Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,961,176	G→C	A40G (GCC→GGC)	cheZ ←	protein phosphatase CheZ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,961,176	0	G	C	91.7%	32.0 / ‑2.8	12	A40G (GCC→GGC)	cheZ	protein phosphatase CheZ
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base C (7/4);  total (7/5)
Fisher's exact test for biased strand distribution p-value = 4.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.60e-01

GCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCT  >  NZ_CP009273/1961087‑1961228                                                                                          |                                                     gcgcCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATgg                                                      >  1:474758/1‑90 (MQ=255)                  tGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGt                                     <  1:38865/90‑1 (MQ=255)                          cATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCaa                             <  2:474758/90‑1 (MQ=255)                          cATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCaa                             <  1:443313/90‑1 (MQ=255)                                  caacaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTcgc                     >  1:432747/1‑90 (MQ=255)                                    acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                   <  1:28995/90‑1 (MQ=255)                                    acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                   <  2:65711/90‑1 (MQ=255)                                         gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt              >  1:38081/1‑90 (MQ=255)                                         gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt              >  2:281563/1‑90 (MQ=255)                                              aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg         >  2:174516/1‑90 (MQ=255)                                              aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg         >  2:313536/1‑90 (MQ=255)                                                   tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg    >  1:524601/1‑90 (MQ=255)                                                     gcgcgcATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCt  >  2:287511/1‑90 (MQ=255)                                                                                          |                                                     GCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCT  >  NZ_CP009273/1961087‑1961228

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: ‑