Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,214,413	A→C	I457L (ATT→CTT)	rpoD →	RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,214,413	0	A	C	100.0%	159.6 / NA	55	I457L (ATT→CTT)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (34/21);  total (34/21)

TCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATCGC  >  NC_000913/3214273‑3214546                                                                                                                                             |                                                                                                                                      tCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTAGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCTCGCACCATCCGTATTCCGGTGCATATGCtt                                                                                                                                     >  1:853474/1‑143 (MQ=255)     tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTgaga                                                                                                                                 <  2:753873/143‑1 (MQ=255)       tgatgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGAAACGGAGCGCGCCTTCCGTATTCCGGTGCATATGCGTGAGAcc                                                                                                                               >  1:665810/1‑143 (MQ=255)       tgatgaAAGCGGTTGATAAATTCGAATACCGCCGTAGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCAGCATCCGTATTCCGGTGCCTATGCTTGAGAcc                                                                                                                               >  2:488705/1‑143 (MQ=255)         atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCAt                                                                                                                             <  1:591478/143‑1 (MQ=255)          tcgaagcgctgtctAAAGTCGAATACCGCTTTGGTTACTAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACGCGCGCTATCGCGGATCAGGCGCGCACCATCCGTATTCCTGTGCATATGCTTGAGACCATc                                                                                                                            <  2:293512/130‑1 (MQ=255)             aggCGGTTGATGTATTGGACTTCGGCTGTGGTGAGAAGTGCTCGACCTCTGTAACCTGGTGGATCCGTCAGGCGATGACTCGCTCTAGCGGGGATCAGGCGCGCACCAGCGGGATTCCGGTGCATATGCTTGAGACCATcaac                                                                                                                         <  2:231878/141‑1 (MQ=255)                   ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTc                                                                                                                   <  1:454858/143‑1 (MQ=255)                     gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCaa                                                                                                                 >  2:852241/1‑143 (MQ=255)                     gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCACCAACAAGCTCaa                                                                                                                 >  2:238049/1‑143 (MQ=255)                      aTAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCGCAAc                                                                                                                >  1:795268/1‑143 (MQ=255)                          aTTCGGATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCgga                                                                                                            >  1:110246/1‑141 (MQ=255)                          aTTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTa                                                                                                            >  1:840137/1‑143 (MQ=255)                          aTTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCCCTATCGCGGAACAGGCGCGCACCGTCCGTATTCCGGTGCATGTGCTTGCGAGCATCAACACGGTCCACCGTa                                                                                                            >  2:268035/1‑143 (MQ=255)                           ttCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGCTCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTAt                                                                                                           >  1:815257/1‑143 (MQ=255)                            tCGCATACCGCCGTGGTTACAAGTCCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTAtt                                                                                                          <  1:564281/143‑1 (MQ=255)                             cGAAGACCGCCGCGGTTACAAGTGCCCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTAGCGCGGATCAGGCGCGCACCACCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTAttt                                                                                                         <  1:747592/143‑1 (MQ=255)                                                  gtgtgtcACCTCCGCAACCTGGCGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGAACCATCCGTATTCCGGTGAATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAgaga                                                                                    <  1:238692/137‑1 (MQ=255)                                                    tctcCGCCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATg                                                                                  <  1:467709/143‑1 (MQ=255)                                                       ccACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGc                                                                               >  1:551257/1‑143 (MQ=255)                                                        cACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTGTCGCGGATCAGGCGCGCACCATCCGTATGCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCCGCACGCGGTGGGcc                                                                              >  1:758435/1‑143 (MQ=255)                                                        cACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTAACGCGGATCAGGCGCGCACCATCCGTATTCCGGGGCATATGCTAGACACCATCAACAAGCGCAACCGGATATCTCGCCAGATGCAGCAAGAGATGGGcc                                                                              >  2:698452/1‑143 (MQ=255)                                                         aCCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCg                                                                             >  1:692303/1‑143 (MQ=255)                                                          cctgcgcgcccTGGTGGATGCGCCGGCCGATGACCCGCTCGATCGCGGATCAGGCGCGCCCCATCCGTATTCCGGTGCATATGCTGGAGACCATCAACAAGCGCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGt                                                                            <  2:173866/134‑1 (MQ=255)                                                          ccTACGCAACCTGGGGGATCCGTCAGGCGAGCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGGGCATATGCTGGGGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCGAGAGATGGGCCgc                                                                            >  1:436296/1‑142 (MQ=255)                                                             aCGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGaa                                                                         >  1:387953/1‑143 (MQ=255)                                                              cGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATGCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAAc                                                                        <  2:810818/143‑1 (MQ=255)                                                                 aaCCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTCCACGAGATGGGCCGTGAGCCGa                                                                     >  2:699444/1‑143 (MQ=255)                                                                     tggtggCTCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCATGAGACCATCAACAAGCTCAACCGTATTGCTCGCGAGCTGCTGCAACAGACGGGCCGTGAACCGAGGcc                                                                 >  2:10746/1‑143 (MQ=255)                                                                     tggtggATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGcc                                                                 >  1:531974/1‑143 (MQ=255)                                                                            tCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGGGAACGGACGCTGggagaa                                                          >  2:367047/1‑143 (MQ=255)                                                                             ccGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAAc                                                         >  1:667767/1‑143 (MQ=255)                                                                              cGTCAGCCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCTTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACt                                                        <  1:446264/143‑1 (MQ=255)                                                                                tCACGCGACCACCCGCTCTAGCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTgg                                                      <  2:840137/143‑1 (MQ=255)                                                                                    gCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAAACGTATGTCTCGCCGGATGCTGGAAGAGATGGGCCGGGAACCGAGGCCgggacgccgggctga                                                  >  1:577252/1‑130 (MQ=255)                                                                                      gATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTAATCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGTGGCCGCACGAGAGGGGACGCGAACGGAGGCAAGGAGAACGAGCTGAAc                                                >  2:789935/1‑143 (MQ=255)                                                                                          aCCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAAACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTAt                                            >  1:688194/1‑143 (MQ=255)                                                                                           cccGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATg                                           >  1:650814/1‑143 (MQ=255)                                                                                            ccGCTCTATAGCGGATCAGGCGCGCACCATCCGTACTCCGGTGCATATGCTTGAGACCACCAACACGCTCAGCCGTATTTCTCGCCAGATGCTCCACGAGATGGGCCGCGAGGCGAGGACGGAGGGACGGGCAGAACGGATGc                                          >  2:829089/1‑143 (MQ=255)                                                                                              gCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCCCCACCGTATTTCTCGCCAGATGATGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTg                                        >  1:567837/1‑143 (MQ=255)                                                                                                   aTCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGCACTGGCTGAACGTATGCCGCTGcc                                   >  2:486388/1‑143 (MQ=255)                                                                                                      gcgGATCAGGCGCGCACCATCCGTATTCCGGCGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGCGAACCGGCGCCGGAAGCACAGGCCGACCGGAAGCTGAGGGCGGa                                >  2:617628/1‑143 (MQ=255)                                                                                                        ggATCAGGCGCGCACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAg                              <  1:30346/143‑1 (MQ=255)                                                                                                               gcgcgcACCTGCCGTATTCCGGTGCATATGCTTGGGGCCCTCAACATGCTCTTCCGTATTTCTCGCCAGTTGCTGCAAGTGTTGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGAt                       <  2:292845/143‑1 (MQ=255)                                                                                                               ccccgcACCTTCCGTACTCCTGTGCTTATGCTTTAGTCCATCACCAAGCTCAACCGTATTTCTCGCCAGATTCTGCAAGAGATTGGCCGTGAACCGACGCCGGCAGAACTGGCTGATCTTATGCTGATGCCGGAAGACAAGAt                       <  2:706835/140‑1 (MQ=255)                                                                                                                    cACCATCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCACGAGATGGGCCGTGAACCGACGCCGGAAGACCTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGcc                  >  1:188644/1‑142 (MQ=255)                                                                                                                     cgcATCCGTGTTCCGGTGCATGTCCTGGAGACCATCTACGAGCGGAGCGGTATTTCGCGCCAGTTGCTGCGAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCaa                 <  2:536829/141‑1 (MQ=255)                                                                                                                        aTCCGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCGGATGCCGGAAGCCAACATCCGCAAAGt              >  2:321650/1‑143 (MQ=255)                                                                                                                          ccctactCCTGTGCATATGCTTGAGACCATCAACAAGCTCATCCGTATTTCTCGCCAGATGCTGCAAGAGGTGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGc            <  1:791485/137‑1 (MQ=255)                                                                                                                          ccGCATTCCGGTGCATATGCTTGAGACCATCAACACGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATAGGCCGTGAACCGACGCCGGACGAACTGGCTGAACGGAGGCTGATGCCGGAAGACAGGATCCGAACAGTGc            >  2:749827/1‑143 (MQ=255)                                                                                                                           cGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAGCTGGCAGAAGGTATGCCGATGCCGCAAGACATGATCCGCACAGGGCt           >  2:783297/1‑143 (MQ=255)                                                                                                                           cGTATTCCGGTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCt           <  1:558453/143‑1 (MQ=255)                                                                                                                              gttCCGGTGCATATGCTTGAGACCATCAACAAGCTCACCCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGaa        <  2:620003/142‑1 (MQ=255)                                                                                                                                tCCGGCGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCGCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGa      <  1:67233/143‑1 (MQ=255)                                                                                                                                    gTGCATATGCTTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGGATGCTGATGCCGGAAGAAAAGAGCCGCAAAGTGCAGAAGAACGc  >  2:52939/1‑143 (MQ=255)                                                                                                                                             |                                                                                                                                      TCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATCGC  >  NC_000913/3214273‑3214546

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑