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
A19 F74 I1 R1 13 68.8 1581882 91.8% 1452167 133.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
JC CP000730 62,818 +CAATTT intergenic (+83/+228) USA300HOU_0056 → / ← speG hypothetical protein/diamine N‑acetyltransferase

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 = 628170 (0.000)44 (0.690)
+TCAATT		 35/252 1.1 100% intergenic (+82/+229) USA300HOU_0056/speG hypothetical protein/diamine N‑acetyltransferase
?CP000730 62818 = 0 (0.000)intergenic (+83/+228) USA300HOU_0056/speG hypothetical protein/diamine N‑acetyltransferase

AATAGAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000730/62681‑62817
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTAT  >  CP000730/62818‑62949
                                                                                                                                         ||||||                                                                                                                                    
AATAGAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAA                                                                                                                                        <  2:80486/141‑1
    GAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTA                                                                                                                                    >  2:420462/1‑141
    GAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTA                                                                                                                                    >  2:622676/1‑141
         ATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTT                                                                                                                               <  2:335176/141‑1
               ACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAA                                                                                                                         >  2:749294/1‑141
                            GGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCT                                                                                                            <  1:58493/141‑1
                            GGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCT                                                                                                            <  1:258959/141‑1
                            GGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTC                                                                                                                                          <  1:528417/111‑1
                            GGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTC                                                                                                                                          >  2:528417/1‑111
                             acaTACCACAAATAATGTTTGTGTAATTCTGATTACGTCCTATTAAGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCTAAGTGAAGGATGCTCTCAATTAATTTTTCTTGAAATTAATATAAGCTT                                                                                                           <  2:314112/138‑1
                              CTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTC                                                                                                          >  1:200261/1‑141
                               TTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCA                                                                                                         >  2:433609/1‑141
                               TTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCA                                                                                                         >  2:433621/1‑141
                                     CAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGA                                                                                                   <  1:458559/141‑1
                                         AAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGA                                                                                               <  1:392375/141‑1
                                            TGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAG                                                                                            >  2:622722/1‑141
                                                 GTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATT                                                                                       >  1:60232/1‑141
                                                   GTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTTAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAA                                                                                     <  1:48299/141‑1
                                                       TTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAA                                                                                     <  2:199823/137‑1
                                                       TTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAA                                                                                     >  1:199823/1‑137
                                                                CGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTTAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTTATAGATAGTCATTAATAATTGTTTGCAA                                                                        <  2:752311/141‑1
                                                                   CCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATC                                                                     >  2:388781/1‑141
                                                                    CTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCG                                                                    >  1:14834/1‑141
                                                                       TTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTA                                                                 >  1:241080/1‑141
                                                                            TTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAG                                                            <  1:696659/141‑1
                                                                            TTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGAGAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAG                                                            <  1:420462/141‑1
                                                                              AATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTA                                                          <  1:433621/141‑1
                                                                              AATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTA                                                          <  1:433609/141‑1
                                                                               ATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTAC                                                         >  2:330508/1‑141
                                                                                     AATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGT                                                   >  2:719410/1‑141
                                                                                         GACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACA                                               <  2:669438/141‑1
                                                                                           CAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGC                                             >  2:359711/1‑141
                                                                                              AAATAAATTGAGAGCATCCTTCACTTTGCGGTAAGAGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTC                                          >  2:333123/1‑141
                                                                                                 TAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATC                                       <  2:60232/141‑1
                                                                                                     TTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTC                                   >  2:99454/1‑141
                                                                                                     TTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTC                                   >  1:152970/1‑141
                                                                                                       GAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCAT                                 <  2:200261/141‑1
                                                                                                            CATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAAT                            <  2:152970/141‑1
                                                                                                                 CTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCG                       >  2:747507/1‑141
                                                                                                                     CCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCtacgagga                   <  1:112055/141‑9
                                                                                                                     CCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGA                   >  1:243131/1‑141
                                                                                                                        CAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATACAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCtacgaggattt                <  1:622676/141‑12
                                                                                                                              GAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCACATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAA          >  2:422759/1‑141
                                                                                                                               AAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAG         >  1:784378/1‑141
                                                                                                                                 GGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCA                                                                                                         >  1:727653/1‑43
                                                                                                                                 GGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCA                                                                                                         <  2:727653/43‑1
                                                                                                                                      CTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATAGTTTGCAAATCGTTTTTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCCTGTAGATTATATCAAtcctttat  >  1:201755/1‑133
                                                                                                                                         ||||||                                                                                                                                    
AATAGAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000730/62681‑62817
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTAT  >  CP000730/62818‑62949

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A