Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,413 C→T 9.5% V47I (GTC→ATC)  USA300HOU_0026 ← IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,4130CT 9.5% 114.8 / 2.7 51V47I (GTC→ATC) USA300HOU_0026IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base C (22/24);  new base T (3/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 6.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

CACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGT  >  CP000730/36278‑36547
                                                                                                                                       |                                                                                                                                      
cACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTg                                                                                                                                   >  1:181086/1‑141 (MQ=39)
         aaTAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAatgaaaac                                                                                                                          >  2:461892/1‑137 (MQ=255)
                   ttttCCTTTTATTTTGATGTACGTCTGATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGACAAAAAATTGGGGAATATATTTTAACCCAACGGTAAACCGTTGAATGATGAACCATAAcacc                                                                                                                >  2:287151/1‑141 (MQ=11)
                    tttCCTTTTATTTTGTTGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTAcacca                                                                                                               <  2:361280/141‑1 (MQ=255)
                     ttCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTAcaccac                                                                                                              <  1:2304/141‑1 (MQ=39)
                      tCCTCTTACTTTGATGTACGTCCCATCAATACGCTATTTGTAACAAGCTTTATTCTGCTTTTTCTTGCAAATTTGACACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACg                                                                                                             <  1:324436/141‑1 (MQ=11)
                        cTTTTATTTTGATATACGTTTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGtt                                                                                                           <  1:52349/141‑1 (MQ=255)
                         ttttATTTTGATGGACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTCGTCCGTTGAATGATGAACGTTTACACCACGTTc                                                                                                          <  2:14616/141‑1 (MQ=255)
                           ttATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTccc                                                                                                        <  1:214765/141‑1 (MQ=39)
                               tttGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTaa                                                                                                    <  2:348159/141‑1 (MQ=40)
                                  gATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAatct                                                                                                 >  2:12353/1‑139 (MQ=255)
                                  gATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAatat                                                                                                 >  2:55760/1‑141 (MQ=40)
                                            ttcgcaATGCGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGatata                                                                                       <  1:83435/137‑1 (MQ=255)
                                            tcatcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGatata                                                                                       >  1:59382/1‑141 (MQ=255)
                                               tcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAAAGATTAAAGCTCGCGCTCTTAATATTTCAGATATATCa                                                                                    >  1:406835/1‑141 (MQ=11)
                                                  aTACGGCAGTTGTAATAAGCTTTTTTATGCTTGTTCTTCCAAATTTGGTACAAAATTGGGGCATATTCTTGAACCCGACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGa                                                                                 <  2:11958/141‑1 (MQ=14)
                                                    aCGCCATTTGTAATAAGCCTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCTTATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACTTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATa                                                                               <  2:268284/141‑1 (MQ=11)
                                                     cGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATaa                                                                              >  1:345551/1‑141 (MQ=40)
                                                       ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGatatacccccagagcc                                                                            >  2:249490/1‑130 (MQ=11)
                                                       ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCATGATAACt                                                                            >  2:368227/1‑141 (MQ=255)
                                                       ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAAcc                                                                            >  2:66669/1‑140 (MQ=255)
                                                        cATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTc                                                                           >  1:188629/1‑141 (MQ=40)
                                                          tttGTAATAAGCTTTTTTAGGCTTTTGCTTGCAAATGTGATACGAAATTGGGGCATATTCTTGAACCCAACGGGAGACCGATGAATGATGAACGGGTTCACCAAGTTCCCTTAATATTTCAGCTAAATCagggatacacaa                                                                         >  2:231197/1‑130 (MQ=14)
                                                           ttGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAAt                                                                        <  1:372056/141‑1 (MQ=40)
                                                            tGTAAGAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATCCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATg                                                                       <  1:439835/141‑1 (MQ=255)
                                                                ataaGCTTTTTCATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCCATGtatt                                                                   >  2:332872/1‑140 (MQ=255)
                                                                   aGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCt                                                                <  2:345551/141‑1 (MQ=38)
                                                                            aTGCTTTTTCTTCCACATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAtagta                                                       >  1:342785/1‑141 (MQ=25)
                                                                             tGCTTTTTCTCCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTCTGGAACTGGTCCTTAATATTTCAGATATATCACGATAACTCAATGTATATTTTAGAtagtag                                                      >  1:335742/1‑141 (MQ=11)
                                                                                    tcttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATCGTAGCCAACgg                                               >  1:83020/1‑141 (MQ=25)
                                                                                      ttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCCGATATATCACGATAACTCAATGTATATCTTAGATAGTAGccgttggct                                             <  1:66669/141‑8 (MQ=255)
                                                                                         taaaTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACa                                          >  2:180122/2‑141 (MQ=21)
                                                                                          aaaTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAg                                         >  1:114869/1‑141 (MQ=34)
                                                                                           aaTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGt                                        <  2:112489/141‑1 (MQ=35)
                                                                                            aTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGta                                       >  1:83901/1‑140 (MQ=25)
                                                                                             tttGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGa                                      <  2:15677/141‑1 (MQ=34)
                                                                                                 aTACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAAc                                  <  2:250608/141‑1 (MQ=35)
                                                                                                      aaaGTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCt                             <  1:359524/141‑1 (MQ=17)
                                                                                                         ttGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGt                          <  2:423593/141‑1 (MQ=32)
                                                                                                            gggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTaa                       >  1:384228/1‑141 (MQ=32)
                                                                                                             ggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCACCGGCTACAGTGATAACCTCCTTGttcca                      >  2:200829/1‑138 (MQ=12)
                                                                                                                   ttCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTGGTTAAATTGttt                >  1:144317/1‑141 (MQ=17)
                                                                                                                    tCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTta               <  1:155169/141‑1 (MQ=32)
                                                                                                                      ttGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCTAACGGCTACAGTGATAACATCCTTGTTAAATTGTTtata             <  1:12353/141‑1 (MQ=17)
                                                                                                                      ttGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTtata             <  1:178699/141‑1 (MQ=32)
                                                                                                                      ttGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTtata             <  2:330927/141‑1 (MQ=32)
                                                                                                                          aCCCAACTGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTACTATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTg         <  1:152274/141‑1 (MQ=17)
                                                                                                                           cccAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTCAAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGa        >  1:13805/1‑141 (MQ=17)
                                                                                                                             cAACGGTAGACCGTTGAATGATGAACGTTTACCCCCCGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGaaa      <  1:85203/141‑1 (MQ=17)
                                                                                                                               aCGGGAGACCGTTGAAGGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATa    <  2:182092/141‑1 (MQ=17)
                                                                                                                                 ggtctaCCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGt  >  1:229193/6‑141 (MQ=17)
                                                                                                                                       |                                                                                                                                      
CACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGT  >  CP000730/36278‑36547

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: ‑