Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 283,980 A→G 9.5% intergenic (+205/+115) ldh1 → / ← ptsG_2 L‑lactate dehydrogenase 1/PTS system glucose‑specific EIICBA component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE283,9800AG 9.5% 109.6 / 2.5 42intergenic (+205/+115)ldh1/ptsG_2L‑lactate dehydrogenase 1/PTS system glucose‑specific EIICBA component
Reads supporting (aligned to +/- strand):  ref base A (22/16);  new base G (2/2);  total (24/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01

TATTTGATACAACTATATGTGTCGAGTAGCCCTATTTTTAATGTAGTGAAAGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCTGTTGATATTTCGGTTAGTCTTAATCCCCGAGCAATTCT  >  USA300TCH1516_ALE/283841‑284113
                                                                                                                                           |                                                                                                                                     
tATTTGATACAACTATATGTGTCGAGTAGCCCTATTTTTAATGTAGTGAAAGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCAc                                                                                                                                      >  1:40656/1‑141 (MQ=255)
tATTTGATACAACTATATGTGTCGAGTAGCCCTATTTTTAATGTAGTGAAAGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAAGCGATTTGGGGGCTCAc                                                                                                                                      >  1:110581/1‑141 (MQ=255)
   ttGATACAACTATATGTGTCGAGTAGCCCTATTTTTAATGTAGTGAAAGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTAc                                                                                                                                   >  2:315262/1‑141 (MQ=255)
       tACAACTATATGTGTCGAGTAGCCCTATCTTTAATGTAGTGAAAGGCGTTGTTGAAATTAAAATCAAATATGGCGCTTAAGCGTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGGTTTGCGGGATCACTACCGTg                                                                                                                               >  2:238690/1‑141 (MQ=255)
           aCTATATGTGTCGAGTAGCCCTATTTTTAATGTAGTGAAAGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCatg                                                                                                                           <  2:315182/141‑1 (MQ=255)
                       gggTAGCCCTATTTTTAATGTAGTGAAAGTCGTTGTTGAAATTAAATTAAGATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATg                                                                                                               <  1:108844/139‑1 (MQ=255)
                           aGCCCTCTTTTTAATGTAGTGAAAGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTc                                                                                                           <  2:377055/141‑1 (MQ=255)
                           aGCCCTATTTTTAATGTAGTGAAAGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTc                                                                                                           <  1:98441/141‑1 (MQ=255)
                            gCCCTATTTTTAATGTAGTGAAAGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCa                                                                                                          >  1:87791/1‑141 (MQ=255)
                              ccTATTTTTAATGTAGTGAAAGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCaaa                                                                                                        <  1:324401/141‑1 (MQ=255)
                                          gTAGTGAAAGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTaaa                                                                                            >  1:279821/1‑141 (MQ=255)
                                                aaaGTCGTTGTTGAAATTAAATTCAAAGCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATaaa                                                                                      <  1:245032/141‑1 (MQ=255)
                                                  aGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAg                                                                                    >  1:265125/1‑141 (MQ=255)
                                                  aGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAg                                                                                    <  1:284770/141‑1 (MQ=255)
                                                    tCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCa                                                                                  <  1:153149/141‑1 (MQ=255)
                                                    tCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTGCAAATGTAACATTAAAAATAAAAGCa                                                                                  >  1:128249/1‑141 (MQ=255)
                                                      gttgttGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAAc                                                                                >  1:245719/1‑141 (MQ=255)
                                                      gttgttGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGAGTTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAAGTTAATGATTCCAAGGTAACCTTAAAAATAAAAGCaaa                                                                                >  2:379231/1‑140 (MQ=255)
                                                         tatgAAATTAAAGTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGAt                                                                             <  2:170085/139‑1 (MQ=255)
                                                         gttgAAATTAAATTCAAGTCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGAt                                                                             <  1:165385/141‑1 (MQ=255)
                                                         gttgAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGAt                                                                             <  2:357821/141‑1 (MQ=255)
                                                                   aattCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAATTAAAAGCAACGATGTCActcctt                                                                   >  2:181937/1‑141 (MQ=255)
                                                                         aaTCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCTATTTGCGGGCTCGCTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCg                                                             >  2:259726/1‑141 (MQ=255)
                                                                         aaTCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCGCTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCg                                                             >  2:94846/1‑141 (MQ=255)
                                                                              ggCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACAt                                                        <  2:327608/141‑1 (MQ=255)
                                                                                  cTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAACAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGtt                                                    >  1:156332/1‑141 (MQ=255)
                                                                                      aGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCa                                                <  1:155377/141‑1 (MQ=255)
                                                                                      aGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCa                                                <  1:361850/141‑1 (MQ=255)
                                                                                               cATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCTg                                       >  2:222172/1‑141 (MQ=255)
                                                                                                 tAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCTGtt                                     >  1:165161/1‑141 (MQ=255)
                                                                                                     aTTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATAGTTGCCATTCGTTCTGTTGata                                 >  1:382109/1‑141 (MQ=255)
                                                                                                         aGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCTGTTGATATTTc                             <  1:200856/141‑1 (MQ=255)
                                                                                                           atgatTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCTGTTGATATTTCgg                           >  2:22861/1‑141 (MQ=255)
                                                                                                            tgatTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATAGTTGCAATTAGTTCTGTTGATATTTCGGt                          >  2:307346/1‑141 (MQ=255)
                                                                                                             gatTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCTGTTGATATTTCGGtt                         <  1:222172/141‑1 (MQ=255)
                                                                                                                 gTCTAGCAGAGGCGATTTGCGGGCTCGCTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTTGTGCGGTTGATATTTCGGTTAGTc                     <  1:94846/141‑1 (MQ=255)
                                                                                                                 gTCTAGCAGAGGCGATTTGCGGGCTCGCTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCTGTTGATATTTCGGTTAGTc                     <  1:259726/141‑1 (MQ=255)
                                                                                                                   cTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTATGTTGATATTTCGGTTAGTCtt                   >  1:226250/1‑141 (MQ=255)
                                                                                                                        agagGCGATTTGCGGGCTCACTACAGTGCATGCTGCACTTAATGCTTCAAAAGGAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCTGTTGATATTTCGGTTAGTCTTAATcc              >  1:190304/1‑141 (MQ=255)
                                                                                                                               aTTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCTGTTGATATTTCGGTTAGTCTTAATCCCCGAGCa       >  2:140103/1‑141 (MQ=255)
                                                                                                                                tttGCGGGCTCACTACAGTGCATGATGAACTTACTGCCACTAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCGGTTGATATTTCGGGTAGTCTTAATCCCCGAGCaa      >  2:361414/1‑141 (MQ=255)
                                                                                                                                    cGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCTGTTGATATTTCGGTTCGTCTTAATCCCCGAGCAAttct  >  1:391714/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                     
TATTTGATACAACTATATGTGTCGAGTAGCCCTATTTTTAATGTAGTGAAAGTCGTTGTTGAAATTAAATTCAAATCTGGCACTTAAGCTTTAATCATAGCATTAAGATGATTGTCTAGCAGAGGCGATTTGCGGGCTCACTACAGTGCATGATGAACTTAATGCTTCAAATGTAACATTAAAAATAAAAGCAACGATGTCACTTCTTACTTCGTACATCGTTGCCATTAGTTCTGTTGATATTTCGGTTAGTCTTAATCCCCGAGCAATTCT  >  USA300TCH1516_ALE/283841‑284113

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑