Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,528,590	C→T	14.2%	A49V (GCC→GTC)	PP_4017 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,528,590	0	C	T	14.2%	62.2 / 3.1	28	A49V (GCC→GTC)	PP_4017	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (14/10);  new base T (2/2);  total (16/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

CTGATACTCCACTGCAGCTGCTCGGCGGCATCTCGGCCCGCGAATTCATGCGCGACTACTGGCAGAAGAAGCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGACCCTGCTGGTGCAGGCCGT  >  NC_002947/4528458‑4528734                                                                                                                                     |                                                                                                                                                 cTGATACTCCACTGCAGCTGCTCGGCGGCATCTCGGCCCGCGAATTCATGCGCGACTACTGGCAGAAGAAGCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGcc                                                                                                                                                 <  1:122470/134‑1 (MQ=255) cTGATACTCCACTGCAGCTGCTCGGCGGCATCTCGGCCCGCGAATTCATGCGCGACTACTGGCAGAAGAAGCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGcc                                                                                                                                                 >  2:122470/1‑134 (MQ=255)         ccACTGCAGCTGCTCGGCGGCATCTCGGCCCGCGAATTCATGCGCGACTACTGGCAGAAGAAGCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGGCCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAagtc                                                                                                                         <  1:472162/150‑1 (MQ=255)                aGCTGCTCGGCGGCATCTCGGCCCGCGAATTCATGCGCGACTACTGGCAGAAGAAGCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTcgc                                                                                                                  >  1:270787/1‑150 (MQ=255)                             cATCTCGGCCCGCGAATTCATGCGCGACTACTGGCAGAAGAAGCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGa                                                                                                     <  2:540557/150‑1 (MQ=255)                               tctcGGCCCGCGAATTCATGCGCGACTACTGGCAGAAGAAGCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGGGc                                                                                                   >  1:51777/1‑150 (MQ=255)                                   ggCCCGCGAATTCATGCGCGACTACTGGCAGAAGAAGCCGCTGCTGTTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCActg                                                                                               >  2:110719/1‑148 (MQ=255)                                     cccGCGAATTCATGCGCGACTACTGGCAGAAGAAGCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGgcg                                                                                             >  1:505381/1‑150 (MQ=255)                                                              gCAGAAGAAGCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCgg                                                                    >  2:550354/1‑150 (MQ=255)                                                                      agCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGCGCTGCGCCGCGGCCCGTTCa                                                            >  2:77240/1‑150 (MQ=255)                                                                       gCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCaa                                                           <  2:270787/150‑1 (MQ=255)                                                                                       cAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGcc                                           >  1:66357/1‑150 (MQ=255)                                                                                         ggCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGa                                         <  2:505381/150‑1 (MQ=255)                                                                                                   gACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGaa                               >  1:314704/1‑150 (MQ=255)                                                                                                         atcaGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTTGTTGGTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGAc                         <  1:110719/150‑1 (MQ=255)                                                                                                            aGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGAGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTgg                      >  1:582160/1‑150 (MQ=255)                                                                                                             gCCCGATCGACCCCGACGAGCGCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGa                     <  1:116084/150‑1 (MQ=255)                                                                                                               ccGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGAcc                   >  1:364337/1‑150 (MQ=255)                                                                                                               ccGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGAcc                   <  2:314704/150‑1 (MQ=255)                                                                                                                    cGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAAc                                                          >  1:319480/1‑106 (MQ=255)                                                                                                                    cGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAAc                                                          <  2:319480/106‑1 (MQ=255)                                                                                                                       ggccggcgaGCTCGTCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGACCct                 <  2:187064/138‑1 (MQ=255)                                                                                                                       ggccggcgaGCTCGTCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGACCct                 <  2:187065/138‑1 (MQ=255)                                                                                                                       ggccggcgaGCTCGTCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGACCct                 >  1:187065/7‑144 (MQ=255)                                                                                                                       ggccggcgaGCTCGTCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGACCct                 >  1:187064/7‑144 (MQ=255)                                                                                                                       ccccGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAGGACTGGACCCTGCTGGt           >  1:92429/1‑150 (MQ=255)                                                                                                                              gaGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGACCCTGCTGGTGCAGGcc    >  1:503768/1‑150 (MQ=255)                                                                                                                                gCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGACCCTGCTGGTGCAGGCCGt  <  2:364337/150‑1 (MQ=255)                                                                                                                                  tCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGCGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGACCCTGCTGGt           <  2:224792/139‑1 (MQ=255)                                                                                                                                  tCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGACCCTGCTGGt           >  1:224792/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                                 CTGATACTCCACTGCAGCTGCTCGGCGGCATCTCGGCCCGCGAATTCATGCGCGACTACTGGCAGAAGAAGCCGCTGCTGGTACGCCAGGCCTTCCCGGACTTCATCAGCCCGATCGACCCCGACGAGCTCGCCGGCCTGGCCCTGGAAGACGAAGTCGAGTCGCGTATCGTGCTGGAGCACGGCGCACACCCGTGGGAGCTGCGCCGCGGCCCGTTCAACGAAGACACCTTCGCCGAGCTGCCGGAAAAAGACTGGACCCTGCTGGTGCAGGCCGT  >  NC_002947/4528458‑4528734

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑