Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,746,488	G→C	8.5%	intergenic (+35/+64)	PP_5042 → / ← PP_5043	hypothetical protein/PhoPQ‑activated pathogenicity‑like protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,746,488	0	G	C	8.5%	138.5 / 3.2	47	intergenic (+35/+64)	PP_5042/PP_5043	hypothetical protein/PhoPQ‑activated pathogenicity‑like protein
Reads supporting (aligned to +/- strand):  ref base G (26/16);  new base C (2/2);  total (28/19)
Fisher's exact test for biased strand distribution p-value = 6.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.41e-01

AAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAAAACGCT  >  NC_002947/5746341‑5746629                                                                                                                                                     |                                                                                                                                               aaaGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCgcggg                                                                                                                                               <  5:76904/149‑1 (MQ=255)        gCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCCCGCGCGGCGC‑t                                                                                                                                       <  1:358348/149‑1 (MQ=255)              cACCATTTATGACAAGCGCCCGGATACCTGCCGCATACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCAAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCCCGCGCGGCGC‑TCGAta                                                                                                                                  >  1:56592/1‑148 (MQ=39)              cACCATTTATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTc                                                                                                                                 >  2:337701/1‑149 (MQ=255)              cACCATTTATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCCCGCGCGGCGC‑TCGa                                                                                                                                    <  2:56592/146‑1 (MQ=255)              cACCATTTATGACAAGCGCCCGGATACCAGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGAGTc                                                                                                                                 >  8:144143/1‑149 (MQ=255)               aCCATTTATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCt                                                                                                                                >  1:349245/1‑149 (MQ=255)               aCCATTTATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCt                                                                                                                                >  3:139618/1‑149 (MQ=255)                ccATTTATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCtg                                                                                                                               >  3:271674/1‑149 (MQ=255)                 cATTTATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCtgt                                                                                                                              >  7:211781/1‑149 (MQ=255)                  aTTTATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGGTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCtgtg                                                                                                                             >  7:141771/1‑149 (MQ=255)                  aTTTAAGACAAGCGCCCGGATACATGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGAttatctg                                                                                                                             >  2:101319/1‑144 (MQ=255)                   tttATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCATGGTCGGGCCACGGCGGGGGTTTTGCGCTTACATGCCCAAGGTGGTTGGGGTTTGTGTCTTGGGCGGGGGCTTAATTCTAGCGCCGCGCGTGCGGCGC‑TCGATTCTGTgg                                                                                                                            <  2:88938/149‑1 (MQ=255)                        gACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATg                                                                                                                       >  3:96156/1‑149 (MQ=255)                         aaaaGCGCACGGATACCTGCCTCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCATACAAGCCCAAGGTGGTTGGGCGTTGATTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGc                                                                                                                      <  4:229298/147‑1 (MQ=255)                          cAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGa                                                                                                                         >  3:232070/1‑145 (MQ=255)                                cccGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGAtt                                                                                                                                  <  3:59828/130‑1 (MQ=255)                                cccGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGAtt                                                                                                                                  >  4:59828/1‑130 (MQ=255)                                   ggATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGAATAAATCGACCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCCAGCTCGGc                                                                                                            <  1:337701/149‑1 (MQ=255)                                          cgCCCCA‑CCCCCCCCATGGGGGGGCCCCGGGGGGGTTTTTGCGCCCACAACCCCCTGGGTGGTGGGGGTTGTTGCTTGGGCGGGGTCATTAATGCTCGGGCGCGGGGGGGGCGCGTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAg                                                                                                      <  2:349245/148‑1 (MQ=255)                                                a‑aCCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGaa                                                                                               <  7:241147/149‑1 (MQ=255)                                                a‑aCCACCCCAAGGTCGGGCAACGGCCGGGGTATTGCGCCAACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGCCATAAATCGAGCGCCGCGGGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGaa                                                                                               <  2:143149/149‑1 (MQ=255)                                                    caccCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCAAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TAGATTCTGTGGCGAAGCCGAGCTGGCCATGAAGCACTGaa                                                                                               >  7:121167/1‑146 (MQ=255)                                                      ccccAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGa                                                                                                                                    >  1:270733/1‑107 (MQ=255)                                                      ccccAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGa                                                                                                                                    <  2:270733/107‑1 (MQ=255)                                                      ccccAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCAc                                                                                          <  4:271674/149‑1 (MQ=255)                                                       cccAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTAGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCAcc                                                                                         >  7:71702/1‑149 (MQ=255)                                                             gTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTcc                                                                                    >  4:93512/1‑148 (MQ=255)                                                                  gCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTAGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTc                                                                              <  8:71702/149‑1 (MQ=255)                                                                   ccACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCAttt                                                                               >  6:318716/1‑147 (MQ=255)                                                                     aCGGCCGGGGAATTGCGCCTACAACCCCAAGGTGGTGGGGCGTTGAGGCTTCCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTcagc                                                                           <  7:144143/149‑1 (MQ=255)                                                                                   gcgcCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTc                                                             >  3:360849/1‑149 (MQ=255)                                                                                   gcgcCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTc                                                             >  3:113012/1‑149 (MQ=255)                                                                                       cTACAAGCCCAAGGGGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGc                                                         <  3:51268/149‑1 (MQ=255)                                                                                        tACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGGGGGGAAGGTCCGGc                                                         >  4:195474/1‑148 (MQ=255)                                                                                         aCAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGc                                                         >  1:165018/1‑147 (MQ=255)                                                                                              cccAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTc                                                             >  3:338987/1‑138 (MQ=255)                                                                                                 aaGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAAACGAGCGCCGCGCGGGCGGCGC‑TCGAATCTCTGGCGATGCCGAGCTGGTCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCAGGCAAGCAccccc                                               >  1:112836/1‑149 (MQ=255)                                                                                                   ggtggtTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCTCGCGGGCGGCTC‑TCGATTCTGTGGCGATGCCGAGCTTGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCt                                             <  6:375174/149‑1 (MQ=255)                                                                                                                   gTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATg                             <  4:96156/149‑1 (MQ=255)                                                                                                                    tCTTGCGCCGGGGCATAAATCGAGGGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATg                             <  8:211781/148‑1 (MQ=255)                                                                                                                      ttGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTc                          <  2:112836/149‑1 (MQ=255)                                                                                                                                     aaTCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGGCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCgg           <  5:318716/149‑1 (MQ=255)                                                                                                                                       tCGAGCGCCGCCCGCGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCGGGTGGATGCTCAGGATAAGTCTGCGGc          >  4:88286/1‑148 (MQ=255)                                                                                                                                        cGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCCGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCa         >  5:283297/1‑148 (MQ=255)                                                                                                                                         gAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGACATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCAGCgttttg       >  8:335876/1‑144 (MQ=255)                                                                                                                                              ccgcGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAAAACGCt  >  6:359761/1‑149 (MQ=255)                                                                                                                                              ccgcGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAAAACGCt  >  5:11345/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                               AAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCA‑ACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGC‑TCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAAAACGCT  >  NC_002947/5746341‑5746629

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑