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 2,004,062 (A)8→7 intergenic (‑2285/+99) USA300TCH1516_01884 ← / ← perR tRNA‑Ile/Peroxide‑responsive repressor PerR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,004,0550A.100.0% 152.0 / NA 33intergenic (‑2278/+106)USA300TCH1516_01884/perRtRNA‑Ile/Peroxide‑responsive repressor PerR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (22/11);  total (22/11)

TCACTTTATGGATAGTTATTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCATAAAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCATTCTTTACAAACTCCATA  >  USA300TCH1516_ALE/2003914‑2004193
                                                                                                                                             |                                                                                                                                          
tCACTTTATGTATAGTTATTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCATaaaaaaa                                                                                                                                      <  4:347502/148‑1 (MQ=255)
                tATTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCAt                                                                                                                     >  3:238579/1‑148 (MQ=255)
                tATTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCAt                                                                                                                     >  3:108446/1‑148 (MQ=255)
                 aTTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATg                                                                                                                    >  4:54575/1‑148 (MQ=255)
                       tagACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCAt                                                                                                                     >  2:61676/1‑141 (MQ=255)
                        agACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATCTTCTTTTCTTCACTTTAAATATTTNTCAGAATAAGCAT‑CAACAAAGTTAAACAAATTCCacg                                                                                                                    >  2:48688/1‑139 (MQ=255)
                            cTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAActt                                                                                                         >  3:22552/1‑148 (MQ=255)
                                gTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTa                                                                                                     <  4:238525/148‑1 (MQ=255)
                                     aaTATTTTTATGTTTACTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAatat                                                                                                <  4:16808/148‑1 (MQ=255)
                                            ttATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAatat                                                                                                <  2:36379/141‑1 (MQ=255)
                                            ttATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGctt                                                                                         <  4:225379/148‑1 (MQ=255)
                                            ttATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGctt                                                                                         <  4:190042/148‑1 (MQ=255)
                                                   tatttatAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTtata                                                                                  >  3:69500/1‑148 (MQ=255)
                                                        ataAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGcttactta                                                                                    <  1:52963/141‑1 (MQ=255)
                                                         taAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTtat                                                                                   >  2:35790/1‑141 (MQ=255)
                                                                          taGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTa                                                           >  4:321946/1‑148 (MQ=255)
                                                                           aGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTaa                                                          <  4:267480/148‑1 (MQ=255)
                                                                              tAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAAttt                                                       >  4:289974/1‑148 (MQ=255)
                                                                              tAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAAttt                                                       >  4:260777/1‑148 (MQ=255)
                                                                              tAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAAttt                                                       >  3:132705/1‑148 (MQ=255)
                                                                                  aCCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCa                                                   >  3:9634/1‑148 (MQ=255)
                                                                                   ccACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCAt                                                  >  3:354165/1‑148 (MQ=255)
                                                                                         ccGTAGTTAGAATATTCTTTTCTTCAATTTACATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCa                                                   >  1:43649/1‑141 (MQ=255)
                                                                                         ccGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCa                                                   >  1:18285/1‑141 (MQ=255)
                                                                                                        tcttttcttCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAAttattt                             <  3:387803/148‑1 (MQ=255)
                                                                                                         cttttcttCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAAttatttt                            >  4:203281/1‑147 (MQ=255)
                                                                                                         cttttcttCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTGTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAAttattta                            >  4:246810/1‑148 (MQ=255)
                                                                                                          ttttcttCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAAttatttat                           <  4:22552/148‑1 (MQ=255)
                                                                                                                 cAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCa                    >  3:354386/1‑148 (MQ=255)
                                                                                                                      tAAATATTTTTCAGAATAAGCNT‑NAAANAAGTTAAACAACCTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAACTATTTATCTTgg                      <  1:48688/141‑1 (MQ=255)
                                                                                                                      tAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCATTCtt               <  3:54575/148‑1 (MQ=255)
                                                                                                                        aaTATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACATCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATAATTTATCTTGGCa                    >  1:3285/1‑141 (MQ=255)
                                                                                                                              tttCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAACTTATTTATCTTGGCATTCttt              <  1:35790/141‑1 (MQ=255)
                                                                                                                                   gAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCATTCTTTACAAACTCCATa  >  4:76021/1‑148 (MQ=255)
                                                                                                                                   gAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCATTCTTTACAAACTCCATa  >  4:84022/1‑148 (MQ=255)
                                                                                                                                             |                                                                                                                                          
TCACTTTATGGATAGTTATTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCATAAAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCATTCTTTACAAACTCCATA  >  USA300TCH1516_ALE/2003914‑2004193

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

GATK/CNVnator alignment

N/A