Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,935,432	G→A	noncoding (265/1542 nt)	BW25113_RS19520 →	16S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,935,432	0	G	A	91.7%	48.7 / ‑1.9	24	noncoding (265/1542 nt)	BW25113_RS19520	16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (7/15);  total (8/16)
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

ATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCC  >  NZ_CP009273/3935346‑3935479                                                                                       |                                                aTAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCt                                              >  1:136474/1‑90 (MQ=18)       tCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTa                                        >  2:162097/1‑90 (MQ=18)        cGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAg                                       <  2:100693/90‑1 (MQ=25)            aGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcga                                   <  1:175158/90‑1 (MQ=18)             gACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac                                  <  2:741373/90‑1 (MQ=18)             gACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac                                  <  2:646716/90‑1 (MQ=18)             gACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac                                  <  1:314933/90‑1 (MQ=18)             gACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac                                  <  1:767603/90‑1 (MQ=18)              aCCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgacg                                 <  1:991405/90‑1 (MQ=18)              aCCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGATCACCTAGGcgacg                                 <  1:982478/90‑1 (MQ=255)               ccAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgacga                                <  1:500706/90‑1 (MQ=18)                       ggggACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGc                        >  2:978770/1‑90 (MQ=25)                        gggACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCt                       >  2:695219/1‑90 (MQ=33)                        gggACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCt                       <  1:303808/90‑1 (MQ=18)                            ccTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTc                   >  1:297984/1‑90 (MQ=25)                              ttCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGGGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTCTg                 >  2:839665/1‑90 (MQ=255)                                 gggCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTCTgaga              <  1:54012/90‑1 (MQ=18)                                   gCCTCTTGCCATCAGATGTGCACAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAgg            >  1:135917/1‑90 (MQ=255)                                       ctTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac                                  <  1:47321/64‑1 (MQ=255)                                       ctTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac                                  >  2:47321/1‑64 (MQ=255)                                         tGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGAGACGATCCCTAGCTGGTCTGAGAGGATGAcc      <  1:693292/90‑1 (MQ=255)                                             aTCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGcc  <  1:695219/90‑1 (MQ=33)                                             aTCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGcc  <  2:469929/90‑1 (MQ=18)                                             aTCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGcc  <  2:969848/90‑1 (MQ=18)                                                                                       |                                                ATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCC  >  NZ_CP009273/3935346‑3935479

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑