Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,655,520	G→A	7.4%	G139S (GGC→AGC)	PP_4118 →	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,655,520	0	G	A	7.4%	160.8 / 2.3	54	G139S (GGC→AGC)	PP_4118	membrane protein
Reads supporting (aligned to +/- strand):  ref base G (21/29);  new base A (2/2);  total (23/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCCTGGCCGCCTTCCTTTGCGCCCACCTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGCCTGTTCGTGTTCTCCGACAGCCTGATCGGCATCGACCGCTTCATCAGC  >  NC_002947/4655379‑4655666                                                                                                                                              |                                                                                                                                                   ggCCTGGCCGCCTTCCTTTGCGCCCACCTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGtt                                                                                                                                             <  6:248959/149‑1 (MQ=255)  gCCTGGCCGCCTTCCTTTGCGCCCACCTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTg                                                                                                                                            >  1:198395/1‑149 (MQ=255)   ccTGGCCGCCTTCCTTTGCGCCCACCTTGCTTACCTGCGCGGCTATTGCGGCATTA‑CCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCt                                                                                                                                          <  2:42283/149‑1 (MQ=255)         cgccTTCCTTTGCGCCCACCTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATcc                                                                                                                                     <  7:211410/149‑1 (MQ=255)               ccttTGCGCCCACCTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGt                                                                                                                                 <  2:291911/147‑1 (MQ=255)               ccttTGCGCCCACCTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTa                                                                                                                                <  4:218246/148‑1 (MQ=255)                      gcCCACCTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGTCAGCAACGGGCCGAGGCCGTTGCTggc                                                                                                                                       >  2:361470/1‑132 (MQ=255)                      gcCCACCTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGTCAGCAACGGGCCGAGGCCGTTGCTggc                                                                                                                                       <  1:361470/134‑3 (MQ=255)                      gcCCACCTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTa                                                                                                                        >  6:205856/1‑149 (MQ=255)                       cccACCTTGCTTACCTGCGCGGGTATTGCGGCATTACCCTGCGCCCCGCGCTGCGCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTAGTGGCCTGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGctctcttc                                                                                                                       <  5:231206/149‑3 (MQ=255)                            cTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCActc                                                                                                                          >  7:113099/1‑141 (MQ=255)                            cTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCActc                                                                                                                          <  8:113099/141‑1 (MQ=255)                               gCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTgg                                                                                                                <  2:106336/148‑1 (MQ=255)                               gCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGACCCCGGTAGCACTCTACGCCCTg                                                                                                                 <  7:57353/147‑1 (MQ=255)                                 ttACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCa                                                                                                             >  3:373235/1‑149 (MQ=255)                                     cTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAg                                                                                                         >  7:252933/1‑149 (MQ=255)                                       gcgcGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAgcg                                                                                                       >  7:214539/1‑149 (MQ=255)                                          cgGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCa                                                                                                    >  1:242161/1‑149 (MQ=255)                                            gCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATg                                                                                                  <  2:198395/149‑1 (MQ=255)                                                  gCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTg                                                                                             <  4:158900/148‑1 (MQ=255)                                                   cGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGgc                                                                                           >  2:217320/1‑149 (MQ=255)                                                          aCCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCAc                                                                                     <  5:205856/148‑1 (MQ=255)                                                           cccTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGTCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTg                                                                                   <  4:59950/149‑1 (MQ=255)                                                            ccTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCAt                                                                                                   <  4:259499/132‑1 (MQ=255)                                                            ccTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCAt                                                                                                   >  3:259499/1‑132 (MQ=255)                                                            ccTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTgg                                                                                  >  3:125161/1‑149 (MQ=255)                                                                     cgcccTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCgggg                                                                         >  5:175928/1‑149 (MQ=255)                                                                       cccTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGa                                                                       <  2:313233/149‑1 (MQ=255)                                                                        ccTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAg                                                                      <  1:369567/149‑1 (MQ=255)                                                                         cTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGt                                                                     <  7:114353/149‑1 (MQ=255)                                                                          tGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTg                                                                    >  4:169721/1‑149 (MQ=255)                                                                                cACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGgcagca                                                              >  3:162360/1‑149 (MQ=255)                                                                                     aTCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGGCCGAGGCCGTTGCTg                                                                                                                                         >  5:64784/1‑69 (MQ=25)                                                                                     aTCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGGCCGAGGCCGTTGCTg                                                                                                                                         <  6:64784/69‑1 (MQ=25)                                                                                          cAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCg                                                    >  8:41403/1‑149 (MQ=255)                                                                                           aGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCgg                                                   <  4:162360/149‑1 (MQ=255)                                                                                           aGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCg                                                    <  6:175928/148‑1 (MQ=255)                                                                                             cggaaTCACTGGCATCTCGCTGGTCGGAGTAGTGGCCAGCAACTGGCTCGGCGCGTTGCTGATCCCGGTATCACTCTACTCCCTGTACATCAGCGCCATGCTCTGGCGCGGACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGc                                                  <  4:352144/145‑1 (MQ=255)                                                                                              gcAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGc                                                  >  3:352144/1‑147 (MQ=255)                                                                                                     cTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGCCTGTTCgtg                                         >  6:64858/1‑149 (MQ=255)                                                                                                      tGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGCCTGTTCgtgt                                        >  6:279701/1‑149 (MQ=255)                                                                                                        gCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGc                                                                             <  3:77424/110‑1 (MQ=255)                                                                                                        gCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGc                                                                             >  4:77424/1‑110 (MQ=255)                                                                                                        gCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGgca                                                                 <  8:193208/122‑1 (MQ=255)                                                                                                        gCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGgca                                                                 >  7:193208/1‑122 (MQ=255)                                                                                                          aTCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGCCTGTTCGTGTtctc                                    <  1:217320/149‑1 (MQ=255)                                                                                                           tCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCgggg                                                                         <  7:283324/111‑1 (MQ=255)                                                                                                           tCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCgggg                                                                         >  8:283324/1‑111 (MQ=255)                                                                                                              cgcTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGCCTGTTCGTGTTCTCCGAc                                <  7:41403/149‑1 (MQ=255)                                                                                                                            cTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGCCTGTTCGTGTTCTCCGACAGCCTGATCGGCAt                  <  4:125161/149‑1 (MQ=255)                                                                                                                               gCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGc                                                                                 <  6:66502/83‑1 (MQ=255)                                                                                                                               gCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGCCTGTTCGTGTTCTCCGACAGCCTGATCg                      <  7:9569/142‑1 (MQ=255)                                                                                                                               gCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGCCTGTTCGTGTTCTCCGACAGCCTGATCg                      >  8:9569/1‑142 (MQ=255)                                                                                                                                ccAGCAACGGCCTCGGCCCGGTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGCCTGTTCGTGTGCTCCGACAGCCTGATCGGCATCGAc              <  8:252933/149‑1 (MQ=255)                                                                                                                                              ggCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGCCTGTTCGTGTTCTCCGACAGCCTGATCGGCATCGACCGCTTCATCAGc  <  2:242161/147‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                   GGCCTGGCCGCCTTCCTTTGCGCCCACCTTGCTTACCTGCGCGGCTATTGCGGCATTACCCTGCGCCCCGCCCTGCCCGCACTGATCTTCAGCGCAATCACTGGCATCGCGCTGCTCGGCGTACTGGCCAGCAACGGCCTCGGCCCGTTGCTGATCCCGGTAGCACTCTACGCCCTGGCCATCAGCGCCATGCTCTGGCGCGCACTGGCCTGCGGGGGAGTGGCAGCACTGGGTGCCGGCCTGTTCGTGTTCTCCGACAGCCTGATCGGCATCGACCGCTTCATCAGC  >  NC_002947/4655379‑4655666

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: ‑