Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,064,445 Δ1 bp 100% coding (44/1218 nt) USA300HOU_1000 ← LytR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,064,4440A.97.7% 184.0 / ‑3.1 43coding (45/1218 nt)USA300HOU_1000LytR family transcriptional regulator
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  >  CP000730/1064311‑1064577
                                                                                                                                     |                                                                                                                                     
gttCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTATTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATg                                                                                                                                >  1:67206/1‑140 (MQ=255)
 ttcttcGGGATTGACTTTATTCTCGCTGACGTGGGTTTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTCAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGc                                                                                                                               <  2:359014/140‑1 (MQ=255)
 ttcttcGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGc                                                                                                                               >  1:463663/1‑140 (MQ=255)
  tcttcGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCt                                                                                                                              >  1:356330/1‑140 (MQ=255)
         gATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGa                                                                                                                       >  1:90464/1‑140 (MQ=255)
                 ttattaTCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAATGACAATGAGACCAATGCTAGAAGGATCAAAAAg                                                                                                               <  2:441385/140‑1 (MQ=255)
                      atCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTAttt                                                                                                          <  1:194383/140‑1 (MQ=255)
                         tcatcaGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGAGTCGAATGCATGTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTAATGGAACAACAATGAGACCAATGCGAGACGGATCAAAAAGTAGTTTaa                                                                                                       >  2:83320/6‑140 (MQ=255)
                               gTTGGATTGGCTGTTAGCTTTTTTGCTGTTTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTTATGTAGTGATTACTTTTGGAACAACAATGAGACTAATGCTAGAAGGATCAAAAAGTATTTTAAAAAttt                                                                                                 <  2:30359/140‑1 (MQ=255)
                               gTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAACACAAAGCTAGAAGGATCAAAAAGTATTTTAAAAAttt                                                                                                 >  1:423332/1‑140 (MQ=255)
                               gTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCAACTTGGGACGATTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAAttt                                                                                                 >  1:149739/1‑140 (MQ=255)
                                  ggATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTAtt                                                                                              >  1:342192/1‑140 (MQ=255)
                                         cGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCAtgatt                                                                                       <  1:97773/140‑1 (MQ=255)
                                          gATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCAtgattg                                                                                      <  2:119538/140‑1 (MQ=255)
                                               gCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGCTCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCt                                                                                 >  2:234463/1‑140 (MQ=255)
                                                      tGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTatat                                                                          <  2:119755/140‑1 (MQ=255)
                                                      tGCTGTATTGAGAAGAGTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGGATTTTAAAAATTTATTCATGATTGATGCTCCTatat                                                                          <  1:253154/140‑1 (MQ=255)
                                                        ccgTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGATAAAAAAATAAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTa                                                                        <  2:548915/138‑1 (MQ=255)
                                                                         gAATGCATCTTGGGACGGTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATGTTAAAAATTTATTCATGATTGATGATCCTATATTAAATTTTTGTTAaatcat                                                       >  1:128246/1‑140 (MQ=255)
                                                                           aTGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGGTCGAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAaatcataa                                                     >  2:170006/1‑140 (MQ=255)
                                                                                  ttGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATTCTCCTATATTAAATTTTTGTTAAATcataatgttaat                                              >  1:234022/1‑140 (MQ=255)
                                                                                           tttAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTACTATGTTAAATTTTTGTTAAATCATAATCATAATTTTAAAata                                     <  2:90464/140‑1 (MQ=255)
                                                                                             tAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAAtata                                   >  2:275364/1‑140 (MQ=255)
                                                                                              aaaaaGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATaa                                  <  1:53550/140‑1 (MQ=255)
                                                                                              aaaaaGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATaa                                  >  1:459149/1‑140 (MQ=255)
                                                                                               aaaaGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGTATCAAATAGTATTTTAAAAATTTATGCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAAt                                 <  1:194689/140‑1 (MQ=255)
                                                                                                  aGTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAg                              <  2:114696/140‑1 (MQ=255)
                                                                                                   gTAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGt                             >  2:318159/1‑140 (MQ=255)
                                                                                                    tAACGTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGtt                            <  2:403059/140‑1 (MQ=255)
                                                                                                      aCGTAGCAAAGACTATTTGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGa                          <  1:532015/140‑1 (MQ=255)
                                                                                                        gTAGCGAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAAc                        <  1:496013/140‑1 (MQ=255)
                                                                                                        atagaaaaGATTTTTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGAATTTTAAAAATTTATTCATGATTAATGCTCCTATATTAAATTTTTGTTAAATAATAATCATAATTTTAAAATATAATTAGTTGAAc                        >  2:201375/7‑140 (MQ=255)
                                                                                                         tAGCGAAGACTATCGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACg                       >  2:278827/1‑140 (MQ=255)
                                                                                                             gAAGACTATTGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGatat                   <  2:463663/140‑1 (MQ=255)
                                                                                                                  cTATTGGAACAACAATGTGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTtata              <  2:356330/140‑1 (MQ=255)
                                                                                                                     ttGGAACAACAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACaa           <  2:67206/140‑1 (MQ=255)
                                                                                                                      tgtaacaacAATGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCTTGATTTATGCTCCTATATTAAAGTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAAc          <  1:220791/137‑1 (MQ=255)
                                                                                                                       ggAAAAAAAATGAGACCAATGCTAGAAAGATCAAAAAGGATTTTAAAAATTTATTCATTATTGATGCTCCTATATTAAATTTTTGTTAAATTATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACt         <  2:213737/140‑1 (MQ=255)
                                                                                                                        gaccaacaaTGAGACCAATGCTAGAAGGCTCAAAAAGTCTCTTGACCATTTACTCATGATTGATGAATTTTCTGGAAAACCATGCGGCTTAAAAAACATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACtt        <  1:264693/137‑1 (MQ=255)
                                                                                                                           caacaaTGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCAt     <  2:149739/140‑1 (MQ=255)
                                                                                                                           caacaaTGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCAt     <  2:423332/140‑1 (MQ=255)
                                                                                                                           caacaaTGAGACCAATGATAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCAt     <  1:25106/140‑1 (MQ=255)
                                                                                                                              caaTGAGACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTAc  <  1:231966/140‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                     
GTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTAC  >  CP000730/1064311‑1064577

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: