Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,220,870 (A)6→7 intergenic (‑521/+41) USA300HOU_RS11345 ← / ← atpC hypothetical protein/ATP synthase epsilon chain

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,220,8641.A91.3% 64.8 / ‑0.8 23intergenic (‑515/+47)USA300HOU_RS11345/atpChypothetical protein/ATP synthase epsilon chain
Reads supporting (aligned to +/- strand):  ref base . (2/0);  new base A (7/14);  total (9/14)
Fisher's exact test for biased strand distribution p-value = 1.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTTTTACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTC‑A‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGGCTCTATGAATATCAGTATTGTCGTCATCATTTT  >  USA300TCH1516_ALE/2220724‑2220999
                                                                                                                                             |                                                                                                                                        
attattACTAATATATTCATATTTTTAAATACAGATTAGCTGTTATTAATGATAAAAAACCACTACATCATAAATCTTTAATGTTTCTTTATAAATTCCTACCAACCTCTCATATTTTGTATCTTTAAATCAATATAATTc                                                                                                                                           <  2:252782/137‑1 (MQ=255)
aGTTTTACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATATAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTc                                                                                                                                           >  1:122942/1‑141 (MQ=255)
aGTTTTACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTc                                                                                                                                           >  1:136773/1‑141 (MQ=255)
aGTTTTACTCATGTATTCCTAATTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTc                                                                                                                                           <  2:182260/141‑1 (MQ=255)
    ttACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCACCCATCTCATGTTTTGTATTTTTAAATAAATATATTTT‑a‑aaa                                                                                                                                     >  2:141859/1‑141 (MQ=25)
     tACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTT‑a‑aaaa                                                                                                                                    >  1:248409/1‑141 (MQ=255)
      aCTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTC‑a‑aaaaa                                                                                                                                   <  1:95153/141‑1 (MQ=255)
      aCTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCCTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTC‑a‑aaaaa                                                                                                                                   <  1:203438/141‑1 (MQ=255)
       cTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTC‑a‑caaaaa                                                                                                                                  >  1:48499/1‑140 (MQ=255)
              aTTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCATCCACCCTCTCAGGTTTTGTCCCTTTAAATCAATATAATTC‑A‑AAAAAaggggcga                                                                                                                           >  1:38870/1‑136 (MQ=37)
                tCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAg                                                                                                                          <  1:258132/141‑1 (MQ=255)
                 ccTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCGTTATAAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGa                                                                                                                         <  2:131939/141‑1 (MQ=255)
                    tttttcAAATACACCTTAACAGTACATAATCATAAAGAGCCACTACATCATAAATCTTTAATGGTTCTTAATCAATTCCTCACCCCCCCTCATGCTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGatat                                                                                                                      <  2:234608/140‑1 (MQ=255)
                    ttttgtAAATAGACATTATCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCGTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGatat                                                                                                                      <  2:270167/140‑1 (MQ=38)
                    atgtttAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGatat                                                                                                                      <  2:132558/138‑1 (MQ=255)
                    aTTTTTAAATACACATTAGCTTTGTTTAATGATAAAGAAACACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGatat                                                                                                                      <  2:239549/141‑1 (MQ=255)
                           aaTACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATca                                                                                                               <  1:13630/141‑1 (MQ=255)
                                                     aaaGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTAttt                                                                                     <  2:83965/141‑1 (MQ=255)
                                                                 catcatAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGCCGAAGATATGAACTCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCcac                                                                         >  1:8327/1‑141 (MQ=255)
                                                                     atAGATCTTGTATGGTTGGTTATCAAGTCGTTACCCCCTCTAATGTTTTGTATCTTTAAATCAATATGATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCGACACGc                                                                     <  2:133446/141‑1 (MQ=255)
                                                                        aaTCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCaaa                                                                  >  1:242982/1‑141 (MQ=255)
                                                                            tttAATGGTTCTTTATCAATTCCTTCCCCCCTATCATGTTTTGTATCTTTAAATCAATATAATTC‑ACACAAAGTTTCGAAGATATTAAACCACATCTTCGACCCTCTCTTTACTATTTTAATTCAGCCCCACTCacactct                                                              >  2:248869/1‑138 (MQ=255)
                                                                               aaTGGTTCTTTATCAATTCCTTCCCCCCTGTCATGTTTTGTATCTTTACATCAATATAATTCAA‑AAAAAGGGTCGAAGATATAAAATCACAACTTCGACCCTTTATTTACTATTTTAATTCACCCCCCCGCCACCGGTAAt                                                           >  2:280974/1‑141 (MQ=255)
                                                                                            cAATTCCTGCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTaa                                              <  1:274571/141‑1 (MQ=255)
                                                                                               ttccttccCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGc                                           <  2:122942/141‑1 (MQ=255)
                                                                                               ttccttccCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGc                                           <  2:136773/141‑1 (MQ=255)
                                                                                                   ttccACCATCTAAAGTTTTGTCCCTTTACATAATGATAATTCAA‑AAAAAGGGTCGAAGAAATAAGATTGCATCTTCGACGCTTGGTAGACTATTTTAATTCAGCCACACGCAAACGGTTATGTGCTCTCTCTAAGGGTCtt                                       >  2:5106/1‑141 (MQ=255)
                                                                                                            ctcATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGACGCACATTTGTAATACCATGGACGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGGCTCTa                              >  1:280561/1‑141 (MQ=255)
                                                                                                                          ttttAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACTTTGTCTACTCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGGCTCTATGAATATCAGTAtt                <  2:242982/140‑1 (MQ=255)
                                                                                                                                    atatAATTCAA‑AAAAAGGGACGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGTCTCTATGAATATTAGTATTGTCGtcatct      >  1:272486/1‑140 (MQ=255)
                                                                                                                                       taATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGAACCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGGCTCTATGAATATCAGTATTGTCGTCATCAttt   <  1:192829/141‑1 (MQ=255)
                                                                                                                                        aaTTCAA‑AAAAAGGATCGAAGATAAGAAATCACATCTTCGACCCTTTATTTACTATTTTAACTCAGCCACACGCCAACGGTTACTCGCTCTCTCTAAAGCCCTTTCGCCCCTATCAATATCAGCATCACCGCCATCAtttc  >  2:22453/1‑140 (MQ=255)
                                                                                                                                             |                                                                                                                                        
AGTTTTACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTC‑A‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGGCTCTATGAATATCAGTATTGTCGTCATCATTTT  >  USA300TCH1516_ALE/2220724‑2220999

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: ‑