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 F41 I1 R1 11 26.2 606442 94.9% 575513 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,028,191 C→A A152S (GCA→TCA)  USA300HOU_RS10230 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,028,1910CA100.0% 61.5 / NA 20A152S (GCA→TCA) USA300HOU_RS10230hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (17/3);  total (17/3)

CACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATA  >  USA300TCH1516_ALE/2028069‑2028321
                                                                                                                          |                                                                                                                                  
caCGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCaaa                                                                                                                  >  1:2586/1‑140 (MQ=255)
                tAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAAtt                                                                                                  >  1:135486/1‑141 (MQ=255)
                tAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCGGCACTTTACCTAAAATGTGTCTAACAACAATGGTATAATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATGTTTAGGCAGCGAAtt                                                                                                  >  2:176471/1‑141 (MQ=255)
                  aaaaGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAAGATGTAGGTCCCCAGTTct                                                                                                >  1:218847/1‑140 (MQ=255)
                    aaGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCACTATGTAGGTCGCCAATTCCAt                                                                                              >  1:133491/1‑141 (MQ=255)
                                       aaTATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCAAATTCCATGTTGAATTTGTCCATATTc                                                                           >  1:148525/1‑141 (MQ=255)
                                         tatTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTccc                                                                         >  1:105613/1‑141 (MQ=255)
                                          atTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCa                                                                        >  2:236473/1‑141 (MQ=255)
                                            tGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCACACt                                                                      >  2:206405/1‑141 (MQ=255)
                                             gTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACtt                                                                     >  2:148585/1‑141 (MQ=255)
                                              tAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTta                                                                    >  2:72238/1‑141 (MQ=255)
                                                    aCCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACa                                                              >  1:44586/1‑141 (MQ=255)
                                                     ccGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACaa                                                             >  2:258217/1‑140 (MQ=255)
                                                               aaCCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGgtgt                                                   >  1:170160/1‑141 (MQ=255)
                                                                                                   tgTATTATTTTACTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGa               <  1:73780/140‑1 (MQ=255)
                                                                                                         attTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGa         <  2:210989/141‑1 (MQ=255)
                                                                                                         attTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGAAAAATAAAGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGa         >  1:235289/1‑141 (MQ=255)
                                                                                                             tCCTTACTATTTGAATCTTTTGTTAAGTCCCACTCTCTTTCGCTATTTCCATGTTCAATTTGTACATCTTCCCACTTATATACATAATCTCGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTc     <  2:148525/141‑1 (MQ=255)
                                                                                                                ttAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGCTGGTGAAGTCATa  >  2:225511/1‑141 (MQ=255)
                                                                                                                ttAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTCTTTAATAAAAGATGTTTAAGTCCTa  >  2:201308/1‑141 (MQ=255)
                                                                                                                          |                                                                                                                                  
CACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATA  >  USA300TCH1516_ALE/2028069‑2028321

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A