Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,046,852 G→A 7.5% intergenic (+60/+29) putP → / ← USA300HOU_RS10335 Sodium/proline symporter/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,046,8520GA 7.5% 166.9 / 4.3 53intergenic (+60/+29)putP/USA300HOU_RS10335Sodium/proline symporter/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (20/29);  new base A (2/2);  total (22/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

AAGTAAACTTACTAAAAAACCTGGTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAATTTCATAGTTATCGATTTTATC  >  USA300TCH1516_ALE/2046714‑2046991
                                                                                                                                          |                                                                                                                                           
aagtaaACTTACTAAAAAACCTGGTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGt                                                                                                                                           >  2:200032/1‑141 (MQ=255)
    aaaCTTACTAAAAAACCTGGTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACCAATGTTAGTCATAATTTTGATTAACATTAGTACCt                                                                                                                                       <  1:557711/141‑1 (MQ=37)
        ttACTAAAAAACCTGGTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACCAATGTTAGTCATAATTTTGATTAACATTAGTACCttttt                                                                                                                                   <  1:485271/141‑1 (MQ=37)
          aCTAAAAAACCTGGTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTttat                                                                                                                                 <  1:28639/141‑1 (MQ=255)
             aaaaaaCCTGGTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTtattat                                                                                                                              >  2:223084/1‑141 (MQ=255)
             aaaaaaCCTGGTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTtattat                                                                                                                              <  1:572947/141‑1 (MQ=255)
              aaaaaCCTGGTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATc                                                                                                                             <  2:9987/141‑1 (MQ=255)
              aaaaaCCTGGTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATc                                                                                                                             <  2:9975/141‑1 (MQ=255)
              aaaaaCCTGGTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATc                                                                                                                             <  1:258803/141‑1 (MQ=255)
                       gTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTAGGATCTTTAATTTa                                                                                                                    >  1:43025/1‑141 (MQ=255)
                            tttGTTGAAACTTACTTAAACAAAGTTCGTGACATCGTTAGAGTAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACaatt                                                                                                               <  2:15120/141‑1 (MQ=255)
                            tttGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTCTCCGTAATTTACaatt                                                                                                               >  2:269640/1‑141 (MQ=255)
                                  gAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTAc                                                                                                         >  1:662464/1‑141 (MQ=255)
                                  gAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTAc                                                                                                         <  1:497446/141‑1 (MQ=255)
                                         aCTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAat                                                                                                  <  1:421936/141‑1 (MQ=255)
                                          cTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAata                                                                                                 <  1:268477/141‑1 (MQ=255)
                                            tAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATg                                                                                               <  1:705003/141‑1 (MQ=255)
                                                 aaaGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAACATTATGACTAACATTGGTACCTTTCTATTATATTTAATTTACAATTAATTACTGTAAATATGAACtt                                                                                          <  1:676456/141‑1 (MQ=255)
                                                  aaGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTg                                                                                         <  1:276426/141‑1 (MQ=255)
                                                  aaGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTg                                                                                         <  2:27487/141‑1 (MQ=255)
                                                   aGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGc                                                                                        >  1:630171/1‑141 (MQ=255)
                                                        gTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTc                                                                                   >  2:267902/1‑141 (MQ=255)
                                                               cGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCa                                                                            <  2:5140/141‑1 (MQ=255)
                                                                  tAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCt                                                                         <  1:437413/141‑1 (MQ=255)
                                                                   agagAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCtt                                                                        >  2:77522/1‑141 (MQ=255)
                                                                   agagAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCtt                                                                        <  1:724410/141‑1 (MQ=255)
                                                                   agagAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCtt                                                                        <  1:670945/141‑1 (MQ=255)
                                                                    gagaAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCttt                                                                       <  1:225214/141‑1 (MQ=255)
                                                                    gagaAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCttt                                                                       >  1:469763/1‑141 (MQ=255)
                                                                          aataatTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCtt                                                                 <  1:682253/141‑1 (MQ=255)
                                                                             aatTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACt                                                              <  1:255227/141‑1 (MQ=255)
                                                                              cttCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTa                                                             >  2:166118/2‑141 (MQ=255)
                                                                              atTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTa                                                             >  2:166126/1‑141 (MQ=255)
                                                                                      gTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGc                                                     <  1:556171/141‑1 (MQ=255)
                                                                                        cTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCAc                                                   <  1:110335/141‑1 (MQ=255)
                                                                                                aTTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGtggttgg                                           <  1:494475/141‑1 (MQ=255)
                                                                                                   aaaaaGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTa                                        >  1:436358/1‑141 (MQ=255)
                                                                                                     aaaGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTAcc                                      >  1:269595/1‑141 (MQ=255)
                                                                                                           aCTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCttt                                >  1:753114/1‑141 (MQ=255)
                                                                                                           aCTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCttt                                >  1:370245/1‑141 (MQ=255)
                                                                                                           aCTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCttt                                >  1:107059/1‑141 (MQ=255)
                                                                                                               aTGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATa                            <  1:250369/141‑1 (MQ=255)
                                                                                                                tGTTAGTCATAATTTTGATTAACATTAGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATAc                           >  1:441389/1‑141 (MQ=38)
                                                                                                                    aaTCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAAt                       >  1:390182/1‑141 (MQ=255)
                                                                                                                       cAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAATTTc                    >  2:88156/1‑141 (MQ=255)
                                                                                                                             tttgattAACATTAGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAATTTCATAGtt              >  1:139682/7‑141 (MQ=255)
                                                                                                                              aTGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAATTTCATAGTTa             <  1:180697/141‑1 (MQ=255)
                                                                                                                               tGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAATTTCATAGTTAt            >  2:103151/1‑141 (MQ=255)
                                                                                                                                  cTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAATTTCATAGTTATCGa         <  1:497152/141‑1 (MQ=255)
                                                                                                                                   tAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAATTTCATAGTTATCGAt        >  2:71763/1‑141 (MQ=255)
                                                                                                                                    aaCATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAATTTCATAGTTATCGAtt       <  1:273184/141‑1 (MQ=255)
                                                                                                                                         tGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAATTTCATAGTTATCGATTTTATc  <  1:774940/141‑1 (MQ=255)
                                                                                                                                         tGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAATTTCATAGTTATCGATTTTATc  <  2:59877/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                           
AAGTAAACTTACTAAAAAACCTGGTGCATTTGTTGAAACTGACTTAAACAAAGTTCGTGACATCGTTAGAGAAAAATAATTCATAAGTCTTAACAAATTAAAAAGGTACTAATGTTAATCAAAATTATGACTAACATTGGTACCTTTTTATTATCTTTAATTTACAATTAATTACTGTAAATATGAACTTGCGGTTCTTTGTCATCTTTTGTCTTACTAATTAAAGCACGTGGTTGGTTACCATCTTTAATACGAATTTCATAGTTATCGATTTTATC  >  USA300TCH1516_ALE/2046714‑2046991

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: ‑