Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,124	G→A	P174L (CCG→CTG)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,124	0	G	A	100.0%	41.2 / NA	16	P174L (CCG→CTG)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (5/11);  total (5/11)

TTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTA  >  USA300TCH1516_ALE/2028004‑2028241                                                                                                                         |                                                                                                                      ttATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTACTATTGTAATTAACCAGCAATATAACCTGCACttt                                                                                                    >  2:126084/1‑140 (MQ=255)     ccGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCt                                                                                                <  1:226430/140‑1 (MQ=255)      cGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTa                                                                                               >  2:88023/1‑140 (MQ=255)                    cttcATTATGAATATTGTTATTTTTAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTaaca                                                                                 <  2:73167/140‑1 (MQ=255)                    cttcAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTaaca                                                                                 <  1:246811/140‑1 (MQ=255)                    cttaAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCAGTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTaaca                                                                                 <  1:181768/140‑1 (MQ=255)                            tGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGt                                                                         <  1:241808/140‑1 (MQ=255)                               atatTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGtatt                                                                      >  2:237720/1‑140 (MQ=255)                                      tATTTTCAATTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATCAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTGAAATGTGTCTAACAACAATGGTATTATTTTcc                                                               <  2:235615/140‑1 (MQ=255)                                                                ttcaCGTAAGTACGTACATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCATTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATAGTTGCAGCTTTTGTTAAGTc                                     <  2:154281/140‑1 (MQ=255)                                                                tgcaCGTAAGTACTTCCAGAGAAAGCAGCTATATGTAAATTAATATTGTAATTAACCAGCAATATAACCTTCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTc                                     <  2:242467/138‑1 (MQ=255)                                                                   aCGTAAGTAATTTTATAAAAAGCAACTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAat                                  <  1:99692/140‑1 (MQ=255)                                                                     gTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAatat                                <  2:29158/140‑1 (MQ=255)                                                                      ttaGTGCTTCGATAAAAAGCAGCTTGATGTACATTAATATTGTATTTTACCAGCAATATATTCTGCACTTTACCTAAAATGTGTCTATCAACATTGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATg                               <  2:52274/138‑1 (MQ=255)                                                                                                 tGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTg    >  2:23773/1‑140 (MQ=255)                                                                                                   tAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTa  >  2:124767/1‑140 (MQ=255)                                                                                                                         |                                                                                                                      TTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTA  >  USA300TCH1516_ALE/2028004‑2028241

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: ‑