Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,508	A→T	14.3%	V46E (GTA→GAA)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,508	0	A	T	14.3%	155.6 / 13.2	61	V46E (GTA→GAA)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (23/29);  new base T (2/7);  total (25/36)
Fisher's exact test for biased strand distribution p-value = 2.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAACGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTT  >  USA300TCH1516_ALE/2028369‑2028647                                                                                                                                            |                                                                                                                                             aTAACGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAAGTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAGGATATCCTa                                                                                                                                              >  1:259228/1‑140 (MQ=255)    aCGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCACAACGCCAAAAGGCCACGTATTTTATGACAATAAAGATATCCTACAt                                                                                                                                           >  1:40044/1‑140 (MQ=255)    aCGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACAt                                                                                                                                           <  2:610809/140‑1 (MQ=255)      gCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATaa                                                                                                                                         >  1:133813/1‑140 (MQ=255)       cacaACCAGTAATAAGAAAAAGACGAACAAGAAGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATaaa                                                                                                                                        <  1:100210/140‑1 (MQ=255)               gTAATGATAAAGAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACT‑AATaca                                                                                                                               <  1:584905/140‑1 (MQ=255)               gTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATaca                                                                                                                               <  1:716803/140‑1 (MQ=255)               gTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATaca                                                                                                                               >  2:311941/1‑140 (MQ=255)               gTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATaca                                                                                                                               <  1:448054/140‑1 (MQ=255)               gTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCACCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATaca                                                                                                                               <  1:65477/140‑1 (MQ=255)                  ataataaAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACAt                                                                                                                            <  1:435438/140‑1 (MQ=255)                   taataaAAAGACGATCAAGATGATGATTGTATACCTATTAGACAATAAAGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATc                                                                                                                           <  2:253176/140‑1 (MQ=255)                       aaaaaGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGTCACGTATTTTATGAAAATAAAGATATCATACATAACCC‑ATTACACATCCCaa                                                                                                                       <  2:743473/140‑1 (MQ=255)                       aaaaaGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCaa                                                                                                                       >  2:560462/1‑140 (MQ=255)                        aaaaGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCaat                                                                                                                      >  2:627577/1‑140 (MQ=255)                        aaaaGACGAACAAGATGATGATTGTATACTTATTAGACAATAAAGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGCCCACGTATTTTATGAAAATAAAAATATCCTACATCAACT‑AATACACATCCCaaa                                                                                                                      >  2:77999/1‑139 (MQ=255)                         aaaGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGAGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACAAAAACG‑AATACACATACCaata                                                                                                                     >  2:593269/1‑140 (MQ=255)                              cGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGa                                                                                                                >  1:580048/1‑140 (MQ=255)                               gAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACT‑AATACACATCCCAATAATAGaa                                                                                                               <  1:181957/140‑1 (MQ=255)                               gAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGACTATCAAAAACGCCAAAAGGCCACGTATTTTATGAAAATACAGATATCCTACATAAACT‑AATACACATCCCAATAATAGaa                                                                                                               >  1:130323/1‑140 (MQ=255)                                aaCAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAAc                                                                                                              >  1:572574/1‑140 (MQ=255)                                     gatgatgatTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCGACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTa                                                                                                         >  2:378555/1‑140 (MQ=255)                                         atgatTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTaaaaa                                                                                                     <  1:201544/140‑1 (MQ=255)                                          tgatTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAg                                                                                                    >  1:744977/1‑140 (MQ=255)                                                   aCTTAAGAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAAttttt                                                                                           <  1:405074/140‑1 (MQ=255)                                                    cTTATTAGACAATAGTGTGAATGGAATTAATAGCGCTCCTATCCAAAACGGCAAAAGGCCATGTATTTTATGAAAATAAAGATATCCTTCATAAACT‑AATACTATTTTTTTTAATAGAACGAGTAAAAAGCCAAtttttt                                                                                          <  2:130323/140‑1 (MQ=255)                                                            aCAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTATATAAAAAAat                                                                                  >  2:200746/1‑140 (MQ=255)                                                               ataatGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTGTGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATCGAACGAGTAAAAAGCCAATTTTTTCAAAAAataag                                                                               >  1:341880/1‑138 (MQ=255)                                                                taatGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGACACATAATTTATGAAAGGAAA‑TTGAACAACCTTGCCTGAAAACTCATCCCAATAATAGAACGAGCGAAAGGACAATCTTTTCACAAAATATgt                                                                              >  2:162559/1‑140 (MQ=255)                                                                  aggggAACGCAATCAATAGCGCACCCATCCAAAACGCCAAAAGGCCACGTATGTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATgtag                                                                            <  1:283711/136‑1 (MQ=255)                                                                   tgtgAATGCGATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAGCT‑AATACACATCCCAATAATAGGACGAGTAAAAAGCCAATTTTTTCAAAAAATATgtagt                                                                           <  2:285733/140‑1 (MQ=255)                                                                   tgtgAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATgtagt                                                                           >  1:48630/1‑140 (MQ=255)                                                                   tgtgAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATgtagt                                                                           <  2:743916/140‑1 (MQ=255)                                                                     tgAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTaa                                                                         >  1:464198/1‑140 (MQ=255)                                                                            cattgagaGCGCGCCTAGCCAAAACGCCGAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTgg                                                                  <  2:218437/133‑1 (MQ=255)                                                                            aaTTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATACACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTgg                                                                  <  2:572574/140‑1 (MQ=255)                                                                             atcaaTATCCCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGc                                                                 <  2:558806/137‑1 (MQ=255)                                                                               tAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACT‑AATACACATCCCAATAATAGAACGAGGAAAAAGCCAATTTTTTCAAAAAAGATGTAGTAGAAATTGGCag                                                               >  1:170627/1‑139 (MQ=255)                                                                                  tAGCGCGACTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCaataa                                                            <  2:91304/140‑1 (MQ=255)                                                                                   aGCGCGCCTATCAAAAACGCCAACAGGACACGTATTTTATGAAAATAAAGATACCATTCATAAACT‑AATACACACCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCaataat                                                           <  2:688237/140‑1 (MQ=255)                                                                                     cgcgcCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCa                                                         <  1:635657/140‑1 (MQ=255)                                                                                     cgcgcCTACCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCa                                                         <  1:635954/140‑1 (MQ=255)                                                                                      gcgcCTATCCAAAACGGCAAAAGGCCACGTATTGTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCAt                                                        <  2:289201/140‑1 (MQ=255)                                                                                            aTCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGc                                                  >  2:208710/1‑140 (MQ=255)                                                                                             tCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCCCAACATATGTAGTAAAAACTGGCAATAATCATTAATGcc                                                 >  2:323419/1‑139 (MQ=255)                                                                                               cAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACAAAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGt                                               <  2:441070/140‑1 (MQ=255)                                                                                                 aaaCGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTaa                                             >  1:149874/1‑140 (MQ=255)                                                                                                      ccAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATg                                        >  2:413231/1‑140 (MQ=255)                                                                                                         aaaGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATc                                     >  2:604133/1‑140 (MQ=255)                                                                                                             gCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACa                                 <  1:330724/140‑1 (MQ=255)                                                                                                               cctgTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACAtc                               <  1:348695/137‑2 (MQ=255)                                                                                                               cACGTATCTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAAAAGAACGAGTAAAAAGCCAAATTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACAtt                               <  2:725564/140‑1 (MQ=255)                                                                                                                 cGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTg                             <  1:86339/140‑1 (MQ=255)                                                                                                                  gTAATTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCAAAAAAAAAAAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGc                            <  2:197511/140‑1 (MQ=255)                                                                                                                       ttATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGa                       <  1:627577/140‑1 (MQ=255)                                                                                                                       ttATAAAAAGAAAGGTATCCTACATAAACT‑ACTACACAGCCCAATAAGAGAACGAGTAAAAAGCCAATTTGTTCAAAAAATAAGTAGTAAAAATTGGCAATAATCATGAATGCAGTAAAAATGATCAACATTTGCGTTGa                       <  1:77999/140‑1 (MQ=255)                                                                                                                         aTGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTTGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGata                     <  1:50295/140‑1 (MQ=255)                                                                                                                         aTGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGata                     >  1:53287/1‑140 (MQ=255)                                                                                                                                 aaaGAAATCCTTCAAAAAAT‑AATACACAACCCAATAATAGAACGAGTCACATCCCGATTTTTTCAAAAAATATGGAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTtg             <  1:393595/140‑1 (MQ=255)                                                                                                                                    gATATCCTTCATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTtgtgt          <  1:66464/140‑1 (MQ=255)                                                                                                                                           tACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAAttttt                                                                                           <  1:284224/52‑1 (MQ=255)                                                                                                                                           tACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAAttttt                                                                                           >  2:284224/1‑52 (MQ=255)                                                                                                                                            aCATAAAAT‑AATACTAAAACTGATAAACGAACGAGTAAAAAGCCAATGTTTTCAAAAAATAGGGAGTAAAAAGTTGCAATAATCATTAATGCAGTAAACACGTTGGGCCCCTCCTTGGATATATATTTGTGTGTCATGtt  <  2:744977/140‑1 (MQ=255)                                                                                                                                            |                                                                                                                                             ATAACGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACT‑AATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTT  >  USA300TCH1516_ALE/2028369‑2028647

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑