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 F16 I1 R1 9 28.1 657842 93.6% 615740 139.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 1,513,930 A→T L413F (TTA→TTT)  USA300HOU_RS07375 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,513,9300AT100.0% 27.5 / NA 12L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (8/4);  total (8/4)

TTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  USA300TCH1516_ALE/1513814‑1514065
                                                                                                                    |                                                                                                                                       
ttagtaGTAGCCATTGTCATGGGGTTTGTCTATTGGATAAAGCGTAAAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                                  <  2:11194/140‑1 (MQ=255)
    tagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTATTGCTatta                                                                                                              >  2:113726/1‑140 (MQ=255)
        agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                          >  2:188767/1‑140 (MQ=255)
        agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATACCATTATTTg                                                                                                          >  1:150993/1‑140 (MQ=255)
                   tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTATGATTATTAATAACATTAATTGGATTATCACtt                                                                                               >  1:2596/1‑140 (MQ=255)
                                       aaGCGTACAAAAAATACTGCAATAAAAGTTCTACATCGCGTAAAAAAACCAGCATCTATATTTCTTATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATCTATAATTGa                                                                           <  1:15214/140‑1 (MQ=255)
                                              cAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAata                                                                    <  2:213181/140‑1 (MQ=255)
                                                        tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTCTATCACTCATAATATGTTTTATTGTATTAAGATTATTAATACAATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                          >  1:124502/1‑140 (MQ=255)
                                                                 aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTTTATTTATAATTGAATTAATATTATATATTAAATAtcttc                                                 >  2:241626/1‑140 (MQ=255)
                                                                      cacaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCt                                            >  1:20353/1‑140 (MQ=255)
                                                                                         aGCATCTATATCACTCATAATATGTTTTATTTTATTAGGATTATTAATGCCATTATTTGGATCATTACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAATCAATAATGCACTTaaa                         <  2:225625/140‑1 (MQ=255)
                                                                                                                gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGACATTTACa  >  1:130835/1‑140 (MQ=255)
                                                                                                                    |                                                                                                                                       
TTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  USA300TCH1516_ALE/1513814‑1514065

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A