Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,516	C→A	33.0%	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	33.0%	79.8 / 39.9	62	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (20/21);  new base A (10/11);  total (30/32)
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

GAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGA  >  USA300TCH1516_ALE/111378‑111655                                                                                                                                            |                                                                                                                                            gAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTaaa                                                                                                                                           >  1:215208/1‑141 (MQ=255)      aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGCTATTCGGCTAAATATCa                                                                                                                                      >  2:335322/1‑141 (MQ=255)          aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTa                                                                                                                                  >  1:222809/1‑141 (MQ=255)          aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTa                                                                                                                                  >  1:13005/1‑141 (MQ=255)            ggaggaaAAGATAAAAAAAGAAATCGAAAACTTTAAGTTTATTGCGCAATATAGCAATTTGAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                                <  1:615246/137‑1 (MQ=17)             gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATACAGAGGTGC‑CGAGTTACTCAGCTAAATATCAATTAACt                                                                                                                               >  2:115445/1‑141 (MQ=255)                gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAat                                                                                                                            <  1:355742/141‑1 (MQ=255)                gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAat                                                                                                                            <  1:303912/141‑1 (MQ=255)                 aaacaaTAAAAAATGAAAT‑GAAAAATTTAAGTTTTTTGCGCAATATAGTAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                                                                          <  2:200340/136‑1 (MQ=17)                  acaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                                                                          <  1:461766/139‑1 (MQ=255)                   aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGCGCTACAGCATACAATCTAGAGGTACTCGTCTTCTT‑AGCTCAATATCAATTAACTAatgat                                                                                                                         >  1:242937/1‑141 (MQ=21)                     cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                                                                       >  2:409899/1‑141 (MQ=255)                     cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAAtgatga                                                                                                                       >  1:198437/1‑141 (MQ=255)                      aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAATgatgat                                                                                                                      >  1:306293/1‑141 (MQ=255)                        aaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATACAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAATGATGATta                                                                                                                    >  2:383768/1‑141 (MQ=255)                         aaaagaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                                   >  2:461408/1‑141 (MQ=255)                         aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                                   <  2:604620/141‑1 (MQ=255)                         aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                                   >  2:148593/1‑141 (MQ=255)                         aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                                   >  2:342707/1‑141 (MQ=255)                            aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                                >  2:27208/1‑141 (MQ=255)                            aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑AGAGTTATTCGGCTAAATATCAATTAACTAATGATAATTATAAt                                                                                                                >  2:432826/1‑141 (MQ=255)                            aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATAACATCATTCAGAGTTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                                <  1:92744/141‑1 (MQ=21)                             aaGATATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATg                                                                                                               <  2:284571/141‑1 (MQ=255)                              aGAAATCGAAAACTTTAAGTTTTGTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGt                                                                                                              <  1:391804/141‑1 (MQ=255)                                 aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCAAGAGTTGC‑TGAACTATTCGTCTACAAATCAATTAACTACTCATAACGATAATGTaca                                                                                                           >  2:3559/1‑139 (MQ=255)                                 aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATAAAGAGGTGC‑TGAGTTATTCGGCTAAATATCAATTAACTAATTATTATTATAATTTaaa                                                                                                           >  2:4905/1‑141 (MQ=17)                                  aTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaaa                                                                                                          >  1:215142/1‑141 (MQ=255)                                   tCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                                                                         >  1:486477/1‑141 (MQ=255)                                   tCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                                                                         >  1:601640/1‑141 (MQ=255)                                          cTTTAAGTTTTTTGAGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTAATCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                                  <  2:262813/141‑1 (MQ=255)                                          atttAAGATTTTTAAAGAATATATTATTTGTAAAAATTTAATGAATTATAAAGATGAAGATATATAATATAATACAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                                  <  2:257117/140‑1 (MQ=11)                                             tAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                               <  1:539947/141‑1 (MQ=255)                                                gTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAg                                                                                            <  1:11843/141‑1 (MQ=255)                                                   ttttGAGCACTATAGCAATTTTAAAGATTTAGTGAGTTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCCATTAACTAATGATGATTATAATGTAAAACAATTACGCCAAAGata                                                                                         >  2:215824/1‑141 (MQ=14)                                                    tttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGatat                                                                                        >  1:521945/1‑141 (MQ=255)                                                        cgcCATATAGCAATTTTAAAGATTTAATGAAATATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGata                                                                                    <  1:63916/141‑3 (MQ=14)                                                         gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACAt                                                                                   <  1:183501/141‑1 (MQ=255)                                                               taGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgac                                                                             <  1:417282/141‑4 (MQ=14)                                                               taGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaac                                                                             <  2:402198/141‑1 (MQ=255)                                                                      tttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaaa                                                                      <  2:115760/141‑1 (MQ=255)                                                                               ttAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACGAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAg                                                             <  2:186683/141‑1 (MQ=255)                                                                                  aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                          >  1:1627/1‑141 (MQ=255)                                                                                   tGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgt                                                         <  1:586474/141‑1 (MQ=255)                                                                                   tGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgt                                                         <  1:235504/141‑1 (MQ=255)                                                                                    gAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgtt                                                        >  2:186624/1‑141 (MQ=255)                                                                                          taAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaa                                                  <  1:514640/141‑1 (MQ=255)                                                                                           aaaGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaaa                                                 <  2:395982/141‑1 (MQ=255)                                                                                             aGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGCATATCCACAACAACAGTTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                                               >  1:634761/1‑141 (MQ=17)                                                                                             aGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCCACAAATAAAGCGCCGAAGCTGTTGTTGAACgg                                               >  1:173256/1‑141 (MQ=255)                                                                                                         atCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                                   <  2:13005/141‑1 (MQ=255)                                                                                                           cATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                                 <  2:290154/141‑1 (MQ=255)                                                                                                               taATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATACAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAgg                             >  2:314200/1‑141 (MQ=255)                                                                                                               taATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAgg                             <  2:477874/141‑1 (MQ=255)                                                                                                                   ccAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                         <  2:242937/141‑1 (MQ=255)                                                                                                                   ccAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGGtca                         >  1:629520/1‑141 (MQ=255)                                                                                                                    gagagGGGC‑CGAGTTAGTCAGGGAGATATGAGTTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAGCAACAAATAGAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGtatgg                        <  2:636130/140‑5 (MQ=14)                                                                                                                         gTGC‑CGGGTTATTCAGCACAAGATCAAATAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtt                   <  2:367804/141‑1 (MQ=255)                                                                                                                                aGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat             <  1:74739/141‑1 (MQ=255)                                                                                                                                aGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat             >  1:363879/1‑141 (MQ=255)                                                                                                                                    aTTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaa         >  1:58104/1‑141 (MQ=255)                                                                                                                                      tCAGCTCAATATCAAATAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGATATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaa       <  2:53844/141‑1 (MQ=255)                                                                                                                                         gCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGGTCATCAGTACGATACAAAAAAAtt    >  1:464453/1‑141 (MQ=255)                                                                                                                                           tCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGa  <  1:126569/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                            GAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGC‑CGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGA  >  USA300TCH1516_ALE/111378‑111655

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑