Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,314,126	C→T	9.5%	P58L (CCC→CTC)	proP →	osmosensory proline/betaine/H+ permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,314,126	0	C	T	9.5%	111.8 / 3.1	42	P58L (CCC→CTC)	proP	osmosensory proline/betaine/H+ permease
Reads supporting (aligned to +/- strand):  ref base C (22/16);  new base T (2/2);  total (24/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

AGCCAATCGGCCTGAAGGACATCACCATCGTCGACGACGCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGGGCGGCAGAAAATCCTCGCCGCGACCATCGTGATC  >  NC_002947/3313979‑3314271                                                                                                                                                    |                                                                                                                                                  aGCCAATCGGCCTGAAGGACATCACCATCGTCGACGACGCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTccc                                                                                                                                                   >  7:293220/1‑148 (MQ=255) aGCCAATCGGCCTGAAGGACATCACCATCGTCGACGACGCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTccc                                                                                                                                                   >  2:367295/1‑148 (MQ=255)             tGAAGGACATCACCATCGTCGACGACGCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGAccc                                                                                                                                       >  3:156421/1‑148 (MQ=255)                  gACATCACCATCGTCGACGACGCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGt                                                                                                                                 >  8:347248/1‑149 (MQ=255)                     aTCACCATCGTCGACGACGCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGc                                                                                                                               >  1:310450/1‑148 (MQ=255)                        aCCATCGTCGACGACGCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGAccc                                                                                                                                       <  3:213797/137‑1 (MQ=255)                        aCCATCGTCGACGACGCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGAccc                                                                                                                                       >  4:213797/1‑137 (MQ=255)                        aCCATCGTCGACGACGCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCaaa                                                                                                                            >  1:133381/1‑148 (MQ=255)                               tcgACGACGCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATcgcg                                                                                                                    <  1:367295/149‑1 (MQ=255)                                       gCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGc                                                                                                            >  3:141963/1‑149 (MQ=255)                                        ccAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGcc                                                                                                           <  4:156421/149‑1 (MQ=255)                                                 agaagGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCg                                                                                                  <  1:296132/149‑1 (MQ=255)                                                  gaagGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCgg                                                                                                 >  1:286036/1‑149 (MQ=255)                                                    agGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGCTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTa                                                                                               >  7:87394/1‑149 (MQ=255)                                                      gCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTg                                                                                                              <  7:277900/132‑1 (MQ=255)                                                      gCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATCGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTg                                                                                                              >  8:277900/1‑132 (MQ=255)                                                          tCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTc                                                                                         <  2:310450/149‑1 (MQ=255)                                                                   ccgcGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTc                                                                                         <  4:159182/140‑1 (MQ=255)                                                                   ccgcGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTc                                                                                         >  3:159182/1‑140 (MQ=255)                                                                     gcgcTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGcc                                                                              >  3:278572/1‑149 (MQ=255)                                                                          gggCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTg                                                                         <  8:293220/149‑1 (MQ=255)                                                                           ggCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTgg                                                                        <  7:347248/149‑1 (MQ=255)                                                                             cAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCg                                                                      <  2:286036/149‑1 (MQ=255)                                                                                             ttCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCTGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGgcgc                                                      >  6:149580/1‑149 (MQ=255)                                                                                                        ggTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGCTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACa                                           <  8:87394/149‑1 (MQ=255)                                                                                                           atatGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGt                                        >  7:346320/1‑149 (MQ=255)                                                                                                           atatGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCCCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGt                                        >  1:92837/1‑149 (MQ=255)                                                                                                            tatGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTcc                                                                                        <  4:84676/100‑1 (MQ=255)                                                                                                            tatGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTcc                                                                                        >  3:84676/1‑100 (MQ=255)                                                                                                                      tcgCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGggcgg                                >  5:346794/1‑146 (MQ=255)                                                                                                                      tcgCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGggcgg                                >  8:152795/1‑146 (MQ=255)                                                                                                                      tcgCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGggcgg                                >  3:208478/1‑146 (MQ=255)                                                                                                                         cTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCTTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGGGCGGCAGaaa                          <  4:208478/149‑1 (MQ=255)                                                                                                                         cTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGGGCGGCAGaaa                          <  2:133381/149‑1 (MQ=255)                                                                                                                              gCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGGGCGGCAGAAAATCCt                     >  6:340448/1‑149 (MQ=255)                                                                                                                                      cAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGAc                                            >  1:362468/1‑118 (MQ=255)                                                                                                                                      cAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGAc                                            <  2:362468/118‑1 (MQ=255)                                                                                                                                       aaGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGGGCGGCAGAAAATCCTCGCCGCGa             <  4:216742/148‑1 (MQ=255)                                                                                                                                       aaGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGGGCGGCAGAAAATCCTCGCCGCGa             >  3:216742/1‑148 (MQ=255)                                                                                                                                            gtTTTTCCTCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGggcgg                                <  6:228878/124‑1 (MQ=255)                                                                                                                                            gtTTTTCCTCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGggcgg                                <  6:223589/124‑1 (MQ=255)                                                                                                                                            gtTTTTCCTCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGggcgg                                >  5:228878/1‑124 (MQ=255)                                                                                                                                            gtTTTTCCTCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGggcgg                                >  5:223589/1‑124 (MQ=255)                                                                                                                                               tttCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGGGCGGCAGAAAATCCTCGCCGCGACCATCGTGa    >  3:164215/1‑149 (MQ=255)                                                                                                                                                  ccccAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGttct                                                             <  3:235218/89‑1 (MQ=255)                                                                                                                                                  ccccAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGttct                                                             >  4:235218/1‑89 (MQ=255)                                                                                                                                                  ccccAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGGGCGGCAGAAAATCCTCGCCGCGACCATCGTGATc  <  7:152795/148‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                  AGCCAATCGGCCTGAAGGACATCACCATCGTCGACGACGCCAAGATGAAGAAGGCGATCACAGCCGCCGCGCTGGGCAACGCCATGGAGTGGTTCGACTTTGGGGTATATGGCTTCGTCGCTTATGCCTTGGGCAAGGTGTTTTTCCCCAACGCCGACCCCAGCGTGCAAATGATCGCGGCCTTGGCCACCTTCTCGGTACCGTTCCTGATCCGGCCTCTTGGCGGGTTGTTCTTCGGCGCCTTGGGCGACAGGTTCGGGCGGCAGAAAATCCTCGCCGCGACCATCGTGATC  >  NC_002947/3313979‑3314271

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: ‑