Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,848,011	T→C	T76A (ACT→GCT)	ydjE ←	MFS transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,848,011	0	T	C	85.7%	41.5 / 2.8	21	T76A (ACT→GCT)	ydjE	MFS transporter
Reads supporting (aligned to +/- strand):  ref base T (3/0);  new base C (8/10);  total (11/10)
Fisher's exact test for biased strand distribution p-value = 2.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.72e-01

CAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCA  >  NZ_CP009273/1847939‑1848094                                                                         |                                                                                    caATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAAt                                                                    >  1:539794/1‑90 (MQ=255)  aaTACCGACGATGGGAAGCTTTATGCGAAACCCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATa                                                                   >  2:746097/1‑90 (MQ=255)  aaTACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATa                                                                   >  2:496405/1‑90 (MQ=255)   aTACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATaa                                                                  >  2:378795/1‑90 (MQ=255)       cgacgaTGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCaa                                                              <  1:685883/90‑1 (MQ=255)        gacgaTGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCaaa                                                             >  1:446916/1‑90 (MQ=255)               agaagaTTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAAt                                                      <  1:773302/90‑1 (MQ=255)                        aTGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTa                                             >  2:758561/1‑90 (MQ=255)                             aaaCGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTTATGCCGAGGTAAAggc                                        >  1:284144/1‑90 (MQ=255)                             aaaCGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAggc                                        >  2:23083/1‑90 (MQ=255)                                   ccTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCAtt                                  <  1:758651/90‑1 (MQ=255)                                     tGCGCCGCCCAAAGTAGTCACCAATAGACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGa                                <  2:465719/90‑1 (MQ=255)                                     tGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGa                                <  2:721449/90‑1 (MQ=255)                                         ccgccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGaa                            <  1:558224/90‑1 (MQ=255)                                         ccgccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGaa                            <  2:739758/90‑1 (MQ=255)                                           gccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAat                          >  1:804143/1‑90 (MQ=255)                                                   tagtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAc                  <  1:550684/90‑1 (MQ=255)                                                   tagtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAc                  <  1:278434/90‑1 (MQ=255)                                                     gtCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAcca                >  2:365245/1‑90 (MQ=255)                                                                  ccaccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTAcc   <  1:298871/90‑1 (MQ=255)                                                                   caccaGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCa  >  1:418415/1‑90 (MQ=255)                                                                         |                                                                                    CAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCA  >  NZ_CP009273/1847939‑1848094

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑