Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,378 C→T 14.7% L58L (TTG→TTA)  USA300HOU_0026 ← IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,3780CT14.7% 110.7 / 12.8 54L58L (TTG→TTA) USA300HOU_0026IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base C (25/20);  new base T (4/4);  total (30/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.81e-01

CGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAAC  >  CP000730/36238‑36515
                                                                                                                                            |                                                                                                                                         
cGCAAACAAACATGCTATGTATGTCCCTCTGCATCCATGGCACGATATAAATCGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTACGCTTTTTCTTCCAAATTTGATAc                                                                                                                                           <  2:66623/141‑1 (MQ=14)
  cAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAATTTGGATACaa                                                                                                                                         >  2:359524/1‑141 (MQ=255)
    aCCAAATATCTAATGGATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATaaaa                                                                                                                                       <  2:460494/141‑1 (MQ=255)
         atatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCGCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGATTTTTCTTCCAAATTTGATACAAAATTggg                                                                                                                                  >  2:152274/1‑141 (MQ=255)
          tatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTgggg                                                                                                                                 <  2:413688/141‑1 (MQ=255)
          tatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTgggg                                                                                                                                 <  2:348516/141‑1 (MQ=255)
          tatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTATTCTTCCAAATTTGATACAACATTgggg                                                                                                                                 >  2:33162/1‑141 (MQ=255)
                    atgtCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAACATTggggacgatccgtc                                                                                                                       >  1:419953/1‑131 (MQ=255)
                     tgtCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGa                                                                                                                      <  2:387828/141‑1 (MQ=255)
                     tgtCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGa                                                                                                                      <  2:387833/141‑1 (MQ=255)
                       tCCCTCTTCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACTTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACACAATTTGGGCGTATTTTTGGAc                                                                                                                    >  1:45360/1‑141 (MQ=14)
                       tCCCTCTGTATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCACATTTGGTATCAAATTGTGGAGTATGCTTTAAc                                                                                                                    >  1:379607/1‑141 (MQ=11)
                        cccTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGACTATTCTTTAAcc                                                                                                                   >  2:85203/1‑141 (MQ=255)
                         ccTCTGCATCAATGGCACGATATACATAACTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAAccc                                                                                                                  <  2:301031/141‑1 (MQ=255)
                         ccTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAAccc                                                                                                                  >  2:178699/1‑141 (MQ=40)
                            ctGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCTAAc                                                                                                               >  2:251818/1‑141 (MQ=255)
                                aTCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTa                                                                                                           <  2:394022/141‑1 (MQ=18)
                                 tCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGATTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAg                                                                                                          >  1:183236/1‑141 (MQ=255)
                                        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)
                                                                                                                                            |                                                                                                                                         
CGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAAC  >  CP000730/36238‑36515

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: ‑