Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,497,885	A→G	8.0%	intergenic (‑289/+417)	PP_5562 ← / ← PP_5563	hypothetical protein/membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,497,885	0	A	G	8.0%	135.7 / 2.5	50	intergenic (‑289/+417)	PP_5562/PP_5563	hypothetical protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base A (22/24);  new base G (2/2);  total (24/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01

GGGGGATTTTTTCCCCGTTTTGTGACGCTGCGCAATAATGGCGCTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCGGGGTAACTGTATTGTTCAAAACCTGA  >  NC_002947/3497745‑3498028                                                                                                                                                |                                                                                                                                                gggggATTTTTTCCCCGTTTTGTGACGCTGCGCAATAATGGCGCTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGtttt                                                                                                                                         <  2:320390/149‑1 (MQ=255)    ggATTTTTTCCCCGTTTTGTGACGCTGCGCAATAATGGCGCTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGtttttt                                                                                                                                       >  2:348924/1‑148 (MQ=255)          tttCCCCGTTTTGTGACGCTGCGCAATAATGGCGCTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCaaaa                                                                                                                                 <  1:348924/148‑1 (MQ=255)           ttCCCCGTTTTGTGACGCTGCGCAATAATGGCGCTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCaaaaa                                                                                                                                <  3:189817/148‑1 (MQ=255)             cgcaggtttGTGACGCTGCGCAATAATTGCGCTGTGATATTGACAGAGTGTCTTGGGAGCAGGAGATGGGGGCTCAAGCCCTAAAGACTTGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GATAATCGTTGGCAAAAGTTTTTTTCAAAAAGt                                                                                                                              <  5:57287/142‑1 (MQ=255)               ccGTTTTGTGACGCTGCGCAATAATGGCGCTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑TCGAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGa                                                                                                                            <  1:52416/149‑1 (MQ=255)               ccGTTTTGTGACGCTGCGCAATAATGGCGCTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGa                                                                                                                            >  2:52416/1‑148 (MQ=255)                      gtgACGCTGCGCAATAATGGCGCTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTtc                                                                                                                    >  4:103002/1‑149 (MQ=255)                         aCGCTGCGCAATAATGGCGCTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCa                                                                                                                 <  3:308851/149‑1 (MQ=255)                                           gcTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCgccg                                                                                                     >  7:75224/1‑143 (MQ=255)                                           gcTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCgccg                                                                                                     <  8:75224/143‑1 (MQ=255)                                            cTGTGAAATTGACAGAGTGTCTTGGGCGCACGAGATGGGGGCTCAACCCCTAAAGACTGGGTACGAAAGTCGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCt                                                                                              <  5:264642/149‑1 (MQ=255)                                                           agTGTCTTGGGCGCAGGAGATGGGGGCTCAAACCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATg                                                                               >  1:37788/1‑149 (MQ=255)                                                               tCTTGGGCGCAGGAGATGGGGGCTCAAGCCCT‑AAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGgc                                                                          >  3:317498/1‑149 (MQ=255)                                                                cTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGATGT‑GGAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATgggg                                                                            >  1:104378/1‑149 (MQ=255)                                                                 ttGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGgcg                                                                         >  2:11529/1‑149 (MQ=255)                                                                    ggCGCAGGAGATGGGGGCTCAAGCCCT‑AAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCgt                                                                      <  4:317498/148‑1 (MQ=255)                                                                         aGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAg                                                                 >  8:21391/1‑149 (MQ=255)                                                                            agaTGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGgat                                                              <  1:11529/149‑1 (MQ=255)                                                                            agaTGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGgat                                                              <  3:103002/149‑1 (MQ=255)                                                                                  gggCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATgg                                                         >  4:218139/1‑148 (MQ=255)                                                                                     cTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAAt                                                     <  2:104378/149‑1 (MQ=255)                                                                                      tCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATgg                                                         >  3:279078/1‑144 (MQ=255)                                                                                      tCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATgg                                                         <  4:279078/144‑1 (MQ=255)                                                                                        aaGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGc                                                   >  6:335023/1‑148 (MQ=255)                                                                                          gCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGGGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGcgac                                                >  8:54179/1‑149 (MQ=255)                                                                                              tAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCgg                                                                                   <  8:108337/110‑1 (MQ=255)                                                                                              tAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCgg                                                                                   >  7:108337/1‑110 (MQ=255)                                                                                                 aGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTtc                                         >  4:216217/1‑149 (MQ=255)                                                                                                  gACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGgatgat                                                           >  4:231573/1‑130 (MQ=255)                                                                                                  gACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGgatgat                                                           <  3:231573/130‑1 (MQ=255)                                                                                                         tACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCGAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGcc                                 >  5:226048/1‑149 (MQ=255)                                                                                                         tACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCGAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGcc                                 >  7:37921/1‑149 (MQ=255)                                                                                                         tACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGACTGTGCGTTGAGGGATGGGGGAGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGcc                                 >  5:5538/1‑149 (MQ=255)                                                                                                             aaaGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTtcgtc                                      >  3:15783/1‑140 (MQ=255)                                                                                                             aaaGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTtcgtc                                      <  4:15783/140‑1 (MQ=255)                                                                                                             aaaGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCcggc                             >  7:155592/1‑149 (MQ=255)                                                                                                                  ggCTGTAAAGAGA‑‑T‑GAAAATCTTTGGCAAAACTTTTTTTCAAAAAGTGAATCAGTTCTAATTTTGTGCGCCGGCCTCCTGTGCGTTGCGGGATGGGTGCGCGTGTCAGTATGATGGCAATGAGACGAGTTTCGTCGCGCCCGGCTGGGt                        <  6:5538/149‑1 (MQ=255)                                                                                                                    cTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCggg                          >  5:244368/1‑145 (MQ=255)                                                                                                                    cTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCggg                          <  6:244368/145‑1 (MQ=255)                                                                                                                           gCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCGGGGTAACTGTAtt               <  3:218139/149‑1 (MQ=255)                                                                                                                           gCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCGGGGTAACTGTAtt               <  7:54179/149‑1 (MQ=255)                                                                                                                             gA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGGCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCGGGGTAACTGTATTGt             >  4:52865/1‑149 (MQ=255)                                                                                                                             gA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAAt                                                     >  1:65623/1‑109 (MQ=255)                                                                                                                             gA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAAt                                                     <  2:65623/109‑1 (MQ=255)                                                                                                                                 t‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCGGGGTAACTGTATTGTTc           <  8:155592/149‑1 (MQ=255)                                                                                                                                       aTCGTTGGCGAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCGGGGTAACTGTATTGTTCAAAAc      <  8:37921/149‑1 (MQ=255)                                                                                                                                       aTCGTTGGCGAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCGGGGTAACTGTATTGTTCAAAAc      <  6:226048/149‑1 (MQ=255)                                                                                                                                          gTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCGGGGTAACTGTATTGTTCAAAACCt    <  2:37788/148‑1 (MQ=255)                                                                                                                                           ttGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCGGGGTAACTGTATTGTTCAAAACCTGa  <  7:21391/149‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                GGGGGATTTTTTCCCCGTTTTGTGACGCTGCGCAATAATGGCGCTGTGATATTGACAGAGTGTCTTGGGCGCAGGAGATGGGGGCTCAAGCCCTAAAGACTGGGTACGAAAGGGGCTGGAAAGCGA‑‑T‑GAAAATCGTTGGCAAAAGTTTTTTTCAAAAAGTGAATCAGTTCTCATTTTGTGCGCCGGCCGCCTGTGCGTTGCGGGATGGGGGCGCGTGTCAGGATGATGGCAATGCGACGAGTTTCGTCGCGCCCGGCGGGGTAACTGTATTGTTCAAAACCTGA  >  NC_002947/3497745‑3498028

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: ‑