Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	336,124:1	+T	100%	coding (209/237 nt)	PP_0278 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	336,124	1	.	T	95.7%	151.1 / ‑0.4	47	coding (209/237 nt)	PP_0278	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base T (23/22);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTTAACCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑A‑TACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAAGCAGCCCCGGCGATTTCAG  >  NC_002947/335976‑336262                                                                                                                                                       |                                                                                                                                           gTTAACCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑a                                                                                                                                             <  5:152950/149‑1 (MQ=255) gTTAACCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑a                                                                                                                                             <  8:39759/149‑1 (MQ=255)     aCCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑A‑ttac                                                                                                                                        <  1:195570/149‑4 (MQ=255)     aCCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑A‑ttac                                                                                                                                        <  6:112123/149‑4 (MQ=255)     aCCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑A‑ttac                                                                                                                                        <  3:298011/149‑4 (MQ=255)     aCCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑A‑ttac                                                                                                                                        <  3:17074/149‑4 (MQ=255)       ccATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑A‑ttacct                                                                                                                                      >  8:231467/1‑144 (MQ=255)                aaTCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACAt                                                                                                                              >  1:211972/1‑149 (MQ=255)                      cTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCa                                                                                                                         <  6:152732/148‑1 (MQ=255)                            gTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCt                                                                                                                  >  4:171626/1‑149 (MQ=255)                             tAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCtg                                                                                                                 <  5:198020/149‑1 (MQ=255)                                  cccGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGaa                                                                                                            >  5:27346/1‑149 (MQ=255)                                  cccGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGaa                                                                                                            >  1:7422/1‑149 (MQ=255)                                     ggCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGTTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGa                                                                                                         <  7:231467/149‑1 (MQ=255)                                          ccccGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATc                                                                                                     >  2:150929/1‑148 (MQ=255)                                           cccGTCGCCGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCACGCACCTGGTGCGCGAGGGCGATATGGAGGACGGCCATAAATTCCTGGGGGCAGCCGCT‑TACCTGTGCGACATGGCCAAGGCGCTGATGTACGATATc                                                                                                     >  4:226685/1‑147 (MQ=255)                                           cccGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCga                                                                                                   <  3:171626/149‑1 (MQ=255)                                            ccGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATc                                                                                                     >  5:237111/1‑146 (MQ=255)                                              gTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGACAAGGCGCTGAAGAACGAAATc                                                                                                     >  2:109604/1‑144 (MQ=255)                                                    gcgGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCaa                                                                                          <  8:249881/149‑1 (MQ=255)                                                        ccTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGt                                                                                      <  1:150929/149‑1 (MQ=255)                                                          tACGAGCATGTCTCGATCCTGATGGGCCACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGt                                                                                      >  6:233921/1‑147 (MQ=255)                                                           aCGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAgg                                                                                                                      <  2:19850/114‑1 (MQ=255)                                                           aCGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAgg                                                                                                                      >  1:19850/1‑114 (MQ=255)                                                            cGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAg                                                                                   <  6:237111/148‑1 (MQ=255)                                                             tcccgcctctcGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGTTGGCGATATGGAGGACGACCATAAATTCCTTGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGgc                                                                                 <  1:109604/142‑1 (MQ=255)                                                                cATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCa                                                                              >  8:59718/1‑149 (MQ=255)                                                                    tctcGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTa                                                                           <  2:211972/148‑1 (MQ=255)                                                                    tctcGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAg                                                                          >  6:272266/1‑149 (MQ=255)                                                                    tctcGATACTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAg                                                                          >  6:267477/1‑149 (MQ=255)                                                                               attggatACATCCAGCACCTGGTGGGCGAGGGCGATATGGAGGACGTCCATATAATCCTGAGGGCATCCGAA‑TACATGAGCGAGATGGCCAAGGCGCTGATGAACGAAATCGAGATCGCCAAGGGTAAGGCGCATAAGGGATTGAcg                                                                 <  6:232070/141‑1 (MQ=255)                                                                               aTGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGAcgcg                                                               <  7:59718/149‑1 (MQ=255)                                                                                tGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCgg                                                              >  1:185344/1‑149 (MQ=255)                                                                                   gCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCa                                                           >  7:7341/1‑149 (MQ=255)                                                                                    cTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCAt                                                          >  6:100930/1‑149 (MQ=255)                                                                                     tACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCAtt                                                         >  2:98826/1‑149 (MQ=255)                                                                                        aTCAAGCACCTGGTGCGCGAGGGTGATATGGAGGACGACCATAAATTCCTGGTGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCAttt                                                        <  4:253935/147‑1 (MQ=255)                                                                                        aTCAAGCACCTGGTGCGCGAGGGTGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCAttt                                                        >  3:253935/1‑147 (MQ=255)                                                                                        aTCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTtgt                                                      <  5:233921/149‑1 (MQ=255)                                                                                        aTCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTtgt                                                      <  6:27346/149‑1 (MQ=255)                                                                                         tCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTtgtg                                                     <  2:7422/149‑1 (MQ=255)                                                                                            aGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGa                                                  <  5:100930/149‑1 (MQ=255)                                                                                             gCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATAGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAg                                                 >  3:197495/1‑149 (MQ=255)                                                                                                 cTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAGc                                                >  7:122150/1‑146 (MQ=255)                                                                                                 cTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAGc                                                <  8:122150/146‑1 (MQ=255)                                                                                                    gTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAGCGGCCtt                                          <  5:272266/149‑1 (MQ=255)                                                                                                    gTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAGCGGCCtt                                          <  5:267477/149‑1 (MQ=255)                                                                                                     tGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAGCGGCCtt                                          <  2:185344/148‑1 (MQ=255)                                                                                                                       aggaCGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCCGc                        >  8:149017/1‑148 (MQ=255)                                                                                                                        ggaCGACCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCaa                      <  3:34007/149‑1 (MQ=255)                                                                                                                            gacCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCAttt                                                        >  6:303745/1‑111 (MQ=255)                                                                                                                            gacCATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCAttt                                                        <  5:303745/111‑1 (MQ=255)                                                                                                                               cATAAATTCCTGGGGGCAGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAGCGGCCTTGCGTCTCGAATGGGCTGCAAATCAGcc               >  1:19324/1‑149 (MQ=255)                                                                                                                                                aGCCG‑ATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAAGCAGCCCCGGCGATTTCag  >  5:261457/1‑145 (MQ=255)                                                                                                                                                       |                                                                                                                                           GTTAACCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCG‑A‑TACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGGTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAAGCAGCCCCGGCGATTTCAG  >  NC_002947/335976‑336262

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: ‑