Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,319,449	T→C	N143S (AAC→AGC)	rcsC ←	sensory histidine kinase RcsC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,319,449	0	T	C	100.0%	158.3 / NA	46	N143S (AAC→AGC)	rcsC	sensory histidine kinase RcsC
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/21);  total (25/21)

ATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGTTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACGCAGGC  >  NC_000913/2319313‑2319580                                                                                                                                         |                                                                                                                                    atcatcTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTa                                                                                                                                  >  2:468512/1‑140 (MQ=255)            gtgCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGcc                                                                                                                       >  2:126579/1‑140 (MQ=255)            gtgCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGcc                                                                                                                       >  2:92830/1‑140 (MQ=255)               cATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCa                                                                                                                    >  1:227583/1‑140 (MQ=255)                         tttattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTAt                                                                                                          >  1:689475/1‑140 (MQ=255)                           tattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATcg                                                                                                        <  1:126579/140‑1 (MQ=255)                           tattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATcg                                                                                                        >  1:49935/1‑140 (MQ=255)                            attGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATcgc                                                                                                       >  2:458536/1‑140 (MQ=255)                              tGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCgcgc                                                                                                     <  1:468512/140‑1 (MQ=255)                                aTGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCa                                                                                                   >  2:520332/1‑140 (MQ=255)                                  gCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGt                                                                                                 <  2:227583/140‑1 (MQ=255)                                   cGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTa                                                                                                >  2:308022/1‑140 (MQ=255)                                   cGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTa                                                                                                >  1:74846/1‑140 (MQ=255)                                     ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCTGCAGAAAAATTATCGCGCCAGTAgc                                                                                              >  1:712873/1‑140 (MQ=255)                                     ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCgcgc                                                                                                     >  2:579275/1‑133 (MQ=255)                                     ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCgcgc                                                                                                     <  1:579275/133‑1 (MQ=255)                                     ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAgc                                                                                              >  2:404862/1‑140 (MQ=255)                                     ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAgc                                                                                              >  1:855221/1‑140 (MQ=255)                                          gCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATa                                                                                         >  2:504544/1‑140 (MQ=255)                                            aaaGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATaaa                                                                                       <  1:92830/140‑1 (MQ=255)                                              aGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAAcc                                                                                     >  2:686726/1‑140 (MQ=255)                                               gCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCa                                                                                    <  1:236198/140‑1 (MQ=255)                                                  ttCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGc                                                                                 >  2:314198/1‑140 (MQ=255)                                                      aCGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAAt                                                                             <  1:308022/140‑1 (MQ=255)                                                      aCGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAAt                                                                             <  1:520332/140‑1 (MQ=255)                                                        gcgGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGa                                                                           <  2:398262/140‑1 (MQ=255)                                                          ggTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACt                                                                         >  2:530544/1‑140 (MQ=255)                                                                   ttCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAAc                                                                <  1:785850/140‑1 (MQ=255)                                                                   ttCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAAc                                                                >  1:655624/1‑140 (MQ=255)                                                                      cACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTc                                                             >  2:190951/1‑140 (MQ=255)                                                                        cTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGc                                                           <  2:74846/140‑1 (MQ=255)                                                                         tGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGcc                                                          <  2:391775/140‑1 (MQ=255)                                                                            cATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAgg                                                       >  2:191735/1‑140 (MQ=255)                                                                                   cGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACt                                                <  1:686726/140‑1 (MQ=255)                                                                                   cGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACt                                                <  2:855221/140‑1 (MQ=255)                                                                                        aCCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTg                                           >  2:54924/1‑140 (MQ=255)                                                                                        aCCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTg                                           >  2:578157/1‑140 (MQ=255)                                                                                           gAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCgg                                        <  1:458536/140‑1 (MQ=255)                                                                                                  gCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATc                                 >  2:744456/1‑140 (MQ=255)                                                                                                    cATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCgg                               >  1:367286/1‑140 (MQ=255)                                                                                                      tGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAg                             <  1:803289/140‑1 (MQ=255)                                                                                                            ggTTATCGCTGCCGATTAAAAATCCCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCa                       <  1:431503/140‑1 (MQ=255)                                                                                                                        cGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCa           <  2:712873/140‑1 (MQ=255)                                                                                                                               aaaTACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACGCAg    <  1:404862/140‑1 (MQ=255)                                                                                                                               aaaTACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACGCAg    <  1:190951/140‑1 (MQ=255)                                                                                                                                 aTACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACGCAGGc  <  1:715878/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                    ATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGTTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACGCAGGC  >  NC_000913/2319313‑2319580

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑