Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 505,514 C→T A469V (GCG→GTG)  treP_1 → PTS system trehalose‑specific EIIBC component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE505,5140CT100.0% 137.9 / NA 41A469V (GCG→GTG) treP_1PTS system trehalose‑specific EIIBC component
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (17/24);  total (17/24)

GTTGGTGGCGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGCGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGTTGTATATCAAATTT  >  USA300TCH1516_ALE/505384‑505645
                                                                                                                                  |                                                                                                                                   
gttggtgGCGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAg                                                                                                                    >  4:41326/1‑148 (MQ=255)
gttggtgGCGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAg                                                                                                                    >  4:216943/1‑148 (MQ=255)
gttggtgGCGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAg                                                                                                                    >  3:286073/1‑148 (MQ=255)
   ggtggCGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGAtt                                                                                                                 >  3:261338/1‑148 (MQ=255)
     tggCGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATtaa                                                                                                               <  3:72680/148‑1 (MQ=255)
        cGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGa                                                                                                                   <  2:35802/141‑1 (MQ=255)
        cGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATtaataa                                                                                                            <  4:144172/148‑1 (MQ=255)
        cGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATtaataa                                                                                                            <  4:97144/148‑1 (MQ=255)
        cGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATtaataa                                                                                                            <  4:43413/148‑1 (MQ=255)
        cGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATtaataa                                                                                                            <  3:151949/148‑1 (MQ=255)
        cGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATtaataa                                                                                                            <  3:373108/148‑1 (MQ=255)
                        tcaattcaaAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGcgt                                                                                            >  3:97088/1‑148 (MQ=255)
                                 aaaGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTAttt                                                                                   <  3:174374/148‑1 (MQ=255)
                                  aaGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTg                                                                                  <  3:327567/148‑1 (MQ=255)
                                      aTTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGACATTGTTGAAGATTAATATTATAAAAATGGGGCGTTCGTTAt                                                                                     <  2:40245/141‑1 (MQ=255)
                                           ggCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCtt                                                                         >  4:341950/1‑148 (MQ=255)
                                           ggCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCtt                                                                         <  4:251605/148‑1 (MQ=255)
                                            gCCAGTATATGTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAAAAAAAAAGGGGCGTTCGTTATTTGGACGTCCttt                                                                        <  4:29954/148‑1 (MQ=255)
                                               aGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTc                                                                            <  1:240/141‑1 (MQ=255)
                                                         aTTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAg                                                           <  4:28771/148‑1 (MQ=255)
                                                                  gctattgctattGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAAtt                                                  <  3:284144/148‑1 (MQ=255)
                                                                    tattgctattgTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATtgt                                                >  3:198204/1‑148 (MQ=255)
                                                                       tgctattgTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATtgtgtg                                             <  4:261338/148‑1 (MQ=255)
                                                                               ttgtACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCgaaaga                                     <  3:370301/148‑1 (MQ=255)
                                                                                   aCCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATa                                 >  4:260335/1‑148 (MQ=255)
                                                                                    ccATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAg                                >  4:317696/1‑148 (MQ=255)
                                                                                             cTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGaa                       >  3:40769/1‑148 (MQ=255)
                                                                                                    ttGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGt                <  3:79811/148‑1 (MQ=255)
                                                                                                    ttGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGt                <  3:230280/148‑1 (MQ=255)
                                                                                                    ttGTGATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGt                <  4:316181/148‑1 (MQ=255)
                                                                                                      gtgATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGTTg              <  3:2833/148‑1 (MQ=255)
                                                                                                      gtgATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGTTg              <  3:67463/148‑1 (MQ=255)
                                                                                                        gATGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGTTGta            >  4:162577/1‑148 (MQ=255)
                                                                                                         aTGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGTTGtat           >  4:192023/1‑148 (MQ=255)
                                                                                                         aTGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGTTGtat           >  4:41557/1‑148 (MQ=255)
                                                                                                         aTGTCTCATTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGTTGtat           >  3:233988/1‑148 (MQ=255)
                                                                                                             ctcAGTTTAGGAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATACGTTCTAAATCa       >  4:327931/1‑148 (MQ=255)
                                                                                                                aTTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATCAAATAAGAAAGGGGCGTTCGTTATTTGGACGCCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGTTGTATATCAAAt    >  3:357729/1‑148 (MQ=255)
                                                                                                                aTTTTAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGTTGTATATCAAAt    >  3:236995/1‑148 (MQ=255)
                                                                                                                  tttAGTAAACAAAAAGTGAAAGAAATTGTTGAATATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAATAAATAGATTGGAGAAAATCCGTTGTATATCAAAttt  <  4:229736/148‑1 (MQ=255)
                                                                                                                  tttAGTAAACAAAAAGTGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGTTGTATATCAAAttt  <  3:391536/148‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                   
GTTGGTGGCGTGCCAGCATTCATTTCAATTCAAAAAGAATTTTGGCCAGTATATCTTATTGTGACAGCTATTGCTATTGTTGTACCATGTATACTAACAATTGTGATGTCTCATTTTAGTAAACAAAAAGCGAAAGAAATTGTTGAAGATTAATAAAATAAAAAAGGGGCGTTCGTTATTTGGACGTCCTTTATTACGTTATAAGGTGGTAATTGTGTGTCGAAAGAAATAGATTGGAGAAAATCCGTTGTATATCAAATTT  >  USA300TCH1516_ALE/505384‑505645

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑