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	88.9%	19.5 / ‑5.0	20	S161R (AGC→CGC)	PP_3661	membrane protein
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base C (10/6);  total (12/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTG  >  NC_002947/4160309‑4160562                                                                                                                                  |                                                                                                                              cccTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGGGGGGCCGCGcccc                                                                                                                        >  1:11598/1‑136 (MQ=255)    tgctgAGCGGCGTGTGGTGTGGAATTAAAGTGTTCACGCGCCCCCGCTATCCCGCCTTGCTGCCCGCCGC‑CGGCAGCGCCATCGGCGGCGCCGCCGCGGGGGTGGCATTCTAATCGGCGCGGCGCAGCGCCCCCCa                                                                                                                     <  2:953387/136‑1 (MQ=255)       tgATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCGCGGCAGCGCCATCTGCGGCGCCCCCCCCGGGCTGCCATACGAATCGGGGCGGCGCccccccccccccc                                                                                                                   >  1:81944/1‑133 (MQ=255)       tgATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCCGCCCCCCCCCTaa                                                                                                                  >  2:836466/1‑136 (MQ=255)         aTCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGCGCGGCGCCCCCCCAaaaa                                                                                                                >  1:899320/1‑136 (MQ=255)         aTCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGCGCCGCCCCCCCCCCaaaa                                                                                                                >  1:721601/1‑136 (MQ=255)         aTCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCCC‑CCGCAGCGCCCTCATCCGCCCCCCCCCCCTGCTGGCATTCGAATAGGCGCCGCCCCCCCCCCCCCCCaaaa                                                                                                                >  2:913542/1‑136 (MQ=255)            ggCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCCGCGCCCCCCCAaaaaacc                                                                                                             >  2:985177/1‑133 (MQ=255)            ggCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCCGCGCCCCCCCAAAAAgcg                                                                                                             >  2:200887/1‑136 (MQ=255)            ggCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGTCGCCGCGCCCCCCCCaaaaaac                                                                                                             >  1:258994/1‑133 (MQ=255)              ccTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGGGGGGCCCCGCCCCCCCGaaaaaaccc                                                                                                           >  1:638448/1‑131 (MQ=255)              ccTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCACCCCCCCCCCTAAAAACGcc                                                                                                           >  2:926689/1‑136 (MQ=255)                          cATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGGGGCGCCCCGCCCCCCCCAAAACCGCCAAGGCAggccgg                                                                                               >  1:546614/1‑131 (MQ=255)                           attaatgtgtTCACGCGCCCCCGCTATCCCGCCTTGCTGCCCGCCGC‑CGCCCGCGCCATCGGCGGCGCCGCCGCGGTGGTGGCATTCTAATCGGCGCGGCGCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGaa                                                                                              <  2:38817/130‑1 (MQ=255)                                       aaGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGCCGGCGCCCCGCCCCCCCAAAAACCGCCCAGGCAGACGGGAGCGGAggggggg                                                                                  >  2:111607/1‑130 (MQ=255)                                            cGACCGCTATACCGCCTTGCTGCCCGCCGG‑GGGCAGCGCATGCTGGGGCGCGGCCGCGGTGGGGGCATTCTATGCGGCGCTGCGCTGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGt                                                                             <  2:553203/136‑1 (MQ=255)                                                     caCCGCCTGGCTCCCCGCCCC‑GGGCAGCGCCTCCGGCGGCGCCGCGGCCGTGCGGGATTTCTACGCGGCGCGGCGCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCg                                                                    <  2:154933/135‑1 (MQ=255)                                                     aaCCGCCTTGCTGCCCGCCGC‑CGGCAGCGCCATCGGCGGCGCCGCGGCGGTGGTGGAATTCTATTGGGCGCGGCGCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCg                                                                    <  2:752664/135‑1 (MQ=255)                                                                                        gggggcgCCGCCGCCGTGCGGCCACGCGACGCGGCGCGGCCCCCCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggct                                  <  2:789288/133‑1 (MQ=255)                                                                                                                        ggCGCTGCGCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGgctg  <  2:371260/136‑1 (MQ=255)                                                                                                                        ggCGCGCCGCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGgctg  <  2:154421/136‑1 (MQ=255)                                                                                                                                  |                                                                                                                              CCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGC‑CGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTG  >  NC_002947/4160309‑4160562

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: ‑