Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,344,389	C→G	10.6%	Q261H (CAG→CAC)	PP_2941 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,344,389	0	C	G	10.6%	141.3 / 8.7	47	Q261H (CAG→CAC)	PP_2941	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (22/20);  new base G (3/2);  total (25/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.80e-01

ATTCTCGAAGGGAAGGTTATGGCTGAACAGTACGTGGAAAGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAGCGCCATCTGCTCGGCTTGTTCGCCCGGCGTCGCGGGTTGC  >  NC_002947/3344243‑3344530                                                                                                                                                   |                                                                                                                                              aTTCTCGAAGGGAAGGTTATGGCTGAACAGTACGTGGAAAGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTGGGGTAGGTCTGATCGGACCCACCGCAACCACACGTAGGCGGACTACGTGCGAATCTGTGCAGCCGCGTCACTGa                                                                                                                                            >  1:606096/1‑150 (MQ=255) aTTCTCGAAGGGAAGGTTATGGCTGAACAGTACGGGGAAAGTCAGAAAAGCGGAGCTTGTGCTTCCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGACGACCACCTGCGAATCTGTGCAGCCGCTTCACTGa                                                                                                                                            >  2:402166/1‑150 (MQ=255) aTTCTCGAAGGGAAGGTTATGGCTGAACAGTAAGTGGAAAGTCAGAAAAGCGGTGCTTGTACTGCCAGGTTAGTTCGCCGCGGTCCGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCGTCACTGa                                                                                                                                            >  1:732097/1‑150 (MQ=255)  ttgtcGAAGGGAAGGTTATGGCTGAACAGTACGTGGAAAGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGaa                                                                                                                                           >  1:1283337/4‑150 (MQ=255)                      gCTGAACAGTACGTGGAAAGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTAtc                                                                                                                                >  2:25686/1‑141 (MQ=255)                      gCTGAACAGTACGTGGAAAGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTAtc                                                                                                                                <  1:25686/141‑1 (MQ=255)                        tGAACAGTACGTGGAAAGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGcc                                                                                                                     >  2:771954/1‑150 (MQ=255)                          aaCAGTACGTGGAAAGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCtt                                                                                                                   <  1:781463/150‑1 (MQ=255)                              gTACGTGGAAAGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTCGGCGAGGTCTGATCGTACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGAtt                                                                                                               <  2:458609/150‑1 (MQ=255)                               tACGTGGAAAGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGctct                                                                                                                                   <  1:1077673/129‑1 (MQ=255)                               tACGTGGAAAGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTCGCCGAGGTCGGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGctct                                                                                                                                   >  2:1077673/1‑129 (MQ=255)                                       aaGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACAtt                                                                                                      <  1:524477/150‑1 (MQ=255)                                                       gCTTGTGCTGCCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTc                                                                                      >  2:388316/1‑150 (MQ=255)                                                           gtgCTGCCAGGTGATTGCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAAGTCGATACCATATGAAGCTGCGCGGCCACTTCACTGAAGCGGATCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTc                                                                                  <  1:1055189/150‑1 (MQ=255)                                                                gcCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATAc                                                                             <  1:388316/150‑1 (MQ=255)                                                                     gTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAg                                                                                                                                          <  1:465362/84‑1 (MQ=255)                                                                     gTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAg                                                                                                                                          >  2:465362/1‑84 (MQ=255)                                                                     gTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTAtca                                                                                                                               <  1:439845/95‑1 (MQ=255)                                                                     gTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTAtca                                                                                                                               >  2:439845/1‑95 (MQ=255)                                                                        aGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGaa                                                                     <  2:1283337/150‑1 (MQ=255)                                                                             gCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGCCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCt                                                                <  2:606096/150‑1 (MQ=255)                                                                                    tCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCggctgg                                                         <  1:771954/150‑1 (MQ=255)                                                                                        aTCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGc                                                                  >  2:253716/1‑137 (MQ=255)                                                                                        aTCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGc                                                                  <  1:253716/137‑1 (MQ=255)                                                                                        aTCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCg                                                     >  2:867261/1‑150 (MQ=255)                                                                                                  ccGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGa                                           >  2:749978/1‑150 (MQ=255)                                                                                                   cGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCAGTGAAGCgg                                                                                                                                       <  1:653478/57‑1 (MQ=255)                                                                                                   cGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCAGTGAAGCgg                                                                                                                                       >  2:653478/1‑57 (MQ=255)                                                                                                   cGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAg                                          >  2:639724/1‑150 (MQ=255)                                                                                                   cGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAg                                          >  2:232824/1‑150 (MQ=255)                                                                                                         cACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAGCGCCAt                                    <  2:1152212/150‑1 (MQ=255)                                                                                                              gCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTc                                                                                  <  1:1001945/99‑1 (MQ=255)                                                                                                              gCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTc                                                                                  >  2:1001945/1‑99 (MQ=255)                                                                                                              gCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCa                                                                           <  2:250940/106‑1 (MQ=255)                                                                                                              gCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCa                                                                           >  1:250940/1‑106 (MQ=255)                                                                                                                     gACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAGCGCCATCTGCTCGGCTTg                        >  2:758970/1‑150 (MQ=255)                                                                                                                         accTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAGCGCCATCTGCTCGGCTTGTTCg                    >  2:1171442/1‑150 (MQ=255)                                                                                                                               gAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAGCGCCATCTGCTCGGCTTGTTCGCCCGGc              <  1:639724/150‑1 (MQ=255)                                                                                                                                        gaGCCGCTTCAGTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAGCGCCa                                     <  2:1071278/117‑1 (MQ=255)                                                                                                                                        gaGCCGCTTCAGTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAGCGCCa                                     >  1:1071278/2‑118 (MQ=255)                                                                                                                                         aGCCGCTTCAGTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAGCGCCATCTGCTCGGCTTGTTCGCCCGGCGTCGCGGGtt    >  1:1000773/1‑150 (MQ=255)                                                                                                                                          gCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTgg                                                                                                    >  2:1061588/1‑53 (MQ=255)                                                                                                                                          gCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTgg                                                                                                    <  1:1061588/53‑1 (MQ=255)                                                                                                                                          gCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAGCGCCATCTGCTCGGCTTGTTCGCCCGGCGTCGCGGGTTg   >  2:351758/1‑150 (MQ=255)                                                                                                                                           ccGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAGCGCCATCTGCTCGGCTTGTTCGCCCGGCGTCGCGGGTTGc  <  2:732097/150‑1 (MQ=255)                                                                                                                                                tCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCt                                                                                            >  2:201247/1‑55 (MQ=255)                                                                                                                                                tCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCt                                                                                            <  1:201247/55‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                              ATTCTCGAAGGGAAGGTTATGGCTGAACAGTACGTGGAAAGTCAGAAAAGCGGAGCTTGTGCTGCCAGGTGAGTTCGCCGAGGTCTGATCGGACCCACCGCAACCACGGGCAGGTCGACCACCTGCGAATCTGTGCAGCCGCTTCACTGAAGCGGCTCTATCAGCTCAGCGCCTTGATTGCGAACATTGGCAATGGCTGTGCTCACTCGATACCACTCGAAGGCCTCGGCTGGCTCGCCCAGGTTGAGCGCCATCTGCTCGGCTTGTTCGCCCGGCGTCGCGGGTTGC  >  NC_002947/3344243‑3344530

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑