Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 492,727 A→G 12.3% intergenic (+149/+36) sle1_1 → / ← USA300HOU_RS02345 N‑acetylmuramoyl‑L‑alanine amidase sle1/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE492,7270AG12.3% 78.4 / 4.2 34intergenic (+149/+36)sle1_1/USA300HOU_RS02345N‑acetylmuramoyl‑L‑alanine amidase sle1/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (17/11);  new base G (2/2);  total (20/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

TATAAATATATAATGAATTCCTATTACATTTCACAAGCTGAAAAGTTGGATTGAATCCTAAATTTTATGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGTAACAACTGCCACTGCTTTTTTGAACTTACGTGGT  >  USA300TCH1516_ALE/492590‑492859
                                                                                                                                         |                                                                                                                                    
tataAATATATAATGAATTCCTATTACATTTCACAAGCTGAAAAGTTGGATTGAATCCTAAATTTTATGGCGGGGCTATCAAAGTCGTGAGTGTTGTAATAGGAATTTTTGTATATGAAAAAGGGTTGGTCGAATGAACtt                                                                                                                                   >  1:18297/1‑141 (MQ=255)
       atataATGAATTCCTATTACATTTCACAAGCTGAAAAGTTTGATTGAATCCTAAATTTTATGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTc                                                                                                                            <  2:135346/141‑1 (MQ=255)
                      ttttcATTTCTCAATTTGAAAACTTGGATTGAATCCTAAATTTTATGGCGGGGCTAGCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATc                                                                                                             <  1:192018/137‑1 (MQ=255)
                      aTTACATTTCACAAGCTGAAAAGTTGGATTGAATCCTAAATTTTATGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATc                                                                                                             <  1:1011/141‑1 (MQ=255)
                       ttACATTTCACAAGCTGAAAAGTTGGATTGAATCCTAAATTTTATGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACCTCATGTTCTATTTTTCACCAAtac                                                                                                            >  2:80024/1‑139 (MQ=255)
                        tACATTTCACAAGCTGAAAAGTTGGATTGAATCCTAAATTTTATGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCt                                                                                                           >  1:338141/1‑141 (MQ=255)
                          cATTTCACAAGCTGAAAAGTTGGATTGAATCCTAAATTTTATGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCttt                                                                                                         <  1:361732/141‑1 (MQ=255)
                                  aaGCTGAAAAGTTGGATTGAATCCTAAATTTTATGGCGGGGCTATCAAAGGCGTGATTGTTGTAATAGGAATTTTTGTATATGGAAAAGGATTGGCTGAATGACCTTCATGTTCTATGTTCGACCAACCATTTTTTAAAtt                                                                                                 >  1:374504/1‑141 (MQ=255)
                                        aaaaGTTGGATTGAATCCTAAATTTTATGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAGCTTTATGTTCTATGTTCGACCAATTCTTTTCTGAATTAGtttt                                                                                           >  2:336915/1‑141 (MQ=255)
                                        aaaaGTTGGATTGAATCCTAAATTTTATGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAGCTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTAtt                                                                                           >  2:337523/1‑141 (MQ=255)
                                              gtgATTGAATCGTAAGTTTTAGTGTGGGGCTATCAAAAGCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTCGTACACATggt                                                                                     <  2:51061/139‑3 (MQ=255)
                                                  ttGAATCCTAAATTTTATGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTAc                                                                                 >  1:261770/1‑141 (MQ=255)
                                                                ttATGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAGCTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTg                                                                   <  1:337523/141‑1 (MQ=255)
                                                                ttAGGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAGCTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTg                                                                   <  1:336915/141‑1 (MQ=255)
                                                                  aTGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGGACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTa                                                                 >  1:207033/1‑141 (MQ=255)
                                                                  aTGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTa                                                                 >  1:122981/1‑141 (MQ=255)
                                                                              tCAAAGTCGTGATTGTTGTAATAGGCATTTTTGTATATGAAAAAGGATTGGTCGACTGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTCGTCTTCCTGTTTTACTTTCCCAATGCTTCTTAATAATCTAGCa                                                     >  2:5088/1‑141 (MQ=255)
                                                                                aaaGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCAcc                                                   <  2:338141/141‑1 (MQ=255)
                                                                                    tCGTGATGTTTGTAATAGGAATTTTTGTATATGAAAGAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGttt                                               <  2:136984/141‑1 (MQ=255)
                                                                                     cGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCTAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTg                                              >  2:315457/1‑141 (MQ=255)
                                                                                         aTTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAACACATCACCTTTTGttat                                          >  2:340002/1‑141 (MQ=255)
                                                                                          ttgttgTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGttatt                                         >  1:308809/1‑141 (MQ=255)
                                                                                          ttgttgTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGttatt                                         >  1:267426/1‑141 (MQ=255)
                                                                                               gttctAGGAATTTTTGTATATGAAAAAGGATTTGTCGATTGACTTTTATGTTCTATGTCGGTCCTATCCTTTTCTGATTTCGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGt                                    <  2:141303/137‑1 (MQ=255)
                                                                                               gtAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACAAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGt                                    >  2:148499/1‑141 (MQ=255)
                                                                                                 aaTAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGTaa                                  <  1:255589/141‑1 (MQ=255)
                                                                                                         tttttGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGTAACAACTGcc                          >  1:284158/1‑141 (MQ=255)
                                                                                                           tttGTATATGAAAAAGGATTCGTCGAATGAACTTCATGTTCTATGTTCGCCCAAAACTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGTAACAACTGCCAc                        <  1:14888/141‑1 (MQ=255)
                                                                                                             tGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGTAACAACTGCCACTg                      >  2:40716/1‑141 (MQ=255)
                                                                                                                      aaaaGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGTAACAACTGCCACTGCTTTTTTGa             >  2:34817/1‑141 (MQ=255)
                                                                                                                        aaGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGTAACAACTGCCACTGCTTTTTTGAAc           >  2:106263/1‑141 (MQ=255)
                                                                                                                        aaGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGTAACAACTGCCACTGCTTTTTTGAAc           <  1:78575/141‑1 (MQ=255)
                                                                                                                            aTTTGTCGTATGAACTTCATGTTCTATGTTCGATCAAGCCTTTTCTGAATTAGTATTCATGTTTTACGTTGCGAATGCTTGTAAATAATCTAGCACCTTTTGTTATTAAAGTAACAACTGCCACTGCTTTTTTGAACTTAc       <  2:158743/141‑1 (MQ=255)
                                                                                                                                 tCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGTAACAACTGCCACTGCTTTTTTGAACTTACgtggt  >  2:17051/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                    
TATAAATATATAATGAATTCCTATTACATTTCACAAGCTGAAAAGTTGGATTGAATCCTAAATTTTATGGCGGGGCTATCAAAGTCGTGATTGTTGTAATAGGAATTTTTGTATATGAAAAAGGATTGGTCGAATGAACTTCATGTTCTATGTTCGACCAATCCTTTTCTGAATTAGTATTCATGTTTTACTTTGCGAATGCTTGTAAATAATCTAGCACCGTTTGTTATTAAAGTAACAACTGCCACTGCTTTTTTGAACTTACGTGGT  >  USA300TCH1516_ALE/492590‑492859

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑