Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,087,693	T→C	F10F (TTT→TTC)	rhaS →	HTH‑type transcriptional activator RhaS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,087,693	0	T	C	100.0%	116.5 / NA	33	F10F (TTT→TTC)	rhaS	HTH‑type transcriptional activator RhaS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/6);  total (27/6)

ATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCATGAAAT  >  NZ_CP009273/4087631‑4087776                                                               |                                                                                    aTTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATa                                                          >  2:218574/1‑90 (MQ=255) aTTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATa                                                          >  1:651221/1‑90 (MQ=255)      gCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAAcc                                                     >  2:724619/1‑90 (MQ=255)      gCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAAcc                                                     >  2:267037/1‑90 (MQ=255)         gtgtTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCg                                                  >  1:237947/1‑90 (MQ=255)          tgtTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCgg                                                 <  2:517085/90‑1 (MQ=255)                         gaggCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAt                                  <  1:456341/90‑1 (MQ=255)                           ggCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAttt                                >  2:193463/1‑90 (MQ=255)                            gCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAtttt                               <  1:585373/90‑1 (MQ=255)                               aGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCt                            >  2:492758/1‑90 (MQ=255)                                     aCCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcat                      >  2:367763/1‑90 (MQ=255)                                     aCCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcat                      <  1:318349/90‑1 (MQ=255)                                     aCCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcat                      >  2:152162/1‑90 (MQ=255)                                     aCCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcat                      >  2:129449/1‑90 (MQ=255)                                     aCCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcat                      >  2:606708/1‑90 (MQ=255)                                        gTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcatcat                   >  1:751863/1‑90 (MQ=255)                                          aTTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcatcatca                 >  2:236753/1‑90 (MQ=255)                                          aTTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcatcatca                 >  2:391221/1‑90 (MQ=255)                                                tAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGAttt           >  2:630862/1‑90 (MQ=255)                                                tAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGAttt           >  1:625689/1‑90 (MQ=255)                                                  gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGa                          <  1:686524/73‑1 (MQ=255)                                                  gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGa                          >  2:686524/1‑73 (MQ=255)                                                  gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc         >  2:409806/1‑90 (MQ=255)                                                  gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc         >  1:206520/1‑90 (MQ=255)                                                  gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc         >  2:102718/1‑90 (MQ=255)                                                  gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc         >  1:705981/1‑90 (MQ=255)                                                  gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc         >  1:5987/1‑90 (MQ=255)                                                  gtgtGGATTTTTTCCCGCCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc         >  1:591197/1‑90 (MQ=255)                                                  gtgtGGATTTTTTCCCGCCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAAATCATCATGATTTTc         >  2:301838/1‑90 (MQ=255)                                                  gagtgGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc         >  1:677148/3‑90 (MQ=255)                                                    gtgGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCAt       >  2:284806/1‑90 (MQ=255)                                                       gATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAt                                  <  2:625842/60‑1 (MQ=255)                                                       gATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAt                                  >  1:625842/1‑60 (MQ=255)                                                         ttttttcCCGTCTGGTAACGCGTCCGTGGCGGTAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCATGAAAt  >  2:407653/1‑90 (MQ=255)                                                               |                                                                                    ATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCATGAAAT  >  NZ_CP009273/4087631‑4087776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑