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
A19 F57 I0 R1 30 35.6 800162 95.7% 765755 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,010,363 C→T 100% C146Y (TGT→TAT)  USA300HOU_RS10125 ← Putative multidrug export ATP‑binding/permease protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,010,3630CT100.0% 65.4 / NA 24C146Y (TGT→TAT) USA300HOU_RS10125Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (12/12);  total (12/12)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGTAT  >  USA300TCH1516_ALE/2010230‑2010500
                                                                                                                                     |                                                                                                                                         
aCGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTaa                                                                                                                                    >  1:283127/1‑141 (MQ=255)
            tCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAt                                                                                                                        <  2:316763/141‑1 (MQ=255)
                       cAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACACCTAAAAAGAACATTATGGATAGTGCAATAATCATTGTTATATAATCTAACCAAATATTCTTTAACCCGGTTa                                                                                                             >  2:57899/1‑141 (MQ=255)
                        aaaGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATCGTGTAAGAATAATTGTTATATAATCTAACCAAATATTAATTAATCCGGTTaa                                                                                                            >  1:227571/1‑141 (MQ=255)
                            aaaaCGTACACAGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAGTAACCCGGTTAAAATg                                                                                                        <  1:4715/141‑1 (MQ=255)
                                 gTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACACTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGACATc                                                                                                   >  2:391454/1‑141 (MQ=255)
                                   acacCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCTGGTTAAAATGAAATCtt                                                                                                 >  2:24346/1‑141 (MQ=255)
                                                     atgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATTAAACCTTTGGTTTGTTCAAcatcat                                                                               <  2:283127/141‑1 (MQ=255)
                                                               aaaCAGTGCTGCTAAAGTTAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCActct                                                                     <  1:19500/141‑1 (MQ=255)
                                                                  cAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAGATGAAATCTTTTGGTTGTTCAACATCATTAGTCAATCTaaa                                                                  >  2:267278/1‑139 (MQ=255)
                                                                  cAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTACTCACTCTAGa                                                                  >  1:237074/1‑141 (MQ=255)
                                                                   aGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGat                                                                 >  2:355945/1‑141 (MQ=255)
                                                                           gaaaGTCAATTTCACATCTAAAAAGAACATTATGGATATTGTGATAGTAATTGTTATATAATCTAACCAAATATGCATTAACCCGTCTAAAATTTAATCTTTTATTTGTTGAACATCACTAATCACTCTAGATCTTACGTg                                                         <  2:176286/140‑1 (MQ=255)
                                                                            aaaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGa                                                        <  1:85991/141‑1 (MQ=255)
                                                                             aaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCTGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGAc                                                       <  2:349509/141‑1 (MQ=255)
                                                                              aGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGAcc                                                      >  1:157922/1‑141 (MQ=255)
                                                                                tCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTa                                                    <  1:390460/141‑1 (MQ=255)
                                                                                        acaTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACGTGattt                                            >  1:99055/1‑140 (MQ=255)
                                                                                        acaTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTATAAATATTACTTGACCTACTTGattt                                            >  1:30881/1‑140 (MQ=255)
                                                                                                 aaGAACATTATGGATAGAGCAATAATAATTGTTATATAATCTAACCACATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAGCATCAGTAAGCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaa                                   <  1:264410/141‑1 (MQ=255)
                                                                                                        ttATGGACACTGCAATAATAATTGTTATATAAGCTACNCTAATCTCCATTAACTCGGTTAAAATGACATCTTTTGTTTGTTCCACATCTTTAATCACTCTTGACATTTCTTGACCTACTTGATTATTAGCATAAAATCTCg                            <  2:58917/141‑1 (MQ=255)
                                                                                                          ttGGATCGGGCAATCATAATTGTTATATAATCTAACAAAATGTTCATTGACCCGGTTAAAATGAAATCTTTGGTTTGTTAAACATCATTAGTCACACTAGATATTACTTGACCTACTTGATTATTAGATTAAAATCTAGCa                          >  2:26670/2‑141 (MQ=255)
                                                                                                                   gCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTGAAAGCt                 <  2:8984/141‑1 (MQ=255)
                                                                                                                           aatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAACATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATg         <  1:307742/141‑1 (MQ=255)
                                                                                                                                  atatAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTGGTAAATGGTTGtat  <  1:213810/141‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                         
ACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGTAT  >  USA300TCH1516_ALE/2010230‑2010500

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A