Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,981,418 C→A 82.7% intergenic (‑17/+339) USA300HOU_RS09870 ← / ← liaR hypothetical protein/Transcriptional regulatory protein LiaR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,981,4180CA82.7% 61.4 / 7.7 35intergenic (‑17/+339)USA300HOU_RS09870/liaRhypothetical protein/Transcriptional regulatory protein LiaR
Reads supporting (aligned to +/- strand):  ref base C (3/3);  new base A (16/12);  total (20/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.03e-01

AAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAA  >  USA300TCH1516_ALE/1981287‑1981548
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aaGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTggg                                                                                                                            >  1:189531/1‑140 (MQ=255)
       tttAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAAtttt                                                                                                                     <  2:439306/140‑1 (MQ=255)
              aGTCCAATTTTTTGCGCCATAGTCTCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGa                                                                                                              <  2:360269/140‑1 (MQ=255)
              aGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAATTCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCggc                                                                                                              >  2:344111/1‑139 (MQ=255)
               gTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAACTCTGTAAACCTCTGTCTATCCATTCTGTTATTTAGCTTTATGTTTCAGGAAATTTATCCGCac                                                                                                             >  2:323549/1‑140 (MQ=255)
                     ttGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGa                                                                                                       >  2:398994/1‑140 (MQ=255)
                     ttGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAAGTACATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATCTTTGGGGAATCTTATCCGGccactata                                                                                                       >  2:88516/1‑136 (MQ=255)
                                 ttgTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCaataat                                                                                           <  2:327457/138‑1 (MQ=255)
                                 tAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAATTTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCCTTTTGTTTCTGGAATTTTCTCCGGACACAAGAAATTGCaagaat                                                                                           >  2:329903/1‑140 (MQ=255)
                                 tAGGATCTGGCGGATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCaataat                                                                                           <  2:533534/140‑1 (MQ=255)
                                   gTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATac                                                                                         <  2:475752/140‑1 (MQ=255)
                                     aTCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATacac                                                                                       <  1:382551/140‑1 (MQ=255)
                                              aaaaCCAGCCTCTATACGAACCATTTTAACTTTTGTTTGAATTAAATCTGTACAACTCTGTCTATCCATTCTGTTATCTCCCTTTATGTTCGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGa                                                                              <  1:234367/138‑1 (MQ=255)
                                                aaCCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGaaa                                                                            <  1:351482/140‑1 (MQ=255)
                                                     gCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGGATTTTATCCGGACACAAGAAATTGCAATAGTACACATTTCTTGAAACACAg                                                                       >  1:497747/1‑140 (MQ=255)
                                                      ccTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTTGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGa                                                                      <  1:189269/140‑1 (MQ=255)
                                                       ctctATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGAt                                                                     <  1:413519/140‑1 (MQ=255)
                                                          tataCGAACCATTTTAAATTTTGTTTGAATTAGAGCTGTAAAACTCTGTCTATCCCTTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTCCAATAATACACACTTCTTGAAACACAGATTAc                                                                  >  2:123522/1‑140 (MQ=255)
                                                                     ttttAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAatata                                                       >  1:556544/1‑140 (MQ=255)
                                                                     ttttAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAatata                                                       >  1:350898/1‑140 (MQ=255)
                                                                        tAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCAATTCTGTTATCTAACTTTATGTTTGGGGAATTTTATCAGTACACAAGAACTTGCAATAATAAACATTTATTGAAAAACAAATTACAACTAAAAATAatt                                                    >  2:211637/1‑140 (MQ=255)
                                                                           aTTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGAAATAATACACATTTCTTGAAACACAGATTACATCACAATATAttatta                                                 >  2:322597/1‑140 (MQ=255)
                                                                             tttgtttgAATTAAATCTGTAATTCTCTGTCTATCCATTCAGTTATCTACCTTTATATTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTtaat                                               <  2:215055/140‑1 (MQ=255)
                                                                              ttgtttgAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACGTCTTAATATATTTTtaata                                              >  1:380117/1‑140 (MQ=255)
                                                                                   tgAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAAta                                         >  2:220870/1‑139 (MQ=255)
                                                                                   tgAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATg                                         >  2:155447/1‑140 (MQ=255)
                                                                                     aaTTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACGCAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGaa                                       >  1:124951/1‑140 (MQ=255)
                                                                                                  agaCTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTc                          <  2:238161/138‑1 (MQ=255)
                                                                                                          tCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGt                  <  2:468335/140‑1 (MQ=255)
                                                                                                          tCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATATGt                  >  2:91285/1‑140 (MQ=255)
                                                                                                              tCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCAGATTTGTATTa              >  1:161324/1‑140 (MQ=255)
                                                                                                                    cggTTATCTGCCTGTATGGTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTGCACATTTGTATTAAAtttt        <  1:437339/138‑1 (MQ=255)
                                                                                                                      gTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGa      >  1:259413/1‑140 (MQ=255)
                                                                                                                      gTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACACTTGTATTAAATTTTGa      >  2:161110/1‑140 (MQ=255)
                                                                                                                          tCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCaa  <  2:165304/140‑1 (MQ=255)
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AAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAA  >  USA300TCH1516_ALE/1981287‑1981548

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: ‑