Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,516	C→A	30.4%	Q196K (CAA→AAA)	USA300HOU_RS00520 →	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	111,516	0	C	A	30.4%	57.7 / 28.4	48	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (16/17);  new base A (7/8);  total (23/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111379‑111651                                                                                                                                          |                                                                                                                                        aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTTTTTTTTTTTGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCTGAGGTGCCGAGTTATTCTGCTAAat                                                                                                                                      >  2:376732/1‑141 (MQ=18)  ggAAGTTAAAGAAGAATACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                     >  1:190692/1‑141 (MQ=255)  ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAACCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                     <  1:309460/141‑1 (MQ=255)     aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                  <  2:357487/141‑1 (MQ=255)        tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAtt                                                                                                                               <  1:318219/141‑1 (MQ=255)           agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAACATAGCACCTTTAAAGATTTATTGAATTATAAAGATGAAGATATATCATAACATACCGAGGTGACGATTTATTCGTCTATATATCAATTaca                                                                                                                            >  2:50529/1‑139 (MQ=17)             aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCAAAATATCAATTAACTa                                                                                                                          <  1:189908/141‑1 (MQ=255)               gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTAAGCTAAATATCAATTAACTAat                                                                                                                        >  2:69801/1‑141 (MQ=255)                   aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATAAATTAACTAatgata                                                                                                                    >  2:32151/1‑140 (MQ=255)                       aaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGGTAAttt                                                                                                                >  2:187990/1‑140 (MQ=255)                       aaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATta                                                                                                                >  1:311738/1‑141 (MQ=255)                       aaaaaaaGAAATCGAAAACGTTAAGTTTTTTGCGCAATATAGCAGTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATta                                                                                                                >  1:209545/1‑141 (MQ=255)                          aacaGAAATCGAACACTTTAAGTATCTCGCGCAATATAACAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATaa                                                                                                             <  1:317667/138‑1 (MQ=17)                            aaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATg                                                                                                           >  2:313021/1‑141 (MQ=255)                              aaaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTa                                                                                                         <  1:187548/140‑1 (MQ=255)                              aaaaTCGAAAACTTGAAGTTTTTTGCGAAATATAGTAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTa                                                                                                         <  2:359575/140‑1 (MQ=255)                                   cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                                                    >  2:334282/1‑141 (MQ=255)                                   cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTGAATGAATTATAAAGATGGAGATATATAATATAATCCAGAGGAGCCGAGTTATTCAGCTCAATTTCAATTAACTAATGATGATTATAATGTAAAACa                                                                                                    >  2:210024/1‑141 (MQ=255)                                    gAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                                                                   <  1:367739/141‑1 (MQ=255)                                    gAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                                                                   >  1:147285/1‑141 (MQ=255)                                    gAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                                                                   <  1:72316/141‑1 (MQ=255)                                     aaaaCTTTAAGTTTTTTGCGCAATATAGTAATTTTAAAGATTTAATAAATTATAAATATGGATGAATATCATATATTCTTGTGGTTGCGCTTTATTAAAAGCAATGTCAATTAACTAATGATGATTATAATGTAAAACaag                                                                                                  <  2:125913/141‑2 (MQ=16)                                     aaaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:266367/141‑1 (MQ=255)                                     aaaaCTTTAAGGTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGTTCGAGGTATATCAGATAATCCTGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  2:126731/141‑1 (MQ=21)                                          tttAAGTTTTTTGCGCAACATACCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  1:364006/141‑2 (MQ=17)                                              aGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaaa                                                                                         >  1:59656/1‑141 (MQ=255)                                                     tGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCCGCCAAAAATCAATGAACGAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGa                                                                                  <  2:367564/141‑1 (MQ=17)                                                       cgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGata                                                                                <  1:179514/141‑3 (MQ=255)                                                           atatAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAcc                                                                            <  1:45234/141‑1 (MQ=255)                                                                    ttttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGCTATGACATACCAACAAATac                                                                   <  2:65252/141‑2 (MQ=255)                                                                    ttttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaa                                                                   <  1:371655/141‑1 (MQ=255)                                                                      ttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaaaa                                                                 >  2:224553/1‑140 (MQ=255)                                                                                 aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACGTTTCAACAAATAAAGCGCCGAAGCtg                                                      <  2:368942/141‑1 (MQ=255)                                                                                 aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                      <  1:299403/141‑1 (MQ=255)                                                                                   gAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgtt                                                    >  1:100468/1‑141 (MQ=255)                                                                                           aaGATTGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAg                                            <  1:297641/141‑1 (MQ=255)                                                                                            aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAGTAACTAATGATGATTATAATGTAAAACAAAAACGTAAAAGATATGAAATACCAACAAATAAAACGCCGAAGCTGTTGATGAAAgg                                           >  2:46101/1‑141 (MQ=17)                                                                                                   gacttatCATATAACCCAGAGGTGCCGAGTTATTCAGGTCAATATCAATCAACCAACGATGATTATAATCTCAAACAATTCCTTAAAAGATATGACATACCAACATGTAAAGCTGCTAAGCTGTTGTTGAACGGTACTggg                                    <  2:143002/137‑1 (MQ=14)                                                                                                     tatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGaa                                  <  2:17349/141‑1 (MQ=255)                                                                                                        atCATATAATGCAGAGCTGCCGAGTTATTCAGCTCACTATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                               <  1:1604/141‑1 (MQ=255)                                                                                                                aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGtt                       >  2:68091/1‑141 (MQ=255)                                                                                                                       ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACAAACAAATAAAGTGGCGAAGCGGTGGTTGAAAGGTACAGGGAGTTTAAAAGGTTCATCAGt                >  1:124217/1‑141 (MQ=17)                                                                                                                         tGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTg              >  1:187062/1‑141 (MQ=255)                                                                                                                         tGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTg              >  1:357032/1‑141 (MQ=255)                                                                                                                           ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGa            >  2:308716/1‑141 (MQ=255)                                                                                                                               gTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGAtata        >  2:242744/1‑141 (MQ=255)                                                                                                                                 tactCAACTCAAAATCACATAACTAAGAATGATTATAATTTAAAACAATTACGGAAAAGATATGACATACCAACAAATTAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAATAGGATCATTATTTGGATATaaa      <  2:272112/138‑1 (MQ=14)                                                                                                                                     cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTTAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaaa  >  2:158299/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                        AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111379‑111651

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: ‑