Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,732,905 T→A 10.8% intergenic (+91/+146) limB_2 → / ← USA300HOU_RS08645 Limonene 1,2‑monooxygenase/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,732,9050TA10.8% 111.6 / 7.4 37intergenic (+91/+146)limB_2/USA300HOU_RS08645Limonene 1,2‑monooxygenase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (21/12);  new base A (2/2);  total (23/14)
Fisher's exact test for biased strand distribution p-value = 6.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.19e-01

GTTCAAGAATGTTATAAATCAGATAAATGAAAAAAACACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGGCGCTTTCAAAATATTGAAAAGCATATCCAAAATTTAA  >  USA300TCH1516_ALE/1732769‑1733044
                                                                                                                                        |                                                                                                                                           
gTTCAAGAATGTTATAAATCAGATAAATGAAAAAAACACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAAt                                                                                                                                         <  1:246148/141‑1 (MQ=255)
              taAATCAGATAAATGAAAAAAACACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTAAATCATTTATTTTAGTa                                                                                                                           >  2:457095/1‑141 (MQ=255)
                   cAGATAAATGAAAAAAACACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGAt                                                                                                                      >  2:355467/1‑141 (MQ=255)
                   cAGATAAATGAAAAAAACACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTACAATCATTTATTTTAGTAATGAt                                                                                                                      >  1:73519/1‑141 (MQ=255)
                   cAGATAAATGAAAAAAACACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTACAATCATTTATTTTAGTAATGAt                                                                                                                      >  1:229666/1‑141 (MQ=255)
                         aaTGAAAAAAACACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAAt                                                                                                                >  2:179351/1‑141 (MQ=255)
                         aaTGAAAAAAACACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAAt                                                                                                                >  1:63244/1‑141 (MQ=255)
                         aaTGAAAAAAACACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAAt                                                                                                                >  1:430675/1‑141 (MQ=255)
                         aaTGAAAAAAACACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAAt                                                                                                                >  1:260642/1‑141 (MQ=255)
                              aaaaaaCACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACt                                                                                                           >  2:429302/1‑141 (MQ=255)
                                         tataATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTaa                                                                                                <  1:341967/141‑1 (MQ=255)
                                              tgtgATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATTAAATATGTCTTTATTGTTCAATCATTGATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCaa                                                                                           >  1:114953/1‑141 (MQ=255)
                                                 gATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAata                                                                                        <  1:228212/141‑1 (MQ=255)
                                                       taaaCTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAg                                                                                  <  1:287338/141‑1 (MQ=255)
                                                         aaCTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAgcg                                                                                >  2:232128/1‑141 (MQ=255)
                                                                tGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTc                                                                         <  2:351101/141‑1 (MQ=255)
                                                                        tgtatCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTac                                                                 >  1:83132/1‑141 (MQ=255)
                                                                         gtatCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTaca                                                                >  1:328150/1‑141 (MQ=255)
                                                                                        ataaAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTa                                                 <  1:355467/141‑1 (MQ=255)
                                                                                        ataaAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTACAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTa                                                 <  2:73519/141‑1 (MQ=255)
                                                                                        ataaAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTACAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTa                                                 <  2:229666/141‑1 (MQ=255)
                                                                                                ataCAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATgg                                         >  2:441329/1‑141 (MQ=255)
                                                                                                    aGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGgcg                                     <  1:40398/141‑1 (MQ=255)
                                                                                                    aGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGgcg                                     <  1:123215/141‑1 (MQ=255)
                                                                                                    aGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGgcg                                     <  1:329475/141‑1 (MQ=255)
                                                                                                    aGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGgcg                                     <  1:269668/141‑1 (MQ=255)
                                                                                                    aGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGgcg                                     <  1:244876/141‑1 (MQ=255)
                                                                                                        aCAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGGCGCttt                                 >  2:442035/1‑141 (MQ=255)
                                                                                                          aGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGGCGCTTTCa                               >  2:171433/1‑141 (MQ=255)
                                                                                                          aGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGGCGCTTTCa                               >  2:366796/1‑141 (MQ=255)
                                                                                                          aGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGGCGCTTTCa                               >  1:47244/1‑141 (MQ=255)
                                                                                                          aGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGGCGCTTTCa                               >  1:244403/1‑141 (MQ=255)
                                                                                                               tttGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGGCGCTTTCAAAata                          >  1:186881/1‑141 (MQ=255)
                                                                                                               tttGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGGCGCTTTCAAAata                          >  1:105734/1‑141 (MQ=255)
                                                                                                                         aGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGGCGCTTTCAAAATATTGAAAAGCa                <  1:179351/141‑1 (MQ=255)
                                                                                                                                 ttATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCACATTTATACTGTGTAAGTGTTTATTTGATGGGGCGCTTTCAAAATATTGAAAAGCATATCCaaa        >  1:8270/1‑141 (MQ=255)
                                                                                                                                 ttATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGATTATTTGATGGGGCGCTTTCAAAATATTGAAAAGCatattctaa        >  1:441547/1‑136 (MQ=255)
                                                                                                                                       ttCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGGCGCTTTCAAAATATTGAAAAGCATATCCAAAATTTaa  <  1:150274/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                           
GTTCAAGAATGTTATAAATCAGATAAATGAAAAAAACACTTTATAATGTGATAAATAAACTAAGTGAAAGTATGTATCCATAATATTAATAAAAATATACAGTAACAGCATTTTGAATGAAAGATGTCTTTATTGTTCAATCATTTATTTTAGTAATGATTCAAATTCACTTAAAATTCTAATGCAAATATGAAAGCGCCCCTTCAACTTTACACTGTGTAAGTGTTTATTTGATGGGGCGCTTTCAAAATATTGAAAAGCATATCCAAAATTTAA  >  USA300TCH1516_ALE/1732769‑1733044

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