Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000731 1,590 G→A 28.2% intergenic (+375/‑481) repA → / → USA300HOU_pUSA300HOUMR0003 replication protein A/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007311,5900GA28.2% 62.6 / 28.5 46intergenic (+375/‑481)repA/USA300HOU_pUSA300HOUMR0003replication protein A/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (15/18);  new base A (4/9);  total (19/27)
Fisher's exact test for biased strand distribution p-value = 5.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.14e-01

GACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATGATAGCAAATTTCCCTTATGCTCTTACG  >  CP000731/1451‑1727
                                                                                                                                            |                                                                                                                                         
gACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGc                                                                                                                                          >  1:102451/1‑141 (MQ=255)
gACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGc                                                                                                                                          <  1:222995/141‑1 (MQ=255)
   gaagaaAAAAAGCACATGCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATACtgt                                                                                                                                       <  1:60849/141‑1 (MQ=255)
        aaaaaaTTATATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATACtgtatgta                                                                                                                                  <  1:160673/141‑1 (MQ=255)
            aaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATACTGTATGTAgtgt                                                                                                                              <  2:68632/141‑1 (MQ=255)
              gCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATCAGTAATAACTAATGTC‑TTTTTTGAAATTGTTT‑TGAGAATAATTGCTGTATTAAAGAGGTGACAAATGCTGTATGTAGTGTcac                                                                                                                           >  1:171977/1‑141 (MQ=2)
                acaTTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTcaca                                                                                                                          <  1:226128/141‑1 (MQ=255)
                acaTTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATACTGTATGTAGTGTcaca                                                                                                                          <  2:33763/141‑1 (MQ=255)
                  aatCAATAAGCGCAATTTTGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATACTGTATGTAGTGTCACaaa                                                                                                                        <  1:99675/139‑1 (MQ=18)
                    tCAATTACCGTAATTTGTAATTTCGAAAAGCAATATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCAAAAAAg                                                                                                                      <  2:98561/141‑1 (MQ=255)
                           tcgaaaTTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGaca                                                                                                               <  2:131149/137‑1 (MQ=255)
                           ccGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGaca                                                                                                               <  2:1905/141‑1 (MQ=255)
                            cGCAATTTGGAATTTCGAAAAGCAAAATTATAATTTAAGACAATAATGAAAAAAGATGTC‑TATTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGacac                                                                                                              >  1:73468/1‑141 (MQ=18)
                                   tGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCt                                                                                                       <  1:180502/141‑1 (MQ=255)
                                     gAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCttt                                                                                                     >  1:108914/1‑141 (MQ=255)
                                     gAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATACTGTATGTAGTGTCACAAAAGTGTGACACTACAGCttt                                                                                                     >  1:7162/1‑141 (MQ=255)
                                           cGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATACTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGa                                                                                               <  1:174347/141‑1 (MQ=255)
                                                    aaaTTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACttt                                                                                      >  1:39981/1‑141 (MQ=255)
                                                    aaaTTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATAGATAATCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACttt                                                                                      <  2:150107/141‑1 (MQ=255)
                                                      attattattTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTaa                                                                                    <  2:206276/141‑1 (MQ=255)
                                                        aattattTAAGACATTAGGGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTaaaa                                                                                  <  2:7181/140‑1 (MQ=255)
                                                             tttAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACt                                                                             <  1:226324/141‑1 (MQ=255)
                                                             tttAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACt                                                                             <  2:35648/141‑1 (MQ=255)
                                                               tAAGACAGTAGTAATAACTGATGGC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTa                                                                           <  1:232247/141‑1 (MQ=255)
                                                                    cATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGAGCTGTCTTATTTTTGTGACATATACTGTATGTAGTGTCACAAAAGTGTGGCATTACAGGTTTGTATGCTATCATTTTAAACTAACTTAAAAcc                                                                      >  2:122077/1‑141 (MQ=25)
                                                                           gATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAACGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAACACCCTTGGaa                                                               >  2:119923/1‑141 (MQ=255)
                                                                               aCTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTc                                                           >  2:41473/1‑141 (MQ=255)
                                                                                 tGATGTCTTTTTTTTATTTTTTTTCAGTGGGAAGTTCGTCTCTTATTTTTGTGACAAATGCTGTTTGTAGTGTCGCGGATTGGGGACATTACAGCTTTGGAGGATATCACTTTTAAATAACTTAAAACCCTTGCAATGTCt                                                          >  2:219040/1‑141 (MQ=255)
                                                                                          ttttttATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTGTGGCCTTGcc                                                 >  1:97703/1‑141 (MQ=255)
                                                                                          tttttgATTGTTGTTCTGGAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGcc                                                 <  2:225562/141‑1 (MQ=255)
                                                                                                aatGTATTTCTGGAAAAAAGTGCTGTCTTATATTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCt                                           <  1:71657/139‑1 (MQ=255)
                                                                                                aTTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCt                                           <  2:114228/141‑1 (MQ=255)
                                                                                                       ttCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCAttt                                    >  1:13430/1‑141 (MQ=255)
                                                                                                            tAAAAAAGTGCTGTCTTATTTTTGTGACAAATACTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGaa                               >  1:151837/1‑141 (MQ=255)
                                                                                                                aaaGTGCTGTCTTATTTTTGTGACAAATACTGTATGTAGTGTCACAACAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATgca                           >  2:151781/1‑139 (MQ=255)
                                                                                                                   gTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATGATAGc                        >  2:50353/1‑141 (MQ=255)
                                                                                                                     gCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATGATAGCaa                      >  2:106081/1‑141 (MQ=255)
                                                                                                                      cTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATGATAGCaaa                     >  1:188915/1‑141 (MQ=255)
                                                                                                                       tGTCTTATTTTTGTGACAAATACTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATGATAGCAAAt                    <  1:84683/141‑1 (MQ=255)
                                                                                                                       tGTCTTATTTTTGTGACAAATACTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATGATAGCAAAt                    <  1:138774/141‑1 (MQ=255)
                                                                                                                        gTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATGATAGCAAAtt                   >  1:16189/1‑141 (MQ=255)
                                                                                                                               ttttGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGTCAGATCTATCATTTTTGAATGATAGCAAATTTCCCTTa            <  2:33235/141‑1 (MQ=255)
                                                                                                                                  tgtgACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATGATAGCAAATTTCCCTTATGc         >  1:200417/1‑141 (MQ=255)
                                                                                                                                    tgACAAATACTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATGATAGCAAATTTCCCTTATGctc       <  2:7162/141‑1 (MQ=255)
                                                                                                                                         aaTGCTGTATGTAGTGTCATAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATGATAGCAAATTTCCCTTATGCTCTTACg  <  2:15325/141‑1 (MQ=255)
                                                                                                                                         aaTGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTCGCCTTGCCAGATCTATCATTTTTGAATGATAGCAAATTTCCCTTATGCTCTTACg  <  2:117174/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                         
GACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTC‑TTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACTTAAAACCCTTGGAATGTCTGGCCTTGCCAGATCTATCATTTTTGAATGATAGCAAATTTCCCTTATGCTCTTACG  >  CP000731/1451‑1727

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑