Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	4,163,459	T→G	L159R (CTG→CGG)	PP_3661 →	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,163,459	0	T	G	90.9%	10.3 / ‑6.4	12	L159R (CTG→CGG)	PP_3661	membrane protein
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base G (6/4);  total (7/5)
Fisher's exact test for biased strand distribution p-value = 4.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTG  >  NC_002947/4163342‑4163562                                                                                                                      |                                                                                                        tgATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGGGGGGCCGCGccccccccaa                                                                                       >  1:21097/1‑132 (MQ=255) tgATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGGGGCGCCGccccccccccca                                                                                       >  1:222707/1‑132 (MQ=255)   aTCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCCCGCCCCCCCCaaaa                                                                                     >  2:41088/1‑136 (MQ=255)   aTCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCCGCGCCCCCCCCCCCCAaaaa                                                                                     >  2:532689/1‑136 (MQ=255)                     aTGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCGCGCCCCCCCAAAAAACGCCCAGGCAGGCGGaa                                                                   >  2:14380/1‑136 (MQ=255)                         aaGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCAATCGAATCGGCGCGGGGGCGCGCCCCCCCAAAAAACGCCAAGGCCCTCGGGAggag                                                               >  2:585549/1‑133 (MQ=255)                                 aaGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGGGGCGCGGGGCCCCCCCCAAAAACACCACAGCAGTCCGAACCGAAGTggagt                                                       >  1:171986/1‑132 (MQ=255)                                               acccGCCTTGCTGCCGGCCGCCGGCAGCGCCATCTGCGGCGCGGCCGCCGGGGTGGATTTCGAATCGGCGCGGCGCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCg                                         <  2:212282/134‑1 (MQ=255)                                                              cgccgccgGCCGCGCCCGCGGCGGCGCCGCCGCCGTGCTGGCATTCCACGCGGCGCGGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCa                          <  1:222842/136‑1 (MQ=255)                                                                                 ggcggcgCCGCCGCGGTGCTGGCATTCGCCGCGGCGCGGCGCCCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggct       <  1:41088/135‑1 (MQ=255)                                                                                 cgcggcgCCGCCGCGGTGCTCGCATTCCACCCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggct       <  1:544525/135‑1 (MQ=255)                                                                                      cgccgcggcGGTGGTGGCATTCGGCGCGGCGCGCCCCCCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGgctggctg  <  1:8232/136‑1 (MQ=255)                                                                                                                      |                                                                                                        TGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTG  >  NC_002947/4163342‑4163562

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑