Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 741,261 C→A 13.5% intergenic (‑103/‑258) USA300HOU_0686 ← / → USA300HOU_0687 possible LysM domain protein/hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730741,2610CA13.5% 87.2 / 2.2 37intergenic (‑103/‑258)USA300HOU_0686/USA300HOU_0687possible LysM domain protein/hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base C (16/14);  new base A (2/3);  total (19/18)
Fisher's exact test for biased strand distribution p-value = 6.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGCTGTTATTGCAAATGCTAATTTTTTCAAAGGGACTCCTCCTTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATAAAAGCGTTTTAGTGATTTTAACTAATTATAAAAAATT  >  CP000730/741128‑741399
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ttGCTGTTATTGCAAATGCTAATTTTTTCAAAGGGACTCCTCCTTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATa                                                                                                                                     <  1:248600/141‑1 (MQ=255)
  gCTGTTATTGCAAATGCTAATTTTTTCAAAGGGACTCCTCCTTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTCAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAg                                                                                                                                   >  1:176290/1‑141 (MQ=255)
            cAAATGCTAATTTTTTCAAAGGGACTCCTCCTTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTtgtg                                                                                                                         <  1:355913/141‑1 (MQ=255)
                tGCTAATTTTTTCAAAGGGACTCCTCCTTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGt                                                                                                                     <  2:157665/141‑1 (MQ=255)
                          ttCAAAGGAACTCCTCCTTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTtattat                                                                                                           <  1:94499/141‑1 (MQ=255)
                               aGGGAATCCTCCTTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTTTATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGt                                                                                                      <  1:338160/141‑1 (MQ=255)
                                gggACTCCTCCTTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTa                                                                                                     >  1:297760/1‑141 (MQ=255)
                                  gACTCCTCCTTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTTTGTGGTTTGTTATTATCTTGTAat                                                                                                   >  2:8066/1‑141 (MQ=255)
                                    ctcctcCTTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAatat                                                                                                 <  1:114697/141‑1 (MQ=255)
                                      cctcctTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTTTTTTCTTGTAAtatta                                                                                               >  1:143290/1‑141 (MQ=255)
                                        ttctTAATATTATGTTTTAATACGTATAAAAATTATTAAGACCATTTATATAGTAAATTAAGTTTTTGTTTTATATTACGATTTAAAAAAAAAAAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATattatt                                                                                             <  2:227311/139‑1 (MQ=255)
                                        tcctTAATATTTTTTTTTAGTACTTTAAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTTGTTTTATATTTCGATTTAAAAAAAAAAAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATattatt                                                                                             <  2:172492/141‑1 (MQ=255)
                                        tcctTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATattatt                                                                                             <  2:240567/141‑1 (MQ=255)
                                        ccctTAAAATTATGTTTTACTACATTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCAAAATAAAAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATattatt                                                                                             <  2:100254/140‑1 (MQ=255)
                                         cctTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATCTTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATAttatta                                                                                            <  1:312093/141‑1 (MQ=255)
                                                        ttACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATc                                                                             >  1:35126/1‑141 (MQ=255)
                                                        ttACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATc                                                                             >  2:134420/1‑141 (MQ=255)
                                                         tactacTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCg                                                                            <  2:179557/141‑1 (MQ=255)
                                                            tactTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGtt                                                                         <  2:297760/141‑1 (MQ=255)
                                                                        ttattaAGACAATTTATATAGTACATTAAGTTTTCGTTATCTATTCAAGTTTCCGTATTATTAAAAGAAATTTGTTTTATGTGGTTGTTTATTATCTTAGAGTATTATTAACATTTTAGGATATCGGTTCATATTTTtata                                                             <  2:221741/141‑1 (MQ=255)
                                                                                aCAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGa                                                     <  1:134420/141‑1 (MQ=255)
                                                                                   aTTTGTATAGTAAATTAAGTTTTCGTTTTAAATTACGATTTACATATTGTGAAAAGAAAGTAGCTTGGTGTGGTTTGTTATTATCTTGTAAGATTATTAACATTTTAGGATATCGGTTCATCTGTTTATAAATGCTGAttt                                                  >  2:232457/1‑141 (MQ=255)
                                                                                      tatataGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTGATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGAt                                               >  2:67619/1‑141 (MQ=255)
                                                                                      tatataGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCGTATTTTTATAATTGCTGATTTGAt                                               >  2:88538/1‑141 (MQ=255)
                                                                                                 ttAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATaaaa                                    >  2:21297/1‑141 (MQ=255)
                                                                                                    aGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATAAAAGCg                                 >  1:34903/1‑141 (MQ=255)
                                                                                                     gTTTTCGTTTTATATTACGATTTCCATATTATCAAAAAAAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATAAAAGCGt                                >  1:339901/1‑141 (MQ=255)
                                                                                                     gTTTTCGTTTTATATTACGATTTCCATATTATAAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTCGGATATCGGTTCATATTTTTATAAATGCTGAATTGACAGTGTATAAAAGCGt                                >  2:86532/1‑141 (MQ=255)
                                                                                                     gTTTCCGTTTTATATTACGATTTCAATATTATAAAAAATCAGTAGCTTTGTGTCGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAAAGCTGATTTGATAGAGTATAAGAGcat                                >  2:233640/1‑139 (MQ=255)
                                                                                                        ttCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATAAAAgagatat                             >  2:323418/1‑135 (MQ=255)
                                                                                                            ttttATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATAAAAGCGTTTTAGTg                         >  1:106915/1‑141 (MQ=255)
                                                                                                                 tactACGATTTGCATATTATCCAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATAGTTTTATAAATGCTGATTTGATAGTGTATAAAAGCGTTTTAGTGAtttt                    <  1:148478/138‑1 (MQ=255)
                                                                                                                        aTTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATAAAAGCGTTTTAGTGATTTTAACTAAt             <  1:18829/141‑1 (MQ=255)
                                                                                                                              atatTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATAAAAGCGTTTTAGTGATTTTGACTAATTATaaa       >  2:344655/1‑141 (MQ=255)
                                                                                                                              atatTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATAAAAGCGTTTTAGTGATTTTAACTAATTATaaa       >  1:370237/1‑141 (MQ=255)
                                                                                                                               tattatCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATAAAAGCGTTTTAGTGATTTTAACTAATTATaaaa      >  2:328918/1‑141 (MQ=255)
                                                                                                                                   atCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATAAAAGCGTTTTAGTGATTTTAACTAATTATAAAAAAtt  <  2:22228/141‑1 (MQ=255)
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TTGCTGTTATTGCAAATGCTAATTTTTTCAAAGGGACTCCTCCTTAAAATTATGTTTTACTACTTTTAAAAATTATTAAGACAATTTATATAGTAAATTAAGTTTTCGTTTTATATTACGATTTCCATATTATCAAAAATAAGTAGCTTTGTGTGGTTTGTTATTATCTTGTAATATTATTAACATTTTAGGATATCGGTTCATATTTTTATAAATGCTGATTTGATAGTGTATAAAAGCGTTTTAGTGATTTTAACTAATTATAAAAAATT  >  CP000730/741128‑741399

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: