Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	277,467	0	C	T	42.1%	6.8 / 15.9	19	L98F (CTT→TTT)	USA300HOU_RS01215	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (7/4);  new base T (1/7);  total (8/11)
Fisher's exact test for biased strand distribution p-value = 5.87e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TAAAGCGCATGAAACAGCGCAAAATACAGATTTAAAAAACGAAGCAAGAAGTTTATTTGATAATGCAACCAAATCAATCGGTAGACTAGCGGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTTGTGACATATCAGAAGAATGGGGGAAGCCATGGCTCTTTTCTCGAGTATTCATCGCT  >  USA300TCH1516_ALE/277337‑277607                                                                                                                                   |                                                                                                                                             caaaGCGCATGAAACAGCGCAAAATGCAGATTTAAAAACCGAAGCAAGAAGTTTATTTGATAATGCAACCAAATCAATCGGTAGACTAGCCGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGTTTTCTGAAGt                                                                                                                                    <  1:173985/140‑1 (MQ=255) caaaGCGCATGAAACAGCGCAAAATGCAGATTTAAAAACCGAAGCAAGAAGTTTATTTGATAATGCAACCAAATCAATCGGTAGACTAGCCGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGTTTTCTGAAGt                                                                                                                                    <  1:174003/140‑1 (MQ=255) caaaGCGCATGAAACAGCGCAAAATGCAGATTTAAAAACCGAAGCAAGAAGTTTATTTGATAATGCAACCAAATCAATCGGTAGACTAGCCGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGTTTTCTGAAGt                                                                                                                                    <  2:144451/140‑1 (MQ=255)     gcgcATGAAACAGCGCAAAATGCAGATTTAAAAACCGAAGCAAGAAGTTTATTTGATAATGCAACCAAATCAATCGGTAGACTAGCCGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGTTTTCTGAAGTAttt                                                                                                                                >  1:115885/1‑141 (MQ=255)                             gATTTAAAAAACGAAGCAAGAAGTTTATTTGATAATGCAACCAAATCAATCGGTAGACTAGCGGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCa                                                                                                        <  2:395218/141‑1 (MQ=255)                             gATTTAAAAAACGAAGCAAGAAGTTTATTTGATAATGCAACCAAATCAATCGGTAGACTAGCGGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCa                                                                                                        <  1:242143/141‑1 (MQ=255)                                                                 gCAACCAAATCAATCGGTAGACTAGCGGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACg                                                                    >  1:37373/1‑141 (MQ=255)                                                                 gCAACCAAATCAATCGGTAGACTAGCGGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACg                                                                    >  2:39228/1‑141 (MQ=255)                                                                          tcaatcGGTAGACTAGCGGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAAtt                                                           >  1:346582/1‑141 (MQ=255)                                                                              tcGGTAGACTAGCGGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTtgtg                                                       <  1:290786/141‑1 (MQ=255)                                                                                     aCTAGCCGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGGTATGTTTTCTGAAGTATTTAAGCCACATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTTGTGATATATc                                                <  2:263930/141‑1 (MQ=255)                                                                                     aCTAGCCGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGTTTTCTGAAGTATTTAAGCCACATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTTGTGATATATc                                                <  2:267730/141‑1 (MQ=255)                                                                                     aCTAGCCGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGTTTTCTGAAGTATTTAAGCCACATACTAAAAACGAAGCAGATGAAATATTTATAGAAAAAAAAAAAAAAACTACGCCAGCAATTTGTGATATATc                                                <  2:1399/141‑1 (MQ=255)                                                                                           cggCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGTTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTTGTGACATATCagaaga                                          <  2:115885/140‑1 (MQ=255)                                                                                             gCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTTGTGACATATCAGAAGAAt                                        >  1:221040/1‑141 (MQ=255)                                                                                              cAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTTGTGACATATCAGAAGAATg                                       <  2:120569/141‑1 (MQ=255)                                                                                                  gatgaAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTTGTGACATATCAGAAGAATggggg                                   >  1:336350/1‑141 (MQ=255)                                                                                                   atgaAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTTGTGACATATCAGAAGAATGGGGGa                                  >  1:74328/1‑141 (MQ=255)                                                                                                        aGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTTGTGACATATCAGAAGAATGGGGGAAGccc                             >  2:287525/1‑140 (MQ=255)                                                                                                                                   cTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTTGTGACATATCAGAAGAATGGGGGAAGCCATGGCTCTTTTCTCGAGTATTCATCGCt  >  2:352124/1‑141 (MQ=255)                                                                                                                                   |                                                                                                                                             TAAAGCGCATGAAACAGCGCAAAATACAGATTTAAAAAACGAAGCAAGAAGTTTATTTGATAATGCAACCAAATCAATCGGTAGACTAGCGGGCAATGATGAAAGCTTAAATCTTAATTTAAAAGATATGCTTTCTGAAGTATTTAAGCCGCATACTAAAAACGAAGCAGATGAAATATTTATAGCGGGTACTGCTAAAACTACGCCAGCAATTTGTGACATATCAGAAGAATGGGGGAAGCCATGGCTCTTTTCTCGAGTATTCATCGCT  >  USA300TCH1516_ALE/277337‑277607

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑