Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,380,750	C→T	28.6%	intergenic (+564/‑328)	opuD_1 → / → acnA	Glycine betaine transporter OpuD/Aconitate hydratase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,380,750	0	C	T	28.6%	18.3 / 7.0	14	intergenic (+564/‑328)	opuD_1/acnA	Glycine betaine transporter OpuD/Aconitate hydratase A
Reads supporting (aligned to +/- strand):  ref base C (6/4);  new base T (2/2);  total (8/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.44e-01

CCAACACAGAAGCTGACGAAAAGTCAGCTTACAATAATGTGCAAGTTGGGGATGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCATCAAAAGAATGACATTGAAAAAAATATTAAAGTTTGGTGCCATAATTTTCTTTCTGCTCAATGAAATAATACGTTTAAAAATT  >  USA300TCH1516_ALE/1380619‑1380860                                                                                                                                    |                                                                                                               ccAACACAGAAGCTGACGAAAAGTCAGCTTACAATAATGTGCAAGTTGGGGATGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATc                                                                                                       >  1:118200/1‑141 (MQ=35)     cacaGAAGCTGACGAAAAGTCAGCTTACAATAATGTGCAAGTTGGGGATGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATCAttt                                                                                                   >  1:9258/1‑141 (MQ=39)          aaGCTGACGAAAAGTCAGCTTACAATAATGTGCAAGTTGGGGATGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTc                                                                                              <  2:66030/141‑1 (MQ=38)            gCTGACGAAAAGTCAGCTTACAATAATGTGCAAGTTGGGGATGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTccc                                                                                            <  1:69146/141‑1 (MQ=38)            gCTGACGAAAAGTCAGCTTACAATAATGTGCAAGTTGGGGATGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTccc                                                                                            <  2:73878/141‑1 (MQ=38)                           gCTTACAATAATGTGCAAGTTGGGGATGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCATCAAAAGa                                                                             <  2:50011/141‑1 (MQ=255)                                 aataatGTGCAAGTTGGGGATGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGTGAAAATATCATTTCTGTCCCACTCCCATCAAAAGAATGACa                                                                       >  1:2368/1‑141 (MQ=255)                                 aataatGTGCAAGTTGGGGATGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGTGAAAATATCATTTCTGTCCCACTCCCATCAAAAGAATGACa                                                                       >  1:2373/1‑141 (MQ=255)                                                                           ggATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGTGAAAATATCATTTCTGTCCCACTCCCATCAAAAGAATGACATTGAAAAAAATATTAAAGTTTGGTGCCATAATTTTCTTTCTg                             <  2:2368/141‑1 (MQ=255)                                                                           ggATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGTGAAAATATCATTTCTGTCCCACTCCCATCAAAAGAAAGACAATAAAAAAAATATTAAAGTTTGGTGCCATAATTTTCTTTCTg                             <  2:2373/141‑1 (MQ=255)                                                                            gATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCATCAAAAGAATGACATTGAAAAAAATATTAAAGTTTGGTGCCATAATTTTCTTTCTGc                            >  1:6970/1‑141 (MQ=255)                                                                                  cAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCATCAAAAGAATGACATTGAAAAAAATATTAAAGTTTGGTGCCATAATTTTCTTTCTGCTCAATg                      >  1:52515/1‑141 (MQ=255)                                                                                                     aaGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCATCAAAAGAATGACATTGAAAAAAATATTAAAGTTTGGTGCCATAATTTTCTTTCTGCTCAATGAAATAATACGTTTAAAaat   >  1:91021/1‑141 (MQ=255)                                                                                                      aGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCATCAAAAGAATGACATTGAAAAAAATATTAAAGTTTGGTGCCATAATTTTCTTTCTGCTCAATGAAATAATACGTTTAAAaatt  >  2:89992/1‑141 (MQ=255)                                                                                                                                    |                                                                                                               CCAACACAGAAGCTGACGAAAAGTCAGCTTACAATAATGTGCAAGTTGGGGATGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCATCAAAAGAATGACATTGAAAAAAATATTAAAGTTTGGTGCCATAATTTTCTTTCTGCTCAATGAAATAATACGTTTAAAAATT  >  USA300TCH1516_ALE/1380619‑1380860

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑