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%	168.7 / NA	44	R20C (CGC→TGC)	soxR	redox‑sensitive transcriptional activator SoxR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (22/22);  total (22/22)

TCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC  >  NZ_CP009273/4267370‑4267538                                                                                     |                                                                                     tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 <  1:899260/90‑1 (MQ=255) tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 >  1:744133/1‑90 (MQ=255) tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 >  2:231380/1‑90 (MQ=255) tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 >  1:492025/1‑90 (MQ=255) tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 >  1:491105/1‑90 (MQ=255)    aGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGgt                                                                              >  1:135855/1‑90 (MQ=255)         aCTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGc                                                                         >  2:725613/1‑90 (MQ=255)              aGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGtgtg                                                                           >  2:820339/1‑83 (MQ=255)              aGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGtgtg                                                                           <  1:820339/83‑1 (MQ=255)                  aaaGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgc                                                                <  1:319549/90‑1 (MQ=255)                  aaaGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgc                                                                >  1:1020565/1‑90 (MQ=255)                     gCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCt                                                             <  2:962042/90‑1 (MQ=255)                       gATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGc                                                           <  2:424523/90‑1 (MQ=255)                         tttATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTTCAt                                                         >  1:181823/1‑90 (MQ=255)                         tttATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCAt                                                         >  1:473038/1‑90 (MQ=255)                                  aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa                                                <  1:1044052/90‑1 (MQ=255)                                  aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa                                                <  2:662227/90‑1 (MQ=255)                                  aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa                                                <  1:818594/90‑1 (MQ=255)                                       aTTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTaa                                           <  1:945202/90‑1 (MQ=255)                                       aTTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTaa                                           <  2:123515/90‑1 (MQ=255)                                          aCCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAgg                                        <  2:473038/90‑1 (MQ=255)                                            cccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt                                      <  2:744133/90‑1 (MQ=255)                                            cccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt                                      <  2:825110/90‑1 (MQ=255)                                             ccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgc                                                                >  2:244764/1‑63 (MQ=255)                                             ccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgc                                                                <  1:244764/63‑1 (MQ=255)                                               gCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 <  1:885407/44‑1 (MQ=255)                                               gCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc                                                                                 >  2:885407/1‑44 (MQ=255)                                                    aaaGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTAcc                              <  2:610227/90‑1 (MQ=255)                                                      aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGAATACCAg                            <  2:750922/90‑1 (MQ=255)                                                        cgcTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTa                          <  1:57916/90‑1 (MQ=255)                                                         gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTTTGAAAGGAAAAGGGTGATTACCAGTAt                         >  2:638488/1‑90 (MQ=255)                                                         gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGGAAAGGGGTGGTTACCAGTAt                         >  2:445550/1‑90 (MQ=255)                                                         gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCCGCCTTTCTATGAAAGGAAAGGGGTGATTACCAGTAt                         >  2:104747/1‑90 (MQ=255)                                                          ctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGATTACCAGTATc                        >  1:200165/1‑90 (MQ=255)                                                                    ccGGCGAGGTGGCGAAATGCAGCGGTGTGGCGGCATCCGTGCCTCGTGTCTTTGGGAGGAAAGGGTTGATTACCAGGATCCGTAACGGCg              >  2:1012842/1‑90 (MQ=255)                                                                    ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCg              >  1:860969/1‑90 (MQ=255)                                                                      ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg                            >  2:305156/1‑74 (MQ=255)                                                                      ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg                            <  1:305156/74‑1 (MQ=255)                                                                      ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGc            >  2:415045/1‑90 (MQ=255)                                                                      ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAAAAAAAGGGTGATTACCAGGATCCGTAACAGCGGc            >  2:987964/1‑90 (MQ=255)                                                                           aGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa                                                >  2:318540/1‑49 (MQ=255)                                                                           aGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa                                                <  1:318540/49‑1 (MQ=255)                                                                                cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc  <  2:345079/90‑1 (MQ=255)                                                                                cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc  <  1:966047/90‑1 (MQ=255)                                                                                     |                                                                                     TCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC  >  NZ_CP009273/4267370‑4267538

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑