Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	59,270	T→C	9.0%	intergenic (‑86/+46)	PP_0050 ← / ← PP_0051	hypothetical protein/sigma‑54 dependent transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	59,270	0	T	C	9.0%	121.5 / 2.9	45	intergenic (‑86/+46)	PP_0050/PP_0051	hypothetical protein/sigma‑54 dependent transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (20/20);  new base C (2/2);  total (22/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.64e-01

TTGCCAGCGGTGTGCTGAGCATGAGCGCGGCGCAGATCACGGTTAGGGCTTTCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGCCAGTTCACTGCGCGAGCCTTTGAACTGCTCCAGCGC  >  NC_002947/59127‑59417                                                                                                                                                |                                                                                                                                                    ttGCCAGCGGTGTGCTGAGCATGAGCGCGGGGCAGATCACGGTTAGGGCTTTCTTCATTTTGAGGCGTTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGt                                                                                                                                               >  2:123642/1‑150 (MQ=255)   gCCAGCGGTGTGCTGAGCATGAGCGCGGCGCAGATCACGGTTAGGGCTTTCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCa                                                                                                                                             <  1:663229/150‑1 (MQ=255)                 gAGCATGAGCGCGGCGCAGATCACGGTTAGGGCTTTCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAg                                                                                                                               <  2:327692/150‑1 (MQ=255)                       gAGCGCGGCGCAGATCACGGTTAGGGCTTTCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAAGTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCgg                                                                                                                         <  1:509714/150‑1 (MQ=255)                       gAGCGCGGCGCAGATCACGGTTAGGGCTATCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTCATTGCCAGGTTCGGTTAAATGATCAGACCACGATTTTTCCCTTTCAGTGTCAGGGCGCAGGTCAAggcacgg                                                                                                                         >  2:207026/1‑145 (MQ=255)                              gcgcAGATCACGGTTAGGGCTTTCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTc                                                                                                                  <  1:631141/150‑1 (MQ=255)                                gcAGATCACGGTTAGGGCTTTCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTGACGTTGCCTTGGCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTg                                                                                                                <  2:85648/150‑1 (MQ=255)                                    aTCACGGTTAGGGCTTTCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTGTGGCGt                                                                                                            >  1:31072/1‑150 (MQ=255)                                         ggTTAGGGCTTTCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCttt                                                                                                       <  2:459951/150‑1 (MQ=255)                                           ttAGGGCTTTCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTttca                                                                                                     <  1:112054/150‑1 (MQ=255)                                              gggCTTTCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTttcagtt                                                                                                  <  2:674818/150‑1 (MQ=255)                                                     cttcATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCg                                                                                           >  2:683422/1‑150 (MQ=255)                                                                       ctctGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCTTTTTAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAgcggcgc                                                                         >  2:258965/1‑149 (MQ=255)                                                                            ccTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAgc                                                                              <  2:91466/140‑1 (MQ=255)                                                                            ccTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAgc                                                                              >  1:91466/1‑140 (MQ=255)                                                                               gTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTTTTTTTTTTTTTCAGGTCGCAGGTAACGGTCCGGTAAAGTCTGTCGTTCTTTCAGTTCAGCCCCAGCGCTTTCAAGCGGCGATACTgcct                                                                 >  2:634624/1‑148 (MQ=255)                                                                                 tAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAgcgtgc                                                               <  2:447497/150‑1 (MQ=255)                                                                                  aaTCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAgcgtgcg                                                              >  2:206893/1‑150 (MQ=255)                                                                                   aTCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAACGTCCGGTAATGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAgcgtgcgt                                                             <  1:207026/150‑1 (MQ=255)                                                                                    tCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGtt                                                            >  1:386026/1‑150 (MQ=255)                                                                                             aaGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGc                                                   >  2:108872/1‑150 (MQ=255)                                                                                               gTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCa                                                 >  1:204741/1‑150 (MQ=255)                                                                                                tATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCACTCAAAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCaa                                                >  2:442097/1‑150 (MQ=255)                                                                                                tATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCaa                                                >  2:310042/1‑150 (MQ=255)                                                                                                  ttgattgCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCACTGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGa                                              <  1:164342/150‑1 (MQ=255)                                                                                                     attgCCAGGTTCGGTTAACTGATCAGACCACGCTTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGa                                           <  2:498523/150‑1 (MQ=255)                                                                                                       tgCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACt                                         <  1:206893/150‑1 (MQ=255)                                                                                                          cAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGc                                      <  1:310042/150‑1 (MQ=255)                                                                                                                  gTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTaaa                                                                                                                                >  1:571160/1‑52 (MQ=255)                                                                                                                  gTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTaaa                                                                                                                                <  2:571160/52‑1 (MQ=255)                                                                                                                     aaCTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGCCAGTTCACTgc                           <  1:123642/150‑1 (MQ=255)                                                                                                                      aCTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGCCAGTTCACTgcg                          >  1:417229/1‑150 (MQ=255)                                                                                                                         gATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGCCAGTTCACTGCGCGa                       <  2:204741/150‑1 (MQ=255)                                                                                                                          aTCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCTTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGACGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGCCAGTTCACTGCGCGAg                      >  1:726931/1‑150 (MQ=255)                                                                                                                               aCCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCCTTCAAGCGGCGATACCGCGTGCGTTCACTCATGCCAAGATGACTGGCGCGTACACTGTGCGAGCCgtt                 <  2:31072/150‑1 (MQ=255)                                                                                                                                 cACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGCCAGTTCACTGCGCGAGTCTTTGa               >  1:300496/1‑150 (MQ=255)                                                                                                                                 cACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGCCAGTTCACTGCGCGAGCCTTTGa               >  1:85723/1‑150 (MQ=255)                                                                                                                                  aCGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCt                                                                                     <  2:362206/79‑1 (MQ=255)                                                                                                                                  aCGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCt                                                                                     >  1:362206/1‑79 (MQ=255)                                                                                                                                  aCGATTTTTCCCTTCCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAg                                               >  2:525041/1‑117 (MQ=255)                                                                                                                                  aCGATTTTTCCCTTCCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAg                                               <  1:525041/117‑1 (MQ=255)                                                                                                                                       ttttCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGCCAGTTCACTGCGCGAGCCTTTGAACTGCt         >  2:581635/1‑150 (MQ=255)                                                                                                                                        tttCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGCCAGTTCACTGCGCGAGCCTTTGAACTGCTc        <  2:417229/150‑1 (MQ=255)                                                                                                                                            ccTTCCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGAt                                             >  2:434140/1‑109 (MQ=255)                                                                                                                                            ccTTCCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGAt                                             <  1:434140/109‑1 (MQ=255)                                                                                                                                              tttCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGCCAGTTCACTGCGCGAGCCTTTGAACTGCTCCAgcgc  >  1:135830/1‑150 (MQ=255)                                                                                                                                                |                                                                                                                                                    TTGCCAGCGGTGTGCTGAGCATGAGCGCGGCGCAGATCACGGTTAGGGCTTTCTTCATTTTGATGCGGTCCTCTGCCTGTTAATCGCCTGGCAAGTATTGATTGCCAGGTTCGGTTAACTGATCAGACCACGATTTTTCCCTTTCAATGTCAGGGCGCAGGTAAAGGTCCGGTAAAGTCTGGCGTTCTTTCAGTTCAGCCCGAGCGCTTTCAAGCGGCGATACAGCGTGCGTTCACTCATGCCAAGATGACTGGCCAGTTCACTGCGCGAGCCTTTGAACTGCTCCAGCGC  >  NC_002947/59127‑59417

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑