Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 693,258 T→A 11.1% I65F (ATT→TTT)  USA300HOU_0636 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730693,2580TA11.1% 97.6 / 6.6 36I65F (ATT→TTT) USA300HOU_0636hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (17/15);  new base A (2/2);  total (19/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01

GGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAATTTATACGACTAGCAACATAGTTTAAAATAG  >  CP000730/693120‑693389
                                                                                                                                          |                                                                                                                                   
ggTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAAttt                                                                                                                                   >  1:260864/1‑141 (MQ=255)
  tCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCGGCCTAAAATTTa                                                                                                                                 <  1:14050/141‑1 (MQ=255)
     tGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCGGCCTAAAATTTacgc                                                                                                                              <  1:306932/141‑4 (MQ=255)
       ttAAATCACTACTTCTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCg                                                                                                                            <  2:242246/141‑1 (MQ=255)
                tAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTAc                                                                                                                   >  2:321341/1‑141 (MQ=255)
                   tACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGt                                                                                                                <  2:80996/141‑1 (MQ=255)
                    aCTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTa                                                                                                               <  1:160342/141‑1 (MQ=255)
                     cTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTAt                                                                                                              <  2:98579/141‑1 (MQ=255)
                      tataTGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTAtt                                                                                                             <  1:136821/141‑1 (MQ=255)
                       atatGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTAttt                                                                                                            >  2:152609/1‑141 (MQ=255)
                        tatGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTAtttt                                                                                                           >  1:119634/1‑141 (MQ=255)
                        tatGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTAtttt                                                                                                           >  2:323631/1‑141 (MQ=255)
                        tatGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTAtttt                                                                                                           >  2:1035/1‑141 (MQ=255)
                                 cATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGt                                                                                                  >  2:62211/1‑141 (MQ=255)
                                        atCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATc                                                                                           >  2:334357/1‑141 (MQ=255)
                                           gCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCAtt                                                                                        >  2:137925/1‑141 (MQ=255)
                                                    aaTACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGa                                                                               >  2:74453/1‑141 (MQ=255)
                                                     aTACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGAc                                                                              >  2:138562/1‑141 (MQ=255)
                                                      tACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACt                                                                             <  2:22202/141‑1 (MQ=255)
                                                                       aCTTGTAGCAGTCTGCCATGTCCTGCGTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTaaa                                                            >  2:4258/1‑141 (MQ=255)
                                                                                  tCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGa                                                 >  2:139805/1‑141 (MQ=255)
                                                                                         tGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTa                                          <  2:291324/141‑1 (MQ=255)
                                                                                                ctacACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGcccc                                   <  2:103279/138‑1 (MQ=255)
                                                                                                  tCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGGCGTCCTTTTAGCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTACTCCTTTAGCTAAAGTCATTAATGAAACCTTATCGCCCCat                                 <  2:62337/141‑2 (MQ=255)
                                                                                                    aCTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAAtt                               >  2:103530/1‑141 (MQ=255)
                                                                                                    aCTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTGCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAAtt                               <  1:158051/141‑1 (MQ=255)
                                                                                                     cTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCTAttt                              >  2:274948/1‑141 (MQ=255)
                                                                                                      tCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAATTta                             <  1:293020/141‑1 (MQ=255)
                                                                                                        aaGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAATTtata                           <  1:126797/141‑1 (MQ=255)
                                                                                                          gCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAATTTATACg                         >  1:33592/1‑141 (MQ=255)
                                                                                                               tACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAATTTATACGACTAg                    <  1:245836/141‑1 (MQ=255)
                                                                                                                         aCAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAATTTATACGACTAGCAACATAGtt          <  1:180006/141‑1 (MQ=255)
                                                                                                                           aaaGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAATTTATACGACTAGCAACATAGTTTa        <  2:15225/141‑1 (MQ=255)
                                                                                                                           aaaGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAATTTATACGACTAGCAACATAGTTTa        >  2:98192/1‑141 (MQ=255)
                                                                                                                                tCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCTCCAATTTATACGACTAGCAACATAGTTTAAAATa   >  2:148937/1‑141 (MQ=255)
                                                                                                                                 cggcctAAAATTTACGCTGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAATTTATACGACTAGCAACATAGTTTAAAATAg  >  2:327578/6‑141 (MQ=255)
                                                                                                                                 cggcctAAAATTTACGCTGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAATTTATACGACTAGCAACATAGTTTAAAATAg  >  2:10320/6‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                   
GGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCCGACCTTTTACCGTATTTTCTTTAACGTAACTATCATTAAATTTAGACTGTATTTCTTTAGCTAAAGTCATTAATGAAACTTTATCGCCCCAATTTATACGACTAGCAACATAGTTTAAAATAG  >  CP000730/693120‑693389

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑