Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,434,377	A→G	F222S (TTC→TCC)	nifJ ←	pyruvate:ferredoxin (flavodoxin) oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,434,377	0	A	G	88.9%	18.1 / ‑2.7	9	F222S (TTC→TCC)	nifJ	pyruvate:ferredoxin (flavodoxin) oxidoreductase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (4/4);  total (4/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.99e-01

GGCAGAGAAATCATTCATCGCCTGTTCAACATGGTCATAGACCGCGTTGTACCATGGGTTGGTGGCTTCGCGAGACTGGAAATAAGTGTCAGGATTGGCGGACGTACCGCGGATCACCGGATGTTCCGGGTTGAGTGCCC  >  NZ_CP009273/1434298‑1434437                                                                                |                                                             ggCAGAGAAATCATTCATCGCCTGTTCAACATGGTCATAGACCGCGTTGTACCATGGGTTGGTGGCTTCGCGAGACTGGAAATAAGTGTc                                                    <  2:107723/90‑1 (MQ=255)               tcatCGCCTGTTCAACATGGTCATAGACCGCGTTGTACCATGGGTTGGTGGCTTCGCGAGACTGGGAATAAGTGTCAGGATTGGCGGACg                                      <  1:296343/90‑1 (MQ=255)                catCGCCTGTTCAACATGGTCATAGACCGCGTTGTACCATGGGTTGGTGGCTTCGCGAGACTGGGAATAAGTGTCAGGATTGGCGGACGt                                     <  1:1700/90‑1 (MQ=255)                                     aTAGACCGCGTTGTACCATGGGTTGGTGGCTTCGCGAGACTGGGAATAAGTGTCAGGATTGGCGGACGTACCGCGGATCACCGGATGTTc                >  2:122584/1‑90 (MQ=255)                                            gcgTTGTACCATGGGTTGGTGGCTTCGCGAGACTGGGAATa                                                          >  1:318240/1‑41 (MQ=255)                                            gcgTTGTACCATGGGTTGGTGGCTTCGCGAGACTGGGAATa                                                          <  2:318240/41‑1 (MQ=255)                                            gcgTTGTACCATGGGTTGGTGGCTTCGCGAGACTGGGAATAAGTGTCAGGATTGGCGGACGTACCGCGGATCACCGGATGTTCCGGGTTg         >  2:140319/1‑90 (MQ=255)                                            gcgTTGTACCATGGGTTGGTGGCTTCGCGAGACTGGGAATAAGTGTCAGGATTGGCGGACGTACCGCGGATCACCGGATGTTCCGGGTTg         >  2:377052/1‑90 (MQ=255)                                                   aCCATGGGTTGGTGGCTTCGCGAGACTGGGAATAAGTGTCAGGATTGGCGGACGTACCGCGGATCACCGGATGTTCCGGGTTGAGTGccc  <  1:204005/90‑1 (MQ=255)                                                                                |                                                             GGCAGAGAAATCATTCATCGCCTGTTCAACATGGTCATAGACCGCGTTGTACCATGGGTTGGTGGCTTCGCGAGACTGGAAATAAGTGTCAGGATTGGCGGACGTACCGCGGATCACCGGATGTTCCGGGTTGAGTGCCC  >  NZ_CP009273/1434298‑1434437

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑