Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	417,373	C→T	P78S (CCA→TCA)	phoB →	response regulator in two‑component regulatory system with PhoR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	417,373	0	C	T	100.0%	198.3 / NA	61	P78S (CCA→TCA)	phoB	response regulator in two‑component regulatory system with PhoR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (32/29);  total (32/29)

AAGATTATGACAGTGCTGTGAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGC  >  NC_000913/417239‑417504                                                                                                                                       |                                                                                                                                    aaGATTATGACAGTGCTGTGAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAgt                                                                                                                                 >  1:530290/1‑139 (MQ=255)                     aaTCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCagag                                                                                                             <  2:530290/139‑1 (MQ=255)                        cAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                          <  2:1405023/139‑1 (MQ=255)                        cAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                          >  1:297886/1‑139 (MQ=255)                        cAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                          >  1:723549/1‑139 (MQ=255)                        cAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                          >  2:1320718/1‑139 (MQ=255)                            tgaatgaaCCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGgaaga                                                                                                      <  1:716135/139‑1 (MQ=255)                             gaatgaaCCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGgaagaa                                                                                                     >  1:1087153/1‑139 (MQ=255)                                 gaaCCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGc                                                                                                                  >  2:1398321/1‑122 (MQ=255)                                 gaaCCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGc                                                                                                                  <  1:1398321/122‑1 (MQ=255)                                        ggCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGAc                                                                                                                     >  2:586689/1‑112 (MQ=255)                                        ggCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGAc                                                                                                                     <  1:586689/112‑1 (MQ=255)                                        ggCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGgaaga                                                                                                      >  1:652427/1‑127 (MQ=255)                                        ggCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGt                                                                                          >  1:638199/1‑139 (MQ=255)                                        ggCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGGGATGTTGACCGCCAGAGGGgaaga                                                                                                      <  2:652427/127‑1 (MQ=255)                                          ccGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTgc                                                                                        <  2:793800/139‑1 (MQ=255)                                           cGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTgcg                                                                                       <  2:723549/139‑1 (MQ=255)                                             gATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGgaaga                                                                                                      <  2:57380/122‑1 (MQ=255)                                             gATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGgaaga                                                                                                      >  1:57380/1‑122 (MQ=255)                                              aTTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                          >  2:34726/1‑117 (MQ=255)                                              aTTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                          <  1:34726/117‑1 (MQ=255)                                                        cctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGaa                                                                             <  1:127081/136‑1 (MQ=255)                                                        cctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGaa                                                                             >  2:127081/1‑136 (MQ=255)                                                         ctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCag                                                                                                               <  2:1356035/101‑1 (MQ=255)                                                         ctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCag                                                                                                               >  1:1356035/1‑101 (MQ=255)                                                           cGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgc                                                                       <  2:1087153/139‑1 (MQ=255)                                                                 gATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGAt                                                                 <  2:638199/139‑1 (MQ=255)                                                                 gATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGAt                                                                 <  2:297886/139‑1 (MQ=255)                                                                        ccTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGAcc                                                                                                                    >  1:706448/1‑81 (MQ=255)                                                                        ccTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGAcc                                                                                                                    <  2:706448/81‑1 (MQ=255)                                                                              ggcTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCa                                                    >  1:228215/1‑139 (MQ=255)                                                                                cTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGAc                                                                                                                     <  1:1268871/72‑1 (MQ=255)                                                                                cTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGAc                                                                                                                     >  2:1268871/1‑72 (MQ=255)                                                                                          cAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCg                                                                         <  2:1446862/106‑1 (MQ=255)                                                                                          cAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCg                                                                         >  1:1446862/1‑106 (MQ=255)                                                                                             ttCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAg                                                                                                                                  >  2:1067490/1‑46 (MQ=255)                                                                                             ttCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAg                                                                                                                                  <  1:1067490/46‑1 (MQ=255)                                                                                             ttCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGa                                     >  1:1003454/1‑139 (MQ=255)                                                                                             ttCATCAAACACCTCAAGCGAGAGACGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGa                                     >  1:863843/1‑139 (MQ=255)                                                                                               catcaAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                          <  2:921125/68‑1 (MQ=255)                                                                                               catcaAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                          >  1:921125/1‑68 (MQ=255)                                                                                                  caAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                      >  2:283078/1‑101 (MQ=255)                                                                                                  caAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                      <  1:283078/101‑1 (MQ=255)                                                                                                         cTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAggg                                                                                                           >  2:1473596/1‑57 (MQ=255)                                                                                                         cTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAggg                                                                                                           <  1:1473596/57‑1 (MQ=255)                                                                                                         cTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCgg                                                                   >  1:1038885/1‑97 (MQ=255)                                                                                                         cTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCgg                                                                   <  2:1038885/97‑1 (MQ=255)                                                                                                            aaGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGgcgc                      >  2:1420712/1‑139 (MQ=255)                                                                                                                 cgAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGTCAGAGGGGAAGAAGAAGATCGCGTGcgcg                                                                                     >  2:21175/1‑71 (MQ=255)                                                                                                                 cgAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGTCAGAGGGGAAGAAGAAGATCGCGTGcgcg                                                                                     <  1:21175/71‑1 (MQ=255)                                                                                                                   aGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                      >  2:178531/1‑84 (MQ=255)                                                                                                                   aGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                      <  1:178531/84‑1 (MQ=255)                                                                                                                   aGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGAt                                                                 >  1:357106/1‑89 (MQ=255)                                                                                                                   aGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGAt                                                                 <  2:357106/89‑1 (MQ=255)                                                                                                                   aGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACtata                                                          <  1:732623/96‑1 (MQ=255)                                                                                                                   aGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACtata                                                          >  2:732623/1‑96 (MQ=255)                                                                                                                   aGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCaa               >  1:1007070/1‑139 (MQ=255)                                                                                                                        aTGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCgg          >  1:1019904/1‑139 (MQ=255)                                                                                                                         tGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACtat                                                           >  1:725598/1‑89 (MQ=255)                                                                                                                         tGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACtat                                                           <  2:725598/89‑1 (MQ=255)                                                                                                                                ggATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATgcgc  <  2:228215/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                    AAGATTATGACAGTGCTGTGAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGC  >  NC_000913/417239‑417504

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑