Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	42,871	G→C	7.4%	R272T (AGA→ACA)	PP_0039 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	42,871	0	G	C	7.4%	166.9 / 2.7	54	R272T (AGA→ACA)	PP_0039	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (26/24);  new base C (2/2);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

CATCATCGATTCCGGCTGGACCCGCCCCAAGTACCCGCTATCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTGAGAATCACAGCGACTACCCGGATGTACCCACTC  >  NC_002947/42725‑43017                                                                                                                                                   |                                                                                                                                                    catcatCGATTCCGGCTGGACCCGCCCCAAGTACCCGCTATCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGa‑a                                                                                                                                                  >  4:217129/1‑149 (MQ=255)   tcatcGATTCCGGCTGGACCCGCCCCAAGTACCCGCTATCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATc                                                                                                                                                >  3:205981/1‑149 (MQ=255)      tcGATTCCGGCTGGACCCGCCACAAGTACCCGCTATCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCtt                                                                                                                                             <  4:200740/149‑1 (MQ=255)             cGGCTGGACCCGCCCCAAGTACCCGCTATCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACgggg                                                                                                                                      >  2:125882/1‑149 (MQ=255)              ggCTGGACCCGCCCCAAGTACCCGCTATCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCtt                                                                                                                                             <  4:2868/141‑1 (MQ=255)              ggCTGGACCCGCCCCAAGTACCCGCTATCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCtt                                                                                                                                             >  3:2868/1‑141 (MQ=255)                    aCCCGCCCCAAGTACCCGCTATCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTg                                                                                                                               <  3:217129/149‑1 (MQ=255)                                  cccGCTATCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCctc                                                                                                                 >  8:219440/1‑149 (MQ=255)                                  cccGCTATCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCctc                                                                                                                 >  4:258852/1‑149 (MQ=255)                                        aTCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGt                                                                                                            >  1:142272/1‑148 (MQ=255)                                            aGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGt                                                                                                       >  7:36339/1‑149 (MQ=255)                                                    acaAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGa                                                                                               <  4:205981/149‑1 (MQ=255)                                                      aaGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGACTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGc                                                                                             >  7:133586/1‑149 (MQ=255)                                                        gagaCCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTcc                                                                                                 <  2:263991/143‑1 (MQ=255)                                                        gagaCCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTcc                                                                                                 >  1:263991/1‑143 (MQ=255)                                                         agaCCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGc                                                                                          <  5:110440/149‑1 (MQ=255)                                                             cTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGCGCCTCTGAGTGACGTGCTTCCGAGCGGCCtt                                                                                       >  2:4933/1‑148 (MQ=255)                                                             cTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCtt                                                                                       >  3:117314/1‑148 (MQ=255)                                                                  tCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATcc                                                                                 <  4:43902/149‑1 (MQ=255)                                                                  tCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATcc                                                                                 >  7:144038/1‑149 (MQ=255)                                                                     aGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTg                                                                              >  5:48889/1‑149 (MQ=255)                                                                      gTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGc                                                                             >  2:26423/1‑149 (MQ=255)                                                                           cGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCg                                                                         >  3:205833/1‑148 (MQ=255)                                                                                    cgcCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGCGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATgg                                                                <  1:4933/148‑1 (MQ=255)                                                                                    cgcCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATggt                                                               >  8:216754/1‑148 (MQ=255)                                                                                        gATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGc                                                            >  7:149115/1‑148 (MQ=255)                                                                                            tgGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAAc                                                       <  3:258852/149‑1 (MQ=255)                                                                                             ggTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAAcc                                                      >  3:207556/1‑149 (MQ=255)                                                                                              gTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAAc                                                                                                                        <  6:108444/82‑1 (MQ=255)                                                                                              gTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAAc                                                                                                                        >  5:108444/1‑82 (MQ=255)                                                                                              gTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCt                                                     >  5:245000/1‑149 (MQ=255)                                                                                                 cTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGcc                                                  <  6:245000/149‑1 (MQ=255)                                                                                                    gcgcgcACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGaa                                               >  3:191067/1‑149 (MQ=255)                                                                                                    gcgcgcACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGaa                                               <  4:191067/149‑1 (MQ=255)                                                                                                     cgcgcACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAAc                                              <  1:125882/149‑1 (MQ=255)                                                                                                            aaaGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCt                                           <  1:18492/145‑1 (MQ=255)                                                                                                            aaaGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCt                                           >  2:18492/1‑145 (MQ=255)                                                                                                            aaaGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTc                                       <  4:207556/149‑1 (MQ=255)                                                                                                            aaaGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTc                                       <  6:48889/149‑1 (MQ=255)                                                                                                                  acacCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCAtt                                    >  2:58501/1‑146 (MQ=255)                                                                                                                  acacCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTga                                  <  4:117314/148‑1 (MQ=255)                                                                                                                   cacCTGGCGCCTGGGAATCATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTgaga                                <  8:144038/149‑1 (MQ=255)                                                                                                                    acCTGGCGCCTGGGAAACATCCTGCGTTCAAGATATCATTGACGGGCCTCCTTGGCATAACGACCCACTGAGTGACGTGCTACCGAGCGGCCTTAAATCCATGCCCCGGATCTATGGGTCCGAAACCTGCCGAACTCTGTTCATTcag                                 >  1:172984/1‑148 (MQ=255)                                                                                                                     ccTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTGAGAAt                              <  2:142272/149‑1 (MQ=255)                                                                                                                                 gAAACATCCTGCGTTCAACA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTga                                  >  2:260973/1‑133 (MQ=255)                                                                                                                                 gAAACATCCTGCGTTCAACA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTga                                  <  1:265143/133‑1 (MQ=255)                                                                                                                                 gAAACATCCTGCGTTCAACA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTga                                  <  1:260973/133‑1 (MQ=255)                                                                                                                                 gAAACATCCTGCGTTCAACA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCACCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTga                                  >  2:265143/1‑133 (MQ=255)                                                                                                                                  aaaCATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGCGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTGAGAATCACAGCGACTAcc                 >  2:83533/1‑149 (MQ=255)                                                                                                                                      aTCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTGAGAATCACAGCGACTACCCGGa             <  7:219440/149‑1 (MQ=255)                                                                                                                                       tCCTTCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTGAGAATCACAGCGACTACCCGGAt            <  8:133586/149‑1 (MQ=255)                                                                                                                                       tCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTGAGAATCACAGCGACTACCCGGAt            <  1:26423/149‑1 (MQ=255)                                                                                                                                         cTGCGTTCAAGA‑ATCCATGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGACCGGCCTTAAATCCCTTCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTGAGAATCACAGCGACTACCCGGATGt          <  7:216754/149‑1 (MQ=255)                                                                                                                                                 aaGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTGAGAATCACAGCGACTACCCGGATGTACCCACTc  <  2:86850/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                    CATCATCGATTCCGGCTGGACCCGCCCCAAGTACCCGCTATCCAGGCAGTCACAAGAGACCTTCATCCAGTATTCGCTTTCTGCGCCGATGTGGTCCTGGCGCGCACAAAGTGACACCTGGCGCCTGGGAAACATCCTGCGTTCAAGA‑ATCCTTGACGGGGCTCCTTGGCATAACGAGCCTCTGAGTGACGTGCTTCCGAGCGGCCTTAAATCCCTGCCCCGGATCTATGGGTGCGAAACCTGCCGAACGCTGTTCATTGAGAATCACAGCGACTACCCGGATGTACCCACTC  >  NC_002947/42725‑43017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑