Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 340,387 A→T 15.3% K19M (AAG→ATG)  esxC → ESAT‑6 secretion system extracellular protein C

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE340,3870AT15.3% 116.2 / 13.8 46K19M (AAG→ATG) esxCESAT‑6 secretion system extracellular protein C
Reads supporting (aligned to +/- strand):  ref base A (24/14);  new base T (2/5);  total (27/19)
Fisher's exact test for biased strand distribution p-value = 1.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.02e-01

AAGCATATATGGTCGCAAACCAAGCTTATCAAAAGATTAGATGGTTTAAATAGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGATATTGAAAGCACAGCAAAGGACGTACAAACTGCAA  >  USA300TCH1516_ALE/340250‑340527
                                                                                                                                         |                                                                                                                                            
aaGCATATATGGTCGCAAACCAAGCTTATCAAAAGATTAGATGGTTTAAATAGCAAAGAAATAAATAGGAGGGAGGGATGTTATGAATTTTAATGATATTGAAACAATGGTGAAGTAGAAATTTGAAGATATTAAAATGCa                                                                                                                                           >  2:498772/1‑141 (MQ=255)
aaGCATATATGGTCGCAAACCAAGCTTATCAAAAGATTAGATGGTATAAATAGCAATGAAGTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCa                                                                                                                                           >  1:519415/1‑141 (MQ=255)
      atatGGTCGCAAACCAAGCTTATCAAAAGATTAGATGGTTTAAATAGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGa                                                                                                                                     <  1:557758/141‑1 (MQ=255)
        atGGTCGCAAACCAAGCTTATCAAAAGATTAGATGGTTTAAATAGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAag                                                                                                                                   <  2:470823/141‑1 (MQ=255)
                   ccAAGCTTATCAAAAGATTAGATGGTTTAAATAGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAATGCATGCTGAAGAGATTGCGCAt                                                                                                                        <  1:332840/141‑1 (MQ=255)
                   ccAAGCTTATCAAAAGATTAGATGGTTTAAATAGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAATGCATGCTGAAGAGATTGCGCAt                                                                                                                        <  1:333027/141‑1 (MQ=255)
                   ccAAACTTATCAAAAGATTAGATGGTTTAAATAGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCAt                                                                                                                        >  2:225526/1‑141 (MQ=255)
                                    ttAGATGGTTTAAATAGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAgttcgttc                                                                                                       <  2:480910/141‑1 (MQ=255)
                                           gTTTAAATAGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGatat                                                                                                <  2:437668/141‑1 (MQ=255)
                                                aaTAGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAg                                                                                           <  2:39422/141‑1 (MQ=255)
                                                 agaggaaTGAATTAAATAGGATGGGGGTATGGTATTAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGa                                                                                          <  1:124640/136‑1 (MQ=255)
                                                 aTAGCAATGAATTAAATAGAAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGATAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTAGTTCTGGATATTTgaga                                                                                          >  1:184865/1‑141 (MQ=255)
                                                   aGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCGTGAAATTGAAGTTCGTTCTGGATGTTTAAGata                                                                                        >  2:36447/1‑139 (MQ=255)
                                                   aGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGaaa                                                                                        <  1:89808/141‑1 (MQ=255)
                                                     cAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAgccacg                                                                                      <  2:462453/141‑6 (MQ=255)
                                                     cAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAg                                                                                      >  2:541383/1‑141 (MQ=255)
                                                      aaTGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGc                                                                                     >  1:572589/1‑141 (MQ=255)
                                                      aaTGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGc                                                                                     >  2:540251/1‑141 (MQ=255)
                                                              aaaTAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAATGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAat                                                                             <  1:352566/141‑1 (MQ=255)
                                                               aaTAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAata                                                                            >  1:224274/1‑141 (MQ=255)
                                                                     agcgaggCATGTTATGAATTTTACTGATATTGAAACAATGGGTGCGTCTAATTTTGAAGATATTAAAAAGCATGCTGAAGAAATTGCGCATGAAATTGAAGTTCGATCGGGATATTTAAGCAAAGGTCAACCATATAAGCg                                                                      >  2:255667/4‑141 (MQ=255)
                                                                                ttATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGaattta                                                           >  1:45590/1‑141 (MQ=255)
                                                                                    gAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATGGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGaatttaattt                                                       >  2:34762/1‑141 (MQ=255)
                                                                                      aTTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTGGAGATATGAGAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGAGTAGAATTTAATTTGa                                                     >  2:556195/1‑141 (MQ=255)
                                                                                      aTTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAATGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGa                                                     >  2:79962/1‑141 (MQ=255)
                                                                                      aTTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAAAATTTAATTTGa                                                     >  2:500598/1‑141 (MQ=255)
                                                                                           aaTGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAATGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGtttt                                                <  2:592556/141‑1 (MQ=255)
                                                                                            aTGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTg                                               >  1:515639/1‑141 (MQ=255)
                                                                                            aTGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTg                                               >  1:29383/1‑141 (MQ=255)
                                                                                             tGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGc                                              <  2:303749/141‑1 (MQ=255)
                                                                                              gATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTAACGAAAACCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCa                                             <  1:117611/141‑1 (MQ=255)
                                                                                                tatTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACt                                           >  1:289371/1‑141 (MQ=255)
                                                                                                 atTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTa                                          <  1:541383/141‑1 (MQ=255)
                                                                                                 atTGAAACAATGGTTAAGTCGAAAATTAAAGATATTAAAAAGCATGCTGAAGAGATAGCGCATGAAATTGAAGATCGTTCAGGATATTTAAGGAAAGCTGAACAATATAAGCGCTTAGAATTTAATTTGAGTTTTACACTa                                          >  2:246624/1‑141 (MQ=255)
                                                                                                     aaaCAATGGTTAAGTCGAAATTTAAAGATATTAAAATGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAgatg                                      <  2:99243/141‑1 (MQ=255)
                                                                                                     aaaCAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAACTTGAGTTTTGCACTAgatg                                      <  2:207761/141‑1 (MQ=255)
                                                                                                       aCAATGGTTAAGTCGATATTTAAAGATATTAAAAAGCATGGTGAAGAGGTTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGACAATTATAAGCGGTTGGAATTTAATTTGAGTTTTGCACTAgatgag                                    >  1:303826/1‑140 (MQ=255)
                                                                                                          aTGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGATAtt                                 <  2:224274/141‑1 (MQ=255)
                                                                                                             gTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTGTTGCACTAGATGATATTGaa                              >  2:534729/1‑141 (MQ=255)
                                                                                                              ttAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATGTAATTTGAGTTTTGCACTAGATGATATTGaaa                             >  1:11676/1‑141 (MQ=255)
                                                                                                                aaGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGATATTGAAAGc                           >  2:350700/1‑141 (MQ=255)
                                                                                                                  gTCGAAATTTAAAGATATTACAAGGGGAGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGATATTGAAAGcac                         >  1:604019/1‑141 (MQ=255)
                                                                                                                  gTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGATATTGAAAGcac                         >  1:399358/1‑141 (MQ=255)
                                                                                                                       aaTTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGATATTGAAAGCACAGCaa                    >  1:18808/1‑141 (MQ=255)
                                                                                                                           taagaataataAAAAGCATGCTGAAGAGATTGCGCATGCAATTGAAGCTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTGTCACTAGATGATATTGAAAGCACAGCAAAGGa                <  1:22664/136‑1 (MQ=255)
                                                                                                                               gATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGAAAATGAAAGCACAGCAAAGGACGTa            >  1:289782/1‑141 (MQ=255)
                                                                                                                                       aaaGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGATATTGAAAGCACAGCAAAGGACGTACAAGCTGc    >  1:221265/1‑141 (MQ=255)
                                                                                                                                        aaGTATGCTGAAGAGATTGCGCATGAAATTGAATTTCGTTCTGGATATTTAAGAAAATCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGATATTGAAAGCACAGCAAAGGACGTACAAACTGCa   <  2:414929/141‑1 (MQ=255)
                                                                                                                                        aaGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGATATTGAAAGCACAGCAAAGGACGAACAAACTGCa   >  1:456975/1‑141 (MQ=255)
                                                                                                                                         aGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGATATTGAAAGCACAGCAAAGGACGTACAAACTGCaa  <  1:225526/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                            
AAGCATATATGGTCGCAAACCAAGCTTATCAAAAGATTAGATGGTTTAAATAGCAATGAATTAAATAGGAGGGAGGTATGTTATGAATTTTAATGATATTGAAACAATGGTTAAGTCGAAATTTAAAGATATTAAAAAGCATGCTGAAGAGATTGCGCATGAAATTGAAGTTCGTTCTGGATATTTAAGAAAAGCTGAACAATATAAGCGATTAGAATTTAATTTGAGTTTTGCACTAGATGATATTGAAAGCACAGCAAAGGACGTACAAACTGCAA  >  USA300TCH1516_ALE/340250‑340527

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: ‑