Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	921,243	T→C	Y220Y (TAT→TAC)	USA300HOU_RS04565 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	921,243	0	T	C	100.0%	72.4 / NA	23	Y220Y (TAT→TAC)	USA300HOU_RS04565	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (17/6);  total (17/6)

GTGAAAGATGGCAGTGTACCTTTAGTCAATCGAATCACAAATGAAATTGCGTTTGTACGTTATCATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATATGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAATATTAGCACAAAAAGCTAAGAAAGTTTACGTCATATTTAACAATAATTCTGGTGGTCATGCAGCAAATAATGCCAAAACATATCAGCG  >  USA300TCH1516_ALE/921106‑921377                                                                                                                                          |                                                                                                                                       gTGAAAGATGGCAGTGTACCTTTAGTCAATCGAATCACAAATGAAATTGCGTTTGTACGTTATCATGGACGTAATCATTACGGTTGGACTAAGCAAGTTATGTCAGCCCAAGAATGGCGCGATATACGCTATCTATACGAt                                                                                                                                     >  2:199254/1‑141 (MQ=255) gTGAAAGATGGCAGTGTACCTTTAGTCAATCGAATCACAAATGAAATTGCGTTTGTACGTTATCATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGAt                                                                                                                                     >  1:172687/1‑141 (MQ=255)        aTGGCAGTGTACCTTTAGTCAATCGAATCACAAATGAAATTGCGTTTGTACGTTATCATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGATATTTATACGATTATAATg                                                                                                                              >  1:157663/1‑141 (MQ=255)               tgtACCTTTAGTCAATCGAATCACAAATGAAATTGCGTTTGTACGTTATCATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGCTCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGa                                                                                                                       >  1:195682/1‑141 (MQ=255)                gtACCTTTAGTCAATCGAATCACAAATGAAATTGCGTTTGTACGTTATCATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGaa                                                                                                                      <  1:110644/141‑1 (MQ=255)                       tAGTCAAGCGAATCACAAATGAAATTGCGTTTGTACGTTATGATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAg                                                                                                               <  2:185385/141‑1 (MQ=255)                        aGTCAATCGAATCACAAATGAAATTGCGTTTGTACGTTATCATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGa                                                                                                              >  2:15617/1‑141 (MQ=255)                           cAATCGAATCACAAATGAAATTGCGTTTATACGTTATCATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATATACGCTATTTATACAATTATAATGAACAAGAATTAATAGACtt                                                                                                           >  2:122127/1‑141 (MQ=255)                             aTCGAATCACAAATGAAATTGCGTTTGTACGTTATCATGGACGTAATCAGTACGGTTGGACTAAGAAAGATATGACAGATCAAGAATGGCGCGATGTACGCAATTTATACGATTATAATGAGCAAGAATTAATAGACTTgc                                                                                                         >  2:32608/1‑140 (MQ=255)                                          tGAAATTGCGTTTGTACGTTATCATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGcaca                                                                                            >  2:6400/1‑141 (MQ=255)                                              aTTGCGTTTGTACGTTATCATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAata                                                                                        >  1:44024/1‑141 (MQ=255)                                                     ttGTACGTTATCATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAATATTAGcac                                                                                 <  1:15617/141‑1 (MQ=255)                                                                     aCGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAATATTAGCACAAAAAGCTAAGAAAGt                                                                 >  2:186477/1‑141 (MQ=255)                                                                                  ggTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGAATATAATGAGCAAGAATTAATAGCCTTGGCACAAAAGGCAAAAATATTAGCACAAAAAGCTAAGAAAGTTTCCGACagcttt                                                    >  2:121693/1‑136 (MQ=255)                                                                                          tAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAATATTAGCACAAAAAGCTAAGAAAGTTTACGTCATATTTAACaataa                                            <  1:197142/141‑1 (MQ=255)                                                                                           aagaaagaTATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACAATTATAATGAGCAAGAATTAATAGACTTAGCACAAAAGGCACAAATATTAGCACAAAAAGCTAAGAAAGTTTACGTCATATTTAACaataat                                           >  2:82226/1‑141 (MQ=255)                                                                                            agaaagaTATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGAACTAACAATAGCACAAAAAGCTAAGAAAGTTTACGTCATATTTAACAATAAtt                                          >  2:243031/1‑141 (MQ=255)                                                                                             gaaagaTATGTCAGAGCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAATATTAGCACAAAAAGCTAAGAAAGATTACGACATATTTAAAaataaata                                         >  2:263717/1‑138 (MQ=255)                                                                                               aagaTATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAATATTAGCACAAAAAGCTAAGAAAGTTTACGTCATATTTAACAATAATTCtg                                       <  1:136421/141‑1 (MQ=255)                                                                                                 gaTATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAATATTAGCACAAAAAGCTAAGAAAGTTTACGTCATATTTAACAATAATTCtggt                                     >  1:205712/1‑141 (MQ=255)                                                                                                  atatGTCAGATCAAGAATGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAATATTAGCACAAAAAGCTAAGAAAGTTTACGTCATATTTAACAATAATTCtggtg                                    >  2:255650/1‑141 (MQ=255)                                                                                                               aGAAAGGCGCGATGTACGCTATTTATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAATATTAGCACAAAAAGCTAAGAAAGTTTACGTCATATTTAACAATAATTCTGGTGGTCATGCAGCaaa                       <  1:199254/141‑1 (MQ=255)                                                                                                                                    tttATACGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAATATTAGCACAAAAAGCTAAGAAAGTTTACGTCATATTTAACAATAATTCTGGTGGTCATGCAGCAAATAATACCAAAACATATCAGCg  >  2:158446/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                       GTGAAAGATGGCAGTGTACCTTTAGTCAATCGAATCACAAATGAAATTGCGTTTGTACGTTATCATGGACGTAATCATTACGGTTGGACTAAGAAAGATATGTCAGATCAAGAATGGCGCGATGTACGCTATTTATATGATTATAATGAGCAAGAATTAATAGACTTGGCACAAAAGGCACAAATATTAGCACAAAAAGCTAAGAAAGTTTACGTCATATTTAACAATAATTCTGGTGGTCATGCAGCAAATAATGCCAAAACATATCAGCG  >  USA300TCH1516_ALE/921106‑921377

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑