Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	522,654	C→T	T169I (ACA→ATA)	USA300HOU_RS02475 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	522,654	0	C	T	100.0%	54.9 / NA	17	T169I (ACA→ATA)	USA300HOU_RS02475	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (7/10);  total (7/10)

TGATTTTAGAAAATTAGTAAAAATATTAGCGCAACATTTAAAAACACGTATCGAGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTACATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGCTAAGGATCAAAATTTATCATTAAATCCAACTAAAATTTCTGGTGCATGTGGTCGTTTGATGTGTTGTT  >  USA300TCH1516_ALE/522520‑522761                                                                                                                                       |                                                                                                            tGATTTTAGAAAATTAGTAAAAATATTAGCGCAACATTTAAAAACACGTATCGAGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATAttttt                                                                                                       <  1:148567/141‑1 (MQ=255)      ttAGAAAATTAGTAAAAATATTAGCGCAACATTTAAAAACACGTATCGAGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAgggg                                                                                                  <  1:143319/141‑1 (MQ=255)                   aaaaaTATTAGCGCAACATTTAAAAACACGTATCGAGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGt                                                                                     >  2:231255/1‑141 (MQ=255)                          ttAGCGCAACATTTAAAAACACGTATCGAGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGAtt                                                                              <  2:45266/141‑1 (MQ=255)                          ttAGAGCAACATATAAAAACACGTATCGAGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGAtt                                                                              <  2:24166/141‑1 (MQ=255)                              cgcAACATTTAAAAACACGTATCGAGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGATTAAGa                                                                          >  1:172992/1‑141 (MQ=255)                              cgcAACATTTAAAAACACGTATCGAGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGAAGGTCGTTATGTTGTTCTATATGTTTAGGGGATTTTGAACCAGTATCGATTAAGa                                                                          >  2:253782/1‑141 (MQ=255)                                  aCATTTAAAAACACGTATCGAGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGc                                                                      <  2:250417/141‑1 (MQ=255)                                          aaaCACGTATCGAGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGCTAAGGATc                                                              <  2:148927/141‑1 (MQ=255)                                                      aGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGCTAAGGATCAAAATTTATCAt                                                  <  2:210767/141‑1 (MQ=255)                                                           agaCAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGCTAAGGATCAAAATTTATCATTAAAt                                             >  2:66130/1‑141 (MQ=255)                                                                   tGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGCTAAGGATCAAAATTTATCATTAAATCCAACTaa                                     >  1:33100/1‑141 (MQ=255)                                                                                  aGCCAAATTGCTTGGCGGTATCGGACCTTGGGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGCTAAGGATCAAAATTTATCATTAAATCCAACTAACATTTCTGGTGCAtg                      >  2:199649/1‑141 (MQ=255)                                                                                            cTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGCTAAGGATCAAAATTTATCATTAAATCCAACTAAAATTTCTGGTGCATGTGGTCGTTTg            >  1:222141/1‑141 (MQ=255)                                                                                            cTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGCTAAGGATCAAAATTTATCATTAAATCCAACTAAAATTTCTGGTGCATGTGGTCGTTTg            <  1:203708/141‑1 (MQ=255)                                                                                                  ggTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTATATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGCTAAGGATCAAAATTTATCATTAAATCCAACTAAAATTTCTGGTGCATGTGGTCGTTTGATgtgt      <  2:287436/141‑1 (MQ=255)                                                                                                      tCGGACCTTGTGGTAGGTCGTTATGTTGTCCTATATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGCTAAGGATCAAAATTTATCATTAAATCCAACTAAAATTTCTGGTGCATGTGGTCGTTTGATGTgttgtt  <  1:284524/141‑1 (MQ=255)                                                                                                                                       |                                                                                                            TGATTTTAGAAAATTAGTAAAAATATTAGCGCAACATTTAAAAACACGTATCGAGTTGAGACAAATTGGTGTAAGGGATGAAGCCAAATTGCTTGGCGGTATCGGACCTTGTGGTAGGTCGTTATGTTGTTCTACATTTTTAGGGGATTTTGAACCAGTATCGATTAAGATGGCTAAGGATCAAAATTTATCATTAAATCCAACTAAAATTTCTGGTGCATGTGGTCGTTTGATGTGTTGTT  >  USA300TCH1516_ALE/522520‑522761

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑