Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	35,850	C→T	19.6%	intergenic (+81/+27)	USA300HOU_0025 → / ← USA300HOU_0026	hypothetical protein/IS431mec transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	35,850	0	C	T	19.6%	98.5 / 11.2	44	intergenic (+81/+27)	USA300HOU_0025/USA300HOU_0026	hypothetical protein/IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base C (15/20);  new base T (2/7);  total (17/27)
Fisher's exact test for biased strand distribution p-value = 4.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTC  >  CP000730/35712‑35946                                                                                                                                           |                                                                                                 cATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCa                                                                                                <  1:123037/141‑1 (MQ=255)      aCAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAAt                                                                                           <  2:283624/141‑1 (MQ=255)          aGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTAt                                                                                       >  1:108939/1‑141 (MQ=255)               ttAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGt                                                                                  >  1:244234/1‑141 (MQ=255)                  aTGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAg                                                                               >  2:288150/1‑141 (MQ=255)                    gTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAgtg                                                                             >  1:95266/1‑141 (MQ=255)                    gTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGAAAAGTAAAAACATATAGCTAACCACTAATTTATCATGTCAgtg                                                                             >  2:87334/1‑141 (MQ=255)                         aGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGc                                                                        <  1:157007/141‑1 (MQ=255)                             aTTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGCTCTGATAAAAATAGAAGGTTCTGTTGCAACGAAAGAGAAGAAAGCTAACCAATAATTTATCATGTCCGTGTTCGCTTaa                                                                    >  2:78070/1‑141 (MQ=255)                               tCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACt                                                                  >  1:10051/1‑141 (MQ=255)                                     taAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAg                                                            <  1:13430/141‑1 (MQ=255)                                        aGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCat                                                         <  2:231336/141‑1 (MQ=255)                                             tatgaaaaaaaTGATTACTTGAACAAGAGCTAAAATAAAATTGTAATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGc                                                    <  2:104839/135‑1 (MQ=255)                                                  gAAAAATGATTACTTGAACAAGAACTAAAAAAAAATTGTGAACTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAAtt                                               <  2:55627/141‑1 (MQ=255)                                                         gATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGc                                        >  2:75650/1‑141 (MQ=255)                                                            tACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATg                                     <  2:302780/141‑1 (MQ=255)                                                              cTTGAACAAGATTTAAAATAAAATTTTGATCTAATAAGAATAGAAGGTTCTGTTGCAAAGTAAAATAATATAGCTTACCTCTAATTTCTCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGc                                   <  2:158653/141‑1 (MQ=17)                                                              cTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGc                                   <  2:208903/141‑1 (MQ=255)                                                              cTTAAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCGGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGc                                   <  2:243140/141‑1 (MQ=255)                                                                   acaacaGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGaaaa                              >  2:226083/1‑141 (MQ=255)                                                                   aCAAGAGCTAAAATAAAATTGTCATCTAATAAAAATAGACAGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATCTATCATTGGAGGGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGaaaa                              <  1:311465/141‑1 (MQ=17)                                                                       gagCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATTCTAATTTCGTGGCATGGCGAAAATCCg                          >  2:310540/1‑141 (MQ=255)                                                                         gCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTa                        >  2:213002/1‑141 (MQ=255)                                                                          cTAAAATAAAATTGTGATCTAATAAAAATAAAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTCATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATTGCGAAAATCCGTAg                       >  2:178940/1‑141 (MQ=255)                                                                           taaaataaaaTTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGa                      >  2:187007/1‑141 (MQ=255)                                                                               acaaaagagtattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGaa                >  1:261188/15‑141 (MQ=11)                                                                                caaaagagtattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAag               <  1:205985/128‑1 (MQ=11)                                                                                   aagagtattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAACCTTTAGCTAATCACTAATATATCATGTTAGTGTTCGTTTAACTTGCTAGCATGATGATCATTTCGGGGCATGGCGAAAATCCGTAGATCTGAAgtga            <  2:115899/131‑1 (MQ=2)                                                                                    agagtattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc           <  2:338356/132‑1 (MQ=11)                                                                                      tgtgATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc           <  2:108939/141‑1 (MQ=255)                                                                                        tgATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCt         <  2:283779/141‑1 (MQ=255)                                                                                        tgATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCt         >  1:60335/1‑141 (MQ=255)                                                                                        tattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAGTTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGc       <  2:342107/136‑1 (MQ=11)                                                                                        tattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGc       <  1:81528/136‑1 (MQ=11)                                                                                        tattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGc       <  2:213429/136‑1 (MQ=11)                                                                                         gATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTCGATCTGTAAAGACCTg        >  2:10712/1‑141 (MQ=255)                                                                                         attttaataaAAAT‑GATGGTTCTGTTGCAAAG‑AAAAAAATATAGCTAATCACTAATATATCATGTCAGTGGACGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAAACCGTAGATATGAAGAGACCTGCg      >  2:365966/5‑141 (MQ=11)                                                                                          ttttaataaAAAT‑GCTGGTTCTGTTGCAAAGT‑AAAAAATATAGCCAACCACTAATATATCCTGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTGCGTTGCATGGCGAAAATCCGGAGATCTGAAGAGACCTGCgg     <  1:321997/138‑1 (MQ=11)                                                                                          aTCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGc       <  2:10051/141‑1 (MQ=255)                                                                                          aTCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGc       <  2:186990/141‑1 (MQ=255)                                                                                           tCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCg      <  1:213002/141‑1 (MQ=255)                                                                                            ttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGtt   <  2:340933/140‑1 (MQ=11)                                                                                             taagaaAAATTGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATCTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGt    <  2:61688/141‑1 (MQ=255)                                                                                               ataaAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTc  <  2:156609/141‑1 (MQ=38)                                                                                                                                           |                                                                                                 CATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTC  >  CP000730/35712‑35946

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: ‑