Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,535,392	C→T	P159P (CCG→CCA)	envZ ←	sensory histidine kinase in two‑component regulatory system with OmpR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,535,392	0	C	T	100.0%	127.8 / NA	39	P159P (CCG→CCA)	envZ	sensory histidine kinase in two‑component regulatory system with OmpR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (24/15);  total (24/15)

CCTGCAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGCGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTTGC  >  NC_000913/3535283‑3535527                                                                                                              |                                                                                                                                        ccTGCAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGt                                                                                                            >  1:345991/1‑139 (MQ=255)     cAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGc                                                                                                        <  1:798503/139‑1 (MQ=255)       aGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCgg                                                                                                      <  2:434813/139‑1 (MQ=255)       aGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCgg                                                                                                      <  1:72950/139‑1 (MQ=255)           tGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCtgat                                                                                                                      <  2:661629/119‑1 (MQ=255)           tGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCtgat                                                                                                                      >  1:661629/1‑119 (MQ=255)             cGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAACCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCAcgcg                                                                                                >  1:1065226/1‑139 (MQ=255)                 ttCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTAcc                                                                                            <  2:773550/139‑1 (MQ=255)                                cggtcggtTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATA‑TGGGCGACa                                                                            >  1:442829/1‑139 (MQ=255)                                     ggtTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCa                                                                        >  2:348884/1‑139 (MQ=255)                                                 gAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCa                                                            >  2:407414/1‑139 (MQ=255)                                                   aTAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAga                                                          >  2:849238/1‑139 (MQ=255)                                                         aGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATA‑TGGGCGACAGCCAGGTTTTCAGCCAGACGACAgg                                                   <  2:442829/139‑1 (MQ=255)                                                          gCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAgg                                                   <  1:849238/139‑1 (MQ=255)                                                           ccACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGc                                                  >  1:135192/1‑139 (MQ=255)                                                                         tCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTTGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGAc                                    >  2:635336/1‑139 (MQ=255)                                                                                   cATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCgg                                                                                                      >  2:495697/1‑63 (MQ=255)                                                                                   cATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCgg                                                                                                      <  1:495697/63‑1 (MQ=255)                                                                                   cATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCAcg                                                                                                  <  2:842637/67‑1 (MQ=255)                                                                                   cATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCAcg                                                                                                  >  1:842637/1‑67 (MQ=255)                                                                                           ccAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCAcgcg                                                                                                >  1:243428/1‑61 (MQ=255)                                                                                           ccAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCAcgcg                                                                                                <  2:243428/61‑1 (MQ=255)                                                                                             aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGc                                                                          >  2:564289/1‑81 (MQ=255)                                                                                             aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGc                                                                          <  1:564289/81‑1 (MQ=255)                                                                                             aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGtttt                                                                  >  1:527287/1‑89 (MQ=255)                                                                                             aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGtttt                                                                  <  2:527287/89‑1 (MQ=255)                                                                                             aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAAcg                             >  1:515849/1‑126 (MQ=255)                                                                                             aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAAcg                             <  2:515849/126‑1 (MQ=255)                                                                                              gCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCgg               >  1:52729/1‑139 (MQ=255)                                                                                              gCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTACGGTCAGGGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGCCAGGCGAACTTTTGTTAACCTCAACGCGCACTTCCGTCgg               >  2:1016167/1‑139 (MQ=255)                                                                                                      cGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGa                                     >  1:1202231/1‑109 (MQ=255)                                                                                                      cGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGa                                     <  2:1202231/109‑1 (MQ=255)                                                                                                      cGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCa       >  1:477486/1‑139 (MQ=255)                                                                                                         aaCAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGtt    >  1:31999/1‑139 (MQ=255)                                                                                                         aaCAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGtt    >  2:911308/1‑139 (MQ=255)                                                                                                          aCAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTTGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTtg   >  2:584753/1‑139 (MQ=255)                                                                                                          aCAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTtg   <  1:407414/139‑1 (MQ=255)                                                                                                           cAGTGGAGAGAAATCGCCCTGATGAATTTCTGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTtgc  >  1:719209/1‑139 (MQ=255)                                                                                                           cAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCg                   >  2:5969/1‑122 (MQ=255)                                                                                                              |                                                                                                                                        CCTGCAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGCGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTTGC  >  NC_000913/3535283‑3535527

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑