Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,524,377	A→G	intergenic (+182/‑21)	BW25113_RS07645 → / → BW25113_RS26145	RHS repeat protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,524,377	0	A	G	90.9%	23.9 / ‑3.2	11	intergenic (+182/‑21)	BW25113_RS07645/BW25113_RS26145	RHS repeat protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (3/7);  total (3/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01

AAACACCAAAGAGCGTTGAGATATATCTTTCTGAAAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGATA  >  NZ_CP009273/1524294‑1524461                                                                                    |                                                                                     aaaCACCAAAGAGCGTTGAGATATATCTTTCTGAAAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGGATGGTc                                                                                <  2:179601/90‑1 (MQ=255) aaaCACCAAAGAGCGTTGAGATATATCTTTCTGAAAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGGATGGTc                                                                                <  2:446491/90‑1 (MQ=255)                      tatatCTTTCTGAAAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGGATGGTCATTTTATAAGTATAATGGTta                                                           <  2:210885/90‑1 (MQ=255)                         atCTTTCTGAAAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGGATGGTCATTTTATAAGTATAATGGTtaata                                                        >  2:204077/1‑90 (MQ=255)                               cTGAAAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACa                                                  <  1:373093/90‑1 (MQ=255)                                       aaTATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGGATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCAc                                          <  1:280178/90‑1 (MQ=255)                                                   aaaaTAATTAATGACCAAAAAATTAGTAGAGGGGATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGtt                              <  1:192695/90‑1 (MQ=255)                                                           taatGACCAAAAAATTAGTAGAGGGGATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAg                                   >  1:200315/1‑77 (MQ=255)                                                           taatGACCAAAAAATTAGTAGAGGGGATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAg                                   <  2:200315/77‑1 (MQ=255)                                                                               gagGGGATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGata  <  1:462446/90‑1 (MQ=255)                                                                               gagGGGATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGata  >  2:462446/1‑90 (MQ=255)                                                                                    |                                                                                     AAACACCAAAGAGCGTTGAGATATATCTTTCTGAAAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGATA  >  NZ_CP009273/1524294‑1524461

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑