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
A5 F18 I1 R1 9 25.9 593870 94.7% 562394 140.9

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% 32.1 / 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)

GTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTG‑AATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTT  >  USA300TCH1516_ALE/1513802‑1514062
                                                                                                                                |                                                                                                                                     
gtatgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGa                                                                                                                           >  2:88766/1‑141 (MQ=255)
        cgatttATAAATAGAAATAGGAATGGGGTTTGTCTCATGAAAAAAGCGTAAAAAAAATACTGCAATAAAAGTAAAAAAAAAAAAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAAt                                                                                                                   <  2:142077/138‑1 (MQ=255)
            ttattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                                               >  2:139874/1‑141 (MQ=255)
                tagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                                           >  1:171640/1‑141 (MQ=255)
                    agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                                       >  2:35076/1‑141 (MQ=255)
                               aggggTTTGAGTCGTAGATAAAGCGTACAAAAAAGACTTCTAACACCCTGCGAGATTGCGTAAAAAAACCAGCATTTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                            <  2:104417/140‑1 (MQ=255)
                                                     gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTG‑AAtt                                                                     >  1:2266/1‑141 (MQ=255)
                                                              aaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATATGTCAAAGATGATTATCTCTTATGCTTGTATTTATAATTG‑AATTAATATtata                                                            >  1:216166/1‑141 (MQ=255)
                                                                                                            atatCACACATAATATGTTTTATTGTATTAGGATTATTAATGGCATTATTTGGATTATCACTTATCCTTGTATTTATAATTG‑AATTAATATTATATATTATAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGaa              <  2:50786/141‑1 (MQ=255)
                                                                                                                       aataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTG‑AATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAtt   >  2:196143/1‑141 (MQ=255)
                                                                                                                       aataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTG‑AATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAtt   >  2:226736/1‑141 (MQ=255)
                                                                                                                        atatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTA‑AGCTCATCGCAAGTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAttt  <  1:139874/141‑1 (MQ=255)
                                                                                                                                |                                                                                                                                     
GTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTG‑AATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTT  >  USA300TCH1516_ALE/1513802‑1514062

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A