Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,289,113 T→C 14.4% Q126R (CAA→CGA)  USA300HOU_2153 ← hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,289,1130TC14.4% 52.0 / 5.1 28Q126R (CAA→CGA) USA300HOU_2153hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base T (10/14);  new base C (2/2);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-02

TAGGTATAAAGACATTAATTAAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATT  >  CP000730/2288979‑2289247
                                                                                                                                      |                                                                                                                                      
tAGGTATAAAGACATTAATTAAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTATCCATATATTGCACAg                                                                                                                                  >  1:42318/1‑141 (MQ=255)
   gTATAAAGACATTAATTAAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCt                                                                                                                               >  1:191953/1‑141 (MQ=255)
         aGACATTAATTAAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGaaa                                                                                                                         <  2:116066/141‑1 (MQ=255)
            cagtaattaaAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCg                                                                                                                      <  2:221376/138‑1 (MQ=255)
             attaattaAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGa                                                                                                                     <  2:115839/141‑1 (MQ=255)
                  ttaaAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGaa                                                                                                                <  2:191953/141‑1 (MQ=255)
                    aaaaCTTCTTGCGAAACATTTGAATCAATTGCAATACCTGTTTCAAGATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATc                                                                                                              <  1:4860/141‑1 (MQ=255)
                      aaGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCaa                                                                                                            <  1:146189/141‑1 (MQ=255)
                      aaGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCaa                                                                                                            >  1:210329/1‑141 (MQ=255)
                           cTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTtct                                                                                                       >  1:281824/1‑141 (MQ=255)
                              gCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTCATGCACCTATACGTCTTGTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCtt                                                                                                    <  2:147775/141‑1 (MQ=255)
                              gCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATCGAATCAATTTCTCtt                                                                                                    <  1:266453/141‑1 (MQ=255)
                                             ccATTGCAATACCTGTTTCAATATCATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACg                                                                                     <  1:296098/141‑1 (MQ=255)
                                             ccATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACg                                                                                     <  2:85111/141‑1 (MQ=255)
                                                    aaTACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTTTTCATCTTTTTTATACGTATTata                                                                              >  2:160015/1‑139 (MQ=255)
                                                              tCAATATAATCTTGAAGACCTGTTTCTTTTTCAAGGACAATTAATGCACCTATACGTCTTTTAGCCATATATCGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGt                                                                    >  2:163942/1‑141 (MQ=255)
                                                              tCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATCGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGt                                                                    >  2:330352/1‑141 (MQ=255)
                                                               cAATATAATCTTGAAGACCTGTTTCTTTTTGAAAGACAATTAATGCAGCTATACGTCTTTTAGCCATATATTGCACAGCCTTTTAAACCGTTTGACTCAATTTCTCTTCATATTTACTATACGTATTAGAAGTATAGGGtt                                                                   >  1:102133/1‑141 (MQ=255)
                                                                   ataATCCTGAAGACTTTCTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGAGTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTaa                                                               <  1:207327/141‑1 (MQ=255)
                                                                           gAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTAc                                                       >  1:358715/1‑141 (MQ=255)
                                                                            aaGATCTGGTTCTTTTTCAAAGACAATTTATGCCCCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTTTACGTATTAGAAGTATAGCGTTTTAAAAAGCTAcc                                                      <  2:138597/141‑1 (MQ=255)
                                                                                  tGTTTCTTTTTCAAAGACAATTAATGCACCTATGCGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTTTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTAcc                                                <  2:20705/141‑1 (MQ=255)
                                                                                                  aCAATTACTGCACCTTTACGTATTTTAGTCATATATTGCACCGCCTTTGAAGCCGATTACATAAATGTCGCTTCCACTTTACTAGACGCATTTGCAGTAGAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCGAACGCa                                >  2:131780/1‑141 (MQ=255)
                                                                                                  aCAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCa                                >  2:253590/1‑141 (MQ=255)
                                                                                                                   aCGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTg               <  1:164900/141‑1 (MQ=255)
                                                                                                                           tAGCCATATATTGCACAGCCTTTGCCACCAATGGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTa       >  1:85238/1‑141 (MQ=255)
                                                                                                                                atatatCGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTAtt  <  1:330352/141‑1 (MQ=255)
                                                                                                                                atatatCGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTAtt  <  1:163942/141‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                      
TAGGTATAAAGACATTAATTAAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATT  >  CP000730/2288979‑2289247

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: