Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,774,812	G→A	7.8%	P234S (CCA→TCA) ‡	PP_5521 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,774,812	0	G	A	7.8%	146.8 / 2.1	51	P234S (CCA→TCA) ‡	PP_5521	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (24/23);  new base A (2/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.63e-01

AGAACAAGATGTCGGCTGCCTTGCTCACCCACGACGATCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGTCGGTGTGGGCGGCAGGTCGAACGGCTCGAACGGGTAACCT  >  NC_002947/2774667‑2774948                                                                                                                                                  |                                                                                                                                              aGAACAAGATGTCGGCTGCCTTGCTCACCCACGACGATCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGgcag                                                                                                                                            >  4:262745/1‑149 (MQ=255)      aaGATGTCGGCTGCCTTGCTCACCCACGACGATCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGc                                                                                                                                       <  1:48050/149‑1 (MQ=255)      aaGATGTCGGCTGCCTTGCTCACCCACGACGATCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGCCACAGCAgg                                                                                                                                        >  8:112281/1‑148 (MQ=255)      aaGATGTCGGCTGCCTTGCTCACCCACGACGATCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGCCACAGCAGGc                                                                                                                                       <  7:112281/149‑1 (MQ=255)               gCTGCCTTGCTCACCCACGACGATCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCAc                                                                                                                              <  5:235672/149‑1 (MQ=255)                           aCCCACGACGATCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGc                                                                                                                    >  3:252904/1‑147 (MQ=255)                             ccACGACGATCAGCCGGCCATCCGCCGACACCCCACCATGCTCCATGCTCAGCCCCAGCCTGATGTCGTCCGGGTCGGTGCCCTCCGCCAGCTCTTCGAGCACGCGTGCCTCCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAg                                                                                                                 >  7:186196/1‑148 (MQ=255)                              cACGACGATCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTa                                                                                                               <  5:60388/149‑1 (MQ=255)                               acgacgATCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAc                                                                                                              >  5:115185/1‑149 (MQ=255)                                   cgaTCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAg                                                                                                         <  4:252904/149‑1 (MQ=255)                                      tCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGa                                                                                                                         <  8:269240/131‑1 (MQ=255)                                      tCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGa                                                                                                                         >  7:269240/1‑131 (MQ=255)                                        aGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATAc                                                                                                     <  6:260766/148‑1 (MQ=255)                                         gCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑Gaa                                                                                                          <  4:220512/142‑1 (MQ=255)                                         gCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑Gaa                                                                                                          >  3:220512/1‑142 (MQ=255)                                          ccGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑tt                                                                                                 >  1:181087/1‑149 (MQ=255)                                              ccATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGGCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGgc                                                                                             >  1:233373/1‑149 (MQ=255)                                                    gccgACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGc                                                                                                                    >  7:221673/1‑122 (MQ=255)                                                    gccgACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGc                                                                                                                    <  8:221673/122‑1 (MQ=255)                                                     ccgACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCAc                                                                                       >  1:187715/1‑148 (MQ=255)                                                          acCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACc‑‑agc‑ag                                                                              <  2:181087/149‑1 (MQ=255)                                                             gCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGa                                                                                                                                     <  2:9852/96‑1 (MQ=255)                                                             gCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGa                                                                                                                                     >  1:9852/1‑96 (MQ=255)                                                                      tccatgctcAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGAt                                                                                                       >  2:84117/1‑116 (MQ=255)                                                                      tccatgctcAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGAt                                                                                                       <  1:84117/116‑1 (MQ=255)                                                                      tccatgctcAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGCGAGTACT‑GCTggtg                                                                  >  3:296619/1‑147 (MQ=255)                                                                      tccatgctcAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGCGAGTACT‑GCTggtg                                                                  >  3:301434/1‑147 (MQ=255)                                                                        catgctcAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGCGAGTACT‑GCTggtgag                                                                <  4:296619/149‑5 (MQ=255)                                                                        catgctcAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGCGAGTACT‑GCTggtgag                                                                <  4:301434/149‑5 (MQ=255)                                                                            ctcAGCCCCAGGCTGATGTCTTCCGGGTCTGTGCGCTCGGCCAGCTCTTGGTGGACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCAGCTTGAGTGGCCAGTAG‑GATGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTGGCTGGCCATCgg                                                             <  8:186196/148‑1 (MQ=255)                                                                             tcAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCggg                                                            >  3:68016/1‑148 (MQ=255)                                                                                    cAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTgg                                                                    <  8:227371/133‑1 (MQ=255)                                                                                    cAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTgg                                                                    >  7:227371/1‑133 (MQ=255)                                                                                       gCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCa                                                 <  3:262745/149‑1 (MQ=255)                                                                                         tGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAgc                                               >  7:6394/1‑149 (MQ=255)                                                                                           aTGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGACTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAgc                                               <  3:240460/147‑1 (MQ=255)                                                                                              tcgtcCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGcggt                                          >  7:223817/1‑149 (MQ=255)                                                                                                          gTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGAGCGGTCGGTGTGggcgg                              >  7:209987/1‑149 (MQ=255)                                                                                                                tCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACCTTTTTTAAATGACCATAGC‑AGAACACGCGGGCCAGCGGGGAAGGGGGTCAGCGCGGGCGGTGTGggcggcgg                           >  1:101609/1‑147 (MQ=255)                                                                                                                  ggCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGGCGGTGTGGGCGGCAGGTc                        <  6:115185/147‑1 (MQ=255)                                                                                                                     cAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGTCGGTGTGGGCGGCAGGTCGAACg                   <  8:6394/149‑1 (MQ=255)                                                                                                                        ctctTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCgg                                                             <  7:12952/104‑1 (MQ=255)                                                                                                                        ctctTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCgg                                                             >  8:12952/1‑104 (MQ=255)                                                                                                                           ttCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGTCGGTGTGGGCGGCAGGTCGAACGGCTc               <  8:209987/147‑1 (MQ=255)                                                                                                                           ttCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGTCGGTGTGGGCGGCAGGTCGAACGGCTCg              >  1:35249/1‑148 (MQ=255)                                                                                                                               aGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGTCGGTGTGGGCGGCAGGTCGAACGGCTCGAACgg         <  2:35249/149‑1 (MQ=255)                                                                                                                                 cACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGTCGGTGTGGGCGGCAGGTCGAACGGCTCGAACGGGt       <  2:233373/149‑1 (MQ=255)                                                                                                                                    gcgTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAgg                                                       >  6:79486/1‑98 (MQ=255)                                                                                                                                    gcgTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGTCGGTGTGGGCGGCAGGTCGAACGGCTCGAACGGGTAAc    >  1:208706/1‑149 (MQ=255)                                                                                                                                      gTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGTCGGTGTGGGCGGCAGGTCGAACGGCTCGAACGGGTAACCt  >  3:89379/1‑149 (MQ=255)                                                                                                                                       cgCCTGCTGCCACAGCAGGCGAGTCGCACCTTGAGTGGCCAGTACGGAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGTCGGTGTGggc                                >  1:69829/2‑119 (MQ=255)                                                                                                                                       cgCCTGCTGCCACAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGTCGGTGTGggc                                <  2:69829/117‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                              AGAACAAGATGTCGGCTGCCTTGCTCACCCACGACGATCAGCCGGCCATCCGCCGACACCGCACCATGCTCCATGCTCAGCCCCAGGCTGATGTCGTCCGGGTCGGTGCCCTCGGCCAGCTCTTCGAGCACGCGTGCCTGCTGTGGCAGCAGGCGAGTCGCACCTTGAGTGGCCAGTAC‑GAAGATACC‑TTCGGCGCTCACC‑‑AGC‑AGTACTCGCTGGCCATCGGGGAAGGGGATCAGCGCGGTCGGTGTGGGCGGCAGGTCGAACGGCTCGAACGGGTAACCT  >  NC_002947/2774667‑2774948

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: ‑