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 F2 I203 R1 4 36.0 2027912 97.0% 1967074 86.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 2,380,341 G→A intergenic (+31/‑72) yfbL → / → yfbM M28 family metallopeptidase/YfbM family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,380,3410GA76.5% 14.0 / 4.4 17intergenic (+31/‑72)yfbL/yfbMM28 family metallopeptidase/YfbM family protein
Reads supporting (aligned to +/- strand):  ref base G (0/4);  new base A (13/0);  total (13/4)
Fisher's exact test for biased strand distribution p-value = 4.20e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.20e-03

AAAATGGCTCAGGTAGTGGATGGTGTTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGTCCAGAAAAAGCGACATGCACATTTTATTTTCCCTCATCTGTTTTAAGATGCGAAACATGAAATTCAACGGAGG  >  NZ_CP009273/2380257‑2380404
                                                                                    |                                                               
aaaaTGGCTCAGGTAGTGGATGGTGTTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGTCCAGAAAAAGCGACa                                                            <  1:316220/90‑1 (MQ=255)
     ggCTCAGGTAGTGGATGGTGTTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGGCAGAAAAAAAGACAAGcga                                                       >  1:520787/1‑88 (MQ=255)
         cAGGTAGTGGATGGTGTTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCAGAAAAAAGGAAAAGCAAattt                                                   >  2:105101/1‑90 (MQ=255)
                     ggTGTTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCAGAAAAAAAGACAAGCACAATTTTTTTTTCCTcc                                       >  2:153912/1‑89 (MQ=255)
                     ggTGTTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCAGAAAAAAAGAAAAGCACATTTTTTTTTTCCTcc                                       >  2:633909/1‑89 (MQ=255)
                       tgtTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGTCCAGAAAAAGCGACATGCACATTTTATTTTCCCTCATc                                     <  2:400653/90‑1 (MQ=255)
                               cTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCCGAAAAAAAGAAAAGCACATTTTTTTTTTTCTCCTCttttttta                             >  1:370158/1‑88 (MQ=255)
                                tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGTCCCGAAAAAACGACATGCACATTTTTTTTTTCCTCCTCtttttttaa                            >  2:191506/1‑87 (MQ=255)
                                tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCCGAAAAAAAGAAAAGCACATTTTTTTTTTTCTCCTCtttttttaa                            >  1:314225/1‑87 (MQ=255)
                                tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCCGAAAAAAAGAAAAGCACAATTTTTTTTTCCTCCTCtttttttaa                            >  1:33656/1‑87 (MQ=255)
                                tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCAGAAAAAACGGAAAGGACATTTTTTTTTTCCTCCTCtttttttaa                            >  2:23617/1‑87 (MQ=255)
                                tttGCTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGTCCAGAAAAAACGACAAGCACATTTTTTTTTTCCTCATCTGtttttaa                            >  2:159890/1‑87 (MQ=255)
                                       taCAACAGTAAATAATAAAAATTTCTCGAGGCGGGTCCAGAAAAAGCGACATGCACATTTTATTTTCCCTCATCTGTTTTAAGATGCGaa                     <  2:136957/90‑1 (MQ=255)
                                             aGTAAATAATAAAAATTTCTCGAGGCGGGGCCAGAAAAAACGACATGCACATTTTTTTTTTCCTCCTCTTTTTTTAGATGCGGAAAATGa               >  2:161596/1‑90 (MQ=255)
                                                aaaTAATAAAAATTTCTCGAGGCGGGGCCAGAAAAAAAGACAAGCACATTTTTTTTTTCCCCCTCTTTTTTTAAATGCGAAAAAAGaaaa            >  2:321598/1‑89 (MQ=255)
                                                     ataaAAATTTCTCGAGGCGGGTCCCGAAAAAACGACATGCACATTTTTTTTTTCCTCATCTTTTTTTAAATGGGAAAAAAAAAAATCAAc       >  2:935683/1‑90 (MQ=255)
                                                          aaTTTCTCGAGGCGGGTCCAGAAAAAGCGACATGCACATTTTATTTTCCCTCATCTGTTTTAAGATGCGAAACATGAAATTCAACggagg  <  1:1009811/90‑1 (MQ=255)
                                                                                    |                                                               
AAAATGGCTCAGGTAGTGGATGGTGTTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGTCCAGAAAAAGCGACATGCACATTTTATTTTCCCTCATCTGTTTTAAGATGCGAAACATGAAATTCAACGGAGG  >  NZ_CP009273/2380257‑2380404

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A