Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,804,410	C→G	R236P (CGT→CCT)	waaS ←	lipopolysaccharide rhamnose:KdoIII transferase, lipopolysaccharide core biosynthesis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,804,410	0	C	G	85.7%	16.7 / ‑2.0	7	R236P (CGT→CCT)	waaS	lipopolysaccharide rhamnose:KdoIII transferase, lipopolysaccharide core biosynthesis protein
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base G (3/3);  total (3/4)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.27e-01

TTATCCCAATCATCATGACCTATTATAAAAAAGCGAGATTCACTATAGATTTCTGAACCAAATACATTTATATTATTAGTAATTAATTTTTTATTGAAAAATAGTGCCTCAAGTATACGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGTTCTTCTAATATT  >  NC_000913/3804293‑3804483                                                                                                                      |                                                                          ttATCCCAATCATCATGACCTATTATAAAAAAGCGAGATTCACTATAGATTTCTGAACCAGATACATTTATATTATTAGTAATTAATTTTTTATTGAAAAATAGTGCCTCAAGTATACGAAGAGTCCAGCCAGATTGGt                                                      <  2:1062648/139‑1 (MQ=255)                                                                         ttattaGTAATTAATTTTTTATTGAAAAATAGTGCCTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGttctt          >  1:1619549/1‑111 (MQ=255)                                                                         ttattaGTAATTAATTTTTTATTGAAAAATAGTGCCTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGttctt          <  2:1619549/111‑1 (MQ=255)                                                                                          tttATTGAAAAATAGTGCCTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGTTCTTCTAATAtt  <  1:1631124/102‑1 (MQ=255)                                                                                          tttATTGAAAAATAGTGCCTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGTTCTTCTAATAtt  >  2:1631124/1‑102 (MQ=255)                                                                                                           ccTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTg                                              >  1:232854/1‑41 (MQ=255)                                                                                                           ccTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTg                                              <  2:232854/41‑1 (MQ=255)                                                                                                                      |                                                                          TTATCCCAATCATCATGACCTATTATAAAAAAGCGAGATTCACTATAGATTTCTGAACCAAATACATTTATATTATTAGTAATTAATTTTTTATTGAAAAATAGTGCCTCAAGTATACGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGTTCTTCTAATATT  >  NC_000913/3804293‑3804483

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑