Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	35,858	T→A	25.6%	intergenic (+89/+19)	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	35,858	0	T	A	25.6%	90.6 / 23.0	44	intergenic (+89/+19)	USA300HOU_0025/USA300HOU_0026	hypothetical protein/IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base T (15/17);  new base A (2/9);  total (17/27)
Fisher's exact test for biased strand distribution p-value = 1.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.66e-01

AGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATT  >  CP000730/35721‑35990                                                                                                                                          |                                                                                                                                     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                                                   <  2:213429/136‑1 (MQ=11)                                                                               tattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGc                                                   <  1:81528/136‑1 (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                                                   <  2:186990/141‑1 (MQ=255)                                                                                 aTCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGc                                                   <  2:10051/141‑1 (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)                                                                                                                               taatcccTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGGGAAAATCCGTAGATCTGAAGAGACCTACGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGt     <  1:102662/135‑1 (MQ=1)                                                                                                                                  ccgcTAAGTTACCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGAGCGGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACACTCAATACCTTTTAAAGTAtt  <  2:1647/138‑1 (MQ=1)                                                                                                                                          |                                                                                                                                     AGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATT  >  CP000730/35721‑35990

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: ‑