Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,361,729	G→A	P193S (CCA→TCA)	secY ←	Protein translocase subunit SecY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,361,729	0	G	A	100.0%	76.3 / NA	21	P193S (CCA→TCA)	secY	Protein translocase subunit SecY
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (10/11);  total (10/11)

GTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAACTAGTGCTATTAATAAATAACTCATA  >  USA300TCH1516_ALE/2361603‑2361865                                                                                                                               |                                                                                                                                         gTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAGATTGAATTAGACTGGCTGACAACGTTGATaaaa                                                                                                                            <  1:149498/141‑1 (MQ=255) gTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATaaaa                                                                                                                            >  1:178233/1‑141 (MQ=255)                     gTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGataata                                                                                                        >  2:61919/1‑141 (MQ=255)                       tAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGa                                                                                                      <  2:52215/141‑1 (MQ=255)                       tAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGa                                                                                                      >  2:381/1‑141 (MQ=255)                       tAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGa                                                                                                      >  2:205734/1‑141 (MQ=255)                                 aGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTa                                                                                            >  2:5594/1‑141 (MQ=255)                                      cacTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAac                                                                                       >  1:282426/1‑141 (MQ=255)                                      cacTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAac                                                                                       >  1:149887/1‑141 (MQ=255)                                              gTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACt                                                                               >  1:259950/1‑141 (MQ=255)                                              gTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACt                                                                               >  2:244812/1‑141 (MQ=255)                                                  tAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGt                                                                           >  1:25403/1‑141 (MQ=255)                                                                  gCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGc                                                           <  1:778/141‑1 (MQ=255)                                                                            tATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGa                                                 <  1:102309/141‑1 (MQ=255)                                                                                            gaacgCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGt                                 <  1:5594/141‑1 (MQ=255)                                                                                              acgCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCa                               <  1:282766/141‑1 (MQ=255)                                                                                               cgCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCaa                              <  2:178233/141‑1 (MQ=255)                                                                                                  aGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAAc                           <  2:135806/141‑1 (MQ=255)                                                                                                   gTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAACt                          <  1:77448/141‑1 (MQ=255)                                                                                                    tttGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAACTa                         <  1:61919/141‑1 (MQ=255)                                                                                                                   ttAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAACTAGTGCTATTaataaat          <  1:8635/141‑1 (MQ=255)                                                                                                                           gctgacAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAACTAGTGCTATTAATAAATAACTCATa  >  2:21201/1‑141 (MQ=255)                                                                                                                               |                                                                                                                                         GTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAACTAGTGCTATTAATAAATAACTCATA  >  USA300TCH1516_ALE/2361603‑2361865

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑