Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,056,257 C→A 12.8% intergenic (‑1758/+1909) sspA ← / ← USA300HOU_0997 S01 family glutamyl endopeptidase/bifunctional N‑acetylmuramoyl‑L‑alanine amidase/mannosyl‑glycoprotein endo‑beta‑N‑acetylglucosaminidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,056,2570CA12.8% 146.3 / 3.3 58intergenic (‑1758/+1909)sspA/USA300HOU_0997S01 family glutamyl endopeptidase/bifunctional N‑acetylmuramoyl‑L‑alanine amidase/mannosyl‑glycoprotein endo‑beta‑N‑acetylglucosaminidase
Reads supporting (aligned to +/- strand):  ref base C (26/23);  new base A (3/6);  total (29/29)
Fisher's exact test for biased strand distribution p-value = 4.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTGAAAATTGGCGAATACTTGGTGCTCTTAAATATTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATAAAATTATGAATCTTTAAACTGTG  >  CP000730/1056117‑1056396
                                                                                                                                            |                                                                                                                                           
tttGAAAATTGGCGAATACTTGGTGCTCTTAAATATTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCGAAAAATTTAGAAATTAATAATATCCTAACATACTTTTAAAGc                                                                                                                                             >  1:617459/1‑141 (MQ=255)
  tGAAAATTGGCGAATACTTGGTGCTCTTAAATATTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCaa                                                                                                                                           <  2:747030/141‑1 (MQ=255)
    aaaaTTGGCGAATACTTGGTGCTCTTAAATATTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATAAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACAGAATTTTAAAGAaaaa                                                                                                                                         >  2:221983/1‑141 (MQ=255)
            cGAATACTTGGTGCTCTTAAATATTTAGACTTAGAATTTCAAGCAAGTTTAAATAGTGACACCTCAAATAAAATTAAAATTTTGTTGTTAAATTTAGTAAAAAAAATGATCGTGACATACTGTTAAAGCAAAAAAGGGTaa                                                                                                                                 >  2:754812/1‑141 (MQ=255)
            cGAATACTTGGTGCTCTTAAATATTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAAAATACTTTTAAAGAAAAAAAGGGTaa                                                                                                                                 >  2:24233/1‑141 (MQ=255)
              aaTACTTGGTTCTCTTAAATATATAGAATAAGAGTTTAAAGAAAGTTTGATTTGTGACAACTCAAATATTAATCAATTATTGTCTAAAAATTTAGATATTATTATTTTCATTATATAAAAAAAAAAAAAAAAAGGGTAAAt                                                                                                                               <  2:563062/141‑1 (MQ=255)
               aTACTTGGTGCTCTTAAATATTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTAAAATATAAATCAAATATTGTATAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGAAAAAAAGAGTAAAtt                                                                                                                              >  2:692194/1‑141 (MQ=255)
                 aCTTGGTGCTCTTAAATATTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTAc                                                                                                                            >  1:139313/1‑141 (MQ=255)
                    tGGTGCTCTTAAATATTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTa                                                                                                                         <  1:676627/141‑1 (MQ=255)
                        gCTCTTAAATATTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCt                                                                                                                     <  1:367819/141‑1 (MQ=255)
                         cttttAAATATTTAGAATTAGAATTAAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCtt                                                                                                                    <  2:429007/138‑1 (MQ=255)
                            ttAACTATTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTAt                                                                                                                 >  2:531018/1‑141 (MQ=255)
                                atatTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGa                                                                                                             >  1:722787/1‑141 (MQ=255)
                                      aaaattaaaaaaTAAAGAAATTTTCATTTGTGACACCTCAAATATAAATCAAATAATGTCTAAAAATTTAGAAATTAATAATATCATAACATAAAAAAAAAAAAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACg                                                                                                       <  2:699433/139‑1 (MQ=255)
                                       aaattagaaatAAAAAAAATTTTTAATTGTGACAACTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATCATATCATAACATAAAAAAAAAAAAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGa                                                                                                      <  2:708611/140‑1 (MQ=255)
                                        aattagaattTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGaa                                                                                                     >  1:313725/1‑141 (MQ=255)
                                          ttagaattTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGaaaa                                                                                                   >  1:209114/1‑141 (MQ=255)
                                               attTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGtt                                                                                              >  1:704856/1‑140 (MQ=255)
                                               attTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTc                                                                                              <  2:616482/141‑1 (MQ=255)
                                                 ttAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTa                                                                                            <  1:327925/141‑1 (MQ=255)
                                                   aaagaaagTTTCATTTGTGAAAAAACAAAAATAAATCAAATATTCTCTAAAAATTTAGAAATTAATAATATCATAACATAAAAAAAAAAAAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTaaa                                                                                          <  2:85268/141‑1 (MQ=255)
                                                    aagaaagTTCCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCCTTATTTGAAAAACGAAAAATGTCTAAAt                                                                                         <  2:329178/141‑1 (MQ=255)
                                                       atattttCATATGTGACACCTCAACGATAAATCAAATATGGTCTAAACATTTAGAAGTTAATAATATCGTAACATACGTATAAAACAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATaca                                                                                      <  2:326105/137‑1 (MQ=255)
                                                       aaagTTTCATTTGTGACACCTCAAAAATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATAATATTAAAGAAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATaca                                                                                      <  2:130136/141‑1 (MQ=255)
                                                            ttCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTgta                                                                                 <  1:404897/141‑1 (MQ=255)
                                                                 ttGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAac                                                                            >  2:262141/1‑141 (MQ=255)
                                                                   gtgACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTAAAAAACCAAAAAAGTCTAAATACACTGTAGTAacta                                                                          >  2:247772/1‑141 (MQ=255)
                                                                     gACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAACAAGGGTACATTCCTTCAGCTTTATTTGAAAAACGAAAAATGTCAAAATACACTGTCGTAactact                                                                        >  1:345447/1‑141 (MQ=255)
                                                                      acacCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACtt                                                                       <  1:732678/141‑1 (MQ=255)
                                                                         ccTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTc                                                                    >  2:622787/1‑141 (MQ=255)
                                                                             aaaTATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTAaaaa                                                                >  1:113475/1‑141 (MQ=255)
                                                                               atatAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATg                                                              <  1:533102/141‑1 (MQ=255)
                                                                               atatAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATg                                                              <  2:722787/141‑1 (MQ=255)
                                                                                    aaTCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATAAACTGTACTAACTACTTTTCAAAATGAATaa                                                         >  2:621331/1‑141 (MQ=255)
                                                                                          atatTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGt                                                   >  1:43861/1‑141 (MQ=255)
                                                                                                tcaaaaaaTTTAGAAATTATTAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGt                                             <  2:455744/138‑1 (MQ=255)
                                                                                                 cTAAAAATTTAGAAATTCATAATATCATAACATACTTTTAAAGCAAAAGAGGGTAAATTACTTAAGCTTTATTGGAAAAACGAAAAATGACTAACTACACTGTAGTAACTACTTTTCAAAATGAATTAAGTGGTTACAGtt                                            >  1:576945/1‑141 (MQ=255)
                                                                                                  tAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTa                                           <  1:189230/141‑1 (MQ=255)
                                                                                                  aaaaaaTTTAGAAATTAATAATATCATAACATAAAAAAAAAAAAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTa                                           <  2:301704/140‑1 (MQ=255)
                                                                                                       aTTTAGAAATTAATAATATCATAACATACTTATAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTa                                      <  2:323750/141‑1 (MQ=255)
                                                                                                         ttAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACt                                    >  2:427648/1‑141 (MQ=255)
                                                                                                         ttAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACt                                    >  1:214835/1‑141 (MQ=255)
                                                                                                          tAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTATTAACTACTTTTCAAAATGAATAAAGTAGTTACAGTTAATGTACtt                                   >  2:76885/1‑141 (MQ=255)
                                                                                                             aaaTTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGa                                >  1:736177/1‑141 (MQ=255)
                                                                                                             aaaTTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGATTACAGTTAATTAACATAGa                                >  2:79448/1‑141 (MQ=255)
                                                                                                                    taataTCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGAAAGtata                         >  2:44299/1‑141 (MQ=255)
                                                                                                                      atatCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATaaa                       <  2:46067/141‑1 (MQ=255)
                                                                                                                      atatCATAACATACTTGTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATaaa                       <  1:391242/141‑1 (MQ=255)
                                                                                                                        atgaaaaCATTCTTTTAAATCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATAAAAt                     <  1:80712/136‑1 (MQ=255)
                                                                                                                        atCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATAAAAt                     <  1:705744/141‑1 (MQ=255)
                                                                                                                         tCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATAAAAtt                    <  1:261342/141‑1 (MQ=255)
                                                                                                                          cagaaCACACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATAAAATTa                   <  2:223274/138‑1 (MQ=255)
                                                                                                                           aTAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATAAAATTAt                  <  2:746467/141‑1 (MQ=255)
                                                                                                                             aaCATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTGGGCGGGGGGTAAGTGGTTACCATTATTGAAGTTAGACAGTATAAAATTATGa                >  1:174220/1‑141 (MQ=255)
                                                                                                                                   cTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATAAAATTATGAATCttt          >  1:696556/1‑141 (MQ=255)
                                                                                                                                      ttAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTACTGTACCTAGTAATTATAAAATTATGAATCTTTaaa       >  1:516065/1‑141 (MQ=255)
                                                                                                                                      ttAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTAAAGCTAATGGAGGTAGACAGTATAAAATTATGAATCTTTaaa       >  1:590129/1‑141 (MQ=255)
                                                                                                                                          aGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATAAAATTATGAATCTTTAAACtgt   <  1:76217/141‑1 (MQ=255)
                                                                                                                                           gCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATAAAATTATGAATCTTTAAACtgtg  >  1:186881/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                           
TTTGAAAATTGGCGAATACTTGGTGCTCTTAAATATTTAGAATTAGAATTTAAAGAAAGTTTCATTTGTGACACCTCAAATATAAATCAAATATTGTCTAAAAATTTAGAAATTAATAATATCATAACATACTTTTAAAGCAAAAAAGGGTAAATTACTTAAGCTTTATTTGAAAAACGAAAAATGTCTAAATACACTGTAGTAACTACTTTTCAAAATGAATAAAGTGGTTACAGTTAATGTACTTAGACAGTATAAAATTATGAATCTTTAAACTGTG  >  CP000730/1056117‑1056396

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: