Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,064,444 Δ1 bp 100% coding (45/1218 nt) ywtF ← Putative transcriptional regulator YwtF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,064,4440A.97.7% 184.2 / ‑3.1 43coding (45/1218 nt)ywtFPutative transcriptional regulator YwtF
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base . (16/26);  total (17/26)
Fisher's exact test for biased strand distribution p-value = 3.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTAC  >  USA300TCH1516_ALE/1064311‑1064577
                                                                                                                                     |                                                                                                                                     
gttCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTATTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATg                                                                                                                                >  1:67206/1‑140 (MQ=255)
 ttcttcGGGATTGACTTTATTCTCGCTGACGTGGGTTTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTCAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGc                                                                                                                               <  2:359014/140‑1 (MQ=255)
 ttcttcGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGc                                                                                                                               >  1:463663/1‑140 (MQ=255)
  tcttcGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCt                                                                                                                              >  1:356330/1‑140 (MQ=255)
         gATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGa                                                                                                                       >  1:90464/1‑140 (MQ=255)
                 ttattaTCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAATGACAATGAG‑ACCAATGCTAGAAGGATCAAAAAg                                                                                                               <  2:441385/140‑1 (MQ=255)
                      atCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTAttt                                                                                                          <  1:194383/140‑1 (MQ=255)
                         tcatcaGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGAGTCGAATGCATGTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTAATGGAACAACAATGAG‑ACCAATGCGAGACGGATCAAAAAGTAGTTTaa                                                                                                       >  2:83320/6‑140 (MQ=255)
                               gTTGGATTGGCTGTTAGCTTTTTTGCTGTTTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTTATGTAGTGATTACTTTTGGAACAACAATGAG‑ACTAATGCTAGAAGGATCAAAAAGTATTTTAAAAAttt                                                                                                 <  2:30359/140‑1 (MQ=255)
                               gTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGA‑ACACAAAGCTAGAAGGATCAAAAAGTATTTTAAAAAttt                                                                                                 >  1:423332/1‑140 (MQ=255)
                               gTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCAACTTGGGACGATTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAAttt                                                                                                 >  1:149739/1‑140 (MQ=255)
                                  ggATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTAtt                                                                                              >  1:342192/1‑140 (MQ=255)
                                         cGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCAtgatt                                                                                       <  1:97773/140‑1 (MQ=255)
                                          gATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCAtgattg                                                                                      <  2:119538/140‑1 (MQ=255)
                                               gCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGCTCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCt                                                                                 >  2:234463/1‑140 (MQ=255)
                                                      tGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTatat                                                                          <  2:119755/140‑1 (MQ=255)
                                                      tGCTGTATTGAGAAGAGTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGGATTTTAAAAATTTATTCATGATTGATGCTCCTatat                                                                          <  1:253154/140‑1 (MQ=255)
                                                        ccgTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGATAAAAAAATAAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTa                                                                        <  2:548915/138‑1 (MQ=255)
                                                                         gAATGCATCTTGGGACGGTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATGTTAAAAATTTATTCATGATTGATGATCCTATATTAAATTTTTGTTAaatcat                                                       >  1:128246/1‑140 (MQ=255)
                                                                           aTGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGGTCGAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAaatcataa                                                     >  2:170006/1‑140 (MQ=255)
                                                                                  ttGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATTCTCCTATATTAAATTTTTGTTAAATcataatgttaat                                              >  1:234022/1‑140 (MQ=255)
                                                                                           tttAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTACTATGTTAAATTTTTGTTAAATCATAATCATAATTTTAAAata                                     <  2:90464/140‑1 (MQ=255)
                                                                                             tAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAAtata                                   >  2:275364/1‑140 (MQ=255)
                                                                                              aaaaaGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATaa                                  <  1:53550/140‑1 (MQ=255)
                                                                                              aaaaaGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATaa                                  >  1:459149/1‑140 (MQ=255)
                                                                                               aaaaGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGTATCAAATAGTATTTTAAAAATTTATGCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAAt                                 <  1:194689/140‑1 (MQ=255)
                                                                                                  aGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAg                              <  2:114696/140‑1 (MQ=255)
                                                                                                   gTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGt                             >  2:318159/1‑140 (MQ=255)
                                                                                                    tAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGtt                            <  2:403059/140‑1 (MQ=255)
                                                                                                      aCGTAGCAAAGACTATTTGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGa                          <  1:532015/140‑1 (MQ=255)
                                                                                                        gTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAAc                        <  1:496013/140‑1 (MQ=255)
                                                                                                        atagaaaaGATTTTTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGAATTTTAAAAATTTATTCATGATTAATGCTCCTATATTAAATTTTTGTTAAATAATAATCATAATTTTAAAATATAATTAGTTGAAc                        >  2:201375/7‑140 (MQ=255)
                                                                                                         tAGCGAAGACTATCGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACg                       >  2:278827/1‑140 (MQ=255)
                                                                                                             gAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGatat                   <  2:463663/140‑1 (MQ=255)
                                                                                                                  cTATTGGAACAACAATGTG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTtata              <  2:356330/140‑1 (MQ=255)
                                                                                                                     ttGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACaa           <  2:67206/140‑1 (MQ=255)
                                                                                                                      tgtaacaacAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCTTGATTTATGCTCCTATATTAAAGTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAAc          <  1:220791/137‑1 (MQ=255)
                                                                                                                       ggAAAAAAAATGAG‑ACCAATGCTAGAAAGATCAAAAAGGATTTTAAAAATTTATTCATTATTGATGCTCCTATATTAAATTTTTGTTAAATTATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACt         <  2:213737/140‑1 (MQ=255)
                                                                                                                        gaccaacaaTGAG‑ACCAATGCTAGAAGGCTCAAAAAGTCTCTTGACCATTTACTCATGATTGATGAATTTTCTGGAAAACCATGCGGCTTAAAAAACATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACtt        <  1:264693/137‑1 (MQ=255)
                                                                                                                           caacaaTGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCAt     <  2:423332/140‑1 (MQ=255)
                                                                                                                           caacaaTGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCAt     <  2:149739/140‑1 (MQ=255)
                                                                                                                           caacaaTGAG‑ACCAATGATAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCAt     <  1:25106/140‑1 (MQ=255)
                                                                                                                              caaTGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTAc  <  1:231966/140‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                     
GTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTAC  >  USA300TCH1516_ALE/1064311‑1064577

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: ‑