Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,479 T→C 24.0% T25A (ACA→GCA)  USA300HOU_0026 ← IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,4790TC24.0% 62.7 / 14.1 44T25A (ACA→GCA) USA300HOU_0026IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base T (17/15);  new base C (3/7);  total (22/22)
Fisher's exact test for biased strand distribution p-value = 2.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGG  >  CP000730/36340‑36616
                                                                                                                                           |                                                                                                                                         
taataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGta                                                                                                                                          <  2:199253/141‑1 (MQ=40)
  ataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGGTAACTCAATGtata                                                                                                                                        >  2:120543/1‑141 (MQ=255)
   taaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTatat                                                                                                                                       <  1:339836/141‑1 (MQ=40)
        ttttttATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACCGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAg                                                                                                                                  >  2:208074/1‑141 (MQ=37)
              aTGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAtagta                                                                                                                            >  1:286432/1‑141 (MQ=35)
               tGCTTTTTCTTCCAATTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAtagtag                                                                                                                           <  2:342631/141‑1 (MQ=25)
                 ggtgttgttcCAAAGTTGATACAAAAGTGGGGCATATTCCTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCGTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGcc                                                                                                                         <  2:160389/134‑1 (MQ=11)
                    tttCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAAc                                                                                                                      <  2:309676/141‑1 (MQ=35)
                     ttcttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCGTAGATAGTAGCCAACg                                                                                                                     <  2:127356/141‑1 (MQ=25)
                         tcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTa                                                                                                                 >  2:252134/1‑141 (MQ=35)
                                 tGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATa                                                                                                         >  1:359730/1‑141 (MQ=35)
                                   aTACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAAc                                                                                                       >  2:295590/1‑141 (MQ=35)
                                    tACAGAATTGGGGCATATTCTTGACCCAAAAGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATAAAACGCTAACTCAATCTATATCTTACATAGTAGCCACCGGATACAGTATTAAct                                                                                                      >  2:227361/1‑140 (MQ=11)
                                    tACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGCTTACACCCCGTTCCCTTAATATTTCAGATATATCACGCTAACTCAATGGATATCTTAGATAGTAGCCACCGGCTACAGTGATAACa                                                                                                      >  2:369909/1‑141 (MQ=11)
                                      cAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATc                                                                                                    <  1:333134/141‑1 (MQ=33)
                                             ggggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTa                                                                                             <  2:20437/141‑1 (MQ=32)
                                               ggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTaaa                                                                                           >  1:288914/1‑141 (MQ=32)
                                                     ttCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATGACATCCTTGTTAAATTGttt                                                                                     <  1:104879/141‑1 (MQ=17)
                                                         tGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTatat                                                                                 >  2:206222/1‑141 (MQ=32)
                                                               cAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGaaa                                                                           >  2:332419/1‑141 (MQ=32)
                                                                  cGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAg                                                                        >  1:43728/1‑141 (MQ=32)
                                                                      aGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCa                                                                    <  2:140675/141‑1 (MQ=32)
                                                                               aaTGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACagaaga                                                           <  1:331334/141‑1 (MQ=32)
                                                                                 tgatgaACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACt                                                         >  2:41743/1‑141 (MQ=32)
                                                                                   atgaACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTGATACAGAAGACTct                                                       >  2:126307/1‑140 (MQ=17)
                                                                                   atgaACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTcc                                                       <  2:77929/141‑1 (MQ=32)
                                                                                      aaCGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCttt                                                    <  2:324367/141‑1 (MQ=32)
                                                                                        cGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCttttt                                                  >  2:116264/1‑141 (MQ=12)
                                                                                            tACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCATAGAGAGTAGCCAACGGCTACAGTGATAACATCCTTTTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTa                                              >  2:78985/1‑141 (MQ=12)
                                                                                             acacCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGttca                                             >  1:98184/1‑139 (MQ=17)
                                                                                               accacGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTaaaa                                           >  1:335005/1‑141 (MQ=32)
                                                                                                       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)
                                                                                                                                           |                                                                                                                                         
TAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGG  >  CP000730/36340‑36616

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: ‑