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
A16 F1 I1 R1 16 38.1 2332770 98.7% 2302443 76.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 4,163,734 T→C L960P (CTG→CCG)  rpoB → DNA‑directed RNA polymerase subunit beta

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6064,163,7340TC100.0% 68.2 / NA 18L960P (CTG→CCG) rpoBDNA‑directed RNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (12/6);  total (12/6)

CGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCGTGCTGTGCTGGTAGCCGGTGGC  >  REL606/4163663‑4163804
                                                                       |                                                                      
cgATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCCGTCt                                                                    <  1:370470/76‑1 (MQ=255)
   tGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCCGTCTgaa                                                                 <  2:472744/76‑1 (MQ=255)
    ggCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCCGTCTggag                                                                <  1:296563/76‑1 (MQ=255)
     gCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCCGTCTgaaga                                                               <  1:3347/76‑1 (MQ=255)
         aGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCCGTCTGAAGAACTg                                                           >  2:773522/1‑76 (MQ=255)
             aaaGACAAACGTGCGCTGGAAATCAAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCCGTCTGAAGAACTGCAGa                                                       >  1:709580/1‑76 (MQ=255)
                         gcgcTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCCGTCTGAAGAACTGCAGATCCTCGAAGCgg                                           <  2:627346/76‑1 (MQ=255)
                              ggAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTg                                      >  2:26248/1‑76 (MQ=255)
                              ggAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTg                                      >  2:1083417/1‑76 (MQ=255)
                                    cGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGc                                >  2:944437/1‑76 (MQ=255)
                                                gCTCAAACAGGCGAAGAAAGACCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCgtgct                    >  1:231321/1‑76 (MQ=255)
                                                 cTCAAACAGGCGAAGAAAGACCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCgtgctg                   >  1:828616/1‑76 (MQ=255)
                                                        gggCGAAGAAAGACCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCGTGCTGTGCTGGt            <  2:85691/75‑1 (MQ=255)
                                                        aGGCGAAGAAAGCCCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCGTGCTGTGCTGGt            <  2:85684/76‑1 (MQ=255)
                                                           cGAAGAAAGACCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCGTGCTGTGCTGGTAGc         >  1:427013/1‑76 (MQ=255)
                                                            gaagaaAGACCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCGTGCTGTGCTGGTAGcc        >  1:1153045/1‑76 (MQ=255)
                                                              agaaagaCCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCGTGCTGTGCTGGTAGCCgg      >  2:313697/1‑76 (MQ=255)
                                                                 aagaCCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCGTGCTGTGCTGGTAGCCGGTgg   >  2:283392/1‑76 (MQ=255)
                                                                  agaCCCGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCGTGCTGTGCTGGTAGCCGGTGGc  >  1:906773/1‑76 (MQ=255)
                                                                       |                                                                      
CGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCGTGCTGTGCTGGTAGCCGGTGGC  >  REL606/4163663‑4163804

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A