Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,744,494 A→T 27.7% F60I (TTT→ATT)  apt ← Adenine phosphoribosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,744,4940AT27.7% 80.4 / 28.8 54F60I (TTT→ATT) aptAdenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand):  ref base A (16/22);  new base T (10/5);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.13e-01

TTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTT  >  USA300TCH1516_ALE/1744357‑1744629
                                                                                                                                         |                                                                                                                                       
tttGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATCAGCTACAGGACAGCCAATGATAATGcc                                                                                                                                      >  2:687827/1‑141 (MQ=255)
 ttGTGCATTGTTAAAACATTTGTACCATATTCTATGGCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGTTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCa                                                                                                                                     <  2:493211/141‑1 (MQ=255)
  tgtgCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCATTCCCCATTTAATAAGCTACAGGAAAACCAATGATACGGCCAc                                                                                                                                    >  1:627960/1‑141 (MQ=255)
      cATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACgcgc                                                                                                                                <  1:61721/141‑1 (MQ=255)
        ttGTTAAAACATTTGTACCATATTCTAGGTCATAATCATAACCAATGACTGCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAATGCCACGCGCtt                                                                                                                              <  1:320812/141‑1 (MQ=255)
              aaaCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCACATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTc                                                                                                                        <  2:227393/141‑1 (MQ=255)
               aaCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGATGCAAAGCCAATCCCCATTGAATAATCTACAGGACAGCCAATGATAAACCCACGCGCTTCAGGTcc                                                                                                                       >  2:252241/1‑141 (MQ=255)
                   tttGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCTACGCGCTTCAGGTCCTACa                                                                                                                   >  1:420021/1‑141 (MQ=255)
                   tttGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACa                                                                                                                   >  1:156048/1‑141 (MQ=255)
                    ttGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACaa                                                                                                                  >  1:266175/1‑141 (MQ=255)
                        aCCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCATGTCCTGCAACgct                                                                                                              >  1:382174/1‑139 (MQ=255)
                         ccATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGata                                                                                                             >  1:268035/1‑141 (MQ=255)
                                 tAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTACCTTCTTTTCTAACAGTTGCAAAGCCAATCCCCATTAAATAAACTCCGAAGGAGCCACTGATAATACCAAGCGCTTCAGGTCCTACAACAATATCAACAtc                                                                                                     >  2:189626/1‑141 (MQ=255)
                                      cATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCGTCAGGTCCTACAACGATATCAACATCTCTGt                                                                                                <  2:616547/141‑1 (MQ=255)
                                      cATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCAAATGATAATGCCACGCCCTACAGGTCCTACAACGATATCAACATCTATGt                                                                                                >  2:469634/1‑141 (MQ=255)
                                       aTACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTc                                                                                               <  2:570024/141‑1 (MQ=255)
                                          cTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAATGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCttt                                                                                            <  2:754334/141‑1 (MQ=255)
                                          cTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCTACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCttt                                                                                            <  2:394945/141‑1 (MQ=255)
                                          cTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGCACAGGCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCttt                                                                                            <  1:289975/141‑1 (MQ=255)
                                          cTCATAACGAATGACTTCACGAGGGAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCttt                                                                                            <  2:556265/141‑1 (MQ=255)
                                                aCGTATGACTTCACGAGGTAATTTCCCTTCTGTTCTAACAGGTGCAAAGCCAATCCACATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTa                                                                                      <  2:248906/141‑1 (MQ=255)
                                                 cGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCACATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTAt                                                                                     <  1:5244/141‑1 (MQ=255)
                                                     tGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGTTGCAAAGACAAACCCCGTTGAATCACACGCATGACATCCAATGATAAAGCCACGCGATTCAGGTCCTACACCGATATCAACATCTCTGTCTTTTCCGTATTCTa                                                                                 >  1:178677/1‑141 (MQ=255)
                                                          tCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAAtt                                                                            <  1:682751/141‑1 (MQ=255)
                                                                  tcaTTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAATGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACCATTTTATCTGt                                                                    >  2:548952/3‑141 (MQ=255)
                                                                      tcctcctcttTTCCAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCa                                                                <  1:666771/135‑1 (MQ=255)
                                                                        cccTTCTTTTCTAACAGGTGCAAAGCCAATCCACATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATa                                                              <  1:559234/141‑1 (MQ=255)
                                                                          cttcttTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGc                                                            <  1:25109/141‑1 (MQ=255)
                                                                            tcttTTCTAACAGGTGCAAATCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACTATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCa                                                          <  2:393832/141‑1 (MQ=255)
                                                                               tttCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAATGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCatat                                                       >  1:509036/1‑141 (MQ=255)
                                                                                    aacatttGCAAAGCCAATCCCCATGGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACCTCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTc                                                  <  1:697582/135‑1 (MQ=255)
                                                                                    aaCAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGTATAGCCATATGCttt                                                  >  1:451989/1‑140 (MQ=255)
                                                                                       aGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCAcc                                               <  1:530766/141‑1 (MQ=255)
                                                                                       aGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATCCTTCAcc                                               >  1:432101/1‑141 (MQ=255)
                                                                                       aGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTATCATCACCATATGCTTAAca                                               >  2:599669/1‑140 (MQ=255)
                                                                                       aGGAGCAAACCCCATCACCGTTGATTAAGATAAAGGACAGCTAATAATAATGGCGCTCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGTGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCAcc                                               <  2:198307/141‑1 (MQ=255)
                                                                                         gTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACTCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCAt                                             <  2:266175/141‑1 (MQ=255)
                                                                                            cAAAGCCAATCCCCATTGAATAAGCTACAGGACAGACAATGATAATGCCACGCGCTTCAGGTCCTACAAAGATATCAACATCTCTGTTGTGTACGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTAt                                          >  1:672127/1‑141 (MQ=255)
                                                                                             aaaGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAATGTCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTAtt                                         >  1:146501/1‑140 (MQ=255)
                                                                                             aaaGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAATGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATCGCCATATGCTTCACCATTATc                                         >  1:216076/1‑141 (MQ=255)
                                                                                             aaaGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAATGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCCTTATc                                         >  1:530920/1‑141 (MQ=255)
                                                                                             aaaGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAATGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATc                                         >  1:216052/1‑141 (MQ=255)
                                                                                                     cccccATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTg                                 <  1:302052/140‑1 (MQ=255)
                                                                                                      ccccATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTgt                                <  2:627960/141‑1 (MQ=255)
                                                                                                                        aGGACAGCCAATGATACAGCCACGCGCTTCAGGTCCTACAACGATATCAGCGTCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACt              <  2:443723/141‑1 (MQ=255)
                                                                                                                           aCAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATCACATTGaaagtgaa           >  2:172677/1‑136 (MQ=255)
                                                                                                                           aCAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTCCGTATTCTACAATTTTATCTGTTTCATAGCCATATGCTTCACCACTATCCATAATTGTAGTAATATCCTTGAAACTAac           >  2:749475/1‑141 (MQ=255)
                                                                                                                           aCAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTACGTATTCTACAATTTTATCTGTTGCATAGCCATATGTTTCACCATTATCCATAATTGTAGTAATATACTCGAAACTAac           >  2:172690/1‑141 (MQ=255)
                                                                                                                              gCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTATATTTTTAGAATTGTCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACAcc        >  1:175931/1‑141 (MQ=255)
                                                                                                                              gCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACAcc        <  2:515831/141‑1 (MQ=255)
                                                                                                                               ccAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCt       >  2:278366/1‑141 (MQ=255)
                                                                                                                                  aTGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATACTTGTAGTAATATCCTTGAAACTAACACCTCGt    >  2:744831/1‑141 (MQ=255)
                                                                                                                                    gATAATGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGttt  <  1:421497/141‑1 (MQ=255)
                                                                                                                                    gATAATGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCATTGAAACTAACACCTGGttt  <  2:275911/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                       
TTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTT  >  USA300TCH1516_ALE/1744357‑1744629

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: