Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,491,728	G→C	10.0%	L231V (CTG→GTG)	PP_3096 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,491,728	0	G	C	10.0%	144.6 / 5.7	49	L231V (CTG→GTG)	PP_3096	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (23/21);  new base C (3/2);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

GGCTGGAAGCGCTGGTAGTCGGCCAGGCTGAGCGGGCCCAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCTGAACAGCTCACGACGCAATGCTGACGG  >  NC_002947/3491580‑3491875                                                                                                                                                     |                                                                                                                                                    ggCTGGAAGCGCTGGTAGTCGGCCAGGCTGAGCGGGCCCAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAg                                                                                                                                                     <  3:257309/149‑1 (MQ=255)           gcTGGTAGTCGGCCAGGCTGAGCGGGCCCAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCACCTGcagcccg                                                                                                                                           <  8:80977/149‑3 (MQ=255)           gcTGGTAGTCGGCCAGGCTGAGCGGGCCCAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGAGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGcagccag                                                                                                                                           <  8:69554/149‑1 (MQ=255)                  gTCGGCCAGGCTGAGCGGGCCGAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCg                                                                                                                                     <  6:298279/148‑1 (MQ=255)                  gTCGGCCAGGCTGAGCGGGCCCAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCgg                                                                                                                                    <  1:60400/149‑1 (MQ=255)                  gTCGGCCAGGCTGAGCGGGCCCAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGCGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCg                                                                                                                                     <  3:61277/148‑1 (MQ=255)                   tCGGCCAGGCTGAGCGGGCCCAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGc                                                                                                                                   >  4:145879/1‑149 (MQ=255)                   tCGGCCAGGCTGAGCGGGCCCAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGc                                                                                                                                   >  3:171334/1‑149 (MQ=255)                             tGAGCGGGCCCAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTg                                                                                                                          >  5:360932/1‑148 (MQ=255)                               aGCGGGCCCAGCTCGAGGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTAc                                                                                                                       <  6:3616/149‑1 (MQ=255)                                      ccAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATc                                                                                                                <  1:198975/149‑1 (MQ=255)                                        aGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCgg                                                                                                              >  4:96125/1‑149 (MQ=255)                                                gCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTg                                                                                                                          >  8:310185/1‑129 (MQ=255)                                                gCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTg                                                                                                                          <  7:310185/129‑1 (MQ=255)                                                  ggATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAg                                                                                                    <  4:171334/149‑1 (MQ=255)                                                       cACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGaa                                                                                               <  2:12465/149‑1 (MQ=255)                                                       cACGACTGGTAGTCCCAGACCCGGATGCCCGCGAAGGAGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTAGGGCTGCAGGTGCATCCAGCGCCCCGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAg                                                                                                 >  2:363392/1‑147 (MQ=255)                                                        aCGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAg                                                                                              <  5:53396/149‑1 (MQ=255)                                                          gACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGcc                                                                                            >  6:36382/1‑149 (MQ=255)                                                            cTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGcc                                                                                            >  8:100140/1‑147 (MQ=255)                                                            cTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGcc                                                                                            >  3:38642/1‑147 (MQ=255)                                                               gTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCa                                                                                       >  8:114983/1‑149 (MQ=255)                                                                   tCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTa                                                                                                  >  6:90806/1‑134 (MQ=255)                                                                   tCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTGCGGGCTGCAGGGGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTa                                                                                                  <  5:90806/134‑1 (MQ=255)                                                                           ccGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGt                                                                           >  3:340037/1‑149 (MQ=255)                                                                            cGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGtt                                                                          <  7:100140/149‑1 (MQ=255)                                                                                   cGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCa                                                                   >  3:282326/1‑149 (MQ=255)                                                                                         cGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTgcgc                                                             <  5:36382/149‑1 (MQ=255)                                                                                               tgtgGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTc                                                       >  3:266555/1‑149 (MQ=255)                                                                                                 tgGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTc                                                       <  6:360932/147‑1 (MQ=255)                                                                                                 tgGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCt                                                      <  4:266555/148‑1 (MQ=255)                                                                                                   gCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGc                                                   >  6:261679/1‑149 (MQ=255)                                                                                                      gtgCTGGGCATTGGGGGGGCCGAGCTGGGTGCTTTGTTCGGGCTGCAGGTGCTGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGTCGAGGATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGa                                                <  1:363392/147‑1 (MQ=255)                                                                                                         cTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAg                                               >  4:139225/1‑147 (MQ=255)                                                                                                              cATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCg                                        >  1:180049/1‑149 (MQ=255)                                                                                                                ttGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGc                                      <  3:139225/149‑1 (MQ=255)                                                                                                                  gcggcgGCCGAGCTGGGTGCATTGTTCGGGCTGCACGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCa                                     <  2:339872/148‑1 (MQ=255)                                                                                                                    ggcggcCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCaaaa                                  >  1:20871/1‑149 (MQ=255)                                                                                                                       ggcCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAg                               >  7:160124/1‑149 (MQ=255)                                                                                                                         ccGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCt                             <  3:96125/149‑1 (MQ=255)                                                                                                                          cGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGACTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGcgcg                                                            >  2:260031/1‑117 (MQ=255)                                                                                                                                 ggTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCTGAACAGCt                     <  3:145879/149‑1 (MQ=255)                                                                                                                                  gTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCTGAACAGCt                     >  3:57512/1‑148 (MQ=255)                                                                                                                                    gCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCTGAACAGCTCac                  >  1:177923/1‑149 (MQ=255)                                                                                                                                      aTTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCTGAACAGCTCacga                >  8:25951/1‑149 (MQ=255)                                                                                                                                        ggcgctggCTGCACCTGCAGCCCGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCTGAACAGCTCacgacg              >  7:305818/7‑149 (MQ=255)                                                                                                                                           gctggCTGCACCTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCTGAACAGCTCACGACGCaa           >  8:81391/4‑149 (MQ=255)                                                                                                                                             tggCTGCACCTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCTGAACAGCTCACGACGCAATg         >  3:100271/2‑149 (MQ=255)                                                                                                                                             gggCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCTGAACAGCTCACGACGCAATg         <  4:57512/149‑1 (MQ=255)                                                                                                                                                    aGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCTGAACAGCTCACGACGCAATGCTGACgg  <  7:114983/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    GGCTGGAAGCGCTGGTAGTCGGCCAGGCTGAGCGGGCCCAGCTCGATGCGGATGCACGACTGGTAGTCCCAGACCCGGTTGCCGGCGACGGCGCTGTGGCCGAGCTGGGCATTGCGGCGGCCGAGCTGGGTGCATTGTTCGGGCTGCAGGTGCAGCCAGCGCCCGGCGAACGGCTGTACCTTGATCGGCAGCGAGAAGTAGAAGCCGAGCATGCGTTCAAGGTTCAGCGCATTGCGCGGCTTCTGGCTGAGCAGGCCGGCAAAATAGCTGAACAGCTCACGACGCAATGCTGACGG  >  NC_002947/3491580‑3491875

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: ‑