Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	4,160,437	A→C	S161R (AGC→CGC)	PP_3661 →	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,160,437	0	A	C	77.3%	11.3 / ‑1.3	25	S161R (AGC→CGC)	PP_3661	membrane protein
Reads supporting (aligned to +/- strand):  ref base A (2/3);  new base C (12/5);  total (15/10)
Fisher's exact test for biased strand distribution p-value = 3.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCG  >  NC_002947/4160304‑4160557                                                                                                                                       |                                                                                                                         cAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGCGCGGcgccgc                                                                                                                        >  2:759104/1‑136 (MQ=255)      cccTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGCGGCGCACCGcccc                                                                                                                   >  2:803800/1‑136 (MQ=255)       ccTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGCGGCGCCGCGgcccc                                                                                                                  >  2:125688/1‑136 (MQ=255)            tgATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGCGGGGGCGcccccccccaaa                                                                                                             >  1:457521/1‑132 (MQ=255)            tgATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGCGCGGCGCccccccccccccaa                                                                                                             >  2:46810/1‑132 (MQ=255)              aTCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGGGGGGCCGCGcccccccccaaa                                                                                                           >  1:751036/1‑130 (MQ=255)              aTCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGGGGGGCCCCGCCCCCCCCaaaa                                                                                                           >  1:907473/1‑136 (MQ=255)              aTCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGGGGCGGCCCGCCCCCCCCaaaa                                                                                                           >  1:336009/1‑136 (MQ=255)              aTCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGGGGCGCCGCCCCCCCCCCaaaa                                                                                                           >  1:666222/1‑136 (MQ=255)              aTCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGCGCGGCGGCGCGCCCCCCCCaaaa                                                                                                           >  2:699345/1‑136 (MQ=255)              aTCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCACGACCGCGATACCACCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGCGCCGCCGCCCCCCCCCCaaaa                                                                                                           >  1:4942/1‑136 (MQ=255)                           ggggCATTAATGTGTTCATGCGCGACCGCGATACCGCCTTGCTGCCCGCCGCCGGCAGCGCCTTCTGCGGCGCCGCCGCCGTGTTGGCATTCT‑AATCGGGGCTGGGCTGCGCCCCCCATAAAAGCGCCATGGCAGt                                                                                              <  2:710786/134‑1 (MQ=255)                                    aaGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGGGGGGGCGCGCCCCCCCAAAACACGCCAGAGGAGTCgggggcgg                                                                                     >  1:535753/1‑130 (MQ=255)                                    aaGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGCGGCGGCGCGCCCGCCCGCAAAGCGCCCAGGCAGTGGGGAGCgg                                                                                     >  2:382654/1‑135 (MQ=255)                                    aaGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGCGCAGCGCCGCGCCCCCCCAAAAAACGCCAAGGCAGCCGGGAGccg                                                                                     >  2:961469/1‑134 (MQ=255)                                       ggtTCTAGCTCGCCGGCTCTCCCCCTTTGCTGCCCGCCGCGGGCTCCGCCTGGGGCGGGGCCGCGGGCGGGGT‑GCATTAGTAAGGGGCGGGGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGt                                                                                  <  2:526548/135‑1 (MQ=255)                                          tCACGCTCGCCCGCTATACCGCGTTGCGGCCCGCCGCCGGCAGCGCCATCTGGGGGGCCGCGGCGGGGCTGTCTTTCT‑ACTCGGCGGGGGGCTGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCt                                                                               <  2:751036/136‑1 (MQ=255)                                            aaGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGGGGCGGGGCGGCCCCCCCAAAAACCCCCAGCCCGTCGGGAGCGGAggggggg                                                                             >  1:789283/1‑130 (MQ=255)                                            aaGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCAATCG‑AATCGGCCGAGCGCACCGCCCCCCAAAAAACCGCCAAGGCAGACGGAAGCGAAGTGCTgg                                                                             >  2:1126844/1‑135 (MQ=255)                                                 cGACCGCGAACCCGCCTGGCGGCCCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCGGGCATTCC‑AAGCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGt                                                                        <  2:880211/136‑1 (MQ=255)                                                          tACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGGGCGGCGCCGCGGCCCCCCCAAAACCGCCCTGGCGGTGGGGAGGGGTGTGGTGTTGGGGTCCTTGtgg                                                               >  2:259351/1‑134 (MQ=255)                                                                              ccgGCAGCGCCATCTGCGGCGCCGCCGCCGGGCTGGCACTCG‑AAGCGGCGCGGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGc                                           <  2:980281/136‑1 (MQ=255)                                                                                            ggcggcgCCGCCGCGGTGCTGCCTTTCG‑ACCCGGCGCGGCGCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggct                             <  1:602155/135‑1 (MQ=255)                                                                                              cggcgCCGCCGCGGTGCTGCCACTCC‑CCGCGGCGCCCCCCCCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggctgg                           <  1:46810/136‑1 (MQ=255)                                                                                                 ggccggcgcgGGGCTGGCACTCG‑CCGCGGCGCCGCCCCCCCCCCCCCGTAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGgctggctg                        <  1:53479/135‑1 (MQ=255)                                                                                                    cgccgccgTGCTGGCATTCG‑ACGCGGCGCGGCGCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCAt                     <  1:497890/136‑1 (MQ=255)                                                                                                                        gcgggggcgcggcgcCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCg  <  1:212487/131‑1 (MQ=255)                                                                                                                                       |                                                                                                                         CAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCG‑AATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCG  >  NC_002947/4160304‑4160557

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: ‑