Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A3 F1 I1 R1 781 46.9 2231650 93.5% 2086592 109.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,549,000 T→C C65R (TGC→CGC)  fimH → minor component of type 1 fimbriae

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,549,0000TC100.0% 199.6 / NA 56C65R (TGC→CGC) fimHminor component of type 1 fimbriae
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/31);  total (25/31)

TAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTA  >  NC_000913/4548879‑4549126
                                                                                                                           |                                                                                                                              
tAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGTGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCg                                                                                                               <  1:1026276/139‑1 (MQ=255)
  aaaCCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGa                                                                                                             <  1:94939/139‑1 (MQ=255)
    aCCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATTTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGaaa                                                                                                           <  1:1114138/139‑1 (MQ=255)
     ccGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGaa                                                                                                            >  2:1021698/1‑139 (MQ=255)
     ccGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGTCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAAc                                                                                                          <  2:734409/139‑1 (MQ=255)
     ccGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAAc                                                                                                          <  1:1095755/139‑1 (MQ=255)
         cAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCAtt                                                                                                      >  2:393010/1‑139 (MQ=255)
          aaTGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTa                                                                                                     >  2:398993/1‑139 (MQ=255)
            tGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACa                                                                                                   <  1:137578/139‑1 (MQ=255)
                aCCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGa                                                                                                 <  1:1021698/139‑1 (MQ=255)
                      aTCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTca                                                                                         >  2:872174/1‑139 (MQ=255)
                      aTCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTca                                                                                         <  1:185860/139‑1 (MQ=255)
                       tCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTcac                                                                                        >  1:312714/1‑139 (MQ=255)
                       tCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTcac                                                                                        >  2:26601/1‑139 (MQ=255)
                                  ggTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTACGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGAAACGAg                                                                             >  2:774550/1‑139 (MQ=255)
                                   gTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCg                                                                                                               <  2:543527/104‑1 (MQ=255)
                                   gTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCg                                                                                                               >  1:543527/1‑104 (MQ=255)
                                          cgcCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCt                                                                     >  2:51896/1‑139 (MQ=255)
                                             cAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACg                                                                                                                       >  2:892718/1‑86 (MQ=255)
                                             cAATGTT‑‑TATGTAAACCGTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACg                                                                                                                       <  1:892718/86‑1 (MQ=255)
                                                 gTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATggcg                                                              <  1:393010/139‑1 (MQ=255)
                                                             aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCAt                                                                                                                           <  1:171023/68‑1 (MQ=255)
                                                             aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCAt                                                                                                                           >  2:171023/1‑68 (MQ=255)
                                                             aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTa                                                                   >  2:1012596/1‑124 (MQ=255)
                                                             aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTa                                                                   <  1:1012596/124‑1 (MQ=255)
                                                             aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATc                                                    >  1:975177/1‑139 (MQ=255)
                                                                 tGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAAt                                                >  2:979140/1‑139 (MQ=255)
                                                                  gcgcCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGAt                                                                                                                     <  1:947642/69‑1 (MQ=255)
                                                                  gcgcCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGAt                                                                                                                     >  2:947642/1‑69 (MQ=255)
                                                                  gcgcCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATggcg                                                              <  1:777608/124‑1 (MQ=255)
                                                                  gcgcCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATggcg                                                              >  2:777608/1‑124 (MQ=255)
                                                                         tcgtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCgg                                        <  1:872174/139‑1 (MQ=255)
                                                                         tcgtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCgg                                        <  2:886680/139‑1 (MQ=255)
                                                                           gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      <  1:398993/139‑1 (MQ=255)
                                                                           gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      <  1:541182/139‑1 (MQ=255)
                                                                           gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      <  1:51896/139‑1 (MQ=255)
                                                                           gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      <  2:312714/139‑1 (MQ=255)
                                                                             gAATGTGGGGCAAAACCTGGTCGTGGATCTTACGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGAcc                                    <  1:774550/139‑1 (MQ=255)
                                                                                tgtgGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTa                                 <  1:979140/139‑1 (MQ=255)
                                                                                tgtgGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTa                                 <  1:507636/139‑1 (MQ=255)
                                                                                    gggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAAc                                                                                                          >  1:105527/1‑62 (MQ=255)
                                                                                    gggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAAc                                                                                                          <  2:105527/62‑1 (MQ=255)
                                                                                    gggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCg                                                                        <  2:286576/96‑1 (MQ=255)
                                                                                    gggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCg                                                                        >  1:286576/1‑96 (MQ=255)
                                                                                       cAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAAtata                          <  2:958100/139‑1 (MQ=255)
                                                                                          aaCCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTg                       >  1:444860/1‑139 (MQ=255)
                                                                                          aaCCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTg                       >  1:178916/1‑139 (MQ=255)
                                                                                               ggTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGt                  >  1:762204/1‑139 (MQ=255)
                                                                                                   gTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCt              <  2:975177/139‑1 (MQ=255)
                                                                                                         cTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCAt        <  1:26601/139‑1 (MQ=255)
                                                                                                           ttCGACGCAAATCTTTCGCCATAACGATTATCCGGaaa                                                                                                           >  2:1056866/1‑38 (MQ=255)
                                                                                                           ttCGACGCAAATCTTTCGCCATAACGATTATCCGGaaa                                                                                                           <  1:1056866/38‑1 (MQ=38)
                                                                                                           ttCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      >  2:350175/1‑107 (MQ=255)
                                                                                                           ttCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      <  1:350175/107‑1 (MQ=255)
                                                                                                            tCGACGCAAATCATTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTc     >  2:1068487/1‑139 (MQ=255)
                                                                                                               aCGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTa  >  1:583401/1‑139 (MQ=255)
                                                                                                                           |                                                                                                                              
TAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTA  >  NC_000913/4548879‑4549126

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A