Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	514,920	A→C	12.0%	I55S (ATC→AGC)	PP_0426 ←	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	514,920	0	A	C	12.0%	125.5 / 8.4	49	I55S (ATC→AGC)	PP_0426	membrane protein
Reads supporting (aligned to +/- strand):  ref base A (20/23);  new base C (2/4);  total (22/27)
Fisher's exact test for biased strand distribution p-value = 6.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

GCCAGCAGCGACGGGCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAGGTCCTTGGCGTC  >  NC_002947/514775‑515068                                                                                                                                                  |                                                                                                                                                     gCCAGCAGCGACGGGCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCAGCCATGATCa                                                                                                                                                   >  7:32664/1‑149 (MQ=255)  ccAGCAGCGACGGGCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATCCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAg                                                                                                                                                  >  4:190693/1‑149 (MQ=255)   cagaagCGACTGGCTGGACTCTTCGTTGCAGATCGACTGCTAACCAGGTGATCAGCATTATATAGAGTCTGGCTATGATCACCAGCGCTCCGTCACCGACGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGc                                                                                                                                                 <  2:259214/149‑1 (MQ=255)    agcagcGACGGGCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGCGGCTGGCGATGATCAACCGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGCGCAACCAGCCCATTGCCGCCATGATCAg                                                                                                                                                  >  4:178950/1‑147 (MQ=255)       agcGACGGGCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATgg                                                                                                                                             <  4:181433/149‑1 (MQ=255)          gACGGGCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGCTGATCATGgcgg                                                                                                                                          <  7:252348/149‑2 (MQ=255)            cGGGCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGCTGATCATGGCGGCa                                                                                                                                        <  4:229797/149‑1 (MQ=255)             gggCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCa                                                                                                                                        >  3:171348/1‑148 (MQ=255)              ggCTGGACGCGGCGTTGGAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGGGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCCTGCCTCGGTGAGCGACCAGCCCATTGCCGCCATGATCAGCATGgcgcgc                                                                                                                                        >  2:39384/1‑145 (MQ=255)              ggCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCaaa                                                                                                                                      <  1:105558/149‑1 (MQ=255)                                  aTGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCa                                                                                                                  >  6:243961/1‑149 (MQ=255)                                     gAGGGCGATCAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGAAACATGGGCCAGCt                                                                                                               <  5:158551/149‑1 (MQ=255)                                     gAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCt                                                                                                               <  3:190693/149‑1 (MQ=255)                                           gAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGc                                                                                                         >  3:174719/1‑149 (MQ=255)                                                    gATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCAGAAAGCTGCCACgtg                                                                                                >  4:291162/1‑149 (MQ=255)                                                          cagGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCgg                                                                                          >  2:211633/1‑149 (MQ=255)                                                          cagGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCGCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCgg                                                                                          <  4:50783/149‑1 (MQ=255)                                                             gATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGtt                                                                                       >  3:115839/1‑149 (MQ=255)                                                                 taGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCt                                                                                    <  3:291162/148‑1 (MQ=255)                                                                  agagGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTg                                                                                   <  4:171348/148‑1 (MQ=255)                                                                    agGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGt                                                                                                                                    <  3:185769/97‑1 (MQ=255)                                                                    agGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGt                                                                                                                                    >  4:185769/1‑97 (MQ=255)                                                                           cGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAAt                                                                         >  8:224059/1‑149 (MQ=255)                                                                           cGATGATCAACAGCGCGCCGGCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAAt                                                                         <  8:245075/149‑1 (MQ=255)                                                                              tgatCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATgg                                                                                                                      <  4:158451/101‑1 (MQ=255)                                                                               gatCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTCCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGcc                                                                      >  7:43495/1‑148 (MQ=255)                                                                                    aCAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAgg                                                                >  4:131649/1‑149 (MQ=255)                                                                                     cAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCaa                                                                    <  2:83085/144‑1 (MQ=255)                                                                                     cAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAgct                                                               >  1:83085/1‑147 (MQ=255)                                                                                     cAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGCGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGc                                                               <  5:243961/149‑1 (MQ=255)                                                                                       gcgcgcCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCtt                                                             <  6:87184/149‑1 (MQ=255)                                                                                         gcgcCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTg                                                           <  2:55446/149‑1 (MQ=255)                                                                                         gcgcCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTg                                                           >  3:200140/1‑149 (MQ=255)                                                                                          cgcCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTgg                                                          <  1:211633/149‑1 (MQ=255)                                                                                           gcCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGt                                                         >  3:178437/1‑149 (MQ=255)                                                                                             cGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTcc                                                       <  8:121502/149‑1 (MQ=255)                                                                                               tCACCGAGGCTCATCCATGCCTCGTTGAGCAACCAGCCCATTGCGGCCATGATCAGCATGGGGCCAAAGTAGACGGCAACATGGCCCTGTAGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTcctg                                                     <  1:92402/149‑1 (MQ=255)                                                                                                     aGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTcctggcctgg                                               <  4:178437/149‑1 (MQ=255)                                                                                                          cATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTg                                            >  6:145289/1‑147 (MQ=255)                                                                                                                        gtaGCAACCAGCCCATTGCCGCCATGCTCAGCATGGCGCAAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGc                            <  8:272488/147‑1 (MQ=255)                                                                                                                              aCCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGgcg                      >  5:197746/1‑149 (MQ=255)                                                                                                                                 aGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGgcgcgc                   <  7:224059/149‑1 (MQ=255)                                                                                                                                   cccATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGgcgcgcgc                 >  3:171544/1‑149 (MQ=255)                                                                                                                                      tttGGCGCCATGCTGATCATGGCGGCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAg              >  3:157134/2‑149 (MQ=255)                                                                                                                                          gcgccATGCTGATCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGgc                       >  2:304533/2‑136 (MQ=255)                                                                                                                                          gcgccATGCTGATCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGgc                       <  1:304533/135‑1 (MQ=255)                                                                                                                                           cgccATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCTCCAGGTCCt         <  1:315312/149‑1 (MQ=255)                                                                                                                                            gccATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTTGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAGGTCCtt        <  7:134658/149‑1 (MQ=255)                                                                                                                                            gccATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAGGTCCtt        <  7:144862/149‑1 (MQ=255)                                                                                                                                                  aTCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAGGTCCTTGGCGTc  <  3:131649/149‑1 (MQ=255)                                                                                                                                                  aTCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAGGTCCTTGGCGTc  <  5:145289/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                     GCCAGCAGCGACGGGCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAGGTCCTTGGCGTC  >  NC_002947/514775‑515068

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑