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 F42 I1 R1 13 27.6 610674 98.5% 601513 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 1,891,750 G→A T53M (ACG→ATG)  rot ← HTH‑type transcriptional regulator rot

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,891,7500GA100.0% 92.7 / NA 27T53M (ACG→ATG) rotHTH‑type transcriptional regulator rot
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (15/12);  total (15/12)

TTGAAATGAATAATAACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCGTCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTG  >  USA300TCH1516_ALE/1891615‑1891887
                                                                                                                                       |                                                                                                                                         
ttGAAATGAATAATAACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATa                                                                                                                                      <  2:161182/141‑1 (MQ=255)
   aaaTGAATAATAACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGaa                                                                                                                                   >  1:289198/1‑141 (MQ=255)
   aaaTGAATAATAACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCATTAAGCATCATAGaa                                                                                                                                   >  1:253377/1‑141 (MQ=255)
         ataataACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTACTTCAGCTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCtttt                                                                                                                             <  1:295224/141‑1 (MQ=255)
                   ttCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAg                                                                                                                   <  1:143225/141‑1 (MQ=255)
                                 aCAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTTACTTCAACAAATCTGTCCATTTCTTTAATCATCATAGAACCTTTTTGCCATAAAGTTAGtaaaattaaa                                                                                                     >  1:136322/1‑141 (MQ=255)
                                 aCAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGtaaaattaaa                                                                                                     >  1:118210/1‑141 (MQ=255)
                                 aCAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGtaaaattaaa                                                                                                     >  1:156377/1‑141 (MQ=255)
                                 aCAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGtaaaattaaa                                                                                                     >  1:103049/1‑141 (MQ=255)
                                       cGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAACGCTATTAAAATTAAAATttct                                                                                               >  1:2512/1‑141 (MQ=255)
                                       cGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATttct                                                                                               >  1:57719/1‑141 (MQ=255)
                                             ttGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTa                                                                                         <  1:254279/141‑1 (MQ=255)
                                             ttGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTa                                                                                         <  1:305028/141‑1 (MQ=255)
                                                        ttCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTa                                                                              <  2:124838/141‑1 (MQ=255)
                                                                 aaCTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTc                                                                     <  2:124298/141‑1 (MQ=255)
                                                                          attatACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCt                                                            <  2:77788/141‑1 (MQ=255)
                                                                          attatACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCt                                                            <  2:98304/141‑1 (MQ=255)
                                                                                        tACGCTTATACGGTTTAACTTCACTAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTACAATTTCTTCTCCTGACATTTTGTCTTCGCTTTCAATCTCGCTGAAAATTGAGTTaa                                              <  2:257931/141‑1 (MQ=255)
                                                                                        tACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTaa                                              <  2:25023/141‑1 (MQ=255)
                                                                                          cGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATg                                            >  2:255528/1‑141 (MQ=255)
                                                                                                     tttAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAg                                 <  2:73217/141‑1 (MQ=255)
                                                                                                         aCTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGtt                             >  1:235148/1‑141 (MQ=255)
                                                                                                         aCTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGtt                             >  1:63741/1‑141 (MQ=255)
                                                                                                         aCTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGtt                             >  1:225685/1‑141 (MQ=255)
                                                                                                         aCTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGtt                             >  2:170482/1‑141 (MQ=255)
                                                                                                                          cATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTcc            >  2:302711/1‑141 (MQ=255)
                                                                                                                                    aGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAgtg  >  1:58456/1‑141 (MQ=255)
                                                                                                                                       |                                                                                                                                         
TTGAAATGAATAATAACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCGTCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTG  >  USA300TCH1516_ALE/1891615‑1891887

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: ‑

GATK/CNVnator alignment

N/A