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 744,375 A→T 100% I506F (ATT→TTT)  melR_1 → Melibiose operon regulatory protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE744,3750AT100.0% 97.7 / NA 32I506F (ATT→TTT) melR_1Melibiose operon regulatory protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (14/18);  total (14/18)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCGACTTAAATTCGATTCGTTAATAATAGATAATGCAAATTTAAGTAGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATATTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATAGTGCTCCATTAATTTATAAGACATTAAGTGCGCTGTATCACAACTTTGATGGCTTTGG  >  USA300TCH1516_ALE/744239‑744511
                                                                                                                                        |                                                                                                                                        
gCGACTTAAATTCGATTCGTTAATAATAGATAATGCAAATTTAAGTAGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGa                                                                                                                                      >  2:169245/1‑141 (MQ=255)
      tAAATTCGATTCGTTAATAATAGATAATGCAAATTTAAGTAGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGa                                                                                                                                >  1:324765/1‑141 (MQ=255)
                           aGATAATGCAAATTTAAGTAGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGt                                                                                                           >  1:9369/1‑141 (MQ=255)
                           aGATAATGCAAATTTAAGTAGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGAGTTTGAACAAGAAAAGCTGATTTTTCTAAATGt                                                                                                           >  1:9109/1‑141 (MQ=255)
                                   cAAATTTAAGTAGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATc                                                                                                   <  1:38120/141‑1 (MQ=255)
                                    aaaTTTAAGTAGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCa                                                                                                  <  2:327643/141‑1 (MQ=255)
                                     aaTTTAAGTAGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCAt                                                                                                 <  1:169245/141‑1 (MQ=255)
                                     aaTTTAAGTAGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCAt                                                                                                 <  2:190482/141‑1 (MQ=255)
                                     aaTTTAAGTAGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAACCAt                                                                                                 <  2:162341/141‑1 (MQ=255)
                                     aaTTTAAATAGGACTTATTTGATGGGGTAATGTGATGAAAAAAAAAAAAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCAt                                                                                                 <  2:219968/141‑1 (MQ=255)
                                              aGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCtt                                                                                        <  2:350605/141‑1 (MQ=255)
                                              aGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCtt                                                                                        <  1:36122/141‑1 (MQ=255)
                                                         gATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACTAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGa                                                                             <  1:256640/141‑1 (MQ=255)
                                                          aTGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGaa                                                                            <  1:197712/141‑1 (MQ=255)
                                                           tGGGGGAAAGTGATGAGTTCCTATTGATAAATATTTTGCATTTTAAAAATTTAAAAAAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGCTTTTTCTAAATGTTGAAAATCATAAACAGCTTGATAagaaagaag                                                                           >  2:23386/1‑140 (MQ=255)
                                                           tGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAACCTGCTTAATAATAAAGAAc                                                                           >  1:88754/1‑141 (MQ=255)
                                                                gAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGAt                                                                      >  1:339321/1‑141 (MQ=255)
                                                                  acgTGATGAGTTAATAGTGAAAAATATTTGGCATGTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTACATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCt                                                                    >  2:231433/3‑141 (MQ=255)
                                                                   aGTGCTGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTa                                                                   <  1:294626/141‑1 (MQ=255)
                                                                         gaGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTGCTAAATGTTGAAAATCATAAACTGCGTAATAATAAAGAACGAGATCTAAGTAAt                                                             >  1:379004/1‑141 (MQ=255)
                                                                          aGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATa                                                            <  1:29385/141‑1 (MQ=255)
                                                                          aGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATa                                                            <  1:122460/141‑1 (MQ=255)
                                                                                   tGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATAGTGCTCCAt                                                   >  2:368026/1‑141 (MQ=255)
                                                                                    gAAAAATATTTTGCTTTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATAGTGCTCCAtt                                                  <  2:327480/141‑1 (MQ=255)
                                                                                         atatTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATAGTGCTCCATTAAttt                                             >  1:252982/1‑141 (MQ=255)
                                                                                                                  aCAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATAGTGCTCCATTAATTTATAAGACATTAAGTGCGCTGTATca                    <  2:379651/141‑1 (MQ=255)
                                                                                                                  aCAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAATAATAGTGCTCCATTAATTTATAAGACATTAAGTGCGCTGTCTca                    >  2:104159/1‑141 (MQ=255)
                                                                                                                   cAAGTAATTAATGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATAGTGCTCCATTAATTTATAAGACATTAAGTGCGCTGTATcac                   <  1:221484/141‑1 (MQ=255)
                                                                                                                     aGTAATTAATGAATTGGATTTTGAACAAGCAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAGTAAAGAACGAGATCTAAGTAATAGTGCTCCATTAATTTATAAGACATTAAGTGCGCTGTATCACaa                 >  1:346044/1‑141 (MQ=255)
                                                                                                                              tGAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATAGTGCTCCATTAATTTATAAGACATTAAGTGCGCTGTATCACAACTTTGATgg        <  1:193092/141‑1 (MQ=255)
                                                                                                                               gAATTGGATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATAGTGCTCCATTAATTTATAAGACATTAAGTGCGCTGTATCACAACTTTGATGGc       <  2:231421/141‑1 (MQ=255)
                                                                                                                                    ggATTTTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATAGTGCTCCATTAATTTATAAGACATTAAGTGCGCTGTATCACAACTTTGATGGCTTTgg  >  2:319917/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                        
GCGACTTAAATTCGATTCGTTAATAATAGATAATGCAAATTTAAGTAGCCCTTATTTGATGGGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTAATTAATGAATTGGATATTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAACTGCTTAATAATAAAGAACGAGATCTAAGTAATAGTGCTCCATTAATTTATAAGACATTAAGTGCGCTGTATCACAACTTTGATGGCTTTGG  >  USA300TCH1516_ALE/744239‑744511

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