Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,202,240	T→C	63.0%	G63G (GGT→GGC)	PP_2809 →	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,202,240	0	T	C	63.0%	18.5 / 21.7	27	G63G (GGT→GGC)	PP_2809	membrane protein
Reads supporting (aligned to +/- strand):  ref base T (5/5);  new base C (8/9);  total (13/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

TGACAGAGGCTGTTATCGTGGAACTCATAGATTTGTTTGCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGTATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCGCCATCTTTCTGGATGCGTTTTCCCGCGGGGTCGGCGTGCCGGTTATTGCAACGCTCGGGTTGATGGCCGTGACGCATAATTA  >  NC_002947/3202098‑3202383                                                                                                                                               |                                                                                                                                                tGACAGAGGCTGTTATCGTGGAACTCATAGATTTGTTTGCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGTATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGTATTTc                                                                                                                                            <  1:209806/148‑1 (MQ=255)   aCAGAGGCTGTTATCGTGGAACTCATAGATTTGTTTGCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTTTGGTGTTGCATTTATCAGGCGCAAGAAATATTTGTTGGTCGTGGAGTTCTAGATTGTCGGTATTTCCg                                                                                                                                          >  6:275782/1‑148 (MQ=255)      gagGCTGTTATCGTGGAACTCTTAGATTTGTTTGCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGTATTTCCGcaac                                                                                                                                      <  5:275782/149‑1 (MQ=255)                tCGTGGAACTCATAGATTTGTTTGCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGTATTTCCGCAACAAACTTTac                                                                                                                             >  1:189435/1‑148 (MQ=255)                      aaCTGATAGATTTGTATGCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGTATTTCCGCAACAAACTTTACGACGTTc                                                                                                                      <  8:154433/149‑1 (MQ=255)                           aTAGATTTGTTTGCGTTGATCGCATGCGTGCTGCTGTTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCATCg                                                                                                                  <  7:118148/148‑1 (MQ=255)                           aTAGATTTGTTTGCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGCATTTTCGCAACAAACTTTACGACGTTCATCGc                                                                                                                 >  3:38373/1‑149 (MQ=255)                            tAGATTTGTTTGCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGAGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCAt                                                                                                                    <  5:174540/145‑1 (MQ=255)                            tAGATTTGTTTGCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGAGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCAt                                                                                                                    >  6:174540/1‑145 (MQ=255)                                tttgtttgCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCATCGCCACg                                                                                                             <  5:152674/148‑1 (MQ=255)                                  tgtttgCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGCATTTTCGCAACAAACTTTACGACGTTCATCGCCACggg                                                                                                           <  4:38373/148‑1 (MQ=255)                                        cGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGTATTTCCGCAACAAACTTTACGACGTTCATCGCAACGGGGTGGc                                                                                                      >  8:78095/1‑147 (MQ=255)                                        cGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCa                                                                                                     <  7:61617/148‑1 (MQ=255)                                              tCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAAt                                                                                              >  2:163247/1‑149 (MQ=255)                                                     cGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGTATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAATTATaaa                                                                                        <  1:102881/148‑1 (MQ=255)                                                            ctgGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCCCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGTGTGGCAAGCCAATTATAAAGTCGcc                                                                                  <  3:247050/147‑1 (MQ=255)                                                                  atgaGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTGGGGCGTGGAGTTCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCTTCGCCTCTGTGTTGCAAGCCAATTATAAAGTCGCCATCTTTCt                                                                          <  6:253137/149‑1 (MQ=255)                                                                      gTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGTATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCGCCATCTTTCTGGAt                                                                      >  6:29340/1‑149 (MQ=255)                                                                       tGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCTGCATTTCCGCAACAAACTTTTCGACTTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCTCCATCTTTCTGGAt                                                                      <  4:108602/148‑1 (MQ=255)                                                                                                         aaGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCGCCATCTTTCTGGATGCGTTTTCCCGCGGGGTCGGCGTGCCGGTTa                                       <  5:82417/145‑1 (MQ=255)                                                                                                         aaGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCGCCATCTTTCTGGATGCGTTTTCCCGCGGGGTCGGCGTGCCGGTTa                                       >  6:82417/1‑145 (MQ=255)                                                                                                                         gCGTGGAGTTCTTGATTGTCGGTATTTCCGCAACAAACTTTAAGACGTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCGCCATCTTTCTGGATGCGTTTTCCCGCGGGGTCGGCGTGCCGGTTATTGCAACGCTCGGGTTGAt                    <  5:29340/148‑1 (MQ=255)                                                                                                                             ggAGTTCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCGCCATCTTTCTGGATGCGTTTTCCCGCGGGGTCGGCGTGCCGGTTATTGCAACGCTCGGGTTGATGGCCg               >  7:81568/1‑149 (MQ=255)                                                                                                                                 ttCTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCGCCATCTTTCTGGATGCGTTTTCCCGCGGGGTCGGCGTGCCGGTTATTGCAACGCTCGGGTTGATGGCCGTGAc           >  5:34647/1‑149 (MQ=255)                                                                                                                                   cTTGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCGCCATCTTTCTGGATGCGTTTTCCCGCGGGGTCGGCGTGCCGGTTATTGCAACGCTCGGGTTGATGGCCGTGACg          >  5:19049/1‑148 (MQ=255)                                                                                                                                    ttGATTGTCGGCATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCGCCATCTTTCTGGATGCGTTTTCCCGCGGGGTCGGCGTGCCGGTTATTGCAACGCTCGGGTTGATGGCCGTGACGCa        >  4:189795/1‑149 (MQ=255)                                                                                                                                           tCGGTATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCGCCATCTTTCTGGATGCGTTTTCCCGCGGGGTCGGCGTGCCGGTTATTGCAACGCTCGGGTTGATGGCCGTGACGCATAATta  >  3:245949/1‑148 (MQ=255)                                                                                                                                               |                                                                                                                                                TGACAGAGGCTGTTATCGTGGAACTCATAGATTTGTTTGCGTTGATCGCATGCGTGCTGCTGGTGATGAGTGGCTTGGGTTATGGTGTTGCATTTATCAGGCGCAAGAATTATTTGTTGGGCGTGGAGTTCTTGATTGTCGGTATTTCCGCAACAAACTTTACGACGTTCATCGCCACGGGGTGGCAAGCCAATTATAAAGTCGCCATCTTTCTGGATGCGTTTTCCCGCGGGGTCGGCGTGCCGGTTATTGCAACGCTCGGGTTGATGGCCGTGACGCATAATTA  >  NC_002947/3202098‑3202383

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: ‑