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
A1 F169 I0 R1 75 34.0 794130 95.7% 759982 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 169,407 G→A 100% G82E (GGA→GAA)  repE → Replication initiation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE169,4070GA100.0% 122.1 / ‑6.5 40G82E (GGA→GAA) repEReplication initiation protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (19/20);  minor base C (1/0);  total (20/20)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CAATGCTTCATTTATTAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGGAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGTTT  >  USA300TCH1516_ALE/169272‑169542
                                                                                                                                       |                                                                                                                                       
cAATGCTTCATTTATTAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATCAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAGGAGCAAATg                                                                                                                                    >  2:271215/1‑141 (MQ=255)
cAATGCTTCATTTATTAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATg                                                                                                                                    >  1:167148/1‑141 (MQ=255)
  aTGCTTCATTTATTAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGaa                                                                                                                                  >  1:101029/1‑141 (MQ=255)
        cATTTATTAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCaa                                                                                                                            >  1:108487/1‑141 (MQ=255)
               taACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCaaa                                                                                                                     >  1:177973/1‑141 (MQ=255)
                     aCGAAGAAGAGGAATGAGGAAGTTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTCATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACaaa                                                                                                               >  1:203769/1‑141 (MQ=255)
                        aagaagAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCg                                                                                                            <  2:151565/141‑1 (MQ=255)
                         agaagaGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGa                                                                                                           >  2:185954/1‑141 (MQ=255)
                          gaagaGGAATGGGGAAATTTAGAAAGCCGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAACTGAAAACCACTTGCAAAAACAAATCgcc                                                                                                          >  2:154751/1‑139 (MQ=255)
                           aagaGGAATGGGGAAAGTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTACGAGAAAATGAAAACCAATTGCAAAAACAAATCGACt                                                                                                         >  1:219645/1‑141 (MQ=255)
                            agagGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAACTATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACtt                                                                                                        >  2:63451/1‑141 (MQ=255)
                              agGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACtttt                                                                                                      >  1:240692/1‑141 (MQ=255)
                                 aaTGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGt                                                                                                   <  2:218533/141‑1 (MQ=255)
                                   tGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTg                                                                                                 <  1:147355/141‑1 (MQ=255)
                                       gAAATTTAGCAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGaatt                                                                                             <  1:231329/141‑1 (MQ=255)
                                       gAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGaatt                                                                                             <  1:147459/141‑1 (MQ=255)
                                              aGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAattatt                                                                                      <  2:240692/141‑1 (MQ=255)
                                                        aCTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAg                                                                            <  2:269468/141‑1 (MQ=255)
                                                          tcatcataaaaaGAGATATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGaa                                                                          <  2:177973/136‑1 (MQ=255)
                                                                taaataTAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGt                                                                    <  2:101029/141‑1 (MQ=255)
                                                                   atatatatatatGTTGCAAAAGTTGGCGTCTATTGATTTGACAGATTTAATGAAAATATGTTTAAGAGAAAATGAATACCAATTGCCAAACCAAATCGACTTTTGGTTGAATTAATTATTATAACTATAGAACTATGTTCa                                                                 <  2:206332/141‑1 (MQ=255)
                                                                   atacAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCa                                                                 <  1:22401/141‑1 (MQ=255)
                                                                         agaTAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGGTCACTTATg                                                           <  2:254554/141‑1 (MQ=255)
                                                                             aaGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCa                                                       >  1:228691/1‑141 (MQ=255)
                                                                                ttGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCt                                                    <  2:203769/141‑1 (MQ=255)
                                                                                 tGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTa                                                   >  2:181301/1‑141 (MQ=255)
                                                                                   aaaaaTATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACt                                                 >  1:139963/1‑141 (MQ=255)
                                                                                   aaaaaTATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAAACAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAAAACTATGTTCAATTATGATCATCTACt                                                 >  1:260525/1‑141 (MQ=255)
                                                                                       atatAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTaaa                                             <  1:318752/141‑1 (MQ=255)
                                                                                       atatAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTaaa                                             <  1:249711/141‑1 (MQ=255)
                                                                                                    tGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTAtttttt                                <  1:137471/141‑1 (MQ=255)
                                                                                                     taTTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTAtttttct                               <  2:292201/140‑3 (MQ=255)
                                                                                                        ttGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAACCAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTttgtt                            >  1:232984/1‑141 (MQ=255)
                                                                                                          gACAGATTTAAAGAAAATATCTTTAAGAGAAAATGAAAACCAATTTCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTgg                          <  2:41049/141‑1 (MQ=255)
                                                                                                              gATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGtttt                      >  1:377919/1‑141 (MQ=255)
                                                                                                                         aaTATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGtt           <  1:239036/141‑1 (MQ=255)
                                                                                                                            atCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGaa        >  1:161904/1‑141 (MQ=255)
                                                                                                                                 tAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGtt   >  1:342480/1‑141 (MQ=255)
                                                                                                                                 tAAAAGAAATTGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGtt   <  2:97920/141‑1 (MQ=255)
                                                                                                                                  aaGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTTAAAGTAGTTGAAATGtgt  >  2:208604/1‑139 (MQ=255)
                                                                                                                                       |                                                                                                                                       
CAATGCTTCATTTATTAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGGAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGTTT  >  USA300TCH1516_ALE/169272‑169542

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A