Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 51,334 (G)7→8 intergenic (‑132/‑7) USA300HOU_RS00210 ← / → USA300HOU_RS00215 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE51,3271.G97.8% 160.5 / ‑1.7 46intergenic (‑125/‑14)USA300HOU_RS00210/USA300HOU_RS00215hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (29/16);  total (30/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.27e-01

TGCTGCTTAGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑GGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAGCGATTTAAATGAA  >  USA300TCH1516_ALE/51180‑51466
                                                                                                                                                    |                                                                                                                                           
tgctgcTTAGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGa                                                                                                                                              >  4:371691/1‑148 (MQ=255)
   tgctTAGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑ggg                                                                                                                                          <  3:60543/148‑1 (MQ=255)
      ttAGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAAAAAAAAATGGGGA‑gggggg                                                                                                                                       <  4:163450/148‑1 (MQ=255)
      ttAGATTTCTTATTAATTTAAAAAATCCTCAAAAAATTTTTAAGGGGTCAATAAATATCAAAAAGGTTAAACTATCTTCAATTGATTGCTATAAAAAGCATAAATGAAGCATTATGTTAAAAAAAAAAAAAAAAAATGGGGA‑gggggg                                                                                                                                       <  4:180840/148‑1 (MQ=255)
        aGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑gggggggg                                                                                                                                     <  3:60274/148‑2 (MQ=255)
           tttCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGTAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑ggggggggtat                                                                                                                                  >  3:201893/1‑144 (MQ=255)
           tttCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑ggggggagtat                                                                                                                                  >  4:356976/1‑143 (MQ=255)
              tttatcaaTTTTAAAATACCTCCAAGAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAAACAAAAAAAAAAAAATGGGGA‑ggggggg                                                                                                                                      <  2:13177/134‑1 (MQ=255)
               ttATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTatatat                                                                                                                               >  3:89296/1‑148 (MQ=255)
                   tCATTTTAATATTCCTTCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGAt                                                                                                                           <  4:404274/148‑1 (MQ=255)
                     aTTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGtatata                                                                                                                                <  1:56846/141‑1 (MQ=255)
                      ttttAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTatatat                                                                                                                               >  1:24706/1‑141 (MQ=255)
                      ttttAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTTTATATTGATAcc                                                                                                                        >  4:19175/1‑148 (MQ=255)
                      ttttAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATAcc                                                                                                                        >  3:132458/1‑148 (MQ=255)
                                    cAATAATTTTTAAGGAGTAAATAAATATCATATAGGTTAAACTAGCTTCAATTGATTGCTATAATAAGCATAAAGGAAGCATTATGATTAGAAAAAAAAAAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGaaa                                                                                                          <  4:236207/148‑1 (MQ=255)
                                       taatTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑GGGGGGGTATATATTGATACCTACGCTAGAAGAAattat                                                                                                      >  3:250354/1‑148 (MQ=255)
                                         atTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAattatt                                                                                                     >  4:242749/1‑148 (MQ=255)
                                                       aatcactAACATATGAATTAAATAATCTTAACGTGAAAGCTAAAATAAGCAAAAATGAAGAATTATGATTAGACCTGAAACAAAAAATGAGGAGGGGGGGGTATATACTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGaag                                                                                       <  4:268378/148‑2 (MQ=255)
                                                                       gTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTg                                                                       >  3:249390/1‑148 (MQ=255)
                                                                        ttAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGa                                                                      >  3:272631/1‑148 (MQ=255)
                                                                        ttAAACTAACTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGa                                                                      <  4:8298/148‑1 (MQ=255)
                                                                         tAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTCTGATTCTTCGCGGAAGGAAAAATGGGGAGGGGGGGGGATAAATTGATACATACGCTAGACGAACTTATTGATAAGTATGGAAACTTAGTTGATAATTTGaa                                                                     >  4:408010/1‑148 (MQ=255)
                                                                         tAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGaa                                                                     >  3:61888/1‑148 (MQ=255)
                                                                         tAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGAGTATACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGaa                                                                     >  3:303742/1‑148 (MQ=255)
                                                                         tAAACTATCATCAACGTATTGCTATAATAAGCCTAAATGAAGCGTTATGCTTAGACGCGGAACTAGAAATGGGGAGGGGGGGGAATATATTGATACCTACGCTAGCATAACTTATTGATGAGTATGTACCCTTAGCTGAATATTTgca                                                                     >  4:408044/1‑146 (MQ=255)
                                                                             cTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAAttt                                                                 >  3:257145/1‑148 (MQ=255)
                                                                                  ttCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGt                                                            <  4:79932/148‑1 (MQ=255)
                                                                                  ttCAATTGATTGATATAATAAGCATAAAGGAAGCATTATGATTAAAAGAAGAAAAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGt                                                            <  4:381542/148‑1 (MQ=255)
                                                                                       ttgattgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAg                                                       >  3:20255/1‑148 (MQ=255)
                                                                                       ttgattgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGGATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGACTATTTGAAATTTGATGTAACAg                                                       >  4:307536/1‑148 (MQ=255)
                                                                                        tgattgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGt                                                      >  3:318777/1‑148 (MQ=255)
                                                                                            tgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAg                                                  >  3:234398/1‑148 (MQ=255)
                                                                                            tgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAg                                                  >  4:154521/1‑148 (MQ=255)
                                                                                             acTATAATAAGAATAAATGAAGCATTATGATTAGAAAAAAAAAAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAgg                                                 <  4:205350/147‑1 (MQ=255)
                                                                                               tataATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGtt                                               >  3:295161/1‑148 (MQ=255)
                                                                                               tataATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGtt                                               >  3:368999/1‑148 (MQ=255)
                                                                                               tataATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATGATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGCTGTAACAGTTGAGGtt                                               >  3:369008/1‑148 (MQ=255)
                                                                                                ataataAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGttt                                              <  4:28868/148‑1 (MQ=255)
                                                                                                ataataAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGttt                                              <  4:28797/148‑1 (MQ=255)
                                                                                                 taataaGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTa                                             >  4:46456/1‑148 (MQ=255)
                                                                                                 taataaGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGCATATATTGATACCTACGCGAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGAGTATTTGAAATTTGATGTAACAGTTGAGGTTTa                                             >  4:178030/1‑148 (MQ=255)
                                                                                                   ataaGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATAGTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAg                                                  >  2:459/1‑141 (MQ=255)
                                                                                                              tGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATttgttg                                >  3:165833/1‑148 (MQ=255)
                                                                                                               gAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTtgttgt                               <  3:277149/148‑1 (MQ=255)
                                                                                                                 aGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGtta                             <  3:154356/148‑1 (MQ=255)
                                                                                                                 aGCATTATAATTAGTCGCGAAAAAAAAAAGGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGtta                             <  3:175052/148‑1 (MQ=255)
                                                                                                                      tATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTaag                        <  3:242749/148‑1 (MQ=255)
                                                                                                                            tAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGttt                  >  3:43151/1‑148 (MQ=255)
                                                                                                                            tAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGttt                  >  3:78545/1‑148 (MQ=255)
                                                                                                                               aCGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTaagaa                      <  2:24706/141‑1 (MQ=255)
                                                                                                                               aCGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAg               <  4:89296/148‑1 (MQ=255)
                                                                                                                                cgcgGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAGc              >  3:407583/1‑148 (MQ=255)
                                                                                                                                  cgGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGGTTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAGCGa            >  4:105852/1‑148 (MQ=255)
                                                                                                                                            aaTGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAGCGATTTAAATGaa  >  3:228989/1‑148 (MQ=255)
                                                                                                                                                    |                                                                                                                                           
TGCTGCTTAGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑GGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAGCGATTTAAATGAA  >  USA300TCH1516_ALE/51180‑51466

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑