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	96.4%	85.8 / ‑4.0	28	A40G (GCC→GGC)	cheZ	protein phosphatase CheZ
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base C (14/13);  total (15/13)
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

GCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGC  >  NZ_CP009273/1961089‑1961262                                                                                        |                                                                                       gcCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGccc                                                                                      <  1:333803/90‑1 (MQ=255)    cGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGa                                                                                   >  1:390453/1‑90 (MQ=255)              ccTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCa                                                                         <  2:375145/90‑1 (MQ=255)                tGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGt                                                                       <  1:183773/90‑1 (MQ=255)                       tCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCa                                                                >  2:201740/1‑90 (MQ=255)                       tCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCa                                                                >  1:165965/1‑90 (MQ=255)                        cATCTGCACAACATATTACAACCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCaa                                                               <  1:270712/90‑1 (MQ=255)                        cATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCaa                                                               <  2:425250/90‑1 (MQ=255)                                  acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                                     <  2:381724/90‑1 (MQ=255)                                  acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                                     <  2:299196/90‑1 (MQ=255)                                  acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                                     <  2:162022/90‑1 (MQ=255)                                  acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc                                                     >  2:132447/1‑90 (MQ=255)                                       gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt                                                >  1:483736/1‑90 (MQ=255)                                       gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt                                                >  1:249782/1‑90 (MQ=255)                                       gTACAAACGATCACGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt                                                >  1:320662/1‑90 (MQ=255)                                       agtaaaaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt                                                <  2:186830/86‑1 (MQ=255)                                            aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg                                           >  2:153309/1‑90 (MQ=255)                                            aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg                                           >  1:332616/1‑90 (MQ=255)                                               gATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCTGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCgcag                                                   >  2:183083/1‑79 (MQ=255)                                               gATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCTGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCgcag                                                   <  1:183083/79‑1 (MQ=255)                                               gATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCa                                        >  1:345623/1‑90 (MQ=255)                                                 tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg                                      >  2:581909/1‑90 (MQ=255)                                                 tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg                                      >  1:254333/1‑90 (MQ=255)                                                        cATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGa                               >  1:583471/1‑90 (MQ=255)                                                               gATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATgcgcgc                        <  2:92938/90‑1 (MQ=255)                                                                 tGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCaa                      <  2:345623/90‑1 (MQ=255)                                                                  ggCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAAt                     >  1:572692/1‑90 (MQ=255)                                                                                   cAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAAt    <  2:414789/90‑1 (MQ=255)                                                                                     aTGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGc  <  1:449808/90‑1 (MQ=255)                                                                                        |                                                                                       GCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGC  >  NZ_CP009273/1961089‑1961262

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑