Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,516	C→A	30.7%	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	30.7%	87.9 / 46.3	62	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (26/17);  new base A (6/13);  total (32/30)
Fisher's exact test for biased strand distribution p-value = 5.36e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.77e-01

TGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAA  >  USA300TCH1516_ALE/111377‑111650                                                                                                                                            |                                                                                                                                       tGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                        >  1:45077/1‑140 (MQ=255)    ggAAGTTAAAGAATAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                     <  1:677891/140‑1 (MQ=255)    ggAAGTTAAAGAAGAAAATATAAAATAAGAAATCGAAATCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATTTAATATTCTCCAGATGTGCCGAGTTATTCGGCTAAat                                                                                                                                     <  2:252185/140‑1 (MQ=17)    ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                     <  1:684184/140‑1 (MQ=255)    ggAACTTAAAGAAGAAAACATAAAACAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATCTATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                     <  2:388953/140‑1 (MQ=18)     gAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGGTTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAata                                                                                                                                    >  1:300112/1‑140 (MQ=255)     gAAGTTAAAAAAGAAAACATAAAAAAAGAAAGCGAAAACTTTAAGTTTTTTGCGCAATATATCAATTTTAAAGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                    <  2:69977/140‑1 (MQ=18)     gAAATTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAata                                                                                                                                    <  2:473982/140‑1 (MQ=255)      aaGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAatat                                                                                                                                   >  1:565972/1‑140 (MQ=255)         ttAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCaa                                                                                                                                <  2:568457/140‑1 (MQ=255)           aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAtt                                                                                                                              >  1:594929/1‑140 (MQ=255)               aaaaaaaaagaaaaaaagaAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACt                                                                                                                          <  2:423132/137‑1 (MQ=255)                agaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCAAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTa                                                                                                                         >  1:440851/1‑140 (MQ=255)                    aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTCAATATTATTTAACTAatga                                                                                                                     >  1:52710/1‑140 (MQ=255)                     aCATAAAAAAAGAAATCGAAACCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAAGTATAAAGATGGAGCTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                                                    <  2:704831/140‑1 (MQ=17)                      cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCTCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                                   <  1:302442/140‑1 (MQ=255)                       aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAAtgatga                                                                                                                  >  2:232979/1‑140 (MQ=255)                               aGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCCGCTCAATATCAATTAACTAATGATGATTATAATg                                                                                                          >  2:58085/1‑140 (MQ=255)                               aGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATACAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGCAGCTAATAATg                                                                                                          >  2:182950/1‑140 (MQ=21)                                gAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGt                                                                                                         <  2:617425/140‑1 (MQ=255)                                  aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTCATGATGATTATAATGTaa                                                                                                       >  1:317606/1‑140 (MQ=255)                                    tCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaaa                                                                                                     >  1:683134/1‑140 (MQ=255)                                     cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAATATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCGAAATATCAATTAACTAATGAGGATTATAATGTAAAAc                                                                                                    >  2:118225/1‑140 (MQ=18)                                        aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                 <  2:587385/140‑1 (MQ=255)                                            tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATTGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGATCAATATCAATTAACTAATGATGCTTATAATTTAAAACAATTACg                                                                                             <  1:165200/140‑1 (MQ=255)                                            tttAAGTTTTTTGCACAATATAGAAATTTTAAAGATTTAATGGTTTAAAAAGAAAGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                             <  2:681409/140‑1 (MQ=18)                                             ttAAGTTTTGTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCTAAGGTTTCCTAGTTATTCCGCTCAATAGCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                            <  2:427589/140‑1 (MQ=18)                                                 gTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaaa                                                                                        >  1:598950/1‑140 (MQ=255)                                                  ttttttGCGCAATATAGCAATTTTAAAGATATAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAg                                                                                       <  2:585392/140‑1 (MQ=255)                                                          gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGata                                                                               >  2:662650/1‑138 (MQ=255)                                                          gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACa                                                                               <  2:139645/140‑1 (MQ=255)                                                              tataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAcc                                                                           <  1:196213/140‑1 (MQ=14)                                                               atatCAATTGTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                          <  1:217532/140‑2 (MQ=11)                                                               ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                          <  1:51180/140‑2 (MQ=11)                                                               ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                          <  2:617668/140‑2 (MQ=14)                                                                  gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacg                                                                       >  1:605406/1‑139 (MQ=11)                                                                   cAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATATAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                      >  2:279406/1‑140 (MQ=255)                                                                   cAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCAGAGTTATTAAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAAGAAAAAGATATGAAATacaaacaa                                                                      >  2:230072/1‑140 (MQ=18)                                                                       tttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaa                                                                  <  1:232979/140‑1 (MQ=255)                                                                             gATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGcc                                                            <  1:454233/140‑1 (MQ=255)                                                                                       aTTATAAAGATGGAGATATATCATAGAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttg                                                  <  2:135832/140‑1 (MQ=255)                                                                                          ataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGttgttg                                               >  1:646087/1‑140 (MQ=255)                                                                                           taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGa                                              <  1:540590/140‑1 (MQ=255)                                                                                              aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAg                                           >  1:251440/1‑140 (MQ=255)                                                                                               gATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                                          >  2:357941/1‑140 (MQ=255)                                                                                                 tGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTGAGCTCAATATCAATTAACTAATGATGATTATAATGTACAACAATGACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGATGTTGTTGCAAggaa                                        >  2:515793/1‑138 (MQ=14)                                                                                                  ggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTAc                                       <  1:540410/140‑1 (MQ=255)                                                                                                    agaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAg                                     >  1:201782/1‑140 (MQ=255)                                                                                                      atatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAggg                                   <  2:580106/140‑1 (MQ=255)                                                                                                        atatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAGTGGTGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGaa                                 >  2:650454/1‑140 (MQ=255)                                                                                                        atatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCACCGAAACTGTTGTTGAAAGGTACAGCGaa                                 >  2:642189/1‑140 (MQ=255)                                                                                                                  aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGt                       <  2:527428/140‑1 (MQ=255)                                                                                                                     cAGAGGTGCCGAGTTATTCAGCTCGATAACAAGTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                    <  2:278378/140‑1 (MQ=255)                                                                                                                     cAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                    >  2:230873/1‑140 (MQ=255)                                                                                                                       gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc                  >  1:421169/1‑140 (MQ=255)                                                                                                                        agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                 >  1:405739/1‑140 (MQ=255)                                                                                                                          gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGGACAGGGAATTAAAAAGGTTCATCAGt               >  1:598209/1‑140 (MQ=255)                                                                                                                            gCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCAGTTGTTGAACGGTACAGGGAAATTAAAAGGTTCATCAGTTg             >  2:691709/1‑140 (MQ=255)                                                                                                                            gCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACAAACAAATAAAACGCCGAAGCTGTTGTTGAAAACGACCGGGAATATAAAAGGTTCATCAGtag             >  2:309636/1‑138 (MQ=17)                                                                                                                                 gTTATTCAGCTCAAGATCAATTAACTAATGATGATTATAATGTAAAACAAGTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat        <  2:300112/140‑1 (MQ=255)                                                                                                                                   tATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaa      >  2:386057/1‑140 (MQ=255)                                                                                                                                   tATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACACGGAAGCTAAAAGGTTCATCAGTTGGATATaa      >  2:643412/1‑140 (MQ=255)                                                                                                                                       cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaa  >  1:490208/1‑140 (MQ=255)                                                                                                                                            |                                                                                                                                       TGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAA  >  USA300TCH1516_ALE/111377‑111650

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: ‑