Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,581 C→T 17.9% intergenic (‑30/‑493) tpn ← / → USA300HOU_0028 IS431mec transposase/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,5810CT17.9% 95.4 / 11.7 48intergenic (‑30/‑493)tpn/USA300HOU_0028IS431mec transposase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (16/23);  new base T (4/5);  total (20/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATTTAGT  >  CP000730/36443‑36721
                                                                                                                                          |                                                                                                                                            
cccTGAATAGTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACta                                                                                                                                            <  1:191090/141‑1 (MQ=17)
        atTTGAGATAGATCACGCTAACTCAATGTATCTCTTTGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAAGTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTGTTTGTTAAAATTATACTATAAATTCa                                                                                                                                    <  1:126307/141‑1 (MQ=11)
             agttatatCACGATAACTCAATGCATATCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACttt                                                                                                                               <  1:106838/138‑1 (MQ=2)
              gATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTg                                                                                                                              >  1:375573/1‑141 (MQ=35)
                  tatCACTATAGCTCACGGCATATCTTAGATAGTCGCCACCGGCTGTGGTGCTAACATCTCTGTTAAATTCTTTATATCTGAAATGGTGCATACAGATGACTCCTTTTTGCTAAAATTATATTATAAATTCAACTTTGCAAc                                                                                                                          <  2:40976/141‑1 (MQ=255)
                  tatCACGATAGCTCAAGGAATATCTTAGATAGTAGCCAACGACTACAGTGATGACTTCGTCGTTAAATTGTTTGTATCTCAAAAAATGCCAACAAAAGACTCCTATTTGTTACAATAGTATAATAAAATCAACTTTGcgaa                                                                                                                          >  2:21977/1‑138 (MQ=2)
                     caagATAACTTAATGCATATCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGa                                                                                                                       <  2:127887/138‑1 (MQ=2)
                         atagcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTCCATACAGAAGATTCCTGTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCg                                                                                                                   >  2:169527/5‑141 (MQ=11)
                         aTAGCTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCg                                                                                                                   <  1:116264/141‑1 (MQ=25)
                          tagcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATATTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGt                                                                                                                  <  2:248456/138‑1 (MQ=255)
                          tagcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGt                                                                                                                  <  1:298021/138‑1 (MQ=12)
                          tAACACAATGCATATCTTATATAGTAGCCAACGTCTACAGTTATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCTTACAGATGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGt                                                                                                                  <  2:13013/141‑1 (MQ=11)
                            gcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATGGTTCATACAGAAGACTCCTTTTTGTTAAAATCATATTATAAATTCAACTTTGCAACAGAACCGtat                                                                                                                >  2:61439/2‑141 (MQ=255)
                               cAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttt                                                                                                             >  1:13757/1‑139 (MQ=255)
                                 aTGCATATCTTGGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttat                                                                                                           <  2:201462/141‑5 (MQ=255)
                                      tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATag                                                                                                      >  1:55095/1‑141 (MQ=255)
                                        tCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATagag                                                                                                    <  1:27361/141‑1 (MQ=255)
                                          tgaGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGAt                                                                                                  <  1:34467/139‑1 (MQ=255)
                                            agagagTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATCTCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGt                                                                                                <  1:128040/141‑1 (MQ=255)
                                               tagtagCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTgg                                                                                             <  1:332419/141‑1 (MQ=255)
                                               aagtatCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTgg                                                                                             <  1:29368/140‑1 (MQ=255)
                                                agtagCCAACGGCTACAGTGAAAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGt                                                                                            <  1:191585/141‑1 (MQ=255)
                                                       caCGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGGATAGATATGTTGGTAATAttt                                                                                     <  2:226587/140‑1 (MQ=255)
                                                          ggCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAACATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAAGAGAGATGTTGGTACCATTtata                                                                                  >  1:83026/1‑141 (MQ=255)
                                                          ggCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTtata                                                                                  >  1:83023/1‑141 (MQ=255)
                                                          ggCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGAGGTTGGTAACATTtata                                                                                  <  1:208074/141‑1 (MQ=255)
                                                          ggCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAAAGATGTTGGTAACATTtgta                                                                                  >  1:52784/1‑141 (MQ=255)
                                                                 gTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTTTTTTATTTTTACTATAAATTCAACTTTGCAACAGAACCGTATTGTGGAATAGAGATGTTGGTAACATTTATACAgatca                                                                           >  2:140577/1‑137 (MQ=18)
                                                                              tGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGt                                                              <  2:286432/141‑1 (MQ=255)
                                                                                    aTTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAATAGTAATATGGTATAGAGATGTTGGTAGCATTGATACAGGATCATTATACTTAAGTTTAAtt                                                        <  2:359730/141‑1 (MQ=21)
                                                                                     ttGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAAttt                                                       >  2:312868/1‑141 (MQ=255)
                                                                                     tagTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTCTACTATAAATTCAACTTTGCAACAGAACAGTATTATGGAATAGAGATGTTGTTAACACTTATACAGGCTCCTTCTACTTAAGTTTAAatt                                                       >  2:98191/3‑141 (MQ=21)
                                                                                          taaatCTAAAATAGTTCATATAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCCTATTATGTAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGtta                                                  <  1:167059/138‑1 (MQ=25)
                                                                                           atatCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGttat                                                 >  2:125231/1‑141 (MQ=255)
                                                                                            tatCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGAAAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGttatt                                                >  1:252987/1‑141 (MQ=255)
                                                                                                tGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAg                                            <  2:27019/141‑1 (MQ=255)
                                                                                                    aTAGTTCATACAGAAGACTCCTTTTTTTTTTTTTTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAAcc                                        >  2:257233/1‑141 (MQ=38)
                                                                                                      aGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGTTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACcac                                      <  1:51543/141‑1 (MQ=255)
                                                                                                       gTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACcaca                                     <  1:252134/141‑1 (MQ=255)
                                                                                                                 aagaCTCCTTTTTTTTTTTTTTTTACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCTTTATTACAGAACCACACATTATAAcc                           >  2:250847/1‑141 (MQ=255)
                                                                                                                  agccTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTACACTTAAGTTTAATTTCGTCATTACTGAACCACACATTCCAACCa                          <  1:204262/138‑1 (MQ=255)
                                                                                                                    aCTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCaga                        <  2:55095/141‑1 (MQ=255)
                                                                                                                            ttGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAg                <  1:295590/141‑1 (MQ=255)
                                                                                                                                tAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATg            <  1:120543/141‑1 (MQ=255)
                                                                                                                                 aaaaTTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCACCCCGAAGAGAAAGTATGt           >  2:121259/1‑141 (MQ=255)
                                                                                                                                  aaaTTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTGATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTc          >  1:119266/1‑141 (MQ=255)
                                                                                                                                       ataCTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTAttt     >  1:345550/1‑141 (MQ=255)
                                                                                                                                       ataCGATAAATTCAACTTTGCAAGAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCAGACATTCCACTCAGCAGAGAAAGTATGTCTAttt     >  2:247249/1‑141 (MQ=255)
                                                                                                                                          cTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATTTAGt  <  1:312868/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                            
CCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATTTAGT  >  CP000730/36443‑36721

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: ‑