Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,858,458 T→A 9.9% F204L (TTT→TTA)  nhoA → N‑hydroxyarylamine O‑acetyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,858,4580TA 9.9% 108.5 / 3.8 38F204L (TTT→TTA) nhoAN‑hydroxyarylamine O‑acetyltransferase
Reads supporting (aligned to +/- strand):  ref base T (14/20);  new base A (2/2);  total (16/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

AAGACAAGGATATTTTCTATGTTCAAAAATTCGAAAATGATCATTGGCATACAAAATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAATTTGATGTCACTAAAGATAACTATAAAC  >  USA300TCH1516_ALE/2858319‑2858582
                                                                                                                                           |                                                                                                                            
aaGACAAAGATATTTTCTATGTTCAAAAATTCGAAAAAGATCATTTACTTACAAGATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTg                                                                                                                             <  1:111742/141‑1 (MQ=255)
                cTATGTTCAAAAATTCGAAAATGATCATTGGCATACAAAATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTattaat                                                                                                             >  1:288965/1‑141 (MQ=255)
                     ttCAAAAATTCGAAAATGATCATTGGCATACAAAATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACaa                                                                                                        <  1:119884/141‑1 (MQ=255)
                         aaaaTTCGAAAATGATCATTGGCATACAAAATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGcc                                                                                                    <  1:336101/141‑1 (MQ=255)
                            aTTCGAAAATGATCATTGGCATACAAAATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCcaca                                                                                                 <  1:153003/141‑1 (MQ=255)
                             ttCGAAAATGATCATTGGCATACAAAATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATAGCACaa                                                                                                >  2:49995/1‑141 (MQ=255)
                              tCGAAAATGATCATTGGCATACAAAATATGAAGCTGAATTCAAACATAAAGAAATAGAAGAATTAAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACTATGACACAAt                                                                                               >  2:314238/1‑141 (MQ=255)
                               cGAAAATGATCATTGGCATACAAAATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATc                                                                                              >  2:253182/1‑141 (MQ=255)
                               cGAAAATGATCATTGGCATACAAAATATGAAGCTGAACTCAAACCTAAACAAATAGAAGAGTTTAATACCAACCTCCACTATAATCAAACGCATCCAGATTCAATATTTGTCCAGCATTTATTAATTACAATGCCACAATc                                                                                              >  2:88410/1‑141 (MQ=255)
                                             ggCATACAAAATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTAGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTa                                                                                >  2:331312/1‑141 (MQ=255)
                                             ggCATACAAAATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTAGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTa                                                                                >  2:329324/1‑141 (MQ=255)
                                               cATACAAAATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACa                                                                              <  2:236905/141‑1 (MQ=255)
                                                     aaaTATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCt                                                                        <  1:102529/141‑1 (MQ=255)
                                                     aaaTATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGAGTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCt                                                                        <  2:188596/141‑1 (MQ=255)
                                                           aaaGCTGAATGCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAAt                                                                  <  1:14544/140‑1 (MQ=255)
                                                            aaGTTGAATTCAAACCTAAACAAACAGAAGCTTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATc                                                                 <  2:55535/141‑1 (MQ=255)
                                                                       aaaCCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCAtttaacttta                                                      <  1:114238/141‑1 (MQ=255)
                                                                              aaaaaaTAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGa                                               <  2:229719/138‑1 (MQ=255)
                                                                                cAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTACCAAGGAAt                                             >  1:246663/1‑141 (MQ=255)
                                                                                cAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAAt                                             >  1:57553/1‑141 (MQ=255)
                                                                                   aTAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGt                                          <  1:253182/141‑1 (MQ=255)
                                                                                         gaTTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCa                                    <  2:288965/141‑1 (MQ=255)
                                                                                         gaTTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTAGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCa                                    <  1:331312/141‑1 (MQ=255)
                                                                                         gaTTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTAGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCa                                    <  1:329324/141‑1 (MQ=255)
                                                                                         aaccttAATATCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCa                                    <  1:77094/137‑1 (MQ=255)
                                                                                           ttttAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGa                                  <  2:303366/141‑1 (MQ=255)
                                                                                                aTAGCAACATCGAATATAATCAAACGCATCGAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAAt                             <  2:142475/141‑1 (MQ=255)
                                                                                                aTAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAAt                             <  1:149215/141‑1 (MQ=255)
                                                                                                    cAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAATTTGa                         >  1:187823/1‑141 (MQ=255)
                                                                                                       cATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAATTTGATGt                      <  1:18435/141‑1 (MQ=255)
                                                                                                             atatAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTACTACAATGTCTGAAAATCATCTAACTCTAACAAGGAATGGCAGCTCAGAACAATTTAATTTCACTaa                >  2:343490/1‑141 (MQ=255)
                                                                                                              tataATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAATTTGATGTCACTaaa               <  1:257339/141‑1 (MQ=255)
                                                                                                                        cGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAATTTGATGTCACTAAAGATAACtata     >  1:335500/1‑141 (MQ=255)
                                                                                                                        cGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAATTTGATGTCACTAAAGATAACtata     <  1:15307/141‑1 (MQ=255)
                                                                                                                         gCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAGTGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAACCTTTGATGTCACTAAAGATCACTATaa    >  2:245266/1‑141 (MQ=255)
                                                                                                                          cATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAATTTGATGTCACTAAAGATAACTATaaa   >  2:94128/1‑141 (MQ=255)
                                                                                                                          cATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAATTTGATGTCACTAAAGATAACTATaaa   >  1:181183/1‑141 (MQ=255)
                                                                                                                           aTCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAATTTGATGTCACTAAAGATAACTATAAAc  >  1:40481/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                            
AAGACAAGGATATTTTCTATGTTCAAAAATTCGAAAATGATCATTGGCATACAAAATATGAAGCTGAATTCAAACCTAAACAAATAGAAGATTTTAATAGCAACATCGAATATAATCAAACGCATCCAGATTCAATATTTGTACAGCATTTATTAATTACAATGCCACAATCATTTGGCCGTGCTACAATGTCTGAAAATCATTTAACTTTAACAAGGAATGGTAGCTCAGAAAAATTTGATGTCACTAAAGATAACTATAAAC  >  USA300TCH1516_ALE/2858319‑2858582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑