Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,486,216	A→C	8.1%	S30R (AGC→CGC)	PP_3978 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,486,216	0	A	C	8.1%	170.4 / 4.6	59	S30R (AGC→CGC)	PP_3978	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (26/28);  new base C (3/2);  total (29/30)
Fisher's exact test for biased strand distribution p-value = 6.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAGATCAATGCTGCGCCACTACAATTACATCGTTGACGACCCGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAG  >  NC_002947/4486071‑4486363                                                                                                                                                  |                                                                                                                                                    cAAGATCAATGCTGCGCCACTACAATTACATCGTTGACGACCCGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCt                                                                                                                                                  <  3:96078/149‑1 (MQ=255)  aaGATCAATGCTGCGCCACTACAATTACATCGTTGACGACCCGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTg                                                                                                                                                 >  3:380383/1‑149 (MQ=255)      tCAATGCTGCGCCACTACAATTACATCGTTGACGACCCGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCACGACCCGGCAGCGAGCTGCCAt                                                                                                                                             <  2:87636/149‑1 (MQ=255)       cAATGCTGCGCCACTACAATTACATCGTTGACGACCCGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCTCGCTGccgg                                                                                                                                             <  4:345970/148‑3 (MQ=255)                    cTACAATTACATCGTTGACGACCCGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGAt                                                                                                                               <  2:62993/149‑1 (MQ=255)                            aCATCGTTGACGACCCGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCAACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCTCCCTGATGGAGAAtt                                                                                                                       >  2:313217/1‑149 (MQ=255)                              aTCGTTGACGACCCGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTg                                                                                                                     >  6:250113/1‑149 (MQ=255)                               tCGTTGACGACCCGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGc                                                                                                                    >  4:162297/1‑149 (MQ=255)                                   tGAGGACCCGAGCATTCCATAGGTATGTGCACCCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCa                                                                                                                   <  8:175696/146‑1 (MQ=255)                                         cccGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCtt                                                                                                          <  8:298954/149‑1 (MQ=255)                                          ccGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATTGCATCTGGTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCttt                                                                                                         <  5:160960/149‑1 (MQ=255)                                          ccGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCCCCGTGGCtt                                                                                                          >  1:350278/1‑148 (MQ=255)                                          ccGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCttt                                                                                                         <  2:77939/149‑1 (MQ=255)                                             aTCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCttt                                                                                                         >  3:191108/1‑146 (MQ=255)                                             aTCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAg                                                                                                      <  4:40153/149‑1 (MQ=255)                                                    cATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACgg                                                                                                  <  8:54011/146‑1 (MQ=255)                                                    cATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACgg                                                                                                  >  7:54011/1‑146 (MQ=255)                                                    cATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGAt                                                                                               >  2:151488/1‑149 (MQ=255)                                                    cATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGAt                                                                                               >  2:145991/1‑149 (MQ=255)                                                       aGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGa                                                                                            >  6:129670/1‑149 (MQ=255)                                                          tATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATAc                                                                                         <  5:171007/149‑1 (MQ=255)                                                                ccACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAg                                                                                   <  1:151488/149‑1 (MQ=255)                                                                ccACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAg                                                                                   <  1:145991/149‑1 (MQ=255)                                                                  aCCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTg                                                                                 >  3:350108/1‑149 (MQ=255)                                                                    ccGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTggg                                                                               <  3:96623/149‑1 (MQ=255)                                                                    ccGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTggg                                                                               >  6:213117/1‑149 (MQ=255)                                                                         gtgtAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAg                                                                                   <  5:130017/140‑1 (MQ=255)                                                                         gtgtAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAg                                                                                   >  6:130017/1‑140 (MQ=255)                                                                              gCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGc                                                                      <  5:129670/148‑1 (MQ=255)                                                                              gCCACAAACGCAACATCGATGCCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGCGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCg                                                                     >  6:309547/1‑149 (MQ=255)                                                                               ccACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCg                                                                     >  2:235481/1‑148 (MQ=255)                                                                                cacaAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACggg                                                                                                 >  3:244551/1‑119 (MQ=255)                                                                                cacaAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACggg                                                                                                 <  4:244551/119‑1 (MQ=255)                                                                                cacaAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATCAAGCCGCCCTGATGTAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATTGCGt                                                                    >  3:17356/1‑148 (MQ=255)                                                                                          aCATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGc                                                         <  5:191597/149‑1 (MQ=255)                                                                                             tCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCGCCGTGGCttt                                                                                                         >  8:244134/1‑98 (MQ=255)                                                                                               gATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCGTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAAc                                                     <  2:340132/148‑1 (MQ=255)                                                                                               gATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATa                                                                                          <  7:64359/111‑1 (MQ=255)                                                                                               gATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATa                                                                                          >  8:64359/1‑111 (MQ=255)                                                                                                         gcTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCg                                           >  8:185175/1‑148 (MQ=255)                                                                                                         gcTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGa                                          <  4:350108/149‑1 (MQ=255)                                                                                                             ttaGCTCCACAGTCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAATCCGCCCTTATGTAGAATTTGCACCTTGGCTTTAAGACGGGATCGATACCGACAGTGGTCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACt                                       <  1:313217/146‑1 (MQ=255)                                                                                                              gAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTc                                      >  4:282367/1‑148 (MQ=255)                                                                                                                gCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCa                                    <  3:282367/148‑1 (MQ=255)                                                                                                                gCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCa                                    <  7:185175/148‑1 (MQ=255)                                                                                                                   ccACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCAt                                >  3:321754/1‑149 (MQ=255)                                                                                                                           acacaAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAg                                                                                                      >  7:167716/1‑71 (MQ=255)                                                                                                                           acacaAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAg                                                                                                      <  8:167716/71‑1 (MQ=255)                                                                                                                             acaAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAATGGCGAt                      >  4:248833/1‑149 (MQ=255)                                                                                                                              caAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGGCATGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATg                     <  1:235481/149‑1 (MQ=255)                                                                                                                               aaaGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATgg                    >  1:95395/1‑149 (MQ=255)                                                                                                                                   cATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTc                <  2:95395/149‑1 (MQ=255)                                                                                                                                     cttcatggCAGCTCGCTGCCATGAAGCCGCCCTGATTGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCcg              >  4:10672/7‑149 (MQ=37)                                                                                                                                     cttcatggCAGCTCGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGc                                  <  7:247180/123‑1 (MQ=255)                                                                                                                                     cttcatggCAGCTCGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGc                                  >  8:247180/7‑129 (MQ=255)                                                                                                                                       aCCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCcgcg            >  6:85253/1‑149 (MQ=255)                                                                                                                                         ccGGCAGCGAGCTGCCATGAAGCCGCCCTGACGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTa          >  8:6413/1‑149 (MQ=255)                                                                                                                                          cGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTAt         <  4:191108/149‑1 (MQ=255)                                                                                                                                                 gAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAg  <  3:162297/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                    CAAGATCAATGCTGCGCCACTACAATTACATCGTTGACGACCCGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAG  >  NC_002947/4486071‑4486363

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: ‑