Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	494,590	A→G	9.3%	I138T (ATT→ACT)	USA300HOU_RS02360 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	494,590	0	A	G	9.3%	125.1 / 5.4	43	I138T (ATT→ACT)	USA300HOU_RS02360	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (21/18);  new base G (2/2);  total (23/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.37e-01

GTTCGCAGATGTCGCTAAAATTTCTCTACCAACACGCATGCCAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGAAGTAGACCGATAAATAAATGAGTGT  >  USA300TCH1516_ALE/494451‑494729                                                                                                                                            |                                                                                                                                            gtTCGCAGATGTCGCTAAAATTTCTCTACCAACACGCATGCCAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAAt                                                                                                                                            >  1:66542/1‑141 (MQ=255)              gCTAAAATTTCTCTACCAACACGCATGCCAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGaata                                                                                                                               >  2:110577/1‑141 (MQ=255)               cTAAAATTTCTCTACCAACACGCATGCCAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACTGCAAGaataa                                                                                                                              >  1:62460/1‑141 (MQ=255)                  aaaTTTCTCTACCAACACGCATGCCAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAGTAACAGCAAGAATAATAg                                                                                                                           >  1:11771/1‑141 (MQ=255)                  aaaTTTCTCTACCAACACGCATGCCAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAGTAACAGCAAGAATAATAg                                                                                                                           >  1:226213/1‑141 (MQ=255)                           tACCAACACGCATGCCAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACATCTGCAATAACAGCAAGAATAATAGTGAACACCa                                                                                                                  <  1:240418/141‑1 (MQ=255)                             ccAACACGCATGCCAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATa                                                                                                                >  1:185905/1‑141 (MQ=255)                               aaCACGCATGCCAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATaaa                                                                                                              <  1:63329/141‑1 (MQ=255)                                         ccAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCata                                                                                                    >  2:115529/1‑141 (MQ=255)                                         ccAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCata                                                                                                    <  1:193671/141‑1 (MQ=255)                                         ccAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCata                                                                                                    <  1:222077/141‑1 (MQ=255)                                         ccAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCata                                                                                                    <  1:408715/141‑1 (MQ=255)                                           aGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATc                                                                                                  >  1:367323/1‑141 (MQ=255)                                                    taatTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAat                                                                                         <  2:424879/141‑1 (MQ=255)                                                    taatTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAat                                                                                         <  2:326279/141‑1 (MQ=255)                                                      atTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAatat                                                                                       >  2:294079/1‑141 (MQ=255)                                                       ttCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATAtt                                                                                      <  1:457141/141‑1 (MQ=255)                                                          gTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCAt                                                                                   <  1:42881/141‑1 (MQ=255)                                                          gTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCAt                                                                                   >  1:296244/1‑141 (MQ=255)                                                          gTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCAt                                                                                   <  1:93113/141‑1 (MQ=255)                                                          gTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCAt                                                                                   <  1:99865/141‑1 (MQ=255)                                                             ttGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGa                                                                                <  2:446364/141‑1 (MQ=255)                                                             ttGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCAAATATACATTGa                                                                                <  2:18010/141‑1 (MQ=255)                                                                   aaGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATacac                                                                          <  2:185905/141‑1 (MQ=255)                                                                    aGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCGGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATAcaca                                                                         <  1:456090/141‑1 (MQ=255)                                                                         tGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGt                                                                    >  1:225635/1‑141 (MQ=255)                                                                             ttCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCa                                                                >  2:88811/1‑141 (MQ=255)                                                                                 cTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCtt                                                            >  2:368587/1‑141 (MQ=255)                                                                                   tGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCttgt                                                          <  1:8882/141‑1 (MQ=255)                                                                                   tGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCttgt                                                          >  2:297026/1‑141 (MQ=255)                                                                                           ttCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGt                                                  >  2:82646/1‑141 (MQ=255)                                                                                                          aCTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAg                                   >  2:288845/1‑141 (MQ=255)                                                                                                          aCTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAg                                   >  2:331663/1‑141 (MQ=255)                                                                                                                  tAATTGTTAAATCTATCACAGCTGCAGTAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGa                           <  2:226213/141‑1 (MQ=255)                                                                                                                  tAATTGTTAAATCTATCACAGCTGCAGTAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGa                           <  2:11771/141‑1 (MQ=255)                                                                                                                     ttGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGAAGt                        >  2:247882/1‑141 (MQ=255)                                                                                                                           aaTCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGAAGTAGACCg                  >  2:215115/1‑141 (MQ=255)                                                                                                                              cTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGAAGTAGACCGata               >  2:385004/1‑141 (MQ=255)                                                                                                                              cTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGAAGTAGACCGata               <  1:181632/141‑1 (MQ=255)                                                                                                                              cTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAAATGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGAAGTAGACCGata               >  1:401716/1‑141 (MQ=255)                                                                                                                                 tCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGAAGTAGACCGataaat            <  2:296244/141‑1 (MQ=255)                                                                                                                                   acaGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGAAGTAGACCGataaataa          >  1:162481/1‑141 (MQ=255)                                                                                                                                    caGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGAAGTAGACCGAtaaataaa         >  1:172824/1‑141 (MQ=255)                                                                                                                                           aaTAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGAAGTAGACCGATAAATAAATGAgtgt  >  1:248219/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                            GTTCGCAGATGTCGCTAAAATTTCTCTACCAACACGCATGCCAGATTGGAATAATTCGTATTGCGTAAGCGTTGGATTCACTTGATGCAATTCATAAATGGGTGAACTAATGGTAATTGTTAAATCTATCACAGCTGCAATAACAGCAAGAATAATAGTGAACACCATAAATTGAACCATATCAATGCCAATATTCATTGAATACACATATGTTTCATCTTGTTGTTCGGTTGAAAAGCCTTGTAGATGACCGAAGTAGACCGATAAATAAATGAGTGT  >  USA300TCH1516_ALE/494451‑494729

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑