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 F169 I1 R1 62 44.4 970160 98.1% 951726 147.0

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% 69.2 / NA 21L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (6/15);  total (6/15)

TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAA  >  USA300TCH1516_ALE/1513796‑1514041
                                                                                                                                       |                                                                                                               
ttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGat                                                                                                    <  4:408426/148‑1 (MQ=255)
  ttttGTATGTATCGCTTTATGAGTAGCCATTGGCAGGGGGTTTGTCTCTTAGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatta                                                                                                  <  4:368255/147‑1 (MQ=255)
         tgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGc                                                                                           >  3:364720/1‑148 (MQ=255)
           tatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                         <  3:218558/148‑1 (MQ=255)
           tatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                         <  3:310206/148‑1 (MQ=255)
                 tttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGAATACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTAttt                                                                                   <  4:388337/148‑1 (MQ=255)
                          agCCCTTAGGATGGGGTTTGGCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                 <  2:11196/141‑1 (MQ=255)
                          agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                          <  3:25385/148‑1 (MQ=255)
                          agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                          <  3:25386/148‑1 (MQ=255)
                          agCCATTGGCATGGGATTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                          <  3:344846/148‑1 (MQ=255)
                           gCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                          >  3:174672/1‑148 (MQ=255)
                              aTTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                      <  4:147448/148‑1 (MQ=255)
                                                    ggATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTGTCCTTGTATTTATAATTGAAtt                                                <  4:67127/148‑1 (MQ=255)
                                                    ggATAAAGCGTACAAAAAATACTGCAATAAAAGTACAACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                <  4:103705/148‑1 (MQ=255)
                                                    ggATAAAAAATACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                <  4:353049/148‑1 (MQ=255)
                                                             gTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtata                                       >  4:155656/1‑148 (MQ=255)
                                                             gTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtata                                       >  3:131372/1‑148 (MQ=255)
                                                                               tAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                     <  4:283910/148‑1 (MQ=255)
                                                                                    gTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAAc                <  3:385685/148‑1 (MQ=255)
                                                                                                 t‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTa   >  3:73342/1‑148 (MQ=255)
                                                                                                   aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa  >  4:75787/1‑148 (MQ=255)
                                                                                                                                       |                                                                                                               
TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAA  >  USA300TCH1516_ALE/1513796‑1514041

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A