Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,961,177	C→G	A40P (GCC→CCC)	cheZ ←	protein phosphatase CheZ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,961,177	0	C	G	76.2%	40.8 / 11.4	21	A40P (GCC→CCC)	cheZ	protein phosphatase CheZ
Reads supporting (aligned to +/- strand):  ref base C (3/2);  new base G (9/7);  total (12/9)
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

GCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAA  >  NZ_CP009273/1961117‑1961242                                                             |                                                                  gCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGt                                      <  2:691717/90‑1 (MQ=255)      acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                 <  1:485026/90‑1 (MQ=255)      acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                 <  1:488997/90‑1 (MQ=255)      acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                 <  2:149267/90‑1 (MQ=255)      acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                 <  2:467967/90‑1 (MQ=255)      acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                 >  2:164121/1‑90 (MQ=255)         tAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCgcagc                              >  1:97031/1‑90 (MQ=255)            tACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATa                           <  1:597551/90‑1 (MQ=255)            tACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCTCGCAGCATa                           <  2:228949/90‑1 (MQ=255)                gaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg                       >  2:20599/2‑90 (MQ=255)                aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg                       >  1:106346/1‑90 (MQ=255)                aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg                       >  2:68326/1‑90 (MQ=255)                aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg                       >  2:367493/1‑90 (MQ=255)                aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg                       >  2:664537/1‑90 (MQ=255)                aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTAGCGCAGCATAcgcg                       >  1:83368/1‑90 (MQ=255)                  cGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                 <  1:452332/78‑1 (MQ=255)                  cGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                 >  2:452332/1‑78 (MQ=255)                     tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg                  >  2:353806/1‑90 (MQ=255)                     tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg                  >  2:686771/1‑90 (MQ=255)                     tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg                  >  2:771679/1‑90 (MQ=255)                                     tGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCaa  <  1:622698/90‑1 (MQ=255)                                                             |                                                                  GCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAA  >  NZ_CP009273/1961117‑1961242

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑