Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,486,216	A→C	12.3%	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	12.3%	142.8 / 12.0	57	S30R (AGC→CGC)	PP_3978	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (21/29);  new base C (5/2);  total (26/31)
Fisher's exact test for biased strand distribution p-value = 2.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.86e-01

GCAAGATCAATGCTGCGCCACTACAATTACATCGTTGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAG  >  NC_002947/4486070‑4486363                                                                                                                                                    |                                                                                                                                                    gCAAGATCAATGCTGCGCCACTACAATTACATCGTTGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGc                                                                                                                                                   >  1:154711/1‑149 (MQ=255)   aaGATCAATGCTGCGCCACTACAATTACATCGTTGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTg                                                                                                                                                 <  2:102104/149‑1 (MQ=255)     gATCAATGCTGCGCCACTACAATTACATCGTTGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGc                                                                                                                                                >  8:190637/1‑148 (MQ=255)                cgcCACTACAATTACCTCGTTGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGTACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAgccgcc                                                                                                                                    <  4:259469/149‑1 (MQ=255)                cgcCACTACAATTACATCGTTGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAgccgcc                                                                                                                                    <  4:254949/149‑1 (MQ=255)                   cACTACAATTACATCGTTGACGACCCAGATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCAACAGGCACACAAAGCATGACCCGCCAGCGAGCTGCCATGAAGACGCACt                                                                                                                                  >  1:4362/1‑149 (MQ=255)                   cACTACAATTACATCGTTGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCt                                                                                                                                  >  8:262783/1‑148 (MQ=255)                   cACTACAATTACATCGTTGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCt                                                                                                                                  >  3:75495/1‑148 (MQ=255)                        cAATTACATCGTTGACGACCC‑GATCATTCCATAGGGATGTGCCACCCGTGGGGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATg                                                                                                                              <  6:251919/147‑1 (MQ=255)                              cATCGTTGACGACCC‑GATCATTCCATAGGTATGTGCCACTCGTCGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCAttt                                                                                                                      >  1:237414/1‑149 (MQ=255)                              cATCGTTGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGTTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCAttt                                                                                                                      <  2:4362/149‑1 (MQ=255)                                  gTTGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCAc                                                                                                                  >  1:265370/1‑149 (MQ=255)                                   ttGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCAcc                                                                                                                 >  7:236807/1‑149 (MQ=255)                                         acCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCt                                                                                                           >  7:305455/1‑149 (MQ=255)                                           cc‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCtt                                                                                                          >  2:67177/1‑148 (MQ=255)                                                 cATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGAc                                                                                                    >  6:188415/1‑149 (MQ=255)                                                  aTTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGAc                                                                                                    <  5:188415/148‑1 (MQ=255)                                                  aTTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGAc                                                                                                    <  4:75495/148‑1 (MQ=255)                                                           gTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTg                                                                                                              >  6:53985/1‑129 (MQ=255)                                                           gTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTg                                                                                                              <  5:53985/129‑1 (MQ=255)                                                           gTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATa                                                                                          >  6:345973/1‑149 (MQ=255)                                                           gTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATa                                                                                          <  4:90133/149‑1 (MQ=255)                                                              tgtgCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATAcc                                                                                        >  8:235304/1‑148 (MQ=255)                                                                  ccACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAg                                                                                   <  7:262783/149‑1 (MQ=255)                                                                   cACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGt                                                                                  <  2:154711/149‑1 (MQ=255)                                                                    aCCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTg                                                                                 <  1:260354/149‑1 (MQ=255)                                                                    aCCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTg                                                                                 >  6:157098/1‑149 (MQ=255)                                                                      ccGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTggg                                                                               >  2:313958/1‑149 (MQ=255)                                                                      ccGTGGTGTAGCCACAAACGCAACATCGATCGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTggg                                                                               <  4:61169/149‑1 (MQ=255)                                                                       cGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGc                                                                              <  7:68463/149‑1 (MQ=255)                                                                              tAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATgg                                                                       >  8:209633/1‑149 (MQ=255)                                                                              tAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATgg                                                                       <  8:305455/149‑1 (MQ=255)                                                                              tAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATg                                                                        <  7:235304/148‑1 (MQ=255)                                                                                 ccACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACCGGATCGATACCGACAGTGGGCTACATGGCGt                                                                    <  5:226651/149‑1 (MQ=255)                                                                                              aTCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCg                                                        >  6:178030/1‑148 (MQ=255)                                                                                                 gATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAAc                                                     <  5:178030/148‑1 (MQ=255)                                                                                                  aTGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTaa                                                                  <  3:258423/134‑1 (MQ=255)                                                                                                  aTGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTaa                                                                  >  4:258423/1‑134 (MQ=255)                                                                                                     gcagcaGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCAc                                                 <  7:190637/148‑1 (MQ=255)                                                                                                       agcagcTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCtt                                              <  5:157098/149‑1 (MQ=255)                                                                                                         cagcTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTACGCGTCCGGCGAACTCACCTTcc                                            <  7:209633/149‑1 (MQ=255)                                                                                                            cTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGaa                                         <  8:236807/149‑1 (MQ=255)                                                                                                                  gCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAg                                   <  1:67177/149‑1 (MQ=255)                                                                                                                   cTCCACAGGCACACAAAGCATGACCCGGCAGCGAGATGCCAAGAAGCCGCCATGATGGAGCATTAGCACCGTGGCTTAAAGACGGCATCCAAACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGCACTCCAg                                   >  4:73091/1‑148 (MQ=255)                                                                                                                         aGGCACACAAAGCATGACCCGTCAGCGAGCTGCCATGAAGCCGCCCTGATGTAGCATTTGCACCGTGGCTTTAAGACGTGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCGGCATTAAg                            <  7:314836/149‑1 (MQ=255)                                                                                                                           gCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAggg                          >  8:160111/1‑149 (MQ=255)                                                                                                                               acaAAGCATGACCCGGCATCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGAt                      <  7:286087/149‑1 (MQ=255)                                                                                                                                caAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATg                     <  1:313958/149‑1 (MQ=255)                                                                                                                                       cttcatggCAGCTCGCTGCCATGAAGCCGCCCAGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCcg              >  4:68071/7‑149 (MQ=37)                                                                                                                                        ttcatggCAGCTCGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCcgc             >  1:186288/6‑149 (MQ=255)                                                                                                                                          catggCAGCTCGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACTGACAGTGGGCTACATGGCATAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCcgcg            >  6:150002/4‑148 (MQ=37)                                                                                                                                           atggCAGCTCGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTa          >  4:238852/3‑149 (MQ=255)                                                                                                                                            tggCAGCTCGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTa          <  5:336861/147‑1 (MQ=255)                                                                                                                                            tggCAGCTCGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTa          >  6:336861/2‑148 (MQ=255)                                                                                                                                            cGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTAt         <  5:345973/149‑1 (MQ=255)                                                                                                                                              gCAGCTCGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACTGACAGTGGGCTACATGGCATAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTAttt       <  5:150002/149‑1 (MQ=255)                                                                                                                                                   gAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGGTGGTGTCCGCGTATTTTTAAg  <  7:160111/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                    GCAAGATCAATGCTGCGCCACTACAATTACATCGTTGACGACCC‑GATCATTCCATAGGTATGTGCCACCCGTGGTGTAGCCACAAACGCAACATCGATGGCAGCAGCTATGAGCTCCACAGGCACACAAAGCATGACCCGGCAGCGAGCTGCCATGAAGCCGCCCTGATGGAGCATTTGCACCGTGGCTTTAAGACGGGATCGATACCGACAGTGGGCTACATGGCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAG  >  NC_002947/4486070‑4486363

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: ‑