Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,027,561	G→C	49.8%	T129S (ACC→AGC)	vraS ←	Sensor protein VraS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,027,561	0	G	C	49.8%	‑1.0 / 22.2	22	T129S (ACC→AGC)	vraS	Sensor protein VraS
Reads supporting (aligned to +/- strand):  ref base G (7/4);  new base C (6/5);  total (13/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTT  >  USA300TCH1516_ALE/2027426‑2027680                                                                                                                                        |                                                                                                                        ttGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTaat                                                                                                                    >  2:201586/1‑140 (MQ=255) ttGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAg                                                                                                                    >  2:201491/1‑141 (MQ=255)     tagcagatagcaTCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGGAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTCAGtttt                                                                                                                >  1:61908/1‑141 (MQ=255)         agatagcaTCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGt                                                                                                            >  2:75192/1‑141 (MQ=255)             agcaTCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTa                                                                                                        <  1:45541/141‑1 (MQ=255)                      cTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAAc                                                                                               >  1:44886/1‑141 (MQ=255)                             aaaaaaGTTGCTGACTAACAGAATCGAAAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCa                                                                                        <  2:126419/140‑1 (MQ=255)                                  aGTTGCTGACTAACAGAATCATGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCt                                                                                   <  2:138059/141‑1 (MQ=255)                                  aGTTGCTGACTAACAGAATCATGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTCAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCt                                                                                   <  2:137968/141‑1 (MQ=255)                                            tAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACAACATTAATATTATAATTTTCATTGCTTAAGTTTTCAGTTTTAAGTCGCAACTTATGGAATTCTTGATTTAAAg                                                                         <  1:156213/141‑1 (MQ=255)                                                          aGTTCTCGTGCTAGTCTTTCACGTTCATCTTCAATAATATTTTTAACTTTCACAGCATTAATATTATAATTTTGATTTCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATgg                                                           >  2:82064/1‑141 (MQ=255)                                                             tctcGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTAAAAGTGTATGGtat                                                        >  2:163125/1‑141 (MQ=255)                                                              ctcGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGtata                                                       <  1:153682/141‑1 (MQ=255)                                                                cGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATaaa                                                     >  1:114737/1‑141 (MQ=255)                                                                    ctcgTCTTTGACGTTCATCATCAATAATCTTTTTAACTTTCCCATCATTAATATTATCATTTTCATTGGTTAAGTTTTGAGTTTTAAATCGCAACTTATGCAATTCTTGAGTTAAAGATACAAGTGTATGGTATACAtgtc                                                 >  2:144500/4‑138 (MQ=255)                                                                     tAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTaa                                                <  1:47305/141‑1 (MQ=255)                                                                      aGTTTTTGACTTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAAc                                               <  2:242008/141‑1 (MQ=255)                                                                       gTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACg                                              <  1:185317/141‑1 (MQ=255)                                                                                          aataatCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCtat                           >  1:44781/1‑141 (MQ=255)                                                                                                  ttttAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGAt                   >  1:26711/1‑141 (MQ=255)                                                                                                           tCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGc          >  1:15681/1‑141 (MQ=255)                                                                                                                   ttAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGtt  >  2:147641/1‑141 (MQ=255)                                                                                                                                        |                                                                                                                        TTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTT  >  USA300TCH1516_ALE/2027426‑2027680

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: ‑