Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,606,362	G→A	7.5%	L16L (CTG→CTA)	PP_4078 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,606,362	0	G	A	7.5%	151.8 / 2.2	54	L16L (CTG→CTA)	PP_4078	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (26/23);  new base A (2/2);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.60e-01

TGTTCGGCTGCGTGCTCGCGCACTTCTTCGCCCTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTGCGGCTGGCCAGCGACCCGCGCCTGACCTTT  >  NC_002947/4606215‑4606503                                                                                                                                                    |                                                                                                                                               tGTTCGGCTGCGTGCTCGCGCACTTCTTCGCCCTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAgctgc                                                                                                                                               >  3:110103/1‑149 (MQ=255)           cGTGCTCGCGCACTTCTTCGCCCTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAAcgc                                                                                                                                     <  4:110103/149‑1 (MQ=255)            gTGCTCGCGCACTTCTTCGCCCTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAAcgcg                                                                                                                                    >  6:271768/1‑149 (MQ=255)                tCGCGCACTTCTTCGCCCTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCAc                                                                                                                                 >  1:212486/1‑148 (MQ=255)                tCGCGCACTTCTTCGCCCTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCAc                                                                                                                                 >  6:345182/1‑148 (MQ=255)                    gcACTTCTTCGCCCTGTACGCCAGCATCAATTCCTTCAATCAACTGGAAGTGACCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGt                                                                                                                             >  3:270114/1‑148 (MQ=255)                          cttcGCCCTGTACGCCAGCATCAATTCCTTCCATCAATTTTAATTTATTTATACGTCGAACAACGAGATCTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAAc                                                                                                                        <  2:2165/147‑1 (MQ=17)                          cttcGCCCTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAAct                                                                                                                       >  7:275394/1‑148 (MQ=255)                               cccTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACttcttc                                                                                                                  >  5:174577/1‑148 (MQ=255)                               cccTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTACTCGCCAACGCGCACCAGTACAActtctt                                                                                                                   >  6:60988/1‑147 (MQ=255)                               cccTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTACTCGCCAACGCGCACCAGTACAActtctt                                                                                                                   <  5:55561/147‑1 (MQ=255)                               cccTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTACTCGCCAACGCGCACCAGTACAActtctt                                                                                                                   <  5:60988/147‑1 (MQ=255)                               cccTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTACTCGCCAACGCGCACCAGTACAActtctt                                                                                                                   >  6:55561/1‑147 (MQ=255)                               cccTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAACAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACttcttc                                                                                                                  >  8:308779/1‑148 (MQ=255)                                 cTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAg                                                                                                               >  1:345467/1‑149 (MQ=255)                                    tACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGtt                                                                                                             <  5:271768/148‑1 (MQ=255)                                     aCGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGc                                                                                                           >  4:38105/1‑149 (MQ=255)                                       gCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTg                                                                                                         >  7:194216/1‑149 (MQ=255)                                          aGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAg                                                                                                      <  8:275394/149‑1 (MQ=255)                                           gCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAg                                                                                                      >  7:111602/1‑148 (MQ=255)                                           gCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAg                                                                                                      <  8:111602/148‑1 (MQ=255)                                              tCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGCTCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCGAGTTGCTGGAGCGGt                                                                                                  >  4:289744/1‑149 (MQ=255)                                                aaTTCCTTCCATCAACTGGAAGTGACCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTg                                                                                                <  4:270114/149‑1 (MQ=255)                                                      ttccATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGc                                                                                          >  4:34408/1‑149 (MQ=255)                                                      ttccATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGc                                                                                          >  4:93840/1‑149 (MQ=255)                                                        ccATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACATCTTCTTCCAGTTGCTGGAGCGGTTGCATGGc                                                                                          <  5:345182/147‑1 (MQ=255)                                                        ccATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCCGGAGCGGTTGCATGGc                                                                                          <  3:129046/147‑1 (MQ=255)                                                        ccATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCAGAACTACCCGACAAGCAGCTCGCCAACGCGCACCAGTACAACAACTTCCAGTTCCAGGAGCCGTTGCATGGCCt                                                                                        >  3:61575/1‑149 (MQ=18)                                                         cATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCt                                                                                        <  3:38105/148‑1 (MQ=255)                                                             aaCTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAATGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACg                                                                                   >  8:227427/1‑149 (MQ=255)                                                                  gAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGcg                                                                                <  3:93840/147‑1 (MQ=255)                                                                       gATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAATGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGAcc                                                                          <  7:227427/148‑1 (MQ=255)                                                                                  ccaACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGtt                                                             <  2:345467/149‑1 (MQ=255)                                                                                   caacaaCGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTg                                                            >  3:327038/1‑149 (MQ=255)                                                                                      caacGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGc                                                         <  2:212486/149‑1 (MQ=255)                                                                                                tACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAgctg                                                                                                                                                >  3:197306/1‑53 (MQ=255)                                                                                                tACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAgctg                                                                                                                                                <  4:197306/53‑1 (MQ=255)                                                                                                    caTGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCAccc                                           <  3:34408/149‑1 (MQ=255)                                                                                                       ggCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGc                                        >  2:66289/1‑149 (MQ=255)                                                                                                          ccATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATg                                                                                            >  7:93567/1‑95 (MQ=255)                                                                                                          ccATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATg                                                                                            <  8:93567/95‑1 (MQ=255)                                                                                                          ccATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTgc                                     <  8:194216/149‑1 (MQ=255)                                                                                                          ccATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGATGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTgc                                     >  8:225272/1‑149 (MQ=255)                                                                                                               cAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCTCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTg                                <  2:255606/149‑1 (MQ=255)                                                                                                                aGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTGc                               <  3:289744/149‑1 (MQ=255)                                                                                                                aGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTGc                               <  1:66289/149‑1 (MQ=255)                                                                                                                     ggCAAACAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTGCGGCTg                          <  7:308779/149‑1 (MQ=255)                                                                                                                      gcaagcaaCCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCg                                                        >  6:24391/1‑118 (MQ=255)                                                                                                                      gcaagcaaCCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCg                                                        <  5:24391/118‑1 (MQ=255)                                                                                                                      gcaagcaaCCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGa                                                   >  7:185995/1‑123 (MQ=255)                                                                                                                      gcaagcaaCCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGa                                                   <  8:185995/123‑1 (MQ=255)                                                                                                                            atccGCTGAGCTCGCCGACAAGCTTCTCGCCAACGCGCACCAGTACTACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTGCGGGTGGCCAGCg                   <  4:61575/147‑1 (MQ=21)                                                                                                                            aaCCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTGCGGCTGGCCAGCg                   >  1:322426/1‑149 (MQ=255)                                                                                                                               cGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGGTAACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTGCGGCTGGc                        <  1:80238/142‑1 (MQ=255)                                                                                                                               cGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTGCGGCTGGc                        >  2:80238/1‑141 (MQ=255)                                                                                                                                       tAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTGCGGCTGGCCAGCGACCCGCGCCt         >  7:272143/1‑148 (MQ=255)                                                                                                                                             aCAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTGCGGCTGGCCAGCGACCCGCGCCTGACCttt  >  1:227910/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                               TGTTCGGCTGCGTGCTCGCGCACTTCTTCGCCCTGTACGCCAGCATCAATTCCTTCCATCAACTGGAAGTGATCAACACCACCAACAACGAGCACTACACATGGCCCATCCAGACCGGCAAGCAACCGCTGATCTAGCCGACAAGCTGCTCGCCAACGCGCACCAGTACAACTTCTTCCAGTTGCTGGAGCGGTTGCATGGCCTGCACGGCGACGACCTGG‑AACCGCGTTGGGCGGATGAGGCCACCCGGCTGCGCGTGCGGCTGGCCAGCGACCCGCGCCTGACCTTT  >  NC_002947/4606215‑4606503

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: ‑