Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,581 C→T 34.6% intergenic (‑30/‑493) USA300HOU_0026 ← / → USA300HOU_0028 IS431mec transposase/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,5810CT34.6% 54.7 / 40.2 52intergenic (‑30/‑493)USA300HOU_0026/USA300HOU_0028IS431mec transposase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (19/15);  new base T (8/10);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 5.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.09e-01

CCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATTTA  >  CP000730/36443‑36719
                                                                                                                                          |                                                                                                                                          
cccTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACta                                                                                                                                          <  2:7897/141‑1 (MQ=32)
       tacttCAGATATATCACGATAACTCAATGCATATCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTc                                                                                                                                   >  1:304285/4‑141 (MQ=2)
           tctgATAGATCACGATAGAACAACGCATATCTTAGATAGGATCCAACGGCTACAGTTATAACAACCTTTTTAAATTGTGTATATCTGAAATAGTTCATACAGACGACTCCTTTTTGTTAAAAATATATTATAAATTCAACt                                                                                                                               <  2:271922/138‑1 (MQ=1)
             aGATATATCACGATAGCTCAATGGATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAACTTCAACttt                                                                                                                             <  2:214127/141‑1 (MQ=255)
                 atatCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGGTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCaa                                                                                                                         >  1:210175/1‑141 (MQ=25)
                  tatCACGATAGCTCAATGAATATATTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTAATACAGAAGCCTCCTTTTTATTCAAATTATGTTATAAATTCAACTTTGCaag                                                                                                                        >  1:130499/1‑140 (MQ=11)
                   atCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACa                                                                                                                       >  2:272158/1‑141 (MQ=35)
                   atCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACa                                                                                                                       >  1:97397/1‑141 (MQ=35)
                    acacggcaaCTCAATGCATATCTTAGATAGTAGCCAACAGCTACAGTGACAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAg                                                                                                                      <  1:183352/134‑1 (MQ=1)
                        ggtagcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTGAAAATTATATTATAAATTCAACTTTGCAACAGAAcc                                                                                                                  <  1:47459/136‑1 (MQ=11)
                          tagcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGt                                                                                                                >  2:154003/4‑141 (MQ=2)
                          acgcttaaTGCATATCTTAGATAGTAGCCAACGGCTACAGTGAAAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGt                                                                                                                <  2:186749/135‑1 (MQ=11)
                            gcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtat                                                                                                              >  2:95185/2‑141 (MQ=12)
                            gcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtat                                                                                                              >  1:320322/2‑141 (MQ=12)
                              gcaattcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaa                                                                                                            <  2:334111/134‑7 (MQ=1)
                               cAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGtattat                                                                                                           >  1:316680/1‑141 (MQ=255)
                               cAATGCATATCGTAGATAGTAGCCAACGGCTATAGTGATAACATACTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGCCTCTGTTTTGTTAAAATTATATTATTTATGCAACTTTGCAACAGAACCGtatttt                                                                                                           <  2:56836/141‑3 (MQ=11)
                                 atacaaatCTTAGATAGTAGCCAAAGGCTACAGTGATAACATCCTGTTTAAATTGTTTATATCTGAAATATTTCAAACAGAAGACTCCTTTTTGTTAAAATTATATTAGAAATTCAACTTTGCAACAGAACCGtagcttat                                                                                                         <  2:132975/135‑7 (MQ=11)
                                  tGTATATCTTAGATAGTAGCCACCGGCTACAGTGATAACATCCTTGTTAAAGTGTTTATATCTGAAATAGTTCATACAGACGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCCACAGAACGGTCTTATGGa                                                                                                        >  2:51190/1‑141 (MQ=14)
                                   gcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatga                                                                                                       <  1:168875/139‑7 (MQ=255)
                                   gcatatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAcctcatttactat                                                                                                       <  2:149216/139‑12 (MQ=11)
                                   gcatatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAcctcatttactat                                                                                                       <  2:231688/139‑12 (MQ=11)
                                    catatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtat                                                                                                      <  1:55093/140‑13 (MQ=11)
                                    catatCTTAGATAGTAGCCAACAGCTACCGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATCAATTCAACTTTGCACCCGAAcctcatttactata                                                                                                      >  2:62505/2‑129 (MQ=11)
                                     atatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCATTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtatt                                                                                                     >  1:32516/1‑128 (MQ=11)
                                      tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagta                                                                                                    >  1:225113/1‑132 (MQ=255)
                                      tatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAcctcatttactatatg                                                                                                    >  1:90416/1‑127 (MQ=11)
                                       atCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtaa                                                                                                   >  1:57724/1‑131 (MQ=255)
                                       atCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTg                                                                                                                            >  1:171788/1‑116 (MQ=17)
                                       atCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTg                                                                                                                            <  2:171788/116‑1 (MQ=18)
                                         cTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacac                                                                                                 >  1:36129/1‑129 (MQ=11)
                                           tAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacactc                                                                                               <  1:169770/141‑15 (MQ=11)
                                                    gCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACa                                                                                      <  2:58527/141‑1 (MQ=255)
                                                           gCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACCGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATAc                                                                               <  2:166273/141‑1 (MQ=255)
                                                             tACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAg                                                                             >  2:98253/1‑141 (MQ=255)
                                                                         ataattGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACt                                                                 >  2:87820/5‑141 (MQ=255)
                                                                               gTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGtt                                                           >  1:258930/1‑141 (MQ=255)
                                                                                  aaaTTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTTTTTTTTTTTTACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATGGAGATGTTGGTGACCTTTATACAGGATCATTATTCTTAAGTTTaa                                                        >  2:250123/1‑141 (MQ=21)
                                                                                  aaaTTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTaa                                                        >  2:54916/1‑141 (MQ=255)
                                                                                  aaaTTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTaa                                                        >  2:210002/1‑141 (MQ=255)
                                                                                     atGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAAttt                                                     <  1:215603/140‑1 (MQ=255)
                                                                                              tCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTAc                                            <  2:66598/141‑1 (MQ=255)
                                                                                               cTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACa                                           <  1:236258/141‑1 (MQ=255)
                                                                                                      aGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTCTCATAAAGGCAGCGTCATTATCATTTAGTTTAATTTCGTTATTACAGAACcac                                    >  1:241219/1‑141 (MQ=21)
                                                                                                         tCATACAGAAGACTCCTTTTTGTTTATTTTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACcacaca                                 >  2:176892/1‑141 (MQ=255)
                                                                                                                 aagaCTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAAcc                         >  1:194110/1‑141 (MQ=255)
                                                                                                                    ccTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCaga                      <  2:97397/140‑1 (MQ=255)
                                                                                                                    aCTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCaga                      <  1:272158/141‑1 (MQ=255)
                                                                                                                               ttAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTAt           <  2:118378/141‑1 (MQ=255)
                                                                                                                                      tataCTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTAtt    <  2:96160/141‑1 (MQ=255)
                                                                                                                                      tataCCATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTAtt    <  1:87820/141‑1 (MQ=255)
                                                                                                                                        taCTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATTTa  >  1:173502/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                          
CCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATTTA  >  CP000730/36443‑36719

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: ‑