Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	860,710	T→A	11.3%	intergenic (‑39/+65)	PP_0741 ← / ← PP_0742	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	860,710	0	T	A	11.3%	138.7 / 8.7	53	intergenic (‑39/+65)	PP_0741/PP_0742	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (23/24);  new base A (3/3);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.67e-01

GGCACAGGTCGGAGGCCTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCACTGAGCCATGCGCCCTCGACTCGGCCGGACAGGCAC  >  NC_002947/860566‑860853                                                                                                                                                 |                                                                                                                                                 ggCACAGGTCGGAGGCCTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTa                                                                                                                                              <  6:50552/149‑1 (MQ=255)    acaGGTCGGAGGCCTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAg                                                                                                                                           >  4:220164/1‑149 (MQ=255)     caGGTCGGAGGCCTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAgg                                                                                                                                          <  3:220164/149‑1 (MQ=255)     caGGTCGGAGGCCTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAgg                                                                                                                                          >  6:226852/1‑149 (MQ=255)       ggTCGGAGGCCTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCCGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGtt                                                                                                                                        <  2:23645/149‑1 (MQ=255)        gTCGGAGGCCTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGtt                                                                                                                                        >  3:113623/1‑148 (MQ=255)                 cTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑Ca                                                                                                                                <  5:138457/146‑1 (MQ=255)                 cTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑Ca                                                                                                                                >  6:138457/1‑146 (MQ=255)                 cTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACAAGTTTCGAGTCACGTACAGGTTTAtttt                                                                                                                                  <  6:209712/145‑2 (MQ=38)                 cTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACAAGTTTCGAGTCACGTACAGGTTTAtttt                                                                                                                                  >  5:209712/1‑144 (MQ=38)                           ccgTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACCTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACACCGCTGaa                                                                                                                   <  7:94721/149‑1 (MQ=255)                                 tAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTAt                                                                                                              <  5:226852/148‑1 (MQ=255)                                                  ggTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGtt                                                                                                                                        >  4:87062/1‑106 (MQ=255)                                                  ggTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGtt                                                                                                                                        <  3:87062/106‑1 (MQ=255)                                                   gTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGta                                                                                           >  6:236952/1‑149 (MQ=255)                                                        gcaggcGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAgc                                                                                                                         >  6:198725/1‑114 (MQ=255)                                                        gcaggcGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAgc                                                                                                                         <  5:198725/114‑1 (MQ=255)                                                          aggcGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGGTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCg                                                                                    >  5:158278/1‑149 (MQ=255)                                                               cTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATc                                                                               <  6:158278/149‑1 (MQ=255)                                                                       gATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTTACTCTAAACTTTTAAAGGTTTATTTCCAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAg                                                                        <  1:96119/149‑1 (MQ=255)                                                                         tACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACa                                                                                                                                            >  4:210684/1‑79 (MQ=255)                                                                         tACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACa                                                                                                                                            <  3:210684/79‑1 (MQ=255)                                                                            gcgGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTc                                                                  >  1:174026/1‑149 (MQ=255)                                                                              ggCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGa                                                                <  4:113623/149‑1 (MQ=255)                                                                                      gtgGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGtt                                                                                                                >  5:238146/1‑93 (MQ=255)                                                                                      gtgGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGtt                                                                                                                <  6:238146/93‑1 (MQ=255)                                                                                         ggCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGcgccgc                                                     <  5:236952/149‑1 (MQ=255)                                                                                           cGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCgcgc                                                   >  7:144561/1‑149 (MQ=255)                                                                                            ggAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCa                                                                              >  2:98022/1‑121 (MQ=255)                                                                                            ggAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCa                                                                              <  1:98022/121‑1 (MQ=255)                                                                                            ggAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCgct                                                  >  2:201172/1‑149 (MQ=255)                                                                                             gAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCgctg                                                 <  2:174026/149‑1 (MQ=255)                                                                                                  gTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCAt                                                                                <  2:180533/113‑1 (MQ=255)                                                                                                  gTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCAt                                                                                >  1:180533/1‑113 (MQ=255)                                                                                                   tCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCt                                           <  8:181463/149‑1 (MQ=255)                                                                                                   tCGTGCATGGCTGCCGCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCt                                           <  4:268058/149‑1 (MQ=255)                                                                                                      tGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGCGTTCGAGCAAGCGCCGCGCTGCTTCCTGGc                                        >  3:193560/1‑149 (MQ=255)                                                                                                        cATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCa                                      <  1:201172/149‑1 (MQ=255)                                                                                                              tGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTg                                          >  7:332055/1‑139 (MQ=255)                                                                                                              tGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTg                                          <  8:332055/139‑1 (MQ=255)                                                                                                                ccTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCAc                                     >  7:248671/1‑142 (MQ=255)                                                                                                                ccTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCAc                                     <  8:248671/142‑1 (MQ=255)                                                                                                                    ctgaaaTAAACCTGTACAAGTTTCGAGTCACGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCACTGAGCCAt                             >  6:176193/4‑146 (MQ=37)                                                                                                                    ctgaaaTAAACCTGTACAAGTTTCGAGTCACGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCACTGAGCCAt                             <  5:176193/143‑1 (MQ=37)                                                                                                                     tgaaaTAAACCTGTACAAGTTTCGAGTCACGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTc                                             <  7:236875/127‑1 (MQ=37)                                                                                                                     tgaaaTAAACCTGTACAAGTTTCGAGTCACGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTc                                             >  8:236875/3‑129 (MQ=37)                                                                                                                               cTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCACTGAGCCATGCGCCCTCGACTCg               >  3:91266/1‑149 (MQ=255)                                                                                                                                     gTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCACTGAGCCATGCGCCCTCGACTCGGCCGGa         <  4:91266/149‑1 (MQ=255)                                                                                                                                     gTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTAATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCACTGAGCCATGCGCCCTCGACTCGGCCGGa         >  1:246981/1‑149 (MQ=255)                                                                                                                                          tCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCACTGAGCCATGCGCCCTCGACTCGGCCGGACAgg     >  6:294095/1‑148 (MQ=255)                                                                                                                                            gAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCACTGAGCCATGCGCCCTCGACTCGGCCGGACAGGCAc  >  8:261894/1‑149 (MQ=255)                                                                                                                                            gAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGCGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCACTGAGCCATGCGCCCTCGACTCGGCCGGACAGGCAc  <  4:193560/149‑1 (MQ=255)                                                                                                                                              aaCTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCACTGAGCCATGCGCCCTCGACTCGGCCGGACAGGCAc  >  7:255429/1‑147 (MQ=255)                                                                                                                                                 |                                                                                                                                                 GGCACAGGTCGGAGGCCTTGTGGCCGCCGTTGTAGCGCACGCTGTGCCCGGTCAGGCAGGCGCTGATGGCGATACGCGGCTTGCTGTGGGCGGAAGGGTCGTGCATGGCTGCCTCCGAAAATAAACCTGTACGTGACTCGAAACTTGTACAGGTTTATTT‑CAGCACAGCGCTGAAGTTATGCAAACTAGTATTTTTGTATAGTTCGGCATCACTCAAGGTGTTCGAGCAAGCGCCGCGCTGCTTCCTGGCCACTGAGCCATGCGCCCTCGACTCGGCCGGACAGGCAC  >  NC_002947/860566‑860853

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: ‑