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	90.0%	56.2 / 0.6	20	A40G (GCC→GGC)	cheZ	protein phosphatase CheZ
Reads supporting (aligned to +/- strand):  ref base G (0/2);  new base C (12/6);  total (12/8)
Fisher's exact test for biased strand distribution p-value = 1.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-02

CCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATAT  >  NZ_CP009273/1961090‑1961248                                                                                       |                                                                         cccGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCt                                                                       <  2:462848/90‑1 (MQ=255) cccGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCt                                                                       <  1:427672/90‑1 (MQ=255)               tGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGt                                                         <  1:302427/90‑1 (MQ=255)                          cTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACt                                              >  1:73371/1‑90 (MQ=255)                                 acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                       <  1:221508/90‑1 (MQ=255)                                      gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                       >  1:309957/1‑85 (MQ=255)                                      gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                       <  2:309957/85‑1 (MQ=255)                                      gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt                                  >  1:53607/1‑90 (MQ=255)                                      gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt                                  >  2:162985/1‑90 (MQ=255)                                       tACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATa                                 <  2:429439/90‑1 (MQ=255)                                           aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg                             >  1:241760/1‑90 (MQ=255)                                           aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg                             >  2:369307/1‑90 (MQ=255)                                                tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt                                  <  2:279418/80‑1 (MQ=255)                                                tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt                                  >  1:279418/1‑80 (MQ=255)                                                tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg                        >  1:255381/1‑90 (MQ=255)                                                         tCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATg               <  1:279624/90‑1 (MQ=255)                                                                 ggCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAAt       >  2:278467/1‑90 (MQ=255)                                                                 ggCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAAt       >  2:501470/1‑90 (MQ=255)                                                                    ttCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGat    >  2:451589/1‑90 (MQ=255)                                                                      ccgccgCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGatat  >  1:341601/1‑90 (MQ=255)                                                                                       |                                                                         CCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATAT  >  NZ_CP009273/1961090‑1961248

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑