Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,079,114 T→C 69.0% H201R (CAC→CGC)  natA_1 ← ABC transporter ATP‑binding protein NatA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,079,1140TC69.0% 38.1 / 20.9 32H201R (CAC→CGC) natA_1ABC transporter ATP‑binding protein NatA
Reads supporting (aligned to +/- strand):  ref base T (6/4);  new base C (16/6);  total (22/10)
Fisher's exact test for biased strand distribution p-value = 6.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.00e-01

GTACGCTTATGTTCTTCATAAATAAGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAG  >  USA300TCH1516_ALE/2078979‑2079249
                                                                                                                                       |                                                                                                                                       
gTACGCTTATGTTGTTCATAAATATGGAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATg                                                                                                                                    >  2:191627/1‑141 (MQ=255)
                    aataaGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTc                                                                                                                >  2:279865/1‑141 (MQ=255)
                      taaGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTa                                                                                                              >  2:4815/1‑141 (MQ=255)
                        aGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTaaa                                                                                                            >  1:219229/1‑141 (MQ=255)
                          tAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACATTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCGAAATc                                                                                                          >  1:82831/1‑141 (MQ=255)
                          tAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATc                                                                                                          >  1:324135/1‑141 (MQ=255)
                           agagATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCt                                                                                                         >  1:257563/1‑141 (MQ=255)
                            gagaTGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTg                                                                                                        <  2:51208/141‑1 (MQ=255)
                             agaTGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTga                                                                                                       <  2:282187/141‑1 (MQ=255)
                                  cTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATaa                                                                                                  >  2:30007/1‑141 (MQ=255)
                                     aTTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCCCCGTCACTTAAGCGCATGATATCATCAGCTATTTTTTCTAAATCTGAGATAAtgt                                                                                               >  1:52200/1‑141 (MQ=255)
                                     aTTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGACATacatt                                                                                               >  2:275672/1‑137 (MQ=255)
                                       tcatcatcaAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAAtgtgt                                                                                             >  1:245294/1‑141 (MQ=255)
                                               aaGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACAt                                                                                     <  1:56494/141‑1 (MQ=255)
                                                    ccTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAata                                                                                >  1:258375/1‑141 (MQ=255)
                                                        aaTAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGt                                                                            <  1:385662/141‑1 (MQ=255)
                                                              accacTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATATGACATAATGTGTGTCGACATGAATATTGTTTTAtt                                                                      >  2:191489/1‑141 (MQ=255)
                                                                      caACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATGATGTGTGTCGACATGCATATTGTTTTATTTTCATaaa                                                              >  2:16154/1‑141 (MQ=255)
                                                                      caACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGACTATTGTTTTATTTTCATCaa                                                              <  1:239238/141‑1 (MQ=255)
                                                                                tCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTg                                                    >  1:136181/1‑141 (MQ=255)
                                                                                tCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGGCGACATGAATATTGTTTTATTTTCATAAATTAATTATTg                                                    >  2:179825/1‑141 (MQ=255)
                                                                                  tttGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCt                                                  <  2:308343/141‑1 (MQ=255)
                                                                                    tGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGa                                                >  1:178723/1‑141 (MQ=255)
                                                                                        aCAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTTTTTGTTTTTGATAATGTGTGTCGACATGATTATTGTTTTTTTTTATTGGATTTATTCTTGTTGTAttt                                            >  2:286035/1‑140 (MQ=255)
                                                                                                        aCCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCAtt                            >  1:266314/1‑141 (MQ=255)
                                                                                                            tttAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTTTTTCTCTGATAATGTTTGTCGACATGTATATTGTTTTATTTTCGTCACTTAATTATTGTTGAGTTTTTGCCATTAGTTCATTTCtt                        >  2:206316/1‑140 (MQ=255)
                                                                                                                 taTAATTTCACCGTTACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTaa                   <  2:193949/140‑1 (MQ=255)
                                                                                                                   tAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAgg                 <  2:393101/141‑1 (MQ=255)
                                                                                                                     aCTTCACCGTAACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGa               <  1:223029/141‑1 (MQ=255)
                                                                                                                            cGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGAc        >  2:66543/1‑141 (MQ=255)
                                                                                                                                aCTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGa    >  1:27100/1‑141 (MQ=255)
                                                                                                                                  ttAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAg  <  1:72392/141‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
GTACGCTTATGTTCTTCATAAATAAGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAG  >  USA300TCH1516_ALE/2078979‑2079249

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: ‑