Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,424,892	T→C	8.8%	intergenic (+480/‑32)	PP_3039 → / → PP_3040	hypothetical protein/holin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,424,892	0	T	C	8.8%	123.1 / 3.2	46	intergenic (+480/‑32)	PP_3039/PP_3040	hypothetical protein/holin
Reads supporting (aligned to +/- strand):  ref base T (23/18);  new base C (2/2);  total (26/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.45e-01

AACAGACATTCCCCGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGCCGGC  >  NC_002947/3424746‑3425031                                                                                                                                                     |                                                                                                                                            aaCAGACATTCCCCGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCt                                                                                                                                             >  6:233270/1‑147 (MQ=255) aaCAGACATTCCCCGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTgg                                                                                                                                           >  5:208046/1‑149 (MQ=255) aaCAGACATTCCCCGGACGTTTACCACTTATTGCCGGGTCGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCt                                                                                                                                             <  5:233270/147‑1 (MQ=255)   cAGACATTCCCCGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGgcg                                                                                                                                         >  1:38117/1‑149 (MQ=255)      aCATTCCCCGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCAGCCAAACACTGAAAACCCCGGCCCTGGCGCCg                                                                                                                                      >  5:60423/1‑149 (MQ=255)            cccGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCGCCAGGGCCGGGGtt                                                                                                                                 <  8:252072/148‑1 (MQ=255)               ggACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTg                                                                                                                             >  3:142108/1‑149 (MQ=255)                 aCGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGcc                                                                                                                           <  1:112622/149‑1 (MQ=255)                       aCCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTgg                                                                                                                      <  4:142108/148‑1 (MQ=255)                         cACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCGGGCGCCGGGGttt                                                                                                                                >  4:91200/1‑136 (MQ=255)                          aCTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGTAGGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTgggg                                                                                                                    >  1:218756/1‑149 (MQ=255)                          aCTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCTCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGttttt                                                                                                                              <  8:250024/137‑1 (MQ=255)                          aCTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGttttt                                                                                                                              >  7:250024/1‑137 (MQ=255)                                    gggTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAAc                                                                                                        <  6:60423/149‑1 (MQ=255)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTg                                                                                                                             >  2:203657/1‑121 (MQ=255)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTg                                                                                                                             <  1:203657/121‑1 (MQ=255)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCttt                                                                                                                        <  2:35387/126‑1 (MQ=255)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCttt                                                                                                                        >  1:35387/1‑126 (MQ=255)                                              aaaaCTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCCCAAAGCGGCCCGCCAAACACTGAAAACCCCGGCGCCAGGGCCgggg                                                                                                                                   >  2:152615/1‑112 (MQ=255)                                              aaaaCTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCGCCAGGGCCgggg                                                                                                                                   <  1:152615/112‑1 (MQ=255)                                               aaaCTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGagcagc                                                                                              <  6:208046/148‑1 (MQ=255)                                                aaCTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGAt                                                                                                            <  5:184824/133‑1 (MQ=255)                                                     gCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGTCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCg                                                                                         <  5:177785/147‑1 (MQ=255)                                                          ctgcCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGtt                                                                                   >  6:70518/1‑148 (MQ=255)                                                             ccACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTgaga                                                                               <  2:38117/149‑1 (MQ=255)                                                                            ggTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCtggttgg                                                                >  2:89855/2‑149 (MQ=255)                                                                              tAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCTAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTg                                                              <  2:218756/149‑1 (MQ=255)                                                                              tAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCtggttggt                                                               <  5:94979/148‑1 (MQ=255)                                                                                aaaaGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGa                                                             >  6:30220/1‑148 (MQ=255)                                                                                       cccATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCtggt                                                                   <  8:97834/135‑1 (MQ=255)                                                                                       cccATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCtggt                                                                   >  7:97834/1‑135 (MQ=255)                                                                                          aTCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTcc                                                  >  7:52794/1‑149 (MQ=255)                                                                                              tCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTggg                                                                                                                     <  8:69763/78‑1 (MQ=255)                                                                                              tCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTggg                                                                                                                     >  7:69763/1‑78 (MQ=255)                                                                                                              cgcACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGgtgt                                  >  6:23909/1‑147 (MQ=255)                                                                                                                   aaaGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCga                           <  5:23909/149‑1 (MQ=255)                                                                                                                          cccGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTgg                    >  2:260102/1‑149 (MQ=255)                                                                                                                            cGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCg                  >  5:277523/1‑149 (MQ=255)                                                                                                                               cAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGc               <  5:70518/149‑1 (MQ=255)                                                                                                                                aaaCACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCtggttg                                                                 >  3:132425/1‑98 (MQ=255)                                                                                                                                aaaCACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCtggttg                                                                 <  4:132425/98‑1 (MQ=255)                                                                                                                                      tGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCGTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACAt         >  3:195578/1‑148 (MQ=255)                                                                                                                                      tGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCgggg                                     >  2:2814/1‑120 (MQ=255)                                                                                                                                      tGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATg        >  7:93467/1‑149 (MQ=255)                                                                                                                                       aaaaaCCCCGGCGCCAGGGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATgg       >  5:47102/2‑149 (MQ=255)                                                                                                                                         aaaCCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGc      >  7:251184/1‑148 (MQ=255)                                                                                                                                         aaaCCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGc      <  8:251184/148‑1 (MQ=255)                                                                                                                                            ccccGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGCCGGc  >  4:126028/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                            AACAGACATTCCCCGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCG‑A‑GACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCCCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGCCGGC  >  NC_002947/3424746‑3425031

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: ‑