Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,969,323	G→A	10.8%	intergenic (+272/‑43)	PP_3498 → / → PP_3499	transposase/transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,969,323	0	G	A	10.8%	95.6 / 3.0	37	intergenic (+272/‑43)	PP_3498/PP_3499	transposase/transposase
Reads supporting (aligned to +/- strand):  ref base G (17/16);  new base A (2/2);  total (19/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01

AACGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAGGTC  >  NC_002947/3969175‑3969410                                                                                                                                                     |                                                                                        aaCGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCcgcg                                                                                         >  8:108211/1‑149 (MQ=255)  aCGTCACACTGCGAGCTCACCAAGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGt                                                                                        <  3:281759/149‑1 (MQ=255)     gCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTAtt                                                                                     >  8:225736/1‑149 (MQ=255)      cacaCTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTAttt                                                                                    <  1:245782/149‑1 (MQ=255)          cTGCGATCTCTCCACTATTTTGGCCAGAATCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGAAACCGTGTTCCTATTGTAATAGTCCGTCGAACTCACCTTCCGAACTCCAGCATTAATGGCGATGGTGTCCGCGTATTTTTaa                                                                                <  4:28877/149‑1 (MQ=21)           tGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAg                                                                               >  3:100403/1‑149 (MQ=255)                    accacGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGAcgcg                                                                       >  5:312748/1‑148 (MQ=255)                    accacGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGa                                                                      <  5:226750/149‑1 (MQ=255)                      cacGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGAt                                                                     >  1:199727/1‑148 (MQ=255)                      cacGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCATATTTTTAAGCGGACGCGAt                                                                     >  2:324535/1‑148 (MQ=255)                      cacGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTACCTATGGTAAGCGTCCGGCGAACTCACCTACCGAACTCCAGCAATAAGGCCGATGGAGTCCGCATAGTTATAAGCGGACGCGaa                                                                     >  2:324533/1‑147 (MQ=21)                       acGATGTTGGCCAGAAGCAAAAAGCTTGCTCGAATAGGCCTGATACTTAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCATATTTTTAAGCGGACGCGATCa                                                                   <  1:324533/149‑1 (MQ=255)                       acGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCATATTTTTAAGCGGACGCGATCa                                                                   <  1:324535/149‑1 (MQ=255)                          aTGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCAccc                                                                <  6:312748/149‑1 (MQ=255)                          aTGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCAccc                                                                <  4:100403/149‑1 (MQ=255)                                  cAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGc                                                         >  2:213247/1‑148 (MQ=255)                                    gAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAg                                                      <  7:108211/149‑1 (MQ=255)                                    gAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAg                                                      <  1:213247/149‑1 (MQ=255)                                          aaaaGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCAGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTc                                                >  1:287458/1‑149 (MQ=255)                                                  ccTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTAttt                                                                                    <  3:287724/105‑1 (MQ=255)                                                  ccTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTAttt                                                                                    >  4:287724/1‑105 (MQ=255)                                                         tAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCTGGATTTCTATGCGCCAACGAAg                                 <  7:225736/149‑1 (MQ=255)                                                            gCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGctc                              >  4:301823/1‑149 (MQ=255)                                                                     aTAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGctc                              >  4:208494/1‑140 (MQ=255)                                                                     aTAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGctc                              <  3:208494/140‑1 (MQ=255)                                                                     aTAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGa                      >  4:209245/1‑148 (MQ=255)                                                                     aTAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGa                      >  7:142391/1‑148 (MQ=255)                                                                       aGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGaaa                    <  1:35224/148‑1 (MQ=255)                                                                       aGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGaaa                    >  2:35224/1‑148 (MQ=255)                                                                         aTGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCAccc                                                                <  1:355618/102‑1 (MQ=255)                                                                         aTGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCAccc                                                                >  2:355618/1‑102 (MQ=255)                                                                         aTGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCg                 >  1:126061/1‑149 (MQ=255)                                                                              aCCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCaa            <  2:287458/149‑1 (MQ=40)                                                                               ccGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCTGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCaaa           <  3:209245/149‑1 (MQ=255)                                                                               ccGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCa             >  4:204091/1‑147 (MQ=40)                                                                                    ttCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTAttt                                                                                    <  4:229256/71‑1 (MQ=255)                                                                                    ttCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTAttt                                                                                    >  3:229256/1‑71 (MQ=255)                                                                                        tATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAGGTc  >  3:92928/1‑149 (MQ=32)                                                                                                                                                     |                                                                                        AACGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCTTCCTCGAATAGGCCTGATACATAGATGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAGGTC  >  NC_002947/3969175‑3969410

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: ‑