Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 37,746 A→T 30.5% intergenic (+770/‑67) USA300HOU_RS14915 → / → ugpQ_1 hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE37,7460AT30.5% 57.2 / 26.4 39intergenic (+770/‑67)USA300HOU_RS14915/ugpQ_1hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic
Reads supporting (aligned to +/- strand):  ref base A (11/16);  new base T (6/6);  total (17/22)
Fisher's exact test for biased strand distribution p-value = 7.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAGCTCCGGAAAATACAATTGCATCATT  >  USA300TCH1516_ALE/37606‑37877
                                                                                                                                            |                                                                                                                                   
aaaaaCTAGACTTGAATACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATa                                                                                                                                     >  1:256290/1‑141 (MQ=255)
      tAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATAAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTg                                                                                                                               <  2:236500/141‑1 (MQ=255)
         aCTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTACAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGa                                                                                                                            <  1:266491/141‑1 (MQ=255)
            tGAGTACAAAATGGACCTTGGTACATAAATTATTTTTTAAAAATGGGACGCGACGTAGATTAACTCCATAAGCAATACGAATCTATGGACTTCTTTAGTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTa                                                                                                                         <  2:16268/141‑1 (MQ=255)
                    aaaTGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGata                                                                                                                 >  2:43308/1‑141 (MQ=255)
                      aTGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAAATAAAGTGCGATTAATGTGataat                                                                                                               >  2:128611/1‑141 (MQ=255)
                         gAGCTTGGGACATAAATGATTTTTTAAAAATGAGAGGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATTTCTTTTTAATGGAAATAAAAATGCGGTTAATGTGATAATACa                                                                                                            >  1:19435/1‑141 (MQ=255)
                          accTTGGAACAAAAATGATTGTTTAAAAATGAGAAGAGACGTAGATCAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAg                                                                                                           <  2:101022/139‑1 (MQ=255)
                           gCTTGCGACATAAATGATTTTTTAAAAACGACATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGt                                                                                                          <  1:8060/141‑1 (MQ=255)
                            cTTGGGACATAAATGATCTGTTAAAAATGAGATGCGACGTAGATTAACTCCATAATCAATACGAATCTATCGTCTTCTTTATTTATGATATTCGTCTCTTTTTAATGGAAATTAAACTGCGATTAATGTGATAATACAGtt                                                                                                         <  1:128707/141‑1 (MQ=255)
                              tGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATCTGCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTAc                                                                                                       <  1:307499/141‑1 (MQ=255)
                              tGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATTAAAGTGCGATTAATGTGATAATACAGTTAc                                                                                                       >  2:129014/1‑141 (MQ=255)
                                    aTAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATAAAAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATTAAAGTGCGATTAATGTGATAATACAGTTaagaaaaa                                                                                                 <  2:298007/141‑8 (MQ=255)
                                       aaTGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATTAAAGTGCGATTAATGTGATAATACAGTTACGttaattaa                                                                                              >  1:310861/1‑141 (MQ=255)
                                       aaTGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATTAAAGTGCGATTAATGTGATAATACAGTTACGttaattaa                                                                                              >  1:193448/1‑141 (MQ=255)
                                             tttttAAAAATGAGATGAGACCTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAaaaaat                                                                                        >  1:175980/1‑141 (MQ=255)
                                                   aatatgagatgagACGTAGATTAACTCCAAAAAAAATACGAAAAAATGGACTGGTTTAGTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAAAAAAaaaaaaaaaaat                                                                                  <  2:331670/138‑1 (MQ=255)
                                                        gagatgagaCGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATTAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAg                                                                             <  1:228654/141‑1 (MQ=255)
                                                         agatgagaCGTAGATTAACTCAATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAGAGTGCGATTAATGTGATATTACAGTTACGTTAATTAAGAAAATAAAAATGCAAgg                                                                            >  1:15103/1‑141 (MQ=255)
                                                                ccGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTa                                                                     <  1:192606/140‑1 (MQ=255)
                                                                aCGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTa                                                                     <  1:313823/141‑1 (MQ=255)
                                                                      aatAACTCCATAATCAAAACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAACGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGc                                                               <  1:260514/139‑1 (MQ=255)
                                                                      aTTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGc                                                               <  1:307642/141‑1 (MQ=255)
                                                                                 aaTCAATAGGAATCTATCGACTTCTTTATTTAGTATATTCATCTCTTTTAAATGGAAATAAAAGGGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTatat                                                    <  2:306180/141‑1 (MQ=255)
                                                                                     aaTACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATTAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGaa                                                >  1:329972/1‑140 (MQ=255)
                                                                                        aCGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGGGAGGTAATTTGCTAACTGTTTATGGACATa                                             >  1:78312/1‑141 (MQ=255)
                                                                                           aaTCTATCGACTGCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAACGCAAGGAGAGGTAATATGCTAACTGTATATGGACATagag                                          >  1:244128/1‑141 (MQ=255)
                                                                                            aTCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAgg                                         <  2:175980/141‑1 (MQ=255)
                                                                                                          ttatttatGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAg                           <  1:14060/141‑1 (MQ=255)
                                                                                                           tatgtatgATATTCATCTCTTTTTAAGGTAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAATAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAGc                          <  2:253311/141‑1 (MQ=255)
                                                                                                            atttatGATATTCATCTCTTTTTAATGGAAATTAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGAAAGGAGAGGTAATATGCTAACTGTATATGGACATAAAGGATTACCTAGTAAAGCt                         >  2:339570/1‑141 (MQ=255)
                                                                                                              ttatGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAGCTcc                       >  2:53783/1‑141 (MQ=255)
                                                                                                                  gATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAGCTCCGGaa                   >  1:74930/1‑141 (MQ=255)
                                                                                                                     atTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAGCTCCGGAAAAt                >  2:219071/1‑141 (MQ=255)
                                                                                                                      ttCATCCCTTTTTAAAGGAAATTAAAGTTCGATTAATGTGATAAGACAGTTACGTTAAAAAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAGCTCCGGAAAATa               <  2:30461/141‑1 (MQ=255)
                                                                                                                      atcacgtctTTAAAAGGGAAAATAAAGCGCGATTAATGTGATAAGACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAGCTCCGGAAAATa               <  2:58752/135‑1 (MQ=255)
                                                                                                                           ctctTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATTGACATAGAGGATTACCTAGTAAAGCTCCGGAAAATACAAtt          >  2:319680/1‑141 (MQ=255)
                                                                                                                               ttttAATGGAAACAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAGCTCCGGAAAATACAATTGcat      <  2:223000/141‑1 (MQ=255)
                                                                                                                                  tAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAGCTCCGGAAAATACAATTGcatcat   >  2:2268/1‑141 (MQ=255)
                                                                                                                                   aaTGGAAATTAAAGTGCGATTAATGGGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAGCTCCGGAAAATACAATTGCATCAtt  <  1:304978/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                   
AAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATCTCTTTTTAATGGAAATAAAAGTGCGATTAATGTGATAATACAGTTACGTTAATTAAAAAAATAAAAATGCAAGGAGAGGTAATATGCTAACTGTATATGGACATAGAGGATTACCTAGTAAAGCTCCGGAAAATACAATTGCATCATT  >  USA300TCH1516_ALE/37606‑37877

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: ‑