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
A4 F1 I1 R1 765 39.6 1867486 94.4% 1762906 108.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,255,020 G→A *234* (TAG→TAA)  yhaK → redox‑sensitive bicupin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,255,0200GA100.0% 61.2 / NA 20*234* (TAG→TAA) yhaKredox‑sensitive bicupin
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (10/10);  total (10/10)

GCTTACGCATCATGAAGAGAAAGCGGCGCTGACCTGCGGTGATGGGGCGTTTATTCGTGACGAGGCTAACATTACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTATGAAGAGATGTTGAGCGAGCT  >  NC_000913/3254894‑3255149
                                                                                                                              |                                                                                                                                 
gcTTACGCATCATGAAGAGAAAGCGGCGCTGACCTGCGGTGATGGGGCGTTTATTCGTGACGAGGCTAACATTACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAg                                                                                                                       <  1:146044/139‑1 (MQ=255)
            tGAAGAGAAAGCGGCGCTGACCTGCGGTGATGGGGCGTTTATTCGTGACGAGGCTAACATTACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAGGGAgatgatgat                                                                                                           <  2:494208/139‑1 (MQ=255)
                          cgcTGACCTGCGGTGATGGGGCGTTTATTCGTGACGAGGCTAACATTACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACa                                                                                                                        <  1:435936/112‑1 (MQ=255)
                          cgcTGACCTGCGGTGATGGGGCGTTTATTCGTGACGAGGCTAACATTACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACa                                                                                                                        >  2:435936/1‑112 (MQ=255)
                                    cGGTGATGGGGCGTTTATTCGTGACGAGGCTAACATTACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAGGGAgatgatgat                                                                                                           <  2:782201/115‑1 (MQ=255)
                                    cGGTGATGGGGCGTTTATTCGTGACGAGGCTAACATTACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAGGGAgatgatgat                                                                                                           >  1:782201/1‑115 (MQ=255)
                                                                          cGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAGGGAGATGATGATGAGTaaaaaa                                                                                                 <  2:576080/87‑1 (MQ=255)
                                                                          cGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAGGGAGATGATGATGAGTaaaaaa                                                                                                 >  1:576080/1‑87 (MQ=255)
                                                                                          cccACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAAttt                             <  2:928756/139‑1 (MQ=255)
                                                                                                 cgcgcTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAg                                                                                                                       <  2:414816/42‑1 (MQ=255)
                                                                                                 cgcgcTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAg                                                                                                                       >  1:414816/1‑42 (MQ=255)
                                                                                                 cgcgcTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTAt                      >  2:892669/1‑139 (MQ=255)
                                                                                                 cgcgcTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTAt                      >  1:185946/1‑139 (MQ=255)
                                                                                                  gcgcTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAGGGAgatgatg                                                                                                             >  1:776145/1‑51 (MQ=255)
                                                                                                  gcgcTTTGCTGATAGATTTGCCTGTCTAATTGTTTTTACAGGGAgatgatg                                                                                                             <  2:776145/51‑1 (MQ=255)
                                                                                                                   ttGCCTGTCTAATTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTATGAAGAGATGTTgagcgag    <  2:185946/139‑1 (MQ=255)
                                                                                                                   ttGCCTGTCTAATTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTATGAAGAGATGTTgagcgag    >  2:850409/1‑139 (MQ=255)
                                                                                                                     gCCTGTCTAATTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTATGAAGAGATGTTGAGCGAGCt  >  2:225317/1‑139 (MQ=255)
                                                                                                                          tCTAATTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCgtggtg                                                             <  2:548155/75‑1 (MQ=255)
                                                                                                                          tCTAATTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCgtggtg                                                             >  1:548155/1‑75 (MQ=255)
                                                                                                                              |                                                                                                                                 
GCTTACGCATCATGAAGAGAAAGCGGCGCTGACCTGCGGTGATGGGGCGTTTATTCGTGACGAGGCTAACATTACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTATGAAGAGATGTTGAGCGAGCT  >  NC_000913/3254894‑3255149

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A