Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,587,842 C→T 11.8% intergenic (‑239/‑120) relJ ← / → yehR Antitoxin RelJ/putative lipoprotein YehR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,587,8420CT11.8% 81.2 / 3.8 41intergenic (‑239/‑120)relJ/yehRAntitoxin RelJ/putative lipoprotein YehR
Reads supporting (aligned to +/- strand):  ref base C (23/13);  new base T (3/2);  total (26/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.92e-01

TGTTCTTTTCTTCCAACATACCGCCTATAATGCTCAAAAAGAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATACAAATATCGAAAGAAGGCGACTGACTTTGAAAAAATTATG  >  USA300TCH1516_ALE/2587720‑2587975
                                                                                                                          |                                                                                                                                     
tGTTCTTTTCTTCCAACATACCGCCTATAATGCTCAAAAAGAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGATGGATCCGCTtaaataaa                                                                                                                            >  1:187723/1‑134 (MQ=255)
 gtgcttttcttCCAACATACCGCCTATAATGCTCAAAAAGAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAAc                                                                                                                           <  2:603088/131‑1 (MQ=255)
     ttatcttcCAACATACCGCCTATAATGCTCAAAAAGAAATCAGCAGTGGAACACACTACTTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCat                                                                                                                       <  2:303729/131‑1 (MQ=255)
      tttcttCCAACATACCGCCTATAATGCTCAAAAAGAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCTGCTTAAAAAAACTCata                                                                                                                      >  2:189198/1‑134 (MQ=255)
      tttcttCCAACATACCGCCTATAATGCTCAAAAAGAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCTGCTTAAAAAAACTCata                                                                                                                      >  2:453980/1‑134 (MQ=255)
          ttcCAACATACCGCCTATAATGCTCAAAAAGAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCtt                                                                                                                  >  2:162261/1‑134 (MQ=255)
               aCATACCGCCTATAATGCTCAAAAAGAAATCAGCAGTGGAACACCCTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCtaaa                                                                                                             >  2:533568/1‑134 (MQ=255)
                        cTATAATGCTCAAAAAGAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTAATATCTTCAAAAAAAATGACa                                                                                                    >  1:79105/1‑134 (MQ=255)
                             aTGCTCAAAAAGAAATCATCAGTGAAACACACTACGTTCCCTACCCCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAaaatt                                                                                               <  2:163917/134‑1 (MQ=255)
                              tGCTCAAAAAGAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGACTCCGCTTATAAATACTCATATCTTCAAAATAAATAAAAaaattt                                                                                              >  1:329644/1‑134 (MQ=25)
                               gCTCAAAAAGAAATCAGCAGTGGAACACACTACGTTACCTACCGCTTTATACTTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCCTATCTTCAAAAAAAATGACAaaattta                                                                                             >  2:278602/1‑134 (MQ=255)
                                  cAAAAAGAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAaaatttaaat                                                                                          >  1:115448/1‑134 (MQ=255)
                                     aaaGAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAAtttt                                                                                       >  2:191733/1‑134 (MQ=255)
                                        gAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCTGCTTATAAAAATTCTTGTCTTCAAAATAAATGACAATATTTAAAttgttta                                                                                    >  1:263196/1‑132 (MQ=21)
                                            tCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGTCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATaa                                                                                >  2:401336/1‑134 (MQ=255)
                                                     gAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCTGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCAtttt                                                                       <  1:453980/134‑1 (MQ=255)
                                                     gAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCTGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCAtttt                                                                       <  1:189198/134‑1 (MQ=255)
                                                     gAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGATTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCAtttt                                                                       >  1:578967/1‑134 (MQ=255)
                                                      aaCACACTACGTTACCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCGTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCAttttt                                                                      <  1:510733/134‑1 (MQ=255)
                                                       acacacTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCAtttttt                                                                     >  1:329281/1‑134 (MQ=255)
                                                         acatTAAGTTCCCTACAGCTTTATCATTATCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAg                                                                   <  2:398294/134‑1 (MQ=255)
                                                         acacTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGACGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTCAATTTTTGAATCACATCAtttttttc                                                                   >  1:258098/1‑132 (MQ=255)
                                                                 ttCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAACAACCTCATATCTTCAAAAAAAATGACAAAATTTAAATTATTGAATAACATCATTTTTTAGTAAATGtt                                                           >  1:231421/1‑134 (MQ=255)
                                                                  tcacTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTta                                                          <  1:575974/131‑1 (MQ=255)
                                                                  tCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTATTAGTAACTGTta                                                          >  1:208830/1‑134 (MQ=255)
                                                                   cccTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTtat                                                         >  1:89592/1‑134 (MQ=255)
                                                                    ccTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTtata                                                        >  2:506120/1‑134 (MQ=255)
                                                                      tACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAAt                                                      <  1:162261/134‑1 (MQ=255)
                                                                              tagacatttAAGGCTTAAATAATATTAAAATTTTGTGAGAAAACCGATTAAAAAAACTCATATCATCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTtat                                              <  2:329644/128‑1 (MQ=255)
                                                                                tCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTataa                                            <  2:483584/134‑1 (MQ=255)
                                                                                 cATTTTCAGTCTTAAATATTTTTAAAATAAAAAGAGAAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTataat                                           >  2:497443/1‑134 (MQ=255)
                                                                                     ttCATGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATACaa                                       <  1:191733/134‑1 (MQ=255)
                                                                                       cAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATTTTATAATTTTTTTATAATATAAat                                     >  2:199531/1‑134 (MQ=255)
                                                                                        aGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATACAAata                                    >  1:188308/1‑134 (MQ=255)
                                                                                         ggCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATATAAatat                                   >  1:533947/1‑134 (MQ=255)
                                                                                         ggCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATACAAatat                                   >  1:523379/1‑134 (MQ=255)
                                                                                                atatTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATACAAATATCGAaaga                            >  2:385675/1‑134 (MQ=255)
                                                                                                    atttAAAAGTTGCAGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATACAAATATCGAAAGAAGGc                        <  2:277960/133‑1 (MQ=255)
                                                                                                           aTTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATACAAATATCGAAAGAAGGCgactgac                 <  2:523379/134‑1 (MQ=255)
                                                                                                              ttGTGAGGAATCCGCTTAACGAACCTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATACAAATATCGAAAGAAGGCGACTGACttt              <  2:554520/134‑1 (MQ=255)
                                                                                                                  gAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATAAAAATATCGAAAGAAGACGACTAACTTTGaaa          >  1:358452/1‑134 (MQ=255)
                                                                                                                          cGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATACAAATATCGAAAGAAGGCGACTGACTTTGAAAAAATTATg  >  1:462562/1‑134 (MQ=255)
                                                                                                                          |                                                                                                                                     
TGTTCTTTTCTTCCAACATACCGCCTATAATGCTCAAAAAGAAATCAGCAGTGGAACACACTACGTTCCCTACCGCTTTATCATTTTCAGGCTTAAATATTTTTAAAATTTTGTGAGGAATCCGCTTAAAAAAACTCATATCTTCAAAAAAAATGACAAAATTTAAATTTTTGAATAACATCATTTTTTAGTAAATGTTATAATTTCTTTATAATACAAATATCGAAAGAAGGCGACTGACTTTGAAAAAATTATG  >  USA300TCH1516_ALE/2587720‑2587975

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑