Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,560	T→C	17.8%	R210R (CGT→CGC)	USA300HOU_RS00520 →	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	111,560	0	T	C	17.8%	73.0 / 6.5	33	R210R (CGT→CGC)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (16/11);  new base C (3/3);  total (19/14)
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

AAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTACTG  >  USA300TCH1516_ALE/111423‑111699                                                                                                                                          |                                                                                                                                            aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAACACAATTACGCaaa                                                                                                                                          >  2:40120/1‑141 (MQ=255)  aGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaaa                                                                                                                                         >  1:299398/1‑141 (MQ=255)    ttttttGCGTAATATAGCAATTTTAAAGATTTAATGAATTAGAAAGATGGAGATATATTATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATAACAATTAAATAATGATGATTATAATGTAAAACGATTACGCAAAAGa                                                                                                                                       <  2:21049/141‑1 (MQ=17)     tttttGAGTAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGat                                                                                                                                      <  2:228977/141‑1 (MQ=255)         tGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGa                                                                                                                                  <  1:114034/141‑1 (MQ=255)             cAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAAGCAACAGATATGAtata                                                                                                                              >  2:9826/1‑141 (MQ=14)             aaaaataGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATa                                                                                                                              <  2:307927/137‑1 (MQ=255)                   aGCAATTTTAAAGATTTAATGAATTATAAAGATGGGGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAAAAGCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacg                                                                                                                        <  1:354687/141‑5 (MQ=11)                   aGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAcacaca                                                                                                                        >  2:319071/1‑136 (MQ=255)                    gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTAGGCTACACATAGAAGAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacga                                                                                                                       >  1:290007/1‑139 (MQ=11)                    gCAATTTTAAAGAGTGAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                                                                       <  2:138168/141‑1 (MQ=255)                    gCAATTTTAAAGAATTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                                                                       <  2:38331/141‑1 (MQ=255)                           tAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgc                                                                                                                <  2:254928/141‑1 (MQ=255)                           tAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACATAAAAGATATGACATACAAACAAATAAAgc                                                                                                                >  2:255197/1‑141 (MQ=255)                            aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                                                                               >  2:121284/1‑141 (MQ=255)                                    aaTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCt                                                                                                       <  2:179470/141‑1 (MQ=255)                                     aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                                                                      <  1:328507/141‑1 (MQ=255)                                          ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTgttgtt                                                                                                 >  1:160084/1‑141 (MQ=255)                                             taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaa                                                                                              <  1:111929/141‑1 (MQ=255)                                                 gATAGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGt                                                                                          <  2:126758/141‑1 (MQ=255)                                                      agaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGCTTATAATGTAAAACAATTACGTAAAACATATGACATACCAACAAATAAAGCACCGAAACTGTTGTCTAAAGGTACAga                                                                                     >  2:26258/1‑140 (MQ=14)                                                        atatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAATAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGa                                                                                   >  1:355976/1‑141 (MQ=255)                                                                   aaTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTCAAACAATTACGTAACAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGCGAATTTCAAAggc                                                                        >  2:14678/1‑140 (MQ=255)                                                                   aaTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGt                                                                        <  1:76181/141‑1 (MQ=255)                                                                   aaTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGt                                                                        <  1:208466/141‑1 (MQ=255)                                                                          agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAAGAAATAAAGCGCCGAAGCTGTTGTTGATAGGTACATGGAATTTAAACAGTTCATCAg                                                                 >  1:371575/1‑141 (MQ=17)                                                                          agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAGTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACCAGGAATTCAAAAGGTTAATCAg                                                                 >  2:312570/1‑141 (MQ=17)                                                                                      aTTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaa                                                     >  1:67418/1‑141 (MQ=255)                                                                                       ttCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaa                                                    >  1:234496/1‑141 (MQ=255)                                                                                          aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt                                                 >  2:222833/1‑141 (MQ=255)                                                                                                atatCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAAtt                                           >  1:274909/1‑141 (MQ=255)                                                                                                   tCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTAc                                        >  2:214944/1‑141 (MQ=255)                                                                                                                                         gTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTACTg  >  2:327541/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                            AAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTACTG  >  USA300TCH1516_ALE/111423‑111699

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: ‑