Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,496,512 C→T 11.7% intergenic (+23/‑163) leuX → / → intB tRNA‑Leu/pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,496,5120CT11.7% 173.7 / 13.3 60intergenic (+23/‑163)leuX/intBtRNA‑Leu/pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase
Reads supporting (aligned to +/- strand):  ref base C (26/27);  new base T (3/4);  total (29/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.87e-01

AGGTATAATCCACAACGTTTTCCGCATACCTCTTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGTTGGTACAGATGATGGTATTTCCGGTTCGATAATGCTTGTACCAA  >  NC_000913/4496367‑4496659
                                                                                                                                                 |                                                                                                                                                   
aGGTATAATCCACAACGTTTTCCGCATACCTCTTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTg                                                                                                                                                   <  4:66614/148‑1 (MQ=255)
    ataATCCACAACGTTTTCCGCATACCTCTTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGt                                                                                                                                               >  1:632851/1‑148 (MQ=255)
      aaTCCACAACGTTTTCCGCATACCTCTTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCt                                                                                                                                             <  2:632851/148‑1 (MQ=255)
       aTCCACAACGTTTTCCGCATACCTCTTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAGTTGAGGTCta                                                                                                                                            <  2:1059364/148‑2 (MQ=255)
           acaACGTTTTCCGCATACCTCTTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGa                                                                                                                                                  >  2:496512/1‑138 (MQ=255)
           acaACGTTTTCCGCATACCTCTTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGa                                                                                                                                                  <  1:496512/138‑1 (MQ=255)
                          tACCTCTTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCt                                                                                                                                             <  1:618688/128‑1 (MQ=255)
                          tACCTCTTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCt                                                                                                                                             >  2:618688/1‑128 (MQ=255)
                               ctTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATg                                                                                                                                    >  1:297313/1‑132 (MQ=255)
                               ctTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATg                                                                                                                                    <  2:297313/132‑1 (MQ=255)
                                ttCAGTGTCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTTAGGTCTTTTTTTATGCCTGAAATCCAGTGttt                                                                                                                   <  3:971569/148‑1 (MQ=255)
                                     tgtcGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGTCACCAAAAGTATGTAAAAAGACCTCAGTTGAgg                                                                                                                                                <  3:758297/111‑1 (MQ=255)
                                     tGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAAAAGACCTCAGTTGAgg                                                                                                                                                >  4:758297/1‑114 (MQ=255)
                                                  aaaTCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGa                                                                                                                                                  >  1:759157/1‑99 (MQ=255)
                                                  aaaTCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGa                                                                                                                                                  <  2:759157/99‑1 (MQ=255)
                                                                       tCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTg                                                                                                                                                   <  1:564878/77‑1 (MQ=255)
                                                                       tCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTg                                                                                                                                                   >  2:564878/1‑77 (MQ=255)
                                                                       tCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCa                                                                                                                         >  3:1010605/1‑103 (MQ=255)
                                                                       tCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCa                                                                                                                         <  4:1010605/103‑1 (MQ=255)
                                                                         aaaaTCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCg                                                                          >  2:39777/1‑148 (MQ=255)
                                                                          aaaTCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACt                                                                                                                                                    >  2:1126886/1‑73 (MQ=255)
                                                                          aaaTCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACt                                                                                                                                                    <  1:1126886/73‑1 (MQ=255)
                                                                          aaaTCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTc                                                                                                        <  3:325558/117‑1 (MQ=255)
                                                                          aaaTCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTc                                                                                                        >  4:325558/1‑117 (MQ=255)
                                                                           aaTCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGat                                                                        <  1:39777/148‑1 (MQ=255)
                                                                             tCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAAt                                                                                                                            <  4:132774/94‑1 (MQ=255)
                                                                             tCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAAt                                                                                                                            >  3:132774/1‑94 (MQ=255)
                                                                             tCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTta                                                                                                                  <  3:225930/104‑1 (MQ=255)
                                                                             tCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTta                                                                                                                  >  4:225930/1‑104 (MQ=255)
                                                                                               gCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCtttt                                                                                                                                          >  4:113814/1‑62 (MQ=255)
                                                                                               gCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCtttt                                                                                                                                          <  3:113814/62‑1 (MQ=255)
                                                                                                           ccGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCttttttt                                                                                                                                       <  2:981994/53‑1 (MQ=255)
                                                                                                           ccGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCttttttt                                                                                                                                       >  1:981994/1‑53 (MQ=255)
                                                                                                                      cACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTtatcta                                                                                                              <  3:382087/67‑1 (MQ=255)
                                                                                                                      cACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTtatcta                                                                                                              >  4:382087/1‑67 (MQ=255)
                                                                                                                      cACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGt                                              <  1:406487/131‑1 (MQ=255)
                                                                                                                      cACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGt                                              >  2:406487/1‑131 (MQ=255)
                                                                                                                          aaaaGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTtatc                                                                                                                <  3:354192/61‑1 (MQ=255)
                                                                                                                          aaaaGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTtatc                                                                                                                >  4:354192/1‑61 (MQ=255)
                                                                                                                           aaaGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCaa                                                                             >  4:843309/1‑95 (MQ=255)
                                                                                                                           aaaGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCaa                                                                             <  3:843309/95‑1 (MQ=255)
                                                                                                                           aaaGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGTTGGTACAgatgat                                 >  2:829801/1‑139 (MQ=255)
                                                                                                                           aaaGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGTTGGTACAgatgat                                 <  1:829801/139‑1 (MQ=255)
                                                                                                                            aaGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGtt                                             >  4:860419/1‑126 (MQ=255)
                                                                                                                            aaGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGtt                                             <  3:860419/126‑1 (MQ=255)
                                                                                                                                       aaGACCTCAGTTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAActctc                                                                                       <  4:456126/72‑1 (MQ=255)
                                                                                                                                       aaGACCTCAGTTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAActctc                                                                                       >  3:456126/2‑73 (MQ=255)
                                                                                                                                         gACCTCAGTTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGTTGGTACAg                                      >  3:6583/1‑120 (MQ=255)
                                                                                                                                         gACCTCAGTTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGTTGGTACAg                                      <  4:6583/120‑1 (MQ=255)
                                                                                                                                         gACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCTATATCAACGTACATCTa                                                         >  3:1078860/1‑101 (MQ=255)
                                                                                                                                         gACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTa                                                         <  4:1078860/101‑1 (MQ=255)
                                                                                                                                          aCCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCaa                                                                   >  1:541894/1‑90 (MQ=255)
                                                                                                                                          aCCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCaa                                                                   <  2:541894/90‑1 (MQ=255)
                                                                                                                                             tCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTa                                                                                             >  1:983184/1‑61 (MQ=255)
                                                                                                                                             tCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTa                                                                                             <  2:983184/61‑1 (MQ=255)
                                                                                                                                             tCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGTTGGTACAGATGATGGTATTTCCg                       >  2:246948/1‑131 (MQ=255)
                                                                                                                                             tCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGTTGGTACAGATGATGGTATTTCCg                       <  1:246948/131‑1 (MQ=255)
                                                                                                                                                aCTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCtt                                                                                                          >  2:1047414/1‑45 (MQ=255)
                                                                                                                                                aCTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCtt                                                                                                          <  1:1047414/45‑1 (MQ=255)
                                                                                                                                                aCTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGTTGGTACAGATGATGGTATTTCCGGTTCGATAATGCTTGTACCa   >  1:728313/1‑148 (MQ=255)
                                                                                                                                                 cTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGTTGGTACAGATGATGGTATTTCCGGTTCGATAATGCTTGTACCaa  >  3:237628/1‑148 (MQ=255)
                                                                                                                                                 |                                                                                                                                                   
AGGTATAATCCACAACGTTTTCCGCATACCTCTTCAGTGCCGAAGTGGCGAAATCGGTAGACGCAGTTGATTCAAAATCAACCGTAGAAATACGTGCCGGTTCGAGTCCGGCCTTCGGCACCAAAAGTATGTAAATAGACCTCAACTGAGGTCTTTTTTTATGCCTGAAATCCAGTGTTTATCTATCTTTCCCGCTATATTAACTCTCTCAAGGTCAACCGATATCAACGTACATCTACCAACATATGTTGGTACAGATGATGGTATTTCCGGTTCGATAATGCTTGTACCAA  >  NC_000913/4496367‑4496659

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: