Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,874,887 G→A 17.2% L108F (CTT→TTT)  rsuA ← Ribosomal small subunit pseudouridine synthase A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,874,8870GA17.2% 114.3 / 13.1 56L108F (CTT→TTT) rsuARibosomal small subunit pseudouridine synthase A
Reads supporting (aligned to +/- strand):  ref base G (18/27);  new base A (4/6);  total (22/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTGTTACACCCTCTTTAAAAGCTTGAATGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATAACCTTTTGGCTTATTTAA  >  USA300TCH1516_ALE/1874748‑1875016
                                                                                                                                           |                                                                                                                                 
agtGTTACACCCTCTTTAAAAGCTTGAATGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAg                                                                                                                                   <  2:537966/140‑1 (MQ=255)
 gtgtTACACCCTCTTTAAAAGCTTGAATGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTGTAGAAACATGTTTGTTTGGACTCATTAGTTCATGCTTAAAATCACCATCATTCGTTATCAATAAAAGc                                                                                                                                  >  2:595355/1‑140 (MQ=255)
      acacCCTCTTTAAAAGCTTGAATGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTc                                                                                                                             >  1:357272/1‑140 (MQ=255)
       cacCCTCTTTAAAAGCTTGAATGTCGTCTTCAGTGATAGGCTTTGCTGAAATAACTTCATATTTTTTAGAATCATGTTTGTTTGGACTGATTAATTGATGATTAAAATCACCATCATTCGTTATAAATAAAAGccatgat                                                                                                                            >  1:716315/1‑135 (MQ=255)
       cacCCTCTTTAAAAGCTTGAATGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCt                                                                                                                            <  1:504501/140‑1 (MQ=255)
       cacCCTCTTTAAAAGCTTGAATGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCt                                                                                                                            >  2:538527/1‑140 (MQ=255)
              tttAAAAGCTTGAATGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCtt                                                                                                                     >  2:709716/1‑140 (MQ=255)
               ttAAAAGCTTGAATGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTCTCttt                                                                                                                    >  2:451537/1‑140 (MQ=255)
                    aGCTTGAATGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCaa                                                                                                               <  1:91411/140‑1 (MQ=255)
                      actGAATGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATCCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAga                                                                                                             <  1:35387/138‑1 (MQ=255)
                          aaTGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTGAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAgacgac                                                                                                         >  1:676926/1‑140 (MQ=255)
                            tGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATGCATGATTAAAATCACCATCATTCGTTATCAATAAAATCCCTTCTGTATCTTTATCAAGACGACCa                                                                                                       <  1:577588/140‑1 (MQ=255)
                               cgtcTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAAcc                                                                                                    >  1:308697/1‑140 (MQ=255)
                                       gTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAat                                                                                            <  1:395636/140‑1 (MQ=255)
                                          aTAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTGTCTTTATCAAGACGACCAACCGGAAAAatagt                                                                                         >  1:794/1‑138 (MQ=255)
                                                  tGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGtt                                                                                 <  2:458560/140‑1 (MQ=255)
                                                     tGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAACATATTTAGATGTTGGt                                                                              >  1:423343/1‑140 (MQ=255)
                                                     tGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTggg                                                                              >  1:460104/1‑139 (MQ=255)
                                                       aaaTAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTAt                                                                            >  1:547723/1‑140 (MQ=255)
                                                          tAACTTGACATTTTTTAGAAACAGGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCa                                                                         <  2:406681/140‑1 (MQ=255)
                                                          tAACTTCATATTTTTTAGAAACATGTTTGTTTGTACTCATTAATTCATGAGTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCa                                                                         <  1:232376/140‑1 (MQ=255)
                                                            aCTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATTGCTGTCATTCAATATCAATAAAAACCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAgg                                                                       <  1:587442/140‑1 (MQ=255)
                                                             cTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGt                                                                      >  1:219703/1‑140 (MQ=255)
                                                              ttCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCTTGATTAAAATCACCATCATTCGTTATCAATAAAAGCCTTTCTGTATCTTTATTAAAACTACCAACAGAAAACATATTTAGATGTTAGTATTCAGGTa                                                                     >  2:229071/1‑140 (MQ=255)
                                                               tCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTAt                                                                    <  1:145822/140‑1 (MQ=255)
                                                               tCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAACCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTAt                                                                    <  1:786019/140‑1 (MQ=255)
                                                                   atTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTaaa                                                                <  1:166020/140‑1 (MQ=255)
                                                                        ttcgAAACATGCTGGTTTGGACTCATTAATTCATGATTAAAATCACCAGCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAAt                                                           <  1:84948/137‑1 (MQ=255)
                                                                        ttAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAAt                                                           <  1:468924/140‑1 (MQ=255)
                                                                        ttAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTAGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAAt                                                           <  2:121346/140‑1 (MQ=255)
                                                                         tacataCATGGGTGTTGGGACTCGTGAATTCATGATTAAAATCACCACCATTCGTTATGAATAAAAGCCCTGCTGTATCGTTATCAAGACGACCAAGCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATa                                                          <  1:183370/135‑1 (MQ=255)
                                                                         tAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATa                                                          <  1:278853/140‑1 (MQ=255)
                                                                           gAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGAGCAACCGACAAAATATTTAGATCTTGGTATTCAGGTATGAAATCAATAAc                                                        >  2:212393/1‑140 (MQ=255)
                                                                               cATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAACCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAGTATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGtt                                                    >  1:625991/1‑140 (MQ=255)
                                                                               cATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAACCCTTCTGTATCTTTATCAAGACGACAAACCAGAAAAATATTTAGATGTTGTTATTCCGGTATTAAATCCATaaacgtt                                                    >  2:504811/1‑135 (MQ=255)
                                                                                      gtttgGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAat                                             <  2:676926/140‑1 (MQ=255)
                                                                                      gtttgGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAACCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAat                                             <  1:401163/140‑1 (MQ=255)
                                                                                       tttgGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAatg                                            >  2:415456/1‑140 (MQ=255)
                                                                                          ggcctctTTAATTCATGATTAAAATACCCCTCATTCGTTATCAATATAAGCCCTTCTGTATCTTTATCAAGACGACCAACCTGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAatgatg                                         <  2:290818/137‑1 (MQ=255)
                                                                                            aCTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATAGAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATgatgat                                       >  1:30165/1‑140 (MQ=255)
                                                                                              tCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAACCCTTCTGTATCTTTATCAAGACTACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCt                                     <  2:740658/140‑1 (MQ=255)
                                                                                                aTTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTc                                   <  1:709716/140‑1 (MQ=255)
                                                                                                 ttAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAAACCTACCGTATCGTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTACTAAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCa                                  <  1:715955/140‑1 (MQ=255)
                                                                                                  tAATTCATGATTAGAATCCCCACCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAg                                 <  2:794/140‑1 (MQ=255)
                                                                                                             tAAAGTCACTGTCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGTAAAAATATTTAGATGTTTGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGatata                      <  2:133163/140‑1 (MQ=255)
                                                                                                             tAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGatata                      <  1:642640/140‑1 (MQ=255)
                                                                                                                agtCACCAGCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATaa                   <  2:749825/138‑1 (MQ=255)
                                                                                                                 aTCACTGTCAGTCGTTATCAAGAAAAGCCCTTCTTTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATAAc                  <  1:694369/140‑1 (MQ=255)
                                                                                                                 aTCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATAAc                  <  1:607629/140‑1 (MQ=255)
                                                                                                                      catcatTCGTTATCAATAAAAACCCTTCTGTATCTTTATCAAGACGACCAACCGGAACAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATAACCtttt             >  1:265191/1‑140 (MQ=255)
                                                                                                                       atcatTCGTTATCAATAAAAACCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATAACCTTTTg            <  2:724837/140‑1 (MQ=255)
                                                                                                                       atcatTCGTTACCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATGAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATAACCTTTTg            <  1:441828/140‑1 (MQ=255)
                                                                                                                          atTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATAACCTTTTgact         <  1:538527/140‑4 (MQ=255)
                                                                                                                           ttCGTTATGAAGGAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAGATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATAACCTTTTGGCtt        <  2:621508/140‑1 (MQ=255)
                                                                                                                             cGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATAACCTTTTGGCTTAt      <  2:308697/140‑1 (MQ=255)
                                                                                                                               ttATCAATAAAAACCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATATTCAGTTGCTGATATATAACCTTTTGGCTTAttt    >  1:329923/1‑140 (MQ=255)
                                                                                                                                 aTCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATAACCTTTTGGCTTATTTaa  >  2:33067/1‑140 (MQ=255)
                                                                                                                                           |                                                                                                                                 
AGTGTTACACCCTCTTTAAAAGCTTGAATGTCGTCTTCAGTGATAGGATTTGCTGAAATAACTTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAAAGCCCTTCTGTATCTTTATCAAGACGACCAACCGGAAAAATATTTAGATGTTGGTATTCAGGTATTAAATCAATAACGGTTTTTGAATGATGATCTTCAGTTGCTGATATATAACCTTTTGGCTTATTTAA  >  USA300TCH1516_ALE/1874748‑1875016

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: ‑