Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000730 1,605,275 G→T R199L (CGT→CTT)  USA300HOU_1490 → integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,605,2750GT97.2% 95.2 / NA 36R199L (CGT→CTT) USA300HOU_1490integrase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base T (19/16);  minor base A (1/0);  total (20/16)
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

TTACAATTATCCAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACGTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGA  >  CP000730/1605144‑1605404
                                                                                                                                   |                                                                                                                                 
ttACAATTATCCAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGa                                                                                                                                >  2:493308/1‑135 (MQ=255)
                  atatTTGTTAACTAATGTCAAAATTCATAAAACAAAAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGataa                                                                                                              >  1:216309/1‑135 (MQ=255)
                  atatTTGTCAACTAATGTCAAAATTCCTAAAAGAAGAAACACAATCGAGGATATAGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGataa                                                                                                              >  2:83377/1‑135 (MQ=255)
                           aagtAATATCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTaca                                                                                                     <  1:261128/132‑1 (MQ=255)
                                     aaaaTTCCTAAAAGAAGAAAAACAATAAAGGATAACGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTAAACAAGCGAAAt                                                                                           >  1:25178/1‑135 (MQ=255)
                                       aaTTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCg                                                                                         >  2:332878/1‑135 (MQ=255)
                                          taccaaaaGTAGAAAATCAAAAGAGGATATCGAAACCGCTGAATATAAAATGTACAACTATTTAAAAATCAACCAAGCACTACAGATACTTGATCATCTCATAAATGATAATAAATTACACAAGCGcaacccaag                                                                                      >  2:201308/5‑129 (MQ=255)
                                                 agaagaAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAAtt                                                                               >  2:225599/1‑135 (MQ=255)
                                                 agaagaAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAAtt                                                                               >  2:578265/1‑135 (MQ=255)
                                                      aaaaaCAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAg                                                                          >  2:357342/1‑135 (MQ=255)
                                                         aaCAAAAGAGAATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCAt                                                                       <  2:600560/135‑1 (MQ=255)
                                                          aCAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATc                                                                      >  2:671887/1‑135 (MQ=255)
                                                                    atatCGAAAAAGATGAATCTAAAATGTACAACAAATAAAAAATGAACCAAGTACTCCAGATACATGATCATATACTCAAAGATAAAAAGTTACACAAACGAAATCGCATTTTAATTGCCAGCATCTTAGAAATaa                                                            >  1:265132/1‑134 (MQ=255)
                                                                             aaGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTaa                                                   <  2:40193/135‑1 (MQ=255)
                                                                                aTGACTCTAAAATTTAAAACTATTTAGAATTGAACTCAGTACTAAAGATAATTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTg                                                <  1:249513/135‑1 (MQ=255)
                                                                                aTGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCGTCTTAGAAGTACAGGCTTTAACTg                                                <  2:80053/135‑1 (MQ=255)
                                                                                 tGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTgg                                               >  2:269930/1‑135 (MQ=255)
                                                                                                        ttgAAATTAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAg                        <  1:606015/133‑1 (MQ=255)
                                                                                                            aaTGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTATAGGTTTTAACTGGTATGTGCATAGGAGAACTACAAGCACt                    <  1:115803/135‑1 (MQ=255)
                                                                                                            aaTGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACt                    <  1:671887/135‑1 (MQ=255)
                                                                                                            aaTGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACt                    <  1:493308/135‑1 (MQ=255)
                                                                                                            aaTGAACCAAGTCCTACAGATACTTCATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACt                    <  1:351761/135‑1 (MQ=255)
                                                                                                              tGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAATTGGTATGCGCATAGGAGAACTACAAGCACTGc                  <  1:40519/135‑1 (MQ=255)
                                                                                                              tGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGc                  >  2:250454/1‑135 (MQ=255)
                                                                                                              tGAACCAAGTCCTACAGATACTTGATCATATACTAAATGAAAAAAAGTTACAAAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACaaaaaaaaa                  <  2:444929/135‑8 (MQ=255)
                                                                                                               gccccAAGTCCTACATATACTTAATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCa                 >  1:9738/4‑135 (MQ=255)
                                                                                                               gAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAACGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTCCAGGCTTTACCTGGTATCCGCATAGGAGACCTCCAGGCACTGcg                 >  2:448156/1‑134 (MQ=255)
                                                                                                                   cAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTCCAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGaa             >  2:35085/1‑135 (MQ=255)
                                                                                                                         cTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAAGCGCATTTTAATTGCCAGCATCTTAAAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGGACTGCAGGAAAAAGat       >  2:102336/1‑135 (MQ=255)
                                                                                                                            cAGATACTTGATCATGTACTAAATGATAATAAGTTACACGAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACCACAAGCACTGTAGGAAAAAGAtata    >  1:349413/1‑135 (MQ=255)
                                                                                                                             aGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCCTAGGAGCACCACAAGCACTGCAGGCAACAgcgatcg   >  2:372685/1‑129 (MQ=255)
                                                                                                                             aGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAg   >  2:602754/1‑135 (MQ=255)
                                                                                                                              gATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCTCATTTTACTTGCCAGCATCTTAGAACTACAGGCTTTAACTGGTATGCGCATTGGAGAACTTCAAGCATTTCATGAAAAAGATATAgc  <  1:461968/135‑2 (MQ=255)
                                                                                                                              gATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGATAACTACAAGCATTGCAGGAAAAAGATATAGa  <  1:324731/135‑1 (MQ=255)
                                                                                                                              gATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGa  <  1:225599/135‑1 (MQ=255)
                                                                                                                              gATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGa  <  1:578265/135‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                 
TTACAATTATCCAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACGTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGA  >  CP000730/1605144‑1605404

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: ‑