Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,191	C→A	100%	A152S (GCA→TCA)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,191	0	C	A	100.0%	84.8 / NA	29	A152S (GCA→TCA)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (13/16);  total (13/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACC  >  USA300TCH1516_ALE/2028057‑2028324                                                                                                                                        |                                                                                                                                      tGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGACATATGCAGCT‑TTCATTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCttt                                                                                                                                 >  1:72548/1‑141 (MQ=255)         cattcaCGCAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGt                                                                                                                         <  1:274444/141‑1 (MQ=255)                                 aaGCAGCTACATGTAAATTAATATTGTAATTCACCGGAACTATA‑ACCTGCACTTTACCTAAAATGTGTCTAAAAACAATGGTATTATTTTCCTTAATATTTGAAGCTCTTGTTCATTCAATATGTAGCTCTCCCATTCCAt                                                                                                 >  2:97029/1‑141 (MQ=255)                                           aTGTAAATTAATATTGTAATTAACCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTg                                                                                       <  1:30252/141‑1 (MQ=255)                                             gTAATTTAGTATTGGAATTAACCGTCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGACGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTa                                                                                     <  2:164952/141‑1 (MQ=255)                                                  ttAATATTGTAATTAACCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCt                                                                                <  1:93821/141‑1 (MQ=255)                                                    aaTATTGTAATTAACCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACCACTTAGGTGCGATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTc                                                                              <  1:226733/141‑1 (MQ=255)                                                    aaTATTGTAATTAACCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTc                                                                              <  1:226182/141‑1 (MQ=255)                                                     atatTGTAATTAACCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTcc                                                                             >  1:265708/1‑141 (MQ=255)                                                       atTGTAATTAACCTGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATTGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCa                                                                           <  1:20991/141‑1 (MQ=255)                                                         ggTAATTAACCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACt                                                                         <  2:177396/140‑1 (MQ=255)                                                             aTTAACCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTtata                                                                     <  1:114899/141‑1 (MQ=255)                                                             aTTAACCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAAAGATAACAGTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTtata                                                                     >  2:127613/1‑141 (MQ=255)                                                                aaCCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATAc                                                                  >  2:7813/1‑141 (MQ=255)                                                                 aCCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACa                                                                 >  1:3447/1‑141 (MQ=255)                                                                   cGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATa                                                               >  2:153315/1‑141 (MQ=255)                                                                      cAATAAA‑ACTTGATCTTTACCTAAAATGTGTCTAACAACAATTGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAACTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAAc                                                            <  2:171403/141‑1 (MQ=255)                                                                                cTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACg                                                   >  1:122002/1‑141 (MQ=255)                                                                                      tttACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTc                                             >  1:201646/1‑141 (MQ=255)                                                                                        tACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCAc                                           >  2:131337/1‑141 (MQ=255)                                                                                         aCCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTGAct                                          >  1:296495/1‑140 (MQ=255)                                                                                              aaaTGTGTCTAACGACAATGGTTTTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCTATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAAcc                                     <  2:191947/141‑1 (MQ=255)                                                                                               aaagtgtCTAACAACAATGGTATTATTTTGCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGGCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACAGGTGGACGTTGCTCCCCAAACCa                                    <  2:287149/138‑1 (MQ=255)                                                                                                           aacaaTGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTtaat                        >  1:88348/1‑141 (MQ=255)                                                                                                               aTGGTATTATTTGCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGACAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATaaaa                    <  2:229867/141‑1 (MQ=255)                                                                                                                      tattTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTg             <  1:269653/141‑1 (MQ=255)                                                                                                                       attTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGa            <  1:220142/141‑1 (MQ=255)                                                                                                                          ttCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGt         >  1:199064/1‑141 (MQ=255)                                                                                                                                 atgtttGAAGTTTGTGTGAATTCAATATGTAGGGCGCCAATTCCATGTTGAATTTGTACATCTTCCCAGTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATTGTGAAGTCATAAcc  <  2:111913/138‑1 (MQ=255)                                                                                                                                        |                                                                                                                                      TGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATA‑ACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACC  >  USA300TCH1516_ALE/2028057‑2028324

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: ‑