Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 195,286 T→A 100% 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_ALE195,2860TA95.6% 135.9 / ‑1.0 45intergenic (‑97/‑82)USA300HOU_RS00900/USA300HOU_RS00905hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base A (22/21);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.79e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAA  >  USA300TCH1516_ALE/195150‑195417
                                                                                                                                        |                                                                                                                                   
tGTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTaaaa                                                                                                                                  >  1:398922/1‑140 (MQ=255)
 ctttCTAGCTAACCTTGCTACGACAGATTCTTTATCCATAATTATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAaaaa                                                                                                                                 <  1:293107/139‑1 (MQ=255)
      tatatAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTTCAGAATTTTATCTAAATTTTAAAAAAAata                                                                                                                            >  2:10080/5‑140 (MQ=255)
      tAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAata                                                                                                                            >  1:50531/1‑140 (MQ=255)
          tAAACTTGTTACAACAGATTCTTTTTCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCtt                                                                                                                        <  2:347063/140‑1 (MQ=255)
                     cGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTATAAAAAATATCTTAATCTCCTTGt                                                                                                             >  2:17231/1‑140 (MQ=255)
                            ttCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATAATTTACAAAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTATAATCCGa                                                                                                      >  1:254631/1‑140 (MQ=255)
                                    ccATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCAATAAGAAta                                                                                              >  1:246666/1‑139 (MQ=255)
                                       tAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATtata                                                                                           >  2:399809/1‑140 (MQ=255)
                                           gATAGCCCCCTATAAATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTaa                                                                                       <  2:456088/140‑1 (MQ=255)
                                            aTAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAat                                                                                      >  1:324904/1‑140 (MQ=255)
                                              aGCCCCCTATATATATGATTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAAATATAGTAatat                                                                                    >  2:66214/1‑140 (MQ=255)
                                                 catctttatatatTTTTATTTTCTTATATTCTATCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTAGCTAAATATTAAAAAAAATATCTTAATATTCTTATTATCCGATAAGAATTATAGTAATAtttt                                                                                 <  1:131096/134‑1 (MQ=255)
                                                  cccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAttttt                                                                                <  2:324904/140‑1 (MQ=255)
                                                   ccTATATATATGTTTATTCACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAACATCCCTGTAATCCGATAAGAATTATAGTAATAtttttt                                                                               <  1:416942/140‑1 (MQ=255)
                                                      ttatttatGTTTATTTAATTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGGATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCaa                                                                            <  1:96957/139‑1 (MQ=255)
                                                          atatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCAt                                                                        >  1:317586/1‑140 (MQ=255)
                                                             tGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGt                                                                     >  1:497690/1‑140 (MQ=255)
                                                                ttatttaCTTATACCCTAACATGATTTTTATACTCTTTTAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtat                                                                  <  1:10080/140‑1 (MQ=255)
                                                                ttatttaCTTAGTCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATAAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtat                                                                  <  2:66165/140‑1 (MQ=255)
                                                                ttaattaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtat                                                                  <  2:50531/140‑1 (MQ=255)
                                                                 tatttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtata                                                                 <  2:497690/140‑1 (MQ=255)
                                                                  atttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACATAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATag                                                                <  1:276214/140‑1 (MQ=255)
                                                                    ttaCTTATACTTTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTAACTAAATATTAAAAAAAATATCTTAATATCCTTGTAAGCCGATGAGAATGATAGTAATATTTTTTCAACCATCGTTATagga                                                              <  1:403060/140‑1 (MQ=255)
                                                                       cTTATACCCTAACATGATTTTTATACTCTTTGTAACTATATTTTACAGAATTTTATCTATATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATTTTTTTTCAACCATTGTTATaggagga                                                           >  1:28933/1‑139 (MQ=255)
                                                                       cTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGt                                                           >  1:415226/1‑140 (MQ=255)
                                                                             cccTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAAGTCttata                                                     >  1:273585/1‑139 (MQ=255)
                                                                             accTAACATGCTTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATAAAAATAAAAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCttatt                                                     <  2:45292/139‑1 (MQ=255)
                                                                                    aTGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAGAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACa                                              >  1:357400/1‑140 (MQ=255)
                                                                                    aTGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACa                                              <  1:6419/140‑1 (MQ=255)
                                                                                     tGATTTTTATACCCTTTTAAATTATGTTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTCTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACat                                             <  2:259035/140‑1 (MQ=255)
                                                                                       aTTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACatta                                           <  2:480314/140‑1 (MQ=255)
                                                                                          tttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGAACTTAttt                                        >  2:25153/1‑140 (MQ=255)
                                                                                          tttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGCCTTATTAATGACATTAttt                                        >  2:109919/1‑140 (MQ=255)
                                                                                             ataCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAAAGACATTATTTtta                                     >  2:260404/1‑140 (MQ=255)
                                                                                               actatatGAAAATATATTTTACATAATTTTATCTAAAAAAAAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTttatt                                   <  2:534396/134‑1 (MQ=255)
                                                                                                    ttGAAAATATATTTTACAGAAATTTATCTAAATATTAAAAAAAATATCCTAATTTCCTTGTAATCCGATAAGAATTATAGTTATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAg                              <  1:332569/140‑1 (MQ=255)
                                                                                                     tGAAAATATCTTTTACAGAATTTTATATAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTATTGACATTATTTTTATTAGAAGc                             >  1:154242/1‑140 (MQ=255)
                                                                                                      gAAAATATATTTTACAGAATTTTATTTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCt                            <  1:535227/140‑1 (MQ=255)
                                                                                                       aaaaTATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTTTAGTAATATTTTTTTAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTa                           >  1:219790/1‑140 (MQ=255)
                                                                                                            atatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATACGAATTATAGTAATATTTTTTTAACCCTTGTTATAGGAGGGCTTATTAATGCCATTATTTTTCTTAGAAGCTAACAAt                      >  2:27907/1‑140 (MQ=255)
                                                                                                            atatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAAt                      <  2:398922/140‑1 (MQ=255)
                                                                                                            atatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGATAACAAt                      >  1:268066/1‑140 (MQ=255)
                                                                                                                    cAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATATGAATTATAGTAATATTTTTTTAACCATTGTTATAGGAGGTCTTATTATTGACATTATTTTTATTAGAAGCTAACAATCTTGAttt              >  2:108425/1‑140 (MQ=255)
                                                                                                                              tCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACg    >  1:408141/1‑140 (MQ=255)
                                                                                                                                tAAATATTAAAAAAAATATCTTAATCTCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATAGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGaa  <  2:243742/140‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                   
TGTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAA  >  USA300TCH1516_ALE/195150‑195417

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑