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
A10 F1 I1 R1 77 35.1 1569012 96.6% 1515665 112.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,734,535 T→C E167G (GAG→GGG)  yfiH ← UPF0124 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,734,5350TC100.0% 39.8 / NA 13E167G (GAG→GGG) yfiHUPF0124 family protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (8/5);  total (8/5)

AAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGC‑GAA‑‑CCT‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGC  >  NC_000913/2734403‑2734662
                                                                                                                                       |                                                                                                                                
aaaaTTTGCTCAACACCCACCGTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTTGATGCAAGCTCCACTTGCATTGGCGTCTAAAGCCATAAACGCCTCGC‑GAA‑‑Ccc‑cccccc                                                                                                                           <  1:202619/139‑1 (MQ=255)
                             gcccTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCCCTTGCTTTAGCGTCTACTGCCATAAACGCCTCGC‑GAAC‑CCC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                               <  1:9632/136‑1 (MQ=255)
                                                         gCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGC‑GAACCCCC‑CCCCCCCCCCTTCCAAGGCCCGTGGCAAAATTCCCGGCCCTAACCAGCCAGAAATATTTTc                                                                    >  1:386730/1‑139 (MQ=255)
                                                                           tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGC‑GAAC‑CCC‑CCCCCCCCACTTCAAACGCGCGTGGACCAATTGCCGGCCCTACCCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAg                                                 >  1:438358/1‑139 (MQ=255)
                                                                           tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGC‑GAA‑‑CCC‑CCCCCCCCACTTCGTACGTGCGTGCACCAATTGc                                                                                               >  1:166783/1‑92 (MQ=255)
                                                                           tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGC‑GAA‑‑CCC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                               <  2:166783/92‑1 (MQ=255)
                                                                            gCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGC‑GAAC‑CCC‑CCCCCCCCCCTTCGAACCCGCGTGGCCCAATTGCCGGCCCTAACCAGGCGAAAAAATTTTCCGGATTTCCAGCaaacaaga                                                >  1:237494/1‑134 (MQ=255)
                                                                                               tGCTTTAGCGTCTACTGCCATAAACGCCCCCC‑GAACCCCC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCa                              <  1:405246/139‑1 (MQ=255)
                                                                                                        gTCTACTGCCCAAAACCCCCCCCGGAC‑‑CCC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca                    <  2:606750/139‑1 (MQ=255)
                                                                                                        gTCTACCGCCATAAACGCCTCCC‑GAAC‑CCC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca                    <  1:99353/139‑1 (MQ=255)
                                                                                                        ctCTACTGCCAAAAACCCCCCGC‑GAA‑‑CCCCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca                    <  2:237494/138‑1 (MQ=255)
                                                                                                         tCTACTCCCATAAACCCCTCGC‑CAACCCCC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca                    <  2:386730/139‑1 (MQ=255)
                                                                                                           tACTGCCATAAACGCCTCGC‑GAAC‑CCC‑CCCCCCCCACTTCGAACGCGCGTGGACCATTTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATAATCAGCAAAAAAGGAAACCGTCTCTTCCAGCACCCCTGCGCACAg                 >  1:606750/1‑139 (MQ=255)
                                                                                                                ccATAAACGCCTCGC‑GAAC‑CCC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGACTATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGAACGCCTCCGCACAGTCCAc            >  1:141716/1‑139 (MQ=255)
                                                                                                                          cTCGC‑GAAC‑CCC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGCCTCTTCCAGCCCGCCTGCGCACAGTCCACGCcacccagc  >  2:564027/1‑139 (MQ=255)
                                                                                                                          cTCGC‑GAAC‑CCC‑CCCCCCCCACCTCGAACCCCCTGGGACCAATTTCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAAAAGGAAACCGTCCCTTCCAGCACGCCTGCCCACAGCCCACCCcccccagc  >  2:381757/1‑139 (MQ=255)
                                                                                                                                       |                                                                                                                                
AAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGC‑GAA‑‑CCT‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGC  >  NC_000913/2734403‑2734662

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A