Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,064,254 Δ1 bp 100% coding (235/1218 nt) USA300HOU_1000 ← LytR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,064,2530C.92.4% 213.3 / 8.0 52coding (236/1218 nt)USA300HOU_1000LytR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (2/1);  new base . (18/30);  total (20/32)
Fisher's exact test for biased strand distribution p-value = 5.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.55e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGC  >  CP000730/1064116‑1064389
                                                                                                                                         |                                                                                                                                        
tAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTcttt                                                                                                                                       >  2:259567/1‑138 (MQ=255)
  aTCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTtttt                                                                                                                                     >  1:227900/1‑141 (MQ=255)
   tCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCtttttt                                                                                                                                    >  2:225528/1‑141 (MQ=255)
            aaTAGCCAACTCTAGGAATTTAGTTTATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGCTCAGCATCCTGTCTTTTTTTCTTCTTcc                                                                                                                          <  2:218578/141‑1 (MQ=255)
                 ccAACTTTAGGAATGTATGTGATATTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAACTCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGt                                                                                                                     <  2:514387/141‑1 (MQ=255)
                   aaCTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTa                                                                                                                   <  2:389464/141‑1 (MQ=255)
                    aCTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTat                                                                                                                  <  1:249559/141‑1 (MQ=255)
                      tttAGGAATTTAGCTGATATTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTatca                                                                                                                <  2:161185/141‑1 (MQ=255)
                      tttAGGAATGCAGCTGAAAGTATCACGTGGAATACTAAGCATGCTAATTTGAGGTTTTGATTGATTAAAAGTAGTGAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTatca                                                                                                                <  2:15958/141‑1 (MQ=255)
                         aGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCg                                                                                                             >  1:435037/1‑141 (MQ=255)
                            aaTGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTACTTTGATGTTTTGCTTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGGGTTCAGCATCCGGTCTTTTTTTCTTCTTCCATCGTTATCATCGAtc                                                                                                          >  2:418315/1‑140 (MQ=255)
                                gatcTGATAGGATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTa                                                                                                      <  1:45400/138‑1 (MQ=255)
                                  gCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaag                                                                                                    <  1:53584/141‑1 (MQ=255)
                                  gCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaag                                                                                                    <  2:218191/141‑1 (MQ=255)
                                    tGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTTTTCTTCCATCGTTATCATCGATTCATaagaa                                                                                                  >  1:218704/1‑141 (MQ=255)
                                    tGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaagaa                                                                                                  >  2:139767/1‑141 (MQ=255)
                                    tGATAATAACACGTGGAATACTAAGCATTCTAAGTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGGGTGTTCAGCATCCGGTCTTTTTTTCTTCGTCCATCGTTATCATCGATACCTaagaa                                                                                                  <  2:521455/141‑1 (MQ=255)
                                         gTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGTTACCTaagaaaagca                                                                                             >  2:303065/1‑139 (MQ=255)
                                               cGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCTTCGTTATCATCGATACCTAAGAAACGAATagagt                                                                                       >  1:521833/1‑140 (MQ=255)
                                                   gAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTGTTCCATGGTTATCATCGATACCTAACAAAAGAATagagttcgg                                                                                   >  2:546180/1‑136 (MQ=255)
                                                     aTACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgtt                                                                                 >  1:329742/1‑141 (MQ=255)
                                                       aCTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCGTCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgttgt                                                                               <  2:65139/141‑1 (MQ=255)
                                                         tAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgttgttt                                                                             >  2:173364/1‑140 (MQ=255)
                                                          aaGCATTCTAATTTGATGTTTTGATTGATAAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATGTGTACCTAAGATAAGCATAGAGATAGGTCGttct                                                                            >  2:237695/1‑141 (MQ=255)
                                                           aGCATTCCAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGttctt                                                                           <  1:197640/141‑1 (MQ=255)
                                                             cATTCTTATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTTTTCg                                                                         <  2:67493/141‑1 (MQ=255)
                                                             cATTCTAATTTGATGTTTTTATTGATTAAAAGTAGTTNCAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCCTCGTTCTCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCg                                                                         <  2:564468/141‑1 (MQ=255)
                                                              aTTCTAATTTGATGTCTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGGTCTTCgg                                                                        <  1:356451/141‑1 (MQ=255)
                                                               ttCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCggg                                                                       >  1:20544/1‑141 (MQ=255)
                                                                 ttAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGAt                                                                     <  2:513534/140‑1 (MQ=255)
                                                                  tAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGAtt                                                                    >  2:409484/1‑141 (MQ=255)
                                                                   aaTTTGATTTTTTGATGGATTAATAGTAGTTAGTATCATTGCGTCTTATCTAGTGTGTTCAGCATCCTTTCTTTTGTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGAtt                                                                    <  1:400220/141‑1 (MQ=255)
                                                                    aTTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGa                                                                  <  1:259567/141‑1 (MQ=255)
                                                                    aTTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGa                                                                  >  1:569236/1‑141 (MQ=255)
                                                                        gATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATCCCTAAGAAAAGAATAGAGCTAGGTTGTTCATCGGGATTGACttt                                                              <  1:313362/141‑1 (MQ=255)
                                                                         aTGTTTTGATTGATTAAAAGTAGTTAAAGTCATGGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCAGCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTtta                                                             <  1:89387/141‑1 (MQ=255)
                                                                                     attTAAAGTAGTTTAATTCATAGCTTCTCATCTAGAGTGTTCAGCATCCTCTCTCTTTCTCTTCTCCCATCGTTATCATCGATACCTAAGAAAAGAATAGACATAGGTTGTCCTTCGGGATTGACTTTATTATCTCTTAAg                                                 <  2:385678/141‑1 (MQ=255)
                                                                                      ttAAAAGTATTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGt                                                <  1:63343/141‑1 (MQ=255)
                                                                                      ttAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGt                                                <  1:480156/141‑1 (MQ=255)
                                                                                            gtagtTAAAATCATAGCGTCTGCTCTAGAGTGTTCAGCTTCCTGTCTTTGTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATGGACTTTATTATCTCTTGAGTTGGAtt                                          <  2:293662/141‑1 (MQ=255)
                                                                                               gtTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTGCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGAc                                       >  1:391625/1‑141 (MQ=255)
                                                                                               gtTAAAATCATAGCGTCTGATCTAGAGTGTTCAGAATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAGAAGAATAGAGATAGGTTGTTCTTCGGGCTTGACTTTATTCTCTCTTGAGTTGGaggaac                                       >  1:189373/1‑136 (MQ=255)
                                                                                                 acaaaTCATTGCGTCTGATCTTGAGTGTTCAGCATCCTTTCTTTTTTTCGTCTTTCATCGTTATCATCGATACCTAAGAAAAGAATACAGATAGGTTGTTCGTCTGGATTCACTTTCTTATCACTTTAGTTGGATTGACGa                                     <  2:347766/139‑1 (MQ=255)
                                                                                                   aaaTCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGAtt                                   <  1:106624/141‑1 (MQ=255)
                                                                                                           gCGTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCAtttt                           <  1:187631/141‑1 (MQ=255)
                                                                                                             gTCTGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTATTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGAAGATTAGCATTTTTg                         <  1:317039/141‑1 (MQ=255)
                                                                                                                tGATCTAGAGTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTg                      >  1:62039/1‑141 (MQ=255)
                                                                                                                  aTCTAGAGTGTTCCGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTc                    <  1:475339/141‑1 (MQ=255)
                                                                                                                       gagTGTTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTgag               <  2:227900/141‑1 (MQ=255)
                                                                                                                         gtgtTCAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGagaa             <  1:313660/141‑1 (MQ=255)
                                                                                                                              cAGCATCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTc        >  2:350725/1‑141 (MQ=255)
                                                                                                                                  aTCCTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTCTTGTCTTGAGAAGATTCGAAt    >  2:561135/1‑141 (MQ=255)
                                                                                                                                    ccTGTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGc  <  1:409484/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                        
TAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGC  >  CP000730/1064116‑1064389

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: