Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	906,978	C→T	6.9%	intergenic (+87/‑342)	USA300HOU_RS04490 → / → USA300HOU_RS04495	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	906,978	0	C	T	6.9%	166.6 / 2.1	58	intergenic (+87/‑342)	USA300HOU_RS04490/USA300HOU_RS04495	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (26/28);  new base T (2/2);  total (28/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

CGAATAGAGTTTAATAAGCATTTAGAACAAGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCTTATTTACTGAGAAAGT  >  USA300TCH1516_ALE/906841‑907115                                                                                                                                           |                                                                                                                                          cGACTAGGGTTTAATAAGCATTTAGAACAAGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCACT‑GCAAg                                                                                                                                        >  2:662701/1‑141 (MQ=255)    aTAGATTTTAATAAACATTGAAAACAAGTTAAAAAAGACCTTCCATAGATAAGCATGATATCAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGCTGATGAGGAATTAGATAAGGCAGT‑GCAAGATg                                                                                                                                     <  2:385592/141‑1 (MQ=21)    aTAGAGTTTAATAAGCATTTAGAACAAGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATg                                                                                                                                     >  1:212160/1‑141 (MQ=255)         gTTTAATAAGCATTTAGAACAAGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCt                                                                                                                                >  2:707957/1‑141 (MQ=255)           ttAATAAGCATTTAGAACAAGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTaa                                                                                                                              >  1:725539/1‑141 (MQ=255)                   cATTTAGAACAAGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAAcc                                                                                                                      >  2:214810/1‑141 (MQ=255)                         gAACAAGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATc                                                                                                                <  2:314884/141‑1 (MQ=255)                          aaCAAGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCa                                                                                                               >  2:686653/1‑141 (MQ=255)                          aaCAAGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCa                                                                                                               <  2:473648/141‑1 (MQ=255)                             aaGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATAc                                                                                                            <  1:657263/141‑1 (MQ=255)                              aGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACt                                                                                                           >  2:674434/1‑141 (MQ=255)                                  aaaaaaGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGa                                                                                                       >  1:27733/1‑141 (MQ=255)                                  aaaaaaGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGa                                                                                                       >  2:212837/1‑141 (MQ=255)                                   aaaaaGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGAt                                                                                                      >  2:439823/1‑141 (MQ=255)                                    aaaaGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGCATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGAtt                                                                                                     <  2:555365/141‑1 (MQ=255)                                    aaaaGAACTTTCATAGATAAGCATGATATTAACGGGAATATCCCTATATTCATTAACATGGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGAtt                                                                                                     <  1:316022/141‑1 (MQ=255)                                           cTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGgatg                                                                                              >  1:764869/1‑141 (MQ=255)                                           cTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGgatg                                                                                              <  1:635225/141‑1 (MQ=255)                                           cTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATAGTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGgatg                                                                                              <  1:340297/141‑1 (MQ=255)                                              tCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGata                                                                                           >  1:10239/1‑141 (MQ=255)                                                         cATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTagag                                                                                >  2:605765/1‑141 (MQ=255)                                                               atTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTGACCATAAGCATACTGTGATTGTGGATGATATACCGTTAGAGGATTga                                                                          <  2:481167/141‑1 (MQ=255)                                                               atTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTga                                                                          <  1:102956/141‑1 (MQ=255)                                                                ttAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTgaa                                                                         <  1:707957/141‑1 (MQ=255)                                                                  aaCGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTgaaga                                                                       >  1:5618/1‑141 (MQ=255)                                                                  aaCGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGAGGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGCTTgaaga                                                                       >  2:482883/1‑141 (MQ=255)                                                                    cGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGTTGTTGGGGAGTTAGATAAGGCAGT‑GTAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGaaa                                                                     >  1:217543/1‑141 (MQ=17)                                                                    cGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GTAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGaaa                                                                     >  1:229515/1‑141 (MQ=255)                                                                     gggAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGaaaa                                                                    <  2:405843/141‑1 (MQ=255)                                                                      ggAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAAt                                                                   <  2:173202/141‑1 (MQ=255)                                                                               cTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAgctatg                                                          <  2:465543/141‑1 (MQ=255)                                                                                 atatTCATTAATATTGGGGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTATCCCTCATGATACTGTGATTGTGGATGATATACCGTGAGAGGATTGAAGAAAATGAAgctatgct                                                        <  1:334038/141‑1 (MQ=18)                                                                                     tCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGCTGGGGGCGTAGCAGGTTG‑AGCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTAttt                                                    <  2:540161/141‑1 (MQ=21)                                                                                     tCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTAttt                                                    <  1:4581/141‑1 (MQ=255)                                                                                       aTTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTtat                                                  <  2:404576/141‑1 (MQ=255)                                                                                       aTTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTtat                                                  <  1:737014/141‑1 (MQ=255)                                                                                       aTTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTtat                                                  <  1:640056/141‑1 (MQ=255)                                                                                          aaTATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATaaa                                               <  1:320375/141‑1 (MQ=255)                                                                                            tatTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAAtt                                             >  1:529050/1‑141 (MQ=255)                                                                                             atTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTa                                            >  1:619394/1‑141 (MQ=255)                                                                                                 gTGAATGGGACGGAGATGATGAGGAATTAGATAAGACAGT‑GCAAGAAGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTAAAAATTAATAc                                        >  1:203495/1‑141 (MQ=255)                                                                                                  tGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACt                                       <  2:98210/141‑1 (MQ=255)                                                                                                       gggACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGCAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTa                                  >  1:397885/1‑141 (MQ=255)                                                                                                          aCGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGtt                               <  1:442520/141‑1 (MQ=255)                                                                                                          aCGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGtt                               >  2:536444/1‑141 (MQ=255)                                                                                                                 tgatgaGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATAcc                        <  2:598340/141‑1 (MQ=255)                                                                                                                        gAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCtt                 <  1:255700/141‑1 (MQ=255)                                                                                                                           ttAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCTTAtt              <  1:674434/141‑1 (MQ=255)                                                                                                                              gATAAGGCAGT‑GTAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCTTATTTAc           <  2:217543/141‑1 (MQ=255)                                                                                                                              gATAAGGCAGT‑GTAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCTTATTTAc           <  2:229515/141‑1 (MQ=255)                                                                                                                              gATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCTTATTTAc           >  2:658481/1‑141 (MQ=255)                                                                                                                              gATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCTTATTTAc           >  1:628883/1‑141 (MQ=255)                                                                                                                               aTAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCTTATTTACt          >  1:576894/1‑141 (MQ=255)                                                                                                                                 gaGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCTTATTTACTga        <  1:416555/140‑1 (MQ=255)                                                                                                                                  aGGCAGT‑GCAAGATGTATCTAACGGTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCtt                 >  1:490268/1‑131 (MQ=255)                                                                                                                                  aGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCtt                 <  2:490268/131‑1 (MQ=255)                                                                                                                                      aGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCTTATTTACTGAGAAAg   >  1:455809/1‑141 (MQ=255)                                                                                                                                       gT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCTTATTTACTGAGAAAGt  >  1:210017/1‑141 (MQ=255)                                                                                                                                           |                                                                                                                                          CGAATAGAGTTTAATAAGCATTTAGAACAAGTTAAAAAAGAACTTTCATAGATAAGCATGATATTAACGGGAATATTCCTATATTCATTAATATTGGTGAATGGGACGGAGATGATGAGGAATTAGATAAGGCAGT‑GCAAGATGTATCTAACGCTAACCATAATCATACTGTGATTGTGGATGATATACCGTTAGAGGATTGAAGAAAATGAAGCTATGCTATTTATAAATTAATACTAATTAGTTTGATACCATAGCTTATTTACTGAGAAAGT  >  USA300TCH1516_ALE/906841‑907115

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: ‑