Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,041,281 T→C 11.5% intergenic (‑364/+219) USA300HOU_1897 ← / ← USA300HOU_1899 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,041,2810TC11.5% 79.0 / 4.7 35intergenic (‑364/+219)USA300HOU_1897/USA300HOU_1899hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (20/11);  new base C (2/2);  total (22/13)
Fisher's exact test for biased strand distribution p-value = 6.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.50e-01

AAGCTGACAGAAAGTCAGCTTCTATGTTGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTGTTATTTATTCAGCATTTTTTGCCGTTCTTCATTATATAGACT  >  CP000730/2041157‑2041417
                                                                                                                            |                                                                                                                                        
aaGCTGACAGAAAGTCAGCTTCTATGTTGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGt                                                                                                                          <  1:19126/141‑1 (MQ=255)
 aGCTGACAGAAAGTCAGCTTCTATGTTGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTc                                                                                                                         >  1:199992/1‑141 (MQ=255)
     gccaaaaaGTCATCTTCTTTTTTGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGAAATTGAATTTATGACCCAGGCTCAGTCTTAt                                                                                                                     <  1:261974/136‑1 (MQ=25)
       cAGAAAGTCAGCTTCTATGTTGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTCAATTTATGACCCAGCCTCAGTCTTAttt                                                                                                                   >  2:325104/1‑141 (MQ=255)
        aGAAAGTCAGCTTCTATGTTGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACCTTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTtc                                                                                                                  >  1:369150/1‑141 (MQ=255)
          aaaGTCAGCTTCTATGTTGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGCATCTATGACCCAGGCTCAGTCTTATTtcat                                                                                                                >  2:62886/1‑141 (MQ=255)
            aGTCAGCTTCTATGTTGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTCATGACCCAGGCTCAGTCTTATTtcatca                                                                                                              >  1:120466/1‑141 (MQ=255)
            aGTCAGCTTCTACGTTGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTCATGACCCAGGCTCAGTCTTATTtcatca                                                                                                              >  1:355388/1‑141 (MQ=255)
                 gCTTCTATGTTGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGACTTTATGACCCAGGCTCCGTCTTATTTCATCATTCtt                                                                                                         >  1:41746/1‑141 (MQ=255)
                          ttGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGtt                                                                                                >  1:143890/1‑141 (MQ=255)
                                     cTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACCTTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCACCt                                                                                     >  1:331713/1‑141 (MQ=255)
                                     cTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGGGCCTAGGACATTGAATTTATGACCCCGGCTCCGTCTTATTTCATTATTCTTAATATCGTTAAAGTCCAACt                                                                                     >  1:62897/1‑141 (MQ=37)
                                        gAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGt                                                                                  <  1:330943/141‑1 (MQ=255)
                                           ttGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGCCCCCGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATc                                                                               <  1:56108/141‑1 (MQ=255)
                                            tGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCt                                                                              <  1:326255/141‑1 (MQ=255)
                                                 aaaGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTCATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAAc                                                                         <  2:355388/141‑1 (MQ=255)
                                                 aaaGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTCATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAAc                                                                         <  2:120466/141‑1 (MQ=255)
                                                                      ttctttcAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACACATACTACCTTGAGATGTaa                                                    <  2:86531/141‑2 (MQ=255)
                                                                      ttctttcAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTAc                                                    >  2:27043/1‑141 (MQ=255)
                                                                           tcAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGc                                               <  1:376378/141‑1 (MQ=255)
                                                                            cAGTCAACTACAGCCAATATAACCTTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTAAAAAGCt                                              >  1:392191/1‑141 (MQ=255)
                                                                            cAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCt                                              >  2:14422/1‑141 (MQ=255)
                                                                              gTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTg                                            >  2:305920/1‑141 (MQ=255)
                                                                              gTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTg                                            >  1:24232/1‑141 (MQ=255)
                                                                              gTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAAATTGTATCTTAAACAAATACTAATTCAATATGTACAAAGtttt                                            >  2:185358/1‑140 (MQ=255)
                                                                               tCAACTACAGCCAATATAACATTGTAGTGCCTAGGACTTTGAAGTTATGACACAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTAACAATGGCTCTATCTCAATATGTACAAAGCTTGt                                           <  1:191510/141‑1 (MQ=255)
                                                                                        gCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTGTTATTTATTc                                  >  1:302102/1‑141 (MQ=255)
                                                                                           aaTATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTGTTATTTATTCAGc                               <  2:369150/141‑1 (MQ=255)
                                                                                                   cttGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTGTTATTTATTCAGCATTTTTTg                       <  1:245151/140‑1 (MQ=255)
                                                                                                       tAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTGTTATTTATTCAGCATTTTTTGCCGt                   >  2:242614/1‑141 (MQ=255)
                                                                                                       tAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTGTTATTTATTCAGCATTTTTTGCCGt                   >  2:368730/1‑141 (MQ=255)
                                                                                                            ccTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTGTTATTTATTCAGCATTTTTTGCCGttcttc              <  2:199992/141‑1 (MQ=255)
                                                                                                                ggACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTGTTATTTATTAAGCATTTTTTTCCGTTCTTCATta          >  1:183992/1‑141 (MQ=255)
                                                                                                                       gAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTGTTATTTATTCAGCATTTTTTGCCGTTCTTCATTATATAGAc   >  2:323018/1‑141 (MQ=255)
                                                                                                                        aaTTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATCTGTACAAAGCTTGTTATTTATTCAGCATTTTTTGCCGTTCTTCATTATATAGACt  >  2:131821/1‑141 (MQ=255)
                                                                                                                            |                                                                                                                                        
AAGCTGACAGAAAGTCAGCTTCTATGTTGGGGCCCCACTAGAATTGAAAAAAGCTTGTTACAAGCGTATTTTCTTTCAGTCAACTACAGCCAATATAACATTGTAGTGCCTAGGACATTGAATTTATGACCCAGGCTCAGTCTTATTTCATCATTCTTAATATCGTTAAAGACCAACTTGTATCTTAAACAAATACTATCTCAATATGTACAAAGCTTGTTATTTATTCAGCATTTTTTGCCGTTCTTCATTATATAGACT  >  CP000730/2041157‑2041417

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: