Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	514,924	G→T	10.2%	L54M (CTG→ATG) ‡	PP_0426 ←	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	514,924	0	G	T	10.2%	129.5 / 7.1	49	L54M (CTG→ATG) ‡	PP_0426	membrane protein
Reads supporting (aligned to +/- strand):  ref base G (18/26);  new base T (2/3);  total (20/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.60e-02

CCAGCAGCGACGGGCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAGGTCCTTGGCGTCGAAT  >  NC_002947/514776‑515072                                                                                                                                                     |                                                                                                                                                     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                                                                                                                                        >  4:185769/1‑97 (MQ=255)                                                                   agGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGt                                                                                                                                        <  3:185769/97‑1 (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                                                               >  3:200140/1‑149 (MQ=255)                                                                                        gcgcCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTg                                                               <  2:55446/149‑1 (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      <  5:145289/149‑1 (MQ=255)                                                                                                                                                 aTCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAGGTCCTTGGCGTc      <  3:131649/149‑1 (MQ=255)                                                                                                                                                  tCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAGGTCCTTGGCGTc      >  1:133456/1‑148 (MQ=255)                                                                                                                                                     gCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCAGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAGGTCCTTGGCGTCGAAt  >  1:224901/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                     CCAGCAGCGACGGGCTGGACGCGGCGTTGCAGATGGAGGGCGAACAAGGTGATCAGCAGGATATAGAGGCTGGCGATGATCAACAGCGCGCCGTCACCGAGGCTCATCCATGCCTCGGTGAGCAACCAGCCCATTGCCGCCATGATCAGCATGGCGCCAAAGTAGAAGGCAACATGGGCCAGCTGAAAGCTGCCACGTGGTGCGGGTTGCTGGCGCAGGAATGCCAACAGGCTTTGGTCCTGGCCTGGTTGGAGAATGCCTGCTTGCACGGCGCGCGCCAGGTCCTTGGCGTCGAAT  >  NC_002947/514776‑515072

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑