Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,536,496	T→C	Q30R (CAG→CGG)	ompR ←	response regulator in two‑component regulatory system with EnvZ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,536,496	0	T	C	100.0%	186.4 / NA	51	Q30R (CAG→CGG)	ompR	response regulator in two‑component regulatory system with EnvZ
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/24);  total (27/24)

GTTGCTCTGACTACGAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCTGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGCAACAATTTGTAA  >  NC_000913/3536360‑3536619                                                                                                                                         |                                                                                                                            gTTGCTCTGACTACGAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCgg                                                                                                                           <  2:349461/139‑1 (MQ=255)          aCTACGAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGt                                                                                                                  >  1:344006/1‑139 (MQ=255)           cTACGAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGtt                                                                                                                 <  1:420321/139‑1 (MQ=255)            tACGAAGACCTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTc                                                                                                                <  1:594888/139‑1 (MQ=255)               gAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGt                                                                                                             >  2:725070/1‑139 (MQ=255)                    cGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGAt                                                                                                        <  1:337344/139‑1 (MQ=255)                        ggCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACg                                                                                                    >  1:20175/1‑139 (MQ=255)                                        aTCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGcgcacgc                                                                                    >  1:358611/1‑139 (MQ=255)                                          cTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAg                                                                                  >  1:780607/1‑139 (MQ=255)                                               ccAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCa                                                                             <  2:780607/139‑1 (MQ=255)                                                cAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            >  2:738652/1‑107 (MQ=255)                                                cAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            <  1:738652/107‑1 (MQ=255)                                                cAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCAt                                                                            >  1:652635/1‑139 (MQ=255)                                                   gTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATgtc                                                                         >  2:241789/1‑139 (MQ=255)                                                        aTTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCAt                                                                    >  2:493185/1‑139 (MQ=255)                                                        aTTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCAt                                                                    <  2:652635/139‑1 (MQ=255)                                                            aaTCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTc                                                                                                                <  2:168440/91‑1 (MQ=255)                                                            aaTCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTc                                                                                                                >  1:168440/1‑91 (MQ=255)                                                            aaTCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            >  2:446494/1‑95 (MQ=255)                                                            aaTCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            <  1:446494/95‑1 (MQ=255)                                                             aTCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGacc                                                               >  1:914452/1‑139 (MQ=255)                                                                  gTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAg                                                          >  2:748616/1‑139 (MQ=255)                                                                  gTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAg                                                          >  1:77448/1‑139 (MQ=255)                                                                           gATGGAAAGATTCACGAGTCAGCAGGCGACCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATg                                                                           <  2:486841/113‑1 (MQ=255)                                                                           gATGGAAAGATTCACGAGTCAGCAGGCGACCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATg                                                                           >  1:486841/1‑113 (MQ=255)                                                                            aTGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAg                                                <  2:344006/139‑1 (MQ=255)                                                                                aaaGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTtct                                            <  2:77448/139‑1 (MQ=255)                                                                                 aaGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTtctc                                           >  1:119108/1‑139 (MQ=255)                                                                                     ttCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGc                                       <  2:358611/139‑1 (MQ=255)                                                                                      tCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCgg                                                                                                              <  1:401756/67‑1 (MQ=255)                                                                                      tCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCgg                                                                                                              >  2:401756/1‑67 (MQ=255)                                                                                       cACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTa                                                 >  1:455903/1‑127 (MQ=255)                                                                                       cACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTa                                                 <  2:455903/127‑1 (MQ=255)                                                                                              cagcagGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCAttgtttgt                              <  2:119108/139‑1 (MQ=255)                                                                                              cagcagGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCAttgtttgt                              <  1:241789/139‑1 (MQ=255)                                                                                                         ccATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCAttgtttgt                              <  2:449676/128‑1 (MQ=255)                                                                                                         ccATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCAttgtttgt                              >  1:449676/1‑128 (MQ=255)                                                                                                                ttCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGcaa            <  1:725070/139‑1 (MQ=255)                                                                                                                  cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            >  1:380118/1‑41 (MQ=255)                                                                                                                  cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            <  2:380118/41‑1 (MQ=255)                                                                                                                  cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGcgcacg                                                                                     >  2:727714/1‑64 (MQ=255)                                                                                                                  cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGcgcacg                                                                                     <  1:727714/64‑1 (MQ=255)                                                                                                                  cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAAt                                                       >  1:53938/1‑94 (MQ=255)                                                                                                                  cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAAt                                                       <  2:53938/94‑1 (MQ=255)                                                                                                                  cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGcaaca          >  2:487825/1‑139 (MQ=255)                                                                                                                     cATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGCAACAAtt       >  2:494584/1‑139 (MQ=255)                                                                                                                          gCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGCAACAATTTGTaa  >  2:724659/1‑139 (MQ=255)                                                                                                                               gCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGcgcacg                                                                                     >  2:3904/1‑51 (MQ=255)                                                                                                                               gCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGcgcacg                                                                                     <  1:3904/51‑1 (MQ=255)                                                                                                                                     aaCCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCa                                      <  1:648724/92‑1 (MQ=255)                                                                                                                                     aaCCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCa                                      >  2:648724/1‑92 (MQ=255)                                                                                                                                         |                                                                                                                            GTTGCTCTGACTACGAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCTGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGCAACAATTTGTAA  >  NC_000913/3536360‑3536619

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑