Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,518,499	A→G	10.2%	E42E (GAA→GAG)	PP_5579 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,518,499	0	A	G	10.2%	99.5 / 3.2	39	E42E (GAA→GAG)	PP_5579	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (15/20);  new base G (2/2);  total (17/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.10e-01

GATTTGAGGGTTTAAAATGCTGGATTTTCAAAACCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCGAAGCCGCCTAAGGATTTGCTTGATCTTAGGCTTGGAGTAAGTA  >  NC_002947/3518358‑3518632                                                                                                                                              |                                                                                                                                       gATTTGAGGGTTTAAAATGCTGGATTTTCAAAACCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTag                                                                                                                                 <  3:271429/149‑1 (MQ=255)       aGGGTTTAAAATGCTGGATTTTCAAAACCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCt                                                                                                                            <  6:35441/148‑1 (MQ=255)              aaaaTGCTGGATTTTCAAAACCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCt                                                                                                                    >  6:40073/1‑149 (MQ=255)               aaaTGCTGGATTTTCAAAACCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCtt                                                                                                                   <  4:109092/149‑1 (MQ=255)                   gCTGGATTTTCAAAACCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGt                                                                                                                >  1:237273/1‑148 (MQ=255)                            tCAAAACCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAAACGGTAGAGGATGAATTTCTTGGTGCTTATg                                                                                                         >  1:233284/1‑146 (MQ=255)                             cAAAACCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCtt                                                                                                                   >  6:90203/1‑135 (MQ=255)                             cAAAACCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCtt                                                                                                                   <  5:90203/135‑1 (MQ=255)                              aaaaCCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGAc                                                                                                    <  6:79459/149‑1 (MQ=255)                                aaCCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAGCCGGTAGAGGCTGAATTTCt                                                                                                                    <  6:299051/131‑1 (MQ=255)                                aaCCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAGCCGGTAGAGGCTGAATTTCt                                                                                                                    <  6:304487/131‑1 (MQ=255)                                aaCCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAGCCGGTAGAGGCTGAATTTCt                                                                                                                    >  5:304487/1‑131 (MQ=255)                                aaCCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAGCCGGTAGAGGCTGAATTTCt                                                                                                                    >  5:299051/1‑131 (MQ=255)                                 aCCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCtt                                                                                                 <  5:40073/149‑1 (MQ=255)                                      attgatGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAg                                                                                              <  3:60209/147‑1 (MQ=255)                                           tgaAATTGGGCGTGCGAACTTTTTTTCTTAGTTGGGGGAGGTGGCTGATAAATTTGAAAATGTTATTTATATAGAGAGCTTGTTTTAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGTCCTTGAGTGG‑TTAc                                                                                      <  2:94754/149‑1 (MQ=255)                                           tgaAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTAc                                                                                      >  7:3747/1‑149 (MQ=255)                                              aaTTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGa                                                                                   <  2:237273/149‑1 (MQ=255)                                                ttGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTagag                                                                                                                               >  2:136410/1‑104 (MQ=255)                                                ttGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTagag                                                                                                                               <  1:136410/104‑1 (MQ=255)                                                                tttttCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGa                                                                   <  2:220083/147‑1 (MQ=255)                                                                      tAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGt                                                           >  4:309075/1‑149 (MQ=255)                                                                      tAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGt                                                           >  2:265040/1‑149 (MQ=255)                                                                              gggAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGttt                                                   >  5:2469/1‑149 (MQ=255)                                                                                  ggTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTc                                               <  6:2469/149‑1 (MQ=255)                                                                                     ggCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCg                                             >  5:294564/1‑148 (MQ=255)                                                                                      gCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTAc                                                                                      <  7:313564/106‑1 (MQ=255)                                                                                      gCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTAc                                                                                      >  8:313564/1‑106 (MQ=255)                                                                                      gCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGCTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCGaa                                           <  4:89226/149‑1 (MQ=255)                                                                                        tGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCGAAgc                                         >  7:60811/1‑149 (MQ=255)                                                                                              aTTTGAAAATTTTATTTATTTTTAGTGCGTGTTTAAGGTTGTTGTTGTACCGGTAGAGGGTGAAATTGTTTGTGTTTATGAAGACCTTTAGTGGTTTTCCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTGCGAAGCCGCCt                                    <  1:86309/149‑1 (MQ=255)                                                                                               tttGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTTGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTAAAGATTGTCCGTTCAAGTTTTTTCCGAAGCCGCCt                                    >  3:311825/1‑147 (MQ=255)                                                                                               tttGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCGAAGCCGCCTaa                                  <  8:60811/149‑1 (MQ=255)                                                                                               tttGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCGAAGCCGCCTaa                                  <  1:265040/149‑1 (MQ=255)                                                                                                                    gagagCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCGAAGCCGCCTAAGGATTTGCTTGATCTTAGGc              <  8:3747/148‑1 (MQ=255)                                                                                                                             tttAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCGAAGCCGCCTAAGGATTTGCTTGATCTTAGGCTTGGagtaa     <  6:294564/148‑1 (MQ=255)                                                                                                                             tttAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCGAAGCCGCCTAAGGATTTGCTTGATCTTAGGCTTGGagtaa     <  3:309075/148‑1 (MQ=255)                                                                                                                                aaGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCGAAGCCGCCTAAGGATTTGCTTGATCTTAGGCTTGGagtaagta  >  1:91306/1‑148 (MQ=255)                                                                                                                                 aGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACATTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCGAAGCCGCCTAAGGATTTGCTTGATCTTAGGCTTGGagtaagta  >  1:167441/1‑147 (MQ=255)                                                                                                                                              |                                                                                                                                       GATTTGAGGGTTTAAAATGCTGGATTTTCAAAACCTGATTGATGAAATTGGGCGTGCGAACTTTTTTTCTAAGATGGGGGAGGTGGCTGATAAATTTGAAAATGTTATATATATAGAGAGCGTGTTTAAGGTCTTTGTTGAACCGGTAGAGGCTGAATTTCTTGGTGCTTATGAAGACCTTGAGTGG‑TTACCGATCACTCCCACTCAAGATTGTCCGTTCAAGTTTTTTCCGAAGCCGCCTAAGGATTTGCTTGATCTTAGGCTTGGAGTAAGTA  >  NC_002947/3518358‑3518632

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: ‑