Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,240,617	A→T	19.2%	D44V (GAC→GTC)	PP_4618 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,240,617	0	A	T	19.2%	53.0 / 7.0	26	D44V (GAC→GTC)	PP_4618	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (10/11);  new base T (2/3);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.48e-01

CGTCAAGCCTGCCTGGCCTGCCTGGAACGCGAGCCTGTCGACCTGCTGGAAGCCGCACTGTGGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTCAGCAGGATGAATATCACCCCTTGCGCCCCCATGCGGCGATGATGGA  >  NC_002947/5240496‑5240755                                                                                                                          |                                                                                                                                           cGTCAAGCCTGCCTGGCCTGCCTGGAACGCGAGCCTGTCGACCTGCTGGAAGCCGCACTGTGGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTg                                                                                                                <  2:665588/150‑1 (MQ=255)     aaGCCTGCCTGGCCTGCCTGGAACGCGAGCCTGTCGACCTGCTGGAAGCCGCACTGTGGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGa                                                                                                            <  1:378262/150‑1 (MQ=255)     aaGCCTGCCTGGCCTGCCTGGAACGCGAGCCTGTCGACCTGCTGGAAGCCGCACTGTGGATTGCGGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGa                                                                                                            <  2:767488/150‑1 (MQ=255)      aGCCTGCCTGGCCTGCCTGGAACGCGAGCCTGTCGACCTGCTGGAAGCCGCACTGTGGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACTTGCGGCAGCGCGAGATAAGCGCCAACCTGCCGAt                                                                                                           <  1:386682/150‑1 (MQ=255)      aGCCTGCCTGGCCTGCCTGGAACGCGAGCCTGTCGACCTGCTGGAAGCCGCACTGTGGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGAt                                                                                                           <  2:25779/150‑1 (MQ=255)         ctgcctggcctgcctggAACGCGAGCCTGTCGACCTGCTGGAAGCCGCACTGTGGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCt                                                                                                        >  2:155474/1‑150 (MQ=255)            cctggccggccgcgAACGCGAGCCTGTCGACCTGCTGGAAGTCGCACTGTGGATTGCTGCGGAGCACGACCCTGGTGTCGAGCCCGCTGCCTGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAATCGCCAACCTGCCGATGCTTcc                                                                                                     <  2:15029/150‑1 (MQ=255)                       tggAACGCGAGCCTGTCGACCTGCTGGAAGCCGCACTGTGGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTGCCACTATGCGAAc                                                                                          <  2:469232/150‑1 (MQ=255)                              cgAGCCTGTCGACCTGCTGGAAGCCGCCCTGTGGCTTGGTGGCGTGAACGGCCCTGGTGTCGAGCGCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCCCGAGCTAAGCGCCAACCTGCCGATGCTTCCACTATGCTAACTGGCCCa                                                                                   <  2:372955/150‑1 (MQ=255)                                                 gAAGCCGCACTGTGGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTg                                                                >  1:594261/1‑150 (MQ=255)                                                       gCACTGTGGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATgcg                                                          >  2:364577/1‑150 (MQ=255)                                                           tgtgGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTgg                                                      <  2:594261/150‑1 (MQ=255)                                                            gtgGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGGGCCAGCTGAATGCGCTggg                                                     <  2:88483/150‑1 (MQ=255)                                                                    ctgcCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCCGCGCTGCAGGTCGTGCAgcgca                                                                                                                                 <  1:302884/66‑2 (MQ=25)                                                                    ctgcCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCCGCGCTGCAGGTCGTGCAgcgca                                                                                                                                 >  2:302884/1‑65 (MQ=25)                                                                     tgcCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTcagca                                            >  1:371493/1‑150 (MQ=255)                                                                           gCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAACCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCACAGCCACTGCTGCGCTAGCTGACTGCCCTGGGCTTTCGCCAGGATGa                                      >  2:166457/1‑150 (MQ=255)                                                                             aCGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTCAGCAGGATGAat                                    <  1:155474/150‑1 (MQ=255)                                                                             aCGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTCAGCAGGATGAat                                    <  1:364577/150‑1 (MQ=255)                                                                                  ccTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTCAGCAGGATGAATATCAc                               >  1:53757/1‑150 (MQ=255)                                                                                         tCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTCAGCAGGATGAATATCACCCCTTgc                        >  2:671525/1‑150 (MQ=255)                                                                                                           ttGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTCAGCAGGATGAATATCACCCCTTGCGCCCCCATGCGGCgatga      >  2:404570/1‑150 (MQ=255)                                                                                                             gctgcgctgcACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTGCACTATGCGAACTGGGCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTCAGCAGGATGAATATCACCCCTTGCGCCCCCATGCGGCGatgatg    >  2:249899/1‑150 (MQ=255)                                                                                                             ctcgcgctgcAGGTCGTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTCAGCAGGATGAat                                    >  2:256327/4‑118 (MQ=255)                                                                                                             ctcgcgctgcAGGTCGTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTCAGCAGGATGAat                                    <  1:256327/115‑1 (MQ=255)                                                                                                               tgcgctgcACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTCAGCAGGATGAATATCACCCCTTGCGCCCCCATGCGGCGATGATGGa  >  1:120799/1‑150 (MQ=255)                                                                                                                          |                                                                                                                                           CGTCAAGCCTGCCTGGCCTGCCTGGAACGCGAGCCTGTCGACCTGCTGGAAGCCGCACTGTGGATTGCTGCCGAGCACGACCCTGGTGTCGAGCCCGCTGCCAGCCTTGCTGCGCTGCACGACCTGCAGCGCGAGATAAGCGCCAACCTGCCGATGCTTCCACTATGCGAACTGGCCCAGCCACTGCTGCGCCAGCTGAATGCGCTGGGCTTTCAGCAGGATGAATATCACCCCTTGCGCCCCCATGCGGCGATGATGGA  >  NC_002947/5240496‑5240755

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: ‑