Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,981,290	T→C	T38A (ACT→GCT)	USA300HOU_RS09870 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,981,290	0	T	C	100.0%	58.6 / NA	18	T38A (ACT→GCT)	USA300HOU_RS09870	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (3/15);  total (3/15)

TTGTTTGAACGATTTCTAATGGATCACAGCCAAATGTACTGTTTAATACTTCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGG  >  USA300TCH1516_ALE/1981158‑1981425                                                                                                                                     |                                                                                                                                        ttGTCTGAACGATTTCTAATGGATCACAGCCAAATGTACTGTTTAATACTGCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAg                                                                                                                                 <  1:37154/141‑1 (MQ=255)     ttGAACGATTTCTAATGGATCACAGCCAAATGTACTGTTTAATACTTCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATCCTCTCTCTTTTCTGCTCTGTACTAAAGCCTTTTTAGAAAg                                                                                                                             <  1:41720/141‑1 (MQ=255)       gAACGATTTCTAATGGATCACAGCCAAATGTACTGTTTAATACTTCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTc                                                                                                                           >  2:153859/1‑141 (MQ=255)                 taaggtaTCACAGCCAAATGTACTGTTTAATACTTCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTg                                                                                                                 >  2:79210/7‑141 (MQ=255)                      gATCACAGCCAATTGTACTGTTTAATACTTCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCa                                                                                                            <  1:133881/141‑1 (MQ=255)                      gATCACAGCCAAATGTACTGTTTAATACTTCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCa                                                                                                            <  1:76051/141‑1 (MQ=255)                        tCACAGCCAAATGTACTGTTTAATACTTCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCATa                                                                                                          <  2:15544/141‑1 (MQ=255)                                        tGTTTAATACTTCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAAc                                                                                          <  2:122153/141‑1 (MQ=255)                                        tGTTTAATACTTCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAAc                                                                                          <  2:203317/141‑1 (MQ=255)                                         ttttAATAGTTCAGAGTGTCTGGAGAATGCACAAATTGAATTACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGGGCCATATTATCTTGCGTATAAcc                                                                                         <  2:164346/140‑1 (MQ=255)                                               tACTTCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTCTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCctc                                                                                   <  1:115118/141‑1 (MQ=255)                                                             tGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATACCCAGCCTCTATACGAACCAttt                                                                     >  2:2764/1‑141 (MQ=255)                                                                           aTTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGa                                                       <  1:168584/141‑1 (MQ=255)                                                                                     aaGGTGTCCAGTTTGGTAATACTCTCTCTTTTTCGAGTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTg                                             <  2:148587/141‑1 (MQ=255)                                                                                       gTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTa                                           <  1:118909/141‑1 (MQ=255)                                                                                                       aTACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCa                           <  1:25462/141‑1 (MQ=255)                                                                                                       aTACTCTCTCTTTTTCGATTTGTACTAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCa                           <  1:25258/141‑1 (MQ=255)                                                                                                                                tAAAGCCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTgg  <  2:147417/141‑1 (MQ=255)                                                                                                                                     |                                                                                                                                        TTGTTTGAACGATTTCTAATGGATCACAGCCAAATGTACTGTTTAATACTTCAGAGTCTCTGAATAATGCACAAATTGAAATACAAGTTGTCCAGTTTGGTAATACTCTCTCTTTTTCGATTTGTACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGG  >  USA300TCH1516_ALE/1981158‑1981425

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑