Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 529,100 A→G 8.0% K159E (AAA→GAA)  rnmV_1 → Ribonuclease M5

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE529,1000AG 8.0% 141.4 / 2.2 52K159E (AAA→GAA) rnmV_1Ribonuclease M5
Reads supporting (aligned to +/- strand):  ref base A (28/19);  new base G (2/2);  total (30/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

TTTGATGAAGCTTATGAATCAATTGATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAACACCATCAAGAACGCGAGCGTTGTTAGATAAATATGGCTTTA  >  USA300TCH1516_ALE/528962‑529239
                                                                                                                                          |                                                                                                                                           
tttGATGAAGCTTATGAATCAATTGATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATCCCAATGGCAGGCGGTTAATGaaa                                                                                                                                           >  1:6190/1‑141 (MQ=255)
  tgatgaAGCTTATGAATCAATTGATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGaaaaa                                                                                                                                         >  1:309891/1‑141 (MQ=255)
     tgaAGCTTATGAATCAATTGATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTACAATGGTAAGCAGTTATTGAAAAAGtt                                                                                                                                      >  2:47462/1‑141 (MQ=255)
        aGCTTATGAATCAATTGATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTaaa                                                                                                                                   <  1:2028/141‑1 (MQ=255)
         gCTTATGAATCAATTGATAAATCTGTTCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAAt                                                                                                                                  <  1:295173/141‑1 (MQ=255)
           ttATGAATCAATTGATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGc                                                                                                                                <  1:206280/141‑1 (MQ=255)
           ttATGAATCAATTGATAAATCTGTGCTAATAGAGTTGGGGATAATTTTTGTGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGc                                                                                                                                <  1:242608/141‑1 (MQ=255)
           aaaagAATCAATTGAGAAATCTGAGCTTATAGAGTTGGGGTGAAATGTAGGGAAAGATTCAAGGCGCAGTAGAGAAAATTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGTAAAAGTTAACTgg                                                                                                                                <  2:353240/137‑2 (MQ=255)
             aTGAATCAATTGATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCAt                                                                                                                              >  1:59686/1‑141 (MQ=255)
                      ttGATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGGAAAAGTTAAATGCATTTGGTtata                                                                                                                     >  1:117417/1‑141 (MQ=255)
                      ttGATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGGAAAAGTTAAATGCATTTGGTtata                                                                                                                     >  1:130246/1‑141 (MQ=255)
                       tGATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATAc                                                                                                                    >  2:18688/1‑141 (MQ=255)
                        gATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATAcc                                                                                                                   >  2:258760/1‑141 (MQ=255)
                            aaTCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGACAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAg                                                                                                               <  1:65359/141‑1 (MQ=255)
                            aaTCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAg                                                                                                               <  1:219857/141‑1 (MQ=255)
                                 gtgCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGCATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGAGGTTGGTTATACCGAACCGGag                                                                                                          >  1:225713/1‑140 (MQ=255)
                                 gcgCTAGTAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGAt                                                                                                          >  2:310247/3‑141 (MQ=255)
                                  ggcaaacagaaTTGCGGTTAATTGTTAATAAACATGTTTGGCTCCTTAGAGAAATTTTAAGTAGTAAATGTCGAAGCGTCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATg                                                                                                         <  2:337646/134‑1 (MQ=255)
                                     tAATAGAGTTGGGATTAATTCTTCGGCTAGCTGAACGGTTGCTTAGAAATATTTAACCTATAAAATAGCGAATCTCCCATTCGAATTTTAATCAATTAGTGAAAAAGTTAAAGGCAGTTGGTTATACCGAAGCGGATGTaa                                                                                                      <  2:30884/141‑1 (MQ=255)
                                       aTAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGTTTAAACCGAAGCGGAGGTAAgg                                                                                                    >  2:57241/1‑141 (MQ=255)
                                       aTAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAgg                                                                                                    >  1:234043/1‑141 (MQ=255)
                                          gagTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATAGCGAAGCGGATTGAAGGCaa                                                                                                 >  1:45448/1‑141 (MQ=255)
                                            gTTGGGGTTAATTGTCGGGAAAGAGGCAATGCGCCGTAGAGAAATTTTAAGTAGAAAATGGCGAATGGGCCAGTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCCTTTGGTTATACCGAAGCGGATGTAAGGCAAGc                                                                                               <  2:6321/141‑1 (MQ=255)
                                             ttGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCt                                                                                              >  1:321876/1‑141 (MQ=255)
                                              tGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCtt                                                                                             >  1:1041/1‑141 (MQ=255)
                                               ggggTTACTTGTTTGGAAAGATGCAAGGCGCCGTAGATAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCttt                                                                                            <  2:125668/141‑1 (MQ=255)
                                                   ttAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAACGTTAAATGCATTTGGATATACCGAAGCGGATGTAAGGCAACCATTagaa                                                                                        >  1:7116/1‑141 (MQ=255)
                                                   ttAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGAAGTTATTGAAAAATTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCGTTagaa                                                                                        >  2:325224/1‑141 (MQ=255)
                                                      aTTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGGAGCGGATGTAAGGCAAGCTTTAGAAGat                                                                                     >  2:279826/1‑141 (MQ=255)
                                                      aTTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGat                                                                                     <  1:163898/141‑1 (MQ=255)
                                                        tgttgGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGGTATACCGAAGCGGATGTAAGGAAAGCTTTAGAAGatga                                                                                   >  2:286327/1‑141 (MQ=255)
                                                            gggAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGAATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGatgaacgg                                                                               >  2:178089/1‑138 (MQ=255)
                                                              gAAAGATGCAAGGCGCCGTAGAGAGATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAgg                                                                             >  1:343835/1‑141 (MQ=255)
                                                                    tGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGGGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGa                                                                       <  2:36887/141‑1 (MQ=255)
                                                                     gCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTGAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGaa                                                                      >  1:241564/1‑141 (MQ=255)
                                                                      cAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGTGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGCTGAATGAGGAAGTGaaa                                                                     >  1:238806/1‑141 (MQ=255)
                                                                      cAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATGGGCCATTTCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAAGGAGGAAGTGaaa                                                                     >  1:101393/1‑141 (MQ=255)
                                                                            gcCGTAGAGAAATTTTAAGTAGAAAAATGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAACGCAAGCTTTAGAAGATGAATGAGAAAGTGAAAATGTTg                                                               >  2:222061/1‑141 (MQ=255)
                                                                                        ttttAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGat                                                   <  1:18688/141‑1 (MQ=255)
                                                                                          ttAAGTAGAAAATTGCGAATCGACCATTCCAATGGTAAGCAGTTAATGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGatat                                                 >  2:175085/1‑141 (MQ=255)
                                                                                           tAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATAtt                                                >  1:106227/1‑141 (MQ=255)
                                                                                           tAAATAGAAAAATGCGAATCGGCCATTCCAATGGTAAGCAGCTAAACAAAAGCAAACTTAGAGTGAGTTATACCTAAGCGGATGTAAGGCAAGCTATCGAAGATGAATGAGGAATTGAAAATGACGGATAATGAAGATAtt                                                >  2:163415/1‑141 (MQ=255)
                                                                                                  aaaaTTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATTAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAacac                                         <  2:58729/141‑1 (MQ=255)
                                                                                                   aaaTTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAacaac                                        >  1:177850/1‑139 (MQ=255)
                                                                                                      ttGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGGAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAACACCATc                                     <  2:117417/141‑1 (MQ=255)
                                                                                                      ttGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGGAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAACACCATc                                     <  2:130246/141‑1 (MQ=255)
                                                                                                       tGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAACACCATCa                                    >  2:319355/1‑141 (MQ=255)
                                                                                                              cGGCCATTCTAATGGTAAGGAGTTATTGAACAAGTTGATTGCTTTTGGTTGTACCTAAGCGGATGTTTTGCAAGCTTTAGAAGTTGAATGAGGTATTGAAAATGTTGGATAATAAAGATATTGCAACACCATCAAGAAcgc                             <  2:246377/141‑1 (MQ=255)
                                                                                                              cGGCCATTCAAATGGTAAGCAGTTATTGAAAAAGTTAAATTCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAACACCATCAAGAAcgc                             <  2:101250/141‑1 (MQ=255)
                                                                                                              cGGCCAGTCCAATGGTAACCAGTTCTTGAAAAAGTTATATGCAGTTGGTTATACCGAAGCGGATGTAAGGCATTTTTTAGAAGATGAATGAGTTATTGAAAATGTTGGATAATAAAGATATTGCAACACCATCAAGAAcgc                             <  2:246436/141‑1 (MQ=255)
                                                                                                               cgCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAACACCATCAAGAAcgcg                            <  2:13253/140‑1 (MQ=255)
                                                                                                                gCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCCTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAACACCATCAATAAGGCGa                           <  2:309891/141‑1 (MQ=255)
                                                                                                                 ccATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAACACCATCAAGAACGCGAg                          >  1:169522/1‑141 (MQ=255)
                                                                                                                                         gAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAACACCATCAAGAACGCGAGCGTTGTTAGATAAATATGGCTTTa  >  2:56220/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                           
TTTGATGAAGCTTATGAATCAATTGATAAATCTGTGCTAATAGAGTTGGGGTTAATTGTTGGGAAAGATGCAAGGCGCCGTAGAGAAATTTTAAGTAGAAAATTGCGAATCGGCCATTCCAATGGTAAGCAGTTATTGAAAAAGTTAAATGCATTTGGTTATACCGAAGCGGATGTAAGGCAAGCTTTAGAAGATGAATGAGGAAGTGAAAATGTTGGATAATAAAGATATTGCAACACCATCAAGAACGCGAGCGTTGTTAGATAAATATGGCTTTA  >  USA300TCH1516_ALE/528962‑529239

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: ‑