Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,627,280 (AT)5→6 intergenic (‑218/‑107) sarT ← / → sarU HTH‑type transcriptional regulator SarT/HTH‑type transcriptional regulator SarU

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,627,2691.T94.4% 56.7 / ‑2.2 18intergenic (‑207/‑118)sarT/sarUHTH‑type transcriptional regulator SarT/HTH‑type transcriptional regulator SarU
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base T (7/10);  total (7/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01
*USA300TCH1516_ALE2,627,2692.A94.4% 58.1 / ‑2.0 18intergenic (‑207/‑118)sarT/sarUHTH‑type transcriptional regulator SarT/HTH‑type transcriptional regulator SarU
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base A (7/10);  total (7/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01

ATAACTCCAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑TATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGAAAAG  >  USA300TCH1516_ALE/2627122‑2627410
                                                                                                                                                    ||                                                                                                                                             
ataaCTCCAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATGGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTAtttatattt                                                                                                                                                 >  1:233087/1‑148 (MQ=255)
       cAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑tatatat                                                                                                                                        <  1:58478/148‑1 (MQ=255)
            atatTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑Tatatatatata                                                                                                                                   <  2:361826/148‑2 (MQ=255)
                            tctagctaTAAACACATATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATAtt                                                                                                                     <  2:318717/147‑1 (MQ=255)
                                gctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAgg                                                                                                                 >  1:125275/1‑148 (MQ=255)
                                gctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAgg                                                                                                                 <  2:123757/148‑1 (MQ=255)
                                gctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAgg                                                                                                                 >  1:354458/1‑148 (MQ=255)
                                 ctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGt                                                                                                                >  1:172055/1‑148 (MQ=255)
                                            aaTGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCtt                                                                                                     <  1:152978/148‑1 (MQ=255)
                                            aaTGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCtt                                                                                                     >  1:306936/1‑148 (MQ=255)
                                             aTGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCttt                                                                                                    >  2:354769/1‑148 (MQ=255)
                                                                                tGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTATGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTTaatatttt                                                                 >  2:384513/1‑144 (MQ=255)
                                                                                              gATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACa                                                   <  1:87222/148‑1 (MQ=255)
                                                                                                      aTGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGaaaa                                           <  2:172055/148‑1 (MQ=255)
                                                                                                         aaTTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAAtag                                        <  1:361464/148‑1 (MQ=255)
                                                                                                         aaTTTGTCATTTGTTATTATGTGATTTTTAGTTATTTATATTTTATATATATATATTCTATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAAtag                                        <  1:202123/148‑1 (MQ=255)
                                                                                                                       tATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAg                          >  1:13908/1‑148 (MQ=255)
                                                                                                                                    ttAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCaaa             <  1:338454/148‑1 (MQ=255)
                                                                                                                                    ttAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCaaa             <  1:108088/148‑1 (MQ=255)
                                                                                                                                          ttatatttta‑‑tatatATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGaa     <  2:270985/145‑1 (MQ=255)
                                                                                                                                          atttatATTTTATATATATATATTATATATAAAATATTTAGTTTAACATGTATTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCg       <  2:22230/148‑1 (MQ=255)
                                                                                                                                             tatttta‑‑tatatATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGAAAAg  <  1:23152/148‑1 (MQ=255)
                                                                                                                                                    ||                                                                                                                                             
ATAACTCCAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑TATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGAAAAG  >  USA300TCH1516_ALE/2627122‑2627410

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