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 I198 R1 96 36.2 2313912 84.6% 1957569 85.2

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_CP0092732,380,3410GA75.0% 11.8 / 6.1 16intergenic (+31/‑72)yfbL/yfbMM28 family metallopeptidase/YfbM family protein
Reads supporting (aligned to +/- strand):  ref base G (0/4);  new base A (12/0);  total (12/4)
Fisher's exact test for biased strand distribution p-value = 5.49e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.48e-03

GTGGATGGTGTTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGTCCAGAAAAAGCGACATGCACATTTTATTTTCCCTCATCTGTTTTAAGATGCGAAACATGAAATTCAACGGAGGAAAAATAAATGGGAA  >  NZ_CP009273/2380272‑2380419
                                                                     |                                                                              
gTGGATGGTGTTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGTCCCGAAAAAAAGACAAGCACattttttttt                                                            >  1:467095/1‑90 (MQ=255)
        tgtTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGTCCAGAAAAAGCGACATGCACATTTTATTTTCCCTCATc                                                    <  1:536517/90‑1 (MQ=255)
                 tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGTCAGAAAAAACAACAAGCACAATTTATTTTTTCTCCTCtttttttat                                           >  2:304761/1‑87 (MQ=255)
                 tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGTCAGAAAAAAAGAAAAGAAAAATTTATTTTTTCTCCTCtttttttaa                                           >  2:1068455/1‑87 (MQ=255)
                 tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCCGAAAAAAATACAAGTACTTTTTATTTTTCCCCATCACtttttaa                                           >  1:292137/1‑87 (MQ=255)
                 tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCCGAAAAAAAGACAAGCACAATTTTTTTTTCCCCCTCTGtttttaa                                           >  1:681854/1‑87 (MQ=255)
                 tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCCAAAAAAAAGAAAAGCACAATTTTTTTTTCCTCCTCTTTTTTaaa                                           >  1:822339/1‑89 (MQ=255)
                 tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCAGAAAAAACGACAAGCACATTTTTTTTTTTCTCCTCtttttttat                                           >  1:946798/1‑87 (MQ=255)
                 tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCAGAAAAAAAGAAAAGCACATTTTTTTTTTTCTCATCTGtttttaa                                           >  2:656584/1‑87 (MQ=255)
                 tttGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGGCCAGAAAAAAAGAAAAGCACAATTTTTTTTTTCTCTTCTGtttttaa                                           >  2:173481/1‑87 (MQ=255)
                            acaGTAAATAATAAAAATTTCTCGAGGCGGGTCCCGAAAAAAAGACAAGCACAATTTTTTTTTCCCCATTTTTTTTTAAATGCGgaaaaa                                >  1:1030920/1‑87 (MQ=255)
                            acaGTAAATAATAAAAATTTCTCGAGGCGGGTCCAGAAAAAGCGACATGCACATTTTATTTTCCCTCATCTGTTTTAAGATGCGAAACAt                                <  2:56293/90‑1 (MQ=255)
                               gTAAATAATAAAAATTTCTCGAGGCGGGTCCAGAAAAAACGACATGCACATTTTTTTTTTCCTCCTCTGTTTTTAAATGGGAAAAAAGaa                             >  1:231106/1‑90 (MQ=255)
                                      ataaAAATTTCTCGAGGCGGGGCCAGAAAAAAAGACATGCACATTTTATTTTTCCCCATCTGTTTTTAAATGCGAAAAAAGAAAATCAAc                      >  1:56293/1‑90 (MQ=255)
                                                     ggCGGGTCCAGAAAAAGCGACATGCACATTTTATTTTCCCTCATCTGTTTTAAGATGCGAAACATGAAATTCAACGGAGGAAaaataaat       <  1:304761/90‑1 (MQ=255)
                                                          gTCCAGAAAAAGCGACATGCACATTTTATTTTCCCTCATCTGTTTTAAGATGCGAAACATGAAATTCAACGGAGGAAAAATAAATGGGaa  <  2:681854/90‑1 (MQ=255)
                                                                     |                                                                              
GTGGATGGTGTTATAACTTTGTTATACAACAGTAAATAATAAAAATTTCTCGAGGCGGGTCCAGAAAAAGCGACATGCACATTTTATTTTCCCTCATCTGTTTTAAGATGCGAAACATGAAATTCAACGGAGGAAAAATAAATGGGAA  >  NZ_CP009273/2380272‑2380419

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A