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
A2 F1 I1 R1 748 32.0 1685426 92.6% 1560704 103.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,548,854 C→T S16L (TCG→TTG)  fimH → minor component of type 1 fimbriae

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,548,8540CT100.0% 180.0 / NA 56S16L (TCG→TTG) fimHminor component of type 1 fimbriae
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (32/24);  total (32/24)

CCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCG  >  NC_000913/4548736‑4548987
                                                                                                                      |                                                                                                                                     
ccACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCg                                                                                                                   <  1:55214/139‑1 (MQ=255)
         gAACCATTCGGGCCGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGTGATGATTTTAATGCAACGCGACTTTGCCCTGTTTGCTGTACTGCTGATGGGCTGGTTAGTTAATGCCTTGACATTCGCCTGTaaac                                                                                                          <  2:97575/139‑2 (MQ=255)
             cATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGc                                                                                                      >  2:779194/1‑139 (MQ=255)
               ttCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCa                                                                                                    >  2:446847/1‑139 (MQ=255)
                tCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCaa                                                                                                   <  2:96509/139‑1 (MQ=255)
                     cAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTa                                                                                              <  1:446847/139‑1 (MQ=255)
                          aTTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGTTACCGCt                                                                                         >  2:650285/1‑139 (MQ=255)
                                  cACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTAt                                                                                 >  1:470735/1‑139 (MQ=255)
                                    ccTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTAt                                                                                       <  2:262414/131‑1 (MQ=255)
                                    ccTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTAt                                                                                       >  1:262414/1‑131 (MQ=255)
                                           cTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTgg                                                                        <  2:162164/139‑1 (MQ=255)
                                           cTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTgg                                                                        <  2:470735/139‑1 (MQ=255)
                                             aCAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCt                                                                                         >  2:517872/1‑120 (MQ=255)
                                             aCAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCt                                                                                         <  1:517872/120‑1 (MQ=255)
                                             aCAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCa                                                                      >  1:423281/1‑139 (MQ=255)
                                             aCAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCa                                                                      >  1:834415/1‑139 (MQ=255)
                                               aGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAgc                                                                    >  2:443029/1‑139 (MQ=255)
                                                      cccGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATg                                                             >  1:430415/1‑139 (MQ=255)
                                                              gatgatTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTgg                                                                        >  1:332183/1‑120 (MQ=255)
                                                              gatgatTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTgg                                                                        <  2:332183/120‑1 (MQ=255)
                                                               atgatTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTaa                                                    <  1:171589/139‑1 (MQ=255)
                                                                     gTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTg                                              <  2:423281/139‑1 (MQ=255)
                                                                       aaTGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTgcg                                            <  2:834415/139‑1 (MQ=255)
                                                                         tGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGCAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGcc                                          >  2:753655/1‑139 (MQ=255)
                                                                                aGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCt                                                                                         <  2:99899/85‑1 (MQ=255)
                                                                                aGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCt                                                                                         >  1:99899/1‑85 (MQ=255)
                                                                                aGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATg                                                             <  2:226113/113‑1 (MQ=255)
                                                                                aGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATg                                                             >  1:226113/1‑113 (MQ=255)
                                                                                           tGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTc                                                                                                                    <  2:669043/47‑1 (MQ=255)
                                                                                           tGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTc                                                                                                                    >  1:669043/1‑47 (MQ=255)
                                                                                           tGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCa                                                                                                    >  2:502373/1‑63 (MQ=255)
                                                                                           tGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCa                                                                                                    <  1:502373/63‑1 (MQ=255)
                                                                                           tGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCa                        >  2:804346/1‑139 (MQ=255)
                                                                                                  tGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGtt                                                           <  2:442380/97‑1 (MQ=255)
                                                                                                  tGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGtt                                                           >  1:679036/1‑97 (MQ=255)
                                                                                                  tGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGtt                                                           >  1:442380/1‑97 (MQ=255)
                                                                                                  tGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGtt                                                           <  2:679036/97‑1 (MQ=255)
                                                                                                       tgctgATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGcc                                                                 >  1:584107/1‑86 (MQ=255)
                                                                                                       tgctgATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGcc                                                                 <  2:584107/86‑1 (MQ=255)
                                                                                                         ctgATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATcc                                                                                     >  2:837329/1‑64 (MQ=255)
                                                                                                         ctgATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATcc                                                                                     <  1:837329/64‑1 (MQ=255)
                                                                                                         ctgATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTgg          >  2:334131/1‑139 (MQ=255)
                                                                                                         ctgATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTgg          >  2:50104/1‑139 (MQ=255)
                                                                                                         ctgATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATCGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAAcc                   >  2:501700/1‑130 (MQ=255)
                                                                                                         ctgATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATCGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAAcc                   <  1:501700/130‑1 (MQ=255)
                                                                                                            aTGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATc       >  1:32112/1‑139 (MQ=255)
                                                                                                              gggCTGGTTGGTAAATGCCTGGTCATTCGCCTGTaaaa                                                                                                          <  1:102868/38‑1 (MQ=255)
                                                                                                              gggCTGGTTGGTAAATGCCTGGTCATTCGCCTGTaaaa                                                                                                          >  2:102868/1‑38 (MQ=255)
                                                                                                              gggCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTgcgc                                           <  1:429882/101‑1 (MQ=255)
                                                                                                              gggCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTgcgc                                           >  2:429882/1‑101 (MQ=255)
                                                                                                              gggCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCtt     >  2:776781/1‑139 (MQ=255)
                                                                                                              gggCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCtt     >  1:583633/1‑139 (MQ=255)
                                                                                                                gCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTc   >  1:217060/1‑139 (MQ=255)
                                                                                                                 cTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCg  >  2:670493/1‑139 (MQ=255)
                                                                                                                   ggTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATc                                                                                      >  1:25934/1‑53 (MQ=255)
                                                                                                                   ggTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATc                                                                                      <  2:25934/53‑1 (MQ=255)
                                                                                                                      |                                                                                                                                     
CCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCG  >  NC_000913/4548736‑4548987

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A