90‑1 (MQ=255)                                    aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 >  1:485257/1‑57 (MQ=255)                                    aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 <  2:485257/57‑1 (MQ=255)                                    aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa                                                <  1:1088922/90‑1 (MQ=255)                                         aTTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTaa                                           <  1:1347209/90‑1 (MQ=255)                                                 gCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTgg                                   >  2:111186/1‑89 (MQ=255)                                                 gCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAAGGGTGa                                   >  2:932757/1‑90 (MQ=255)                                                    ttAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTa                                <  2:761783/90‑1 (MQ=255)                                                        aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg                            <  1:509187/90‑1 (MQ=255)                                                        aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg                            <  2:798389/90‑1 (MQ=255)                                                         gcgcTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGAtt                                 <  1:455429/84‑1 (MQ=255)                                                         gcgcTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGAtt                                 >  2:455429/1‑84 (MQ=255)                                                          cgcTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTa                          <  1:373936/90‑1 (MQ=255)                                                           gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCGTTTCTTTTAAAGTAAAGGGGTGATTACCAGGAt                         >  1:1098957/1‑90 (MQ=255)                                                           gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCCTTTCTTTGAAAGTAAAGGGGTGATTAACAGTAt                         >  2:876469/1‑90 (MQ=255)                                                           gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTAt                         >  1:138702/1‑90 (MQ=255)                                                           gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGGAAAAGGGTGATTACCAGTAt                         >  2:224398/1‑90 (MQ=255)                                                           gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGGTGCATTTTTATGAAAATAAAGGGGTTATTATCAGTAt                         >  2:962871/1‑90 (MQ=255)                                                            ctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATc                        >  1:488917/1‑90 (MQ=255)                                                                      ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTTTGAAAGTAAAGGGGTGATTACCAGTATCCGTAACAGCg              >  2:1331720/1‑90 (MQ=255)                                                                      ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGAAAAAGGGTGATTACCAGTATCCGTAACAGCg              >  1:7126/1‑90 (MQ=255)                                                                       cGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCgg             <  1:531866/90‑1 (MQ=255)                                                                        ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGc            >  1:325094/1‑90 (MQ=255)                                                                        ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCCGCATTTCTATGAAAGTAAAGGGGTGGTTACCAGTATCCGTAACAGCGGc            >  2:1193064/1‑90 (MQ=255)                                                                                  cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc  <  2:1098957/90‑1 (MQ=255)                                                                                  cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc  <  1:669418/90‑1 (MQ=255)                                                                                  cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc  <  2:667023/90‑1 (MQ=255)                                                                                  cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc  <  1:485741/90‑1 (MQ=255)                                                                                  cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc  <  1:144560/90‑1 (MQ=255)                                                                                       |                                                                                     CCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC  >  NZ_CP009273/4267368‑4267538

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑