Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,003,946	C→G	8.2%	P176R (CCG→CGG)	PP_2627 →	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,003,946	0	C	G	8.2%	143.4 / 4.2	49	P176R (CCG→CGG)	PP_2627	membrane protein
Reads supporting (aligned to +/- strand):  ref base C (25/20);  new base G (2/2);  total (27/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.44e-01

TACCGGCTGCCCTGGTACCTGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGCCCGGTTATGGGAGCACCTG  >  NC_002947/3003804‑3004094                                                                                                                                                |                                                                                                                                                      tACCGGCTGCCCTGGTACCTGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAgg                                                                                                                                                 <  2:305114/149‑1 (MQ=255)    cGGCTGCCCTGGTACCTGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCGGGTAGGcca                                                                                                                                              <  1:100334/149‑3 (MQ=255)        tGCCCTGGTACCTGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCtggtgg                                                                                                                                          >  6:70764/1‑149 (MQ=255)          cccTGGTACCTGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCGGGTAGGccattgc                                                                                                                                          <  3:204347/147‑7 (MQ=255)           ccTGGTACCTGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTc                                                                                                                                       <  3:30772/149‑1 (MQ=255)             tGGTACCTGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAg                                                                                                                                     >  4:275627/1‑149 (MQ=255)                tACCTGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGcga                                                                                                                                  >  4:259094/1‑149 (MQ=255)                   cTGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGcgacga                                                                                                                               <  3:275627/149‑1 (MQ=255)                   cTGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGcgacga                                                                                                                               <  2:196279/149‑1 (MQ=255)                    tGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCGGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGcgacgct                                                                                                                              >  4:305356/1‑147 (MQ=255)                      gtgtTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATg                                                                                                                             <  3:279150/148‑1 (MQ=255)                            ggCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGat                                                                                                                      <  1:274364/149‑1 (MQ=255)                               gacgaACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGat‑cat                                                                                                                  <  5:345475/149‑1 (MQ=255)                                acgaACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGat‑catc                                                                                                                 >  1:176811/1‑149 (MQ=255)                                  gaACAGTCCGGTAAAAGCAGCTTCATCGACCGACACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGCCAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGat‑catc                                                                                                                 >  1:238725/1‑148 (MQ=255)                                   aaCAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGAc                                                                                                              >  6:351702/1‑149 (MQ=255)                                        tCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGAcccgcc                                                                                                         >  3:123492/1‑149 (MQ=255)                                               aaaGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGtt                                                                                                  >  7:353422/1‑149 (MQ=255)                                                aaGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGttt                                                                                                 >  8:86324/1‑149 (MQ=255)                                                     gcTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGCCCCGCCCGGTGtttt                                                                                                >  5:54751/1‑145 (MQ=255)                                                     ccTTCCTCGACCG‑CACCGAGCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGtttt                                                                                                <  6:54751/144‑1 (MQ=255)                                                          aTCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTc                                                                                        <  2:238725/148‑1 (MQ=255)                                                                    aCCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAaccacc                                                                              >  7:57275/1‑149 (MQ=255)                                                                     ccGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCg                                                                             <  8:353422/149‑1 (MQ=255)                                                                          cAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTgg                                                                         >  5:358472/1‑148 (MQ=255)                                                                               cTTTACCCTGACGCGTATCGACCACGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTcgg                                                                   >  8:202040/1‑149 (MQ=255)                                                                                tttACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTcggc                                                                  >  2:61280/1‑149 (MQ=255)                                                                                   aCCCTGACGCGTATCGACCACGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTcggcgg                                                                <  7:202040/148‑1 (MQ=255)                                                                                              tATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCt                                                    >  6:122988/1‑149 (MQ=255)                                                                                                tCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCACCGCCCCCTcc                                                  >  7:287145/1‑149 (MQ=255)                                                                                                           caggcACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCcgc                                       <  5:70764/149‑1 (MQ=255)                                                                                                            aggcACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCcgcg                                      <  2:176811/149‑1 (MQ=255)                                                                                                              gcACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGcc                                                        <  3:220769/129‑1 (MQ=255)                                                                                                              gcACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGcc                                                        >  4:220769/1‑129 (MQ=255)                                                                                                               cACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGcgccg                                   <  3:259094/149‑1 (MQ=255)                                                                                                                       cGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGaa                                               >  2:142089/1‑129 (MQ=255)                                                                                                                       cGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGaa                                               <  1:142089/129‑1 (MQ=255)                                                                                                                        gACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATc                          >  2:234415/1‑149 (MQ=255)                                                                                                                        gACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGAAGGCGTGATACAACCCCCCCCCCGG‑GGTTTGATAAGGCAAAAACCCCCCGTTGGCAGGGCGGCCCACGCCCCCGACGAACCCACCCCCCCCCCCCGCCTc                          >  1:280443/1‑149 (MQ=255)                                                                                                                             aCTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGc                     >  1:366556/1‑149 (MQ=255)                                                                                                                                 aaGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGccc                   <  8:57275/147‑1 (MQ=255)                                                                                                                                 aaGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGCCCgg                 >  6:137993/1‑149 (MQ=255)                                                                                                                                 aaGCAATGGCCTACCCGGTAGGCTGGTGGGACAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGCCCgg                 >  5:200835/1‑149 (MQ=255)                                                                                                                                 aaGCAATGGCCTACCCGGTAGGCGGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGccc                   <  5:351702/147‑1 (MQ=255)                                                                                                                                  aGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGCCCGGt                <  5:122988/149‑1 (MQ=255)                                                                                                                                    caccagCCTACCGGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGCCCGGTTa              >  3:353508/6‑149 (MQ=255)                                                                                                                                      ccagCCTACCGGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCACCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGCCCGGTTATg            >  6:320670/4‑149 (MQ=255)                                                                                                                                       tGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGCCCGGTTATgg           <  1:61280/149‑1 (MQ=255)                                                                                                                                            tACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGCCCGGTTATGGGAGCa      >  8:110562/1‑149 (MQ=255)                                                                                                                                                cGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGCCCGGTTATGGGAGCACCTg  <  2:366556/149‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                      TACCGGCTGCCCTGGTACCTGGTGTTGGGCGACGAACAGTCCGGTAAAAGCAGCTTCATCGACCG‑CACCGATCAGCGCTTTACCCTGACGCGTATCGACCAGGCCCAGGCACGGGGCCGACAGACTCAAGCAATGGCCTACCCGGTAGGCTGGTGGGTCAGCGACGATGCCGTGAT‑CATCGACCCGCCCGGTGTTTTCATCAGTCAAAAACCACCGGTGGGCTCGGCGGCCAACGCCCCCTCCGAAGCCTCCGCGCCGCCCGGCATCCAGGCCCGGTTATGGGAGCACCTG  >  NC_002947/3003804‑3004094

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: ‑