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%	133.5 / NA	43	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 (26/17);  total (26/17)

TGACAGTGCTGTGAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCG  >  NC_000913/417246‑417503                                                                                                                                |                                                                                                                                   tGACAGTGCTGTGAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTAAGTGGTGATg                                                                                                                         >  2:174766/1‑139 (MQ=255)      gTGCTGTGAATCAACTGAATGAACCCTGGGCGGATTTAATTCTCCTCGTCTGGAGGTTATTTGGCGGCTCAGGCACCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAATGGTTATGTTTAc                                                                                                                    >  2:156453/1‑139 (MQ=255)            tgAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCag                                                                                                              >  2:1064599/1‑139 (MQ=255)             gAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAgtg                                                                                                                               >  1:527644/1‑121 (MQ=255)             gAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACAGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAgtg                                                                                                                               <  2:527644/121‑1 (MQ=255)                 cAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         <  2:687513/139‑1 (MQ=255)                 cAACTGAATGAACCCTGGCCGGAATTAATTCTCCTCGACTGGATTTTACCTTGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgcgg                                                                                                         <  1:156453/139‑1 (MQ=255)                   aCTGTATGAACCCTGGCCGGATTTATTTCTCCTCGACTGGATGTTACCTGGCGGCACCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGgaa                                                                                                       >  2:783552/1‑139 (MQ=255)                   aCTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCag                                                                                                              <  1:53050/132‑1 (MQ=255)                   aCTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCag                                                                                                              >  2:53050/1‑132 (MQ=255)                              ccTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGgaaga                                                                                                     <  2:180906/130‑1 (MQ=255)                              ccTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGgaaga                                                                                                     >  1:180906/1‑130 (MQ=255)                              ccTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATcg                                                                                            >  1:873420/1‑139 (MQ=255)                                  gCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         >  2:661709/1‑122 (MQ=255)                                  gCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         <  1:661709/122‑1 (MQ=255)                                                tcctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         <  2:767606/108‑1 (MQ=255)                                                tcctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         >  1:767606/1‑108 (MQ=255)                                                  ctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         <  1:526770/106‑1 (MQ=255)                                                  ctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         >  2:526770/1‑106 (MQ=255)                                                  ctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCg                                                                        >  2:680449/1‑139 (MQ=255)                                                  ctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCg                                                                        <  2:427209/139‑1 (MQ=255)                                                   tcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCgg                                                                       >  1:857196/1‑139 (MQ=255)                                                     gACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                     <  2:873420/139‑1 (MQ=255)                                                       cTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGcgcg                                                                   <  1:680449/139‑1 (MQ=255)                                                          gATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGcgcg                                                                   <  1:308514/136‑1 (MQ=255)                                                          gATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGcgcg                                                                   >  2:308514/1‑136 (MQ=255)                                                          gATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGAt                                                                >  1:39639/1‑139 (MQ=255)                                                               tACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACta                                                           >  1:933649/1‑139 (MQ=255)                                                                            cGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                     >  1:176834/1‑116 (MQ=255)                                                                            cGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                     <  2:176834/116‑1 (MQ=255)                                                                                      ttCATCAAACACCTCAAGTGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGa                                    >  1:555493/1‑139 (MQ=255)                                                                                      ttCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGtt                                                                                                                       >  1:734090/1‑56 (MQ=255)                                                                                      ttCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGtt                                                                                                                       <  2:734090/56‑1 (MQ=255)                                                                                      ttCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGa                                    >  2:772392/1‑139 (MQ=255)                                                                                      ttCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGAATGACTATATCACCAAGCCGTTTTCGCCGa                                    >  1:408243/1‑139 (MQ=255)                                                                                                  cTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                     >  1:817889/1‑94 (MQ=255)                                                                                                  cTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                     <  2:817889/94‑1 (MQ=255)                                                                                                   tCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGgc                       >  2:320275/1‑139 (MQ=255)                                                                                                          cgAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCg                                                                        >  2:274024/1‑83 (MQ=255)                                                                                                          cgAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCg                                                                        <  1:274024/83‑1 (MQ=255)                                                                                                          cgAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATc                >  2:375057/1‑139 (MQ=255)                                                                                                                  tGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGt        >  1:1020988/1‑139 (MQ=255)                                                                                                                     cccGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAAt     <  1:783552/139‑1 (MQ=255)                                                                                                                        gggATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATgcg  >  2:677173/1‑139 (MQ=255)                                                                                                                                |                                                                                                                                   TGACAGTGCTGTGAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCG  >  NC_000913/417246‑417503

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑