Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,027,672	C→A	G92V (GGC→GTC)	vraS ←	Sensor protein VraS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,027,672	0	C	A	100.0%	67.0 / NA	19	G92V (GGC→GTC)	vraS	Sensor protein VraS
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (15/4);  total (15/4)

TTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCG  >  USA300TCH1516_ALE/2027530‑2027815                                                                                                                                               |                                                                                                                                                tttCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTg                                                                                                                                           <  1:218275/149‑1 (MQ=255)           ttAATATTATAATTTTCAGTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAAAGACAACTGTTTAGCATTc                                                                                                                                 >  1:326714/1‑149 (MQ=255)                                 ttAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTc                                                                                                           >  1:184259/1‑149 (MQ=255)                                  tAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCt                                                                                                          >  1:102674/1‑149 (MQ=255)                                  tAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCt                                                                                                          >  1:179241/1‑149 (MQ=255)                                                                      ttGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTAACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGa                                                                      >  1:176337/1‑149 (MQ=255)                                                                               aGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAAc                                                             <  1:69144/149‑1 (MQ=255)                                                                                                 taAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACaata                                           >  1:217636/1‑149 (MQ=255)                                                                                                        aaCGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgat                                    >  1:93924/1‑149 (MQ=255)                                                                                                             ttCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATAtgatgatga                               >  1:314641/1‑149 (MQ=255)                                                                                                                aCTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGAt                            >  1:236052/1‑149 (MQ=255)                                                                                                                aCTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGAt                            <  1:248472/149‑1 (MQ=255)                                                                                                                    tatatTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTtaa                        >  1:79473/1‑149 (MQ=255)                                                                                                                       atTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaa                     >  1:87977/1‑149 (MQ=255)                                                                                                                        tttCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACAGAACAAACAATAATACACAATATTATGATGATGAGATTtaaaaat                    >  1:101362/1‑149 (MQ=255)                                                                                                                                     aTCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGTTGAGATTTAAAAATAAAAAAACTGGTa       >  1:235072/1‑149 (MQ=255)                                                                                                                                     aTCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTa       >  1:228570/1‑149 (MQ=255)                                                                                                                                     aTCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTa       >  1:209980/1‑149 (MQ=255)                                                                                                                                          tAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATCAAAAAACTGGTATTCCg  <  1:299309/149‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                TTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCG  >  USA300TCH1516_ALE/2027530‑2027815

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