Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,531,904	T→A	10.2%	A53A (GCT→GCA)	PP_2222 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,531,904	0	T	A	10.2%	133.2 / 6.1	49	A53A (GCT→GCA)	PP_2222	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (19/25);  new base A (3/2);  total (22/27)
Fisher's exact test for biased strand distribution p-value = 6.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.43e-01

GATGTGGCTGTGATGATAGGGTCGGGTGTGCCGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGTCTTCTAGCAGGCTCACGCCAT  >  NC_002947/2531764‑2532048                                                                                                                                             |                                                                                                                                                 gATGTGGCTGTGATGATAGGGTCGGGTGTGCCGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGgca                                                                                                                                          <  2:304366/149‑1 (MQ=255) gATGTGGCTGTGATGATAGGGTCGGGTGTGCCGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGgc                                                                                                                                           <  4:269921/148‑1 (MQ=255) gATGTGGCTGTGATGATAGGGTCCGGTGTGCCGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGgca                                                                                                                                          <  8:146902/149‑1 (MQ=255)  aTGTGGCTGTGATGATAGGGTCGGGTGTGCCGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCNGgcag                                                                                                                                         <  7:60745/149‑1 (MQ=255)         tgtgATGATAGGGTCGGGTGTGCCTGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCagcagcagc                                                                                                                                  >  4:303008/1‑149 (MQ=255)           tgatgaTAGGGTCGGGTGTGCCGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTg                                                                                                                                <  3:226392/149‑1 (MQ=255)                   gggTCGGGTGTGCCGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAgg                                                                                                                        <  8:185953/149‑1 (MQ=255)                    ggTCGGGTGTGCCGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAggg                                                                                                                       >  5:65511/1‑149 (MQ=255)                    ggTCGGGTGTGCCGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAggg                                                                                                                       >  4:137549/1‑149 (MQ=255)                      tCGGGTGTGCCGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGggct                                                                                                                     >  5:328119/1‑149 (MQ=255)                               ccGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCt                                                                                                             >  8:15289/1‑148 (MQ=255)                                cGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCAGCCTGgcactcaag                                                                                                                                    >  4:79145/1‑118 (MQ=255)                                cGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCAGCCTGgcactcaag                                                                                                                                    <  3:79145/124‑7 (MQ=255)                                    cACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAAt                                                                                                       <  2:302981/149‑1 (MQ=255)                                      ccTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGt                                                                                                     <  3:303008/149‑1 (MQ=255)                                      ccTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGt                                                                                                     <  2:203359/149‑1 (MQ=255)                                       cTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGtt                                                                                                    <  6:328119/149‑1 (MQ=255)                                           cAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTAtt                                                                                                <  7:15289/149‑1 (MQ=255)                                           cAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTAtt                                                                                                <  1:210221/149‑1 (MQ=255)                                            aGGCGCTGGGCAAGCGTATATGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGAGTCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCAGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTg                                                                                               >  8:212300/1‑149 (MQ=255)                                             ggCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGGGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGc                                                                                              <  1:132283/149‑1 (MQ=255)                                                  tGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCTCCTTCGCCACGCGCGAAGAAGCTCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCtctc                                                                                         <  5:47831/149‑1 (MQ=255)                                                  tGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCtctc                                                                                         >  3:161651/1‑149 (MQ=255)                                                          cGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAAAGTTTATTGCCTCTCGACGGGtt                                                                                 >  7:90777/1‑149 (MQ=255)                                                                   tGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACgg                                                                                    >  3:166568/1‑137 (MQ=255)                                                                   tGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACgg                                                                                    <  4:166568/137‑1 (MQ=255)                                                                       tAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCgg                                                                    <  5:118775/149‑1 (MQ=255)                                                                               gTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTTTTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATAttt                                                            <  4:54232/149‑1 (MQ=255)                                                                               gTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATAttt                                                            >  6:345978/1‑149 (MQ=255)                                                                                  aaTGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTc                                                         >  1:157241/1‑149 (MQ=255)                                                                                  aaTGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTc                                                         >  1:159624/1‑149 (MQ=255)                                                                                      gCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTa                                                      <  4:164657/148‑1 (MQ=255)                                                                                                            cGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGc                                 >  4:57262/1‑147 (MQ=255)                                                                                                             gCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCa                               <  3:246375/148‑1 (MQ=255)                                                                                                              ccACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAgg                             >  7:182162/1‑149 (MQ=255)                                                                                                                  gcgcgAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCtt                         <  4:161651/149‑1 (MQ=255)                                                                                                                    gcgAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGt                       >  5:306133/1‑149 (MQ=255)                                                                                                                      gaagaaGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGtct                     >  6:70483/1‑149 (MQ=255)                                                                                                                        agaagCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAggg                            >  4:289822/1‑140 (MQ=255)                                                                                                                        agaagCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAggg                            <  3:289822/140‑1 (MQ=255)                                                                                                                        agaagCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGtcttc                   <  2:159624/149‑1 (MQ=255)                                                                                                                            gcgcTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGTCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGTCTTCTAGc               <  7:212300/149‑1 (MQ=255)                                                                                                                            gcgcTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGTCTTCTAGc               <  8:90777/149‑1 (MQ=255)                                                                                                                                 ctgctGCCAGGCAGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGTCTTCTa                 <  2:218142/138‑1 (MQ=255)                                                                                                                                 ctgctGCCAGGCAGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGTCTTCTa                 >  1:218142/5‑142 (MQ=255)                                                                                                                                  tgctGCCAGGCAGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGTCTTCTAGCAGGCt          >  2:297872/4‑148 (MQ=255)                                                                                                                                   aGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGTCTTCTAGCAGGCTc         <  2:165999/148‑1 (MQ=255)                                                                                                                                        cAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGTCTTCTAGCAGGCTCACGCCa   >  6:304086/1‑149 (MQ=255)                                                                                                                                         aGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGTCTTCTAGCAGGCTCACGCCAt  >  6:194326/1‑149 (MQ=255)                                                                                                                                             |                                                                                                                                                 GATGTGGCTGTGATGATAGGGTCGGGTGTGCCGGCCACCTTGCAGGCGCTGGGCAAGCGTATTTGCTGGGTAGTGCTGGTCAATGGCGAGCGTCGCGGCACCGCCTTCGCCACGCGCGAAGAAGCGCTTGAGTGCCAGGCTGCCTGGCAGCAGCAGCTGAAGAAAGGGCTGGCTGCCTGAAAATGTTTATTGCCTCTCGACGGGTTTCGGTGTTTTCGGGCATATTTGTCCTACAGTAATGCGCACATGGATGCCAGGGCTTGTCTTCTAGCAGGCTCACGCCAT  >  NC_002947/2531764‑2532048

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑