Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,961,177	C→A	A40S (GCC→TCC)	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	A	90.9%	30.3 / ‑2.5	11	A40S (GCC→TCC)	cheZ	protein phosphatase CheZ
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base A (5/5);  total (5/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.20e-01

CGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCA  >  NZ_CP009273/1961092‑1961241                                                                                      |                                                                 cGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGa                                                              >  1:42207/1‑90 (MQ=255)    tCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATcc                                                           <  1:288889/90‑1 (MQ=255)             tGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGt                                                  >  2:6147/1‑90 (MQ=255)                          gCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGt                                     <  2:24080/90‑1 (MQ=255)                               acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                <  1:30860/90‑1 (MQ=255)                                    gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTcgc                                  >  1:192584/1‑83 (MQ=255)                                    gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTcgc                                  <  2:192584/83‑1 (MQ=255)                                                        cGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCCCAGCATACGCGTCAGGCTGCCGATgc       <  1:328701/90‑1 (MQ=255)                                                             aTGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCa  >  1:49005/1‑90 (MQ=255)                                                                          cTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGc                <  1:185384/63‑1 (MQ=255)                                                                          cTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGc                >  2:185384/1‑63 (MQ=255)                                                                                      |                                                                 CGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCA  >  NZ_CP009273/1961092‑1961241

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑