Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 195,286 T→A intergenic (‑97/‑82) USA300HOU_RS00900 ← / → USA300HOU_RS00905 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE195,2860TA100.0% 282.8 / NA 76intergenic (‑97/‑82)USA300HOU_RS00900/USA300HOU_RS00905hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (30/46);  total (30/46)

CCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGAC  >  USA300TCH1516_ALE/195199‑195372
                                                                                       |                                                                                      
ccccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTaaaa                                                                                     >  1:2621550/1‑91 (MQ=255)
ccccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTaaaa                                                                                     <  1:2163610/91‑1 (MQ=255)
    tatatataTGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTaaaaaaaa                                                                                 <  1:3233089/91‑1 (MQ=255)
       atatatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAatat                                                                              <  1:152214/91‑1 (MQ=255)
        tatatGTTTATTTTCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTATAAAAAATTTc                                                                             >  1:166589/1‑91 (MQ=255)
        tatatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATc                                                                             >  1:2644152/1‑91 (MQ=255)
        tatatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATc                                                                             >  1:2644250/1‑91 (MQ=255)
         atatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCt                                                                            <  1:769981/91‑1 (MQ=255)
             gTTGATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAat                                                                        <  1:2992657/91‑1 (MQ=255)
                  tttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCt                                                                   <  1:2577049/91‑1 (MQ=255)
                    taCTTATACCCTAACGTGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTg                                                                 <  1:3347858/91‑1 (MQ=255)
                    taCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTg                                                                 <  1:201287/91‑1 (MQ=255)
                      cTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTa                                                               >  1:313003/1‑91 (MQ=255)
                      cTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTa                                                               >  1:1627638/1‑91 (MQ=255)
                      cTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTa                                                               >  1:709926/1‑91 (MQ=255)
                      cTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTa                                                               >  1:710203/1‑91 (MQ=255)
                        tataCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAAt                                                             <  1:993051/91‑1 (MQ=255)
                            cccTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGa                                                         <  1:2832461/91‑1 (MQ=255)
                            cccTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGa                                                         <  1:2832559/91‑1 (MQ=255)
                            cccTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGa                                                         <  1:2832560/91‑1 (MQ=255)
                               tAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATaa                                                      >  1:2978745/1‑91 (MQ=255)
                                 aCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGa                                                    <  1:2172497/91‑1 (MQ=255)
                                   aTGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAAt                                                  >  1:708213/1‑91 (MQ=255)
                                   aTGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAAt                                                  >  1:2738627/1‑91 (MQ=255)
                                    tGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAACTATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAAtt                                                 >  1:2939639/1‑91 (MQ=255)
                                    tGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAAtt                                                 <  1:647358/91‑1 (MQ=255)
                                    tGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAAtt                                                 <  1:1625099/91‑1 (MQ=255)
                                      aTTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAGTtat                                               >  1:3081233/1‑91 (MQ=255)
                                      aTTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATtat                                               >  1:3506730/1‑91 (MQ=255)
                                       tttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAACAATATCTTAATATCCTTGTAATCCGATAAGTATtata                                              >  1:2619637/1‑91 (MQ=255)
                                       tttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATtata                                              >  1:725693/1‑91 (MQ=255)
                                        ttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAg                                             <  1:3559192/91‑1 (MQ=255)
                                        ttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAg                                             <  1:3425475/91‑1 (MQ=255)
                                         tttATACTCTTTGATAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGt                                            <  1:2701877/91‑1 (MQ=255)
                                         tttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGt                                            <  1:1064432/91‑1 (MQ=255)
                                         tttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGt                                            <  1:3355999/91‑1 (MQ=255)
                                          ttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTa                                           >  1:666978/1‑91 (MQ=255)
                                           tataCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTaa                                          >  1:2387238/1‑91 (MQ=255)
                                            ataCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAat                                         <  1:2336604/91‑1 (MQ=255)
                                            ataCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAat                                         >  1:664030/1‑91 (MQ=255)
                                            ataCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAat                                         <  1:406979/91‑1 (MQ=255)
                                             taCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAata                                        <  1:444827/91‑1 (MQ=255)
                                             taCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAata                                        <  1:97750/91‑1 (MQ=255)
                                              aCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAatat                                       <  1:2675933/91‑1 (MQ=255)
                                              aCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAatat                                       >  1:3502550/1‑91 (MQ=255)
                                              aCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAatat                                       <  1:278516/91‑1 (MQ=255)
                                               ctctTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAtt                                      <  1:2927460/91‑1 (MQ=255)
                                                tctTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAttt                                     >  1:2605024/1‑91 (MQ=255)
                                                 ctTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAtttt                                    >  1:3491106/1‑91 (MQ=255)
                                                   ttGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAtttttt                                  <  1:1259194/91‑1 (MQ=255)
                                                     gAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCa                                <  1:2330864/91‑1 (MQ=255)
                                                     gAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCa                                <  1:950456/91‑1 (MQ=255)
                                                      aaaaTATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCaa                               <  1:1347526/91‑1 (MQ=255)
                                                        aaTATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAAcc                             <  1:141175/91‑1 (MQ=255)
                                                        aaTATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAAcc                             <  1:1969903/91‑1 (MQ=255)
                                                         atatatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCa                            >  1:3091024/1‑91 (MQ=255)
                                                         atatatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCa                            >  1:1826767/1‑91 (MQ=255)
                                                            tatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTg                         <  1:1469252/91‑1 (MQ=255)
                                                              ttttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGtt                       <  1:1270174/91‑1 (MQ=255)
                                                              ttttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGtt                       <  1:2693495/91‑1 (MQ=255)
                                                              ttttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGtt                       <  1:1412182/91‑1 (MQ=255)
                                                              ttttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTAGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGtt                       >  1:3701356/1‑91 (MQ=255)
                                                               tttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTta                      >  1:2887343/1‑91 (MQ=255)
                                                               tttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTta                      <  1:1482350/91‑1 (MQ=255)
                                                               tttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTta                      >  1:2938967/1‑91 (MQ=255)
                                                                  aCAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATag                   <  1:3527132/91‑1 (MQ=255)
                                                                   cAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATagg                  <  1:1212941/91‑1 (MQ=255)
                                                                      aaTTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTACTCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATaggagg               <  1:3710626/91‑1 (MQ=255)
                                                                        ttttATCTAAATATTAAAAAAAATATCTTAATATCCTTTTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTc             >  1:988694/1‑91 (MQ=255)
                                                                         tttATCTAAATATTAAAAGAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCt            <  1:2597042/91‑1 (MQ=255)
                                                                         tttATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGGGGTCt            <  1:2004756/91‑1 (MQ=255)
                                                                         tttATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGGGGTCt            <  1:2004821/91‑1 (MQ=255)
                                                                         tttATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCt            <  1:2597178/91‑1 (MQ=255)
                                                                          ttATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCtt           <  1:40865/91‑1 (MQ=255)
                                                                          ttATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCtt           >  1:971323/1‑91 (MQ=255)
                                                                             tCTAAACATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCttatt        >  1:2877038/1‑91 (MQ=255)
                                                                                 aaTATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATg    <  1:2543869/91‑1 (MQ=255)
                                                                                   tatTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGAc  <  1:3572856/91‑1 (MQ=255)
                                                                                   tatTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGAc  >  1:3544940/1‑91 (MQ=255)
                                                                                       |                                                                                      
CCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGAC  >  USA300TCH1516_ALE/195199‑195372

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑