Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,506,824	G→A	7.5%	A48T (GCT→ACT)	PP_3104 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,506,824	0	G	A	7.5%	150.9 / 2.0	53	A48T (GCT→ACT)	PP_3104	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (26/23);  new base A (2/2);  total (28/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.29e-01

GACCCCATGGGCCTCGGCGGGCAAGACGGCCTTCTCGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGATGAACTGCTGGCCATCAAGGAGAAGGCCGAG  >  NC_002947/3506677‑3506967                                                                                                                                                    |                                                                                                                                                gACCCCATGGGCCTCGGCGGGCAAGACGGCCTTCTCGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGc                                                                                                                                                >  4:215146/1‑149 (MQ=255)  aCCCCATGGGCCTCGGCGGGCAAGACGGCCTTCTCGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCACCGAGTTTCTCGTTGCt                                                                                                                                               >  4:86509/1‑149 (MQ=255)   ccccATGGGCCTCGGCGGGCAAGACGGCCTTCTCGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTg                                                                                                                                              <  4:349055/149‑1 (MQ=255)    cccATGGGCCTCGGCGGGCAAGACGGCCTTCTCGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTgagat                                                                                                                                             >  1:165839/1‑145 (MQ=255)    cccATGGG‑GTCGGCGGGCAAGACGGCCTTCTCGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGTCGCCGAGTTTCTCGTTGCTGaa                                                                                                                                            <  8:53934/149‑1 (MQ=255)          ggCCTCGGCGGGCAAGACGGCCTTCTCGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACa                                                                                                                                       <  1:339558/149‑1 (MQ=255)                ggcggGCAAGACGGCCTTCTCGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAgtcgtc                                                                                                                                 <  7:28204/149‑1 (MQ=255)                               cTTCTCGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAg                                                                                                                  >  3:159252/1‑149 (MQ=255)                               cTTCTCGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAg                                                                                                                  >  1:213331/1‑149 (MQ=255)                                 tctcGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTg                                                                                                                >  6:96626/1‑149 (MQ=255)                                  ctcGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAgtcgt                                                                                                                                  <  3:287636/130‑1 (MQ=255)                                  ctcGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAgtcgt                                                                                                                                  >  4:287636/1‑130 (MQ=255)                                     gggCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAg                                                                                                                  <  7:236453/143‑1 (MQ=255)                                     gggCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAg                                                                                                                  >  8:236453/1‑143 (MQ=255)                                           ggTGACCTGCCGTGGCAAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGc                                                                                                      >  5:338430/1‑149 (MQ=255)                                                 cTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTgacgaagacgaa                                                                                                  >  2:178091/1‑147 (MQ=255)                                                 cTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCgaa                                                                                                  <  1:178091/147‑1 (MQ=255)                                                    ccGTGGCAAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAAt                                                                                              <  6:338430/148‑1 (MQ=255)                                                      gTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATAcg                                                                                           >  8:107883/1‑149 (MQ=255)                                                          ccAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATAcgcg                                                                                         >  6:2083/1‑147 (MQ=255)                                                           cAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAg                                                                                      <  7:67944/149‑1 (MQ=255)                                                            aaGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGt                                                                                     >  6:131965/1‑149 (MQ=255)                                                               tgttgtAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTACTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTAc                                                                                  >  8:2829/1‑149 (MQ=255)                                                               tgttgtAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTACTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTAc                                                                                  >  8:7806/1‑149 (MQ=255)                                                                 ttgtAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCATTATTCGGCTGATCACATGAGTGCCGCCTAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTAAtt                                                                                >  5:250957/1‑149 (MQ=255)                                                                        agcCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGcc                                                                         >  5:249976/1‑149 (MQ=255)                                                                         gcCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCt                                                                        <  1:362129/149‑1 (MQ=255)                                                                         gcCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCt                                                                        >  1:339586/1‑149 (MQ=255)                                                                            aGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCga                                                                                                   <  5:342603/119‑1 (MQ=255)                                                                            aGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCga                                                                                                   >  6:342603/1‑119 (MQ=255)                                                                                     gCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTACTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAAt                                                            <  7:7806/149‑1 (MQ=255)                                                                                     gCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTACTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAAt                                                            <  7:2829/149‑1 (MQ=255)                                                                                        aaGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATgg                                                          >  5:229317/1‑148 (MQ=255)                                                                                                  tAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCggg                                                <  5:96626/148‑1 (MQ=255)                                                                                                       ggCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGttt                                          >  8:36260/1‑149 (MQ=255)                                                                                                        gCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTTAGTGCTGACGAAGCCgaa                                                                                                  >  6:223833/1‑92 (MQ=255)                                                                                                        gCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTTAGTGCTGACGAAGCCgaa                                                                                                  <  5:223833/92‑1 (MQ=255)                                                                                                        gCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGtttt                                         >  5:158523/1‑149 (MQ=255)                                                                                                          cTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGc                                       >  7:160761/1‑149 (MQ=255)                                                                                                           tttATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGcc                                      >  7:59291/1‑149 (MQ=255)                                                                                                            ttATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAg                                                                                                       <  6:219038/83‑1 (MQ=255)                                                                                                            ttATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCACTTGAGTGCTGACGAAg                                                                                                       >  5:219038/1‑83 (MQ=255)                                                                                                                 cGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGa                                 <  7:107883/148‑1 (MQ=255)                                                                                                                  ggCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGtt                                           >  8:86991/1‑137 (MQ=255)                                                                                                                  ggCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGtt                                           <  7:86991/137‑1 (MQ=255)                                                                                                                  ggCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGATg                               <  2:213331/149‑1 (MQ=255)                                                                                                                  ggCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGACCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGATg                               <  7:91412/149‑1 (MQ=255)                                                                                                                    cTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGATGaa                             <  8:160761/149‑1 (MQ=255)                                                                                                                          aCATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGATGAActgctg                       <  4:159252/149‑1 (MQ=255)                                                                                                                          aCATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGATGAActgctg                       <  3:215146/149‑1 (MQ=255)                                                                                                                               aGTGCCACCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGATGAACTGCTGGCCAt                  <  3:86509/149‑1 (MQ=255)                                                                                                                                   ccgccgAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGATGAACTGCTGGCCATCAAg              >  1:127936/1‑149 (MQ=255)                                                                                                                                     gccgAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGATGAACTGCTGGCCATCAAGga            <  5:131965/149‑1 (MQ=255)                                                                                                                                                 gTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGATGAACTGCTGGCCATCAAGGAGAAGGCCgag  >  5:45306/1‑147 (MQ=255)                                                                                                                                                    |                                                                                                                                                GACCCCATGGGCCTCGGCGGGCAAGACGGCCTTCTCGGGCAGGGTGACCTGCCGTGGCCAAGTGTTGTAGCAGCCAGAACCTACGCCAAGATGGATGTAGGTGGCCTTTATTCGGCTGATGACATGAGTGCCGCCGAGTTTCTCGTTGCTGAACTACAGTCGTCCGAAACGCAGTTGAGTGCTGACGAAGCCGAAGAATACGCGCAGTTACTTTATAGCCTGATTGCAAAAATGGAAAAATCGGGGCGTTTTGCCGCGGATGAACTGCTGGCCATCAAGGAGAAGGCCGAG  >  NC_002947/3506677‑3506967

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: ‑