Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,995,314 C→T pseudogene (447/447 nt) ygeN ← pseudogene, orgB family, part of T3SS PAI ETT2 remnant

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,995,3140CT100.0% 100.2 / NA 32pseudogene (447/447 nt)ygeNpseudogene, orgB family, part of T3SS PAI ETT2 remnant
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (17/15);  total (17/15)

AATATAATTAAAAATAAAATTTTTGCGTAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGATTAT  >  NC_000913/2995197‑2995447
                                                                                                                      |                                                                                                                                     
aaTATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGc                                                                                                                   <  2:15353/139‑1 (MQ=255)
        tAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAg                                                                                                           >  1:1042810/1‑139 (MQ=255)
                                                  aaaaaTCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCaa                                                                 <  2:1042810/139‑1 (MQ=255)
                                                       tCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCt                                                                                                                             >  2:819334/1‑74 (MQ=255)
                                                       tCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCt                                                                                                                             <  1:819334/74‑1 (MQ=255)
                                                        cATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAaat                                                           <  1:1066250/139‑1 (MQ=255)
                                                                 atTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCatat                                                                                               >  2:580454/1‑94 (MQ=255)
                                                                 atTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCatat                                                                                               <  1:580454/94‑1 (MQ=255)
                                                                           tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTaaa                                                            <  2:790222/119‑1 (MQ=255)
                                                                           tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTaaa                                                            >  1:790222/1‑119 (MQ=255)
                                                                                  aGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGa                                      >  1:371363/1‑134 (MQ=255)
                                                                                  aGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGa                                      <  2:371363/134‑1 (MQ=255)
                                                                                  aGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCg                                 >  1:923242/1‑139 (MQ=255)
                                                                                    aTTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa                                                                                                  <  2:839680/72‑1 (MQ=255)
                                                                                    aTTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa                                                                                                  >  1:839680/1‑72 (MQ=255)
                                                                                    aTTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAAt                                                                                      <  2:889653/84‑1 (MQ=255)
                                                                                    aTTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAAt                                                                                      >  1:889653/1‑84 (MQ=255)
                                                                                        tatTCAAATCATTAAACTTGAGCCAGGGAGTTATaa                                                                                                                                  >  1:86744/1‑36 (MQ=255)
                                                                                        tatTCAAATCATTAAACTTGAGCCAGGGAGTTATaa                                                                                                                                  >  1:642436/1‑36 (MQ=255)
                                                                                        tatTCAAATCATTAAACTTGAGCCAGGGAGTTATaa                                                                                                                                  <  2:642436/36‑1 (MQ=37)
                                                                                        tatTCAAATCATTAAACTTGAGCCAGGGAGTTATaa                                                                                                                                  <  2:86744/36‑1 (MQ=255)
                                                                                              aaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAGACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCa                     >  2:1060171/1‑139 (MQ=255)
                                                                                               aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCata                                                                                                <  2:347819/63‑1 (MQ=255)
                                                                                               aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCata                                                                                                >  1:347819/1‑63 (MQ=255)
                                                                                                  aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg                 >  2:402153/1‑139 (MQ=255)
                                                                                                  aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg                 <  1:402153/139‑1 (MQ=255)
                                                                                                    tAAGCTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTc                      >  2:443061/1‑132 (MQ=255)
                                                                                                    tAAGCTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTc                      <  1:443061/132‑1 (MQ=255)
                                                                                                            aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttttt                                                                    <  2:352850/78‑1 (MQ=255)
                                                                                                            aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttttt                                                                    >  1:352850/1‑78 (MQ=255)
                                                                                                            aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATg       >  1:1045026/1‑139 (MQ=255)
                                                                                                                 gggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGattat  >  2:734303/1‑139 (MQ=255)
                                                                                                                      |                                                                                                                                     
AATATAATTAAAAATAAAATTTTTGCGTAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGATTAT  >  NC_000913/2995197‑2995447

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: