Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,299,784	G→A	16.1%	Q134* (CAG→TAG)	PP_1134 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,299,784	0	G	A	16.1%	48.6 / 2.6	25	Q134* (CAG→TAG)	PP_1134	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (13/7);  new base A (2/2);  total (15/10)
Fisher's exact test for biased strand distribution p-value = 6.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

ACTTTGCGGCCGTGGTGTTGCGGGTCCTTGATCTGGCTGTACAGCTTGCCGTCCGAGAAGGTACCGGCGCCGCCTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCACGGGCCGAAACCGACCACGATCGGGCGCTCCTGCAGGCCTGCCGGGGCCTGGCCGACGAACT  >  NC_002947/1299636‑1299924                                                                                                                                                     |                                                                                                                                             aCTTTGCGGCCGTGGTGTTGCGGGTCCTTGATCTGGCTGTACAGCTTGCCGTCCGAGAAGGTACCGGCGCCGCCTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTgg                                                                                                                                             >  2:183728/1‑150 (MQ=255)         gCCGTGGTGTTGCGGGTCCTTGATCTGGCTGTACAGCTTGCCGTCCGAGAAGGTACCGGCGCCGCCTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCCAGCGCAccaa                                                                                                                                     <  1:110995/150‑4 (MQ=255)           cGTGGTGTTGCGGGTCCTTGATCTGGCTGTACAGCTTGCCGTCCGAGAAGGTACCGGCGCCGCCTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCCAGCGCAccaag                                                                                                                                    <  2:453155/149‑5 (MQ=255)           cGTGGTGTTGCGGGTCCTTGATCTGGCTGTACAGCTTGCCGTCCGAGAAGGTACCGGCGCCGCCTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCCAGCGCAccaag                                                                                                                                    >  1:453155/1‑145 (MQ=255)              ggtgTTGCGGGTCCTTGATCTGGCTGTACAGCTTGCCGTCCGAGAAGGTACCGGCGCCGCCTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGc                                                                                                                                <  1:332248/150‑1 (MQ=255)                       ggTCCTTGATCTGGCTGTACAGCTTGCCGTCCGAGAAGGTACCGGCGCCGCCTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGa                                                                                                                       <  1:104522/150‑1 (MQ=255)                                    gCTGTACCGCTTGCCGTCCGAGAAGGTACCGGCGCCGCCGTCACCGAGCTGCACGTGGGACTCGGGGTTGAGCACCCTCTTGCGCCCCAGGCCCCAGGTGTCCTTTGTGCGCTGGAGCACTTCCTTGCCACGTTCGAGGATGACCGGCtt                                                                                                          >  2:46180/1‑150 (MQ=255)                                                 ccGTCCGAGAAGGTACCGGCACCGCCTGCACCTAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTtgt                                                                                             <  2:325890/150‑1 (MQ=255)                                                       gagaAGGTACCGGCGCCGCCTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGCTGATCGGCTTGAAGCCCATTTGTGCCAGc                                                                                       >  2:241079/1‑150 (MQ=255)                                                             gTACCGGCGCCGCCTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAgg                                                                                 >  1:306586/1‑150 (MQ=255)                                                             gTACCGGCGCCGCCTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAgg                                                                                 >  2:408189/1‑150 (MQ=255)                                                                      ccgccTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCGACAGGCCGGCAAAg                                                                        >  2:456092/1‑150 (MQ=255)                                                                       cgccTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGa                                                                       <  2:350454/150‑1 (MQ=255)                                                                              aCCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCa                                                                >  2:95649/1‑150 (MQ=255)                                                                                cGAACTGCACGTTGGACTCGCGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGCGCCAGTACTCATTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCACg                                                              <  1:405514/150‑1 (MQ=255)                                                                                     tGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGGGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCATGAACAGGCCGGCAAAGAGGCCGCACGGGCCg                                                         >  2:5268/1‑150 (MQ=255)                                                                                           ttGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCACGGGCCGAAACCg                                                   >  1:515064/1‑150 (MQ=255)                                                                                             ggACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTGCGAGGATGATCGTCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCACGGGCCGAAACCGAc                                                 <  2:177018/150‑1 (MQ=255)                                                                                                 tCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCACGGGCCGAAACCGACCACg                                             >  2:435246/1‑150 (MQ=255)                                                                                                      gTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCACGGGCCGAAACCGACCACGATCgg                                        <  1:95649/150‑1 (MQ=255)                                                                                                                        ccACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGACAATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCACGGGCCGAAACCGACCCCGATCGGGCGCTCCTGCAGGCCTGc                      >  1:246602/1‑150 (MQ=255)                                                                                                                              gCCCCAGCTGTACTTGGTTTGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATAGGCTTGTTCAGGCGAGGTGCCAGCCCTATGCCGGCAAAGATGAACAACGGGCCGAAATCGATCACGATCGGGCGCTCCTGCAGGCCTGCCGGGGc                <  1:183728/150‑1 (MQ=255)                                                                                                                                        tCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCACGGGCCGAAACCGACCACGATCGGGCGCTCCTGCAGGCCTGCCGGGGCCTGGCcgacg      >  1:176260/1‑150 (MQ=255)                                                                                                                                           ttGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCACGGGCCGAAACCGACCACGATCGGGCGCTCCTGCAGGCCTGCCGGGGCCTGGCCGACGAAc   >  2:12513/1‑150 (MQ=255)                                                                                                                                           gaagTGCGCCAGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCACAAAGGCCGAAACCAAGCACGATCGGGCGCTCCTGCAGGCCTGCCGGGGCCTGGCCGACGAAc   >  1:549543/4‑150 (MQ=255)                                                                                                                                            tGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCACGGGCCGAAACCGACCACGATCGGGCGCTCCTCAAGGCCTTCCGGGGCCTGGCCGACGAACt  >  1:36/1‑150 (MQ=255)                                                                                                                                                     |                                                                                                                                             ACTTTGCGGCCGTGGTGTTGCGGGTCCTTGATCTGGCTGTACAGCTTGCCGTCCGAGAAGGTACCGGCGCCGCCTTCACCGAACTGCACGTTGGACTCGGGGTTGAGCACGCTCTTGCGCCACAGGCCCCAGGTGTCCTTGGTGCGCTGGCGCACTTCCTTGCCACGTTCGAGGATGATCGGCTTGAAGCCCATTTGTGCCAGCAACAGGCCGGCAAAGATGCCGCACGGGCCGAAACCGACCACGATCGGGCGCTCCTGCAGGCCTGCCGGGGCCTGGCCGACGAACT  >  NC_002947/1299636‑1299924

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑