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
A7 F67 I1 R1 28 23.6 502806 98.6% 495766 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,236,856 A→T L303I (TTA→ATA)  rho ← Transcription termination factor Rho

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,236,8560AT100.0% 50.7 / NA 20L303I (TTA→ATA) rhoTranscription termination factor Rho
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (8/12);  total (8/12)

TCCTTTAAATTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTAAAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAATTTCTACTAAACGCTTTG  >  USA300TCH1516_ALE/2236725‑2236987
                                                                                                                                   |                                                                                                                                   
tCCTTTAAATTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAgg                                                                                                                            >  1:391710/1‑141 (MQ=255)
       aaTTCTTCGGAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTaaa                                                                                                                     <  1:464520/141‑1 (MQ=255)
          tcttcCTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAacca                                                                                                                  <  1:396432/141‑1 (MQ=255)
                              cATCCGTGAACCCGTATCAACTAATGCAGTTGCAAGTATCGTTAAACTTCCACCCGCCTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACt                                                                                              <  1:332911/141‑1 (MQ=255)
                                  cGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTtggt                                                                                          >  1:385514/1‑141 (MQ=255)
                                       aCCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAAt                                                                                     <  1:167798/141‑1 (MQ=255)
                                       aCCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAAt                                                                                     <  1:183996/141‑1 (MQ=255)
                                           gTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGGATAACt                                                                                 >  1:2159/1‑141 (MQ=255)
                                                   tAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTtata                                                                         <  1:68227/141‑1 (MQ=255)
                                                           ttGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTg                                                                 <  1:476895/141‑1 (MQ=255)
                                                           ttGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTg                                                                 <  1:245604/141‑1 (MQ=255)
                                                              cAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGAGTATAGATGCAGGATCTAAACCCATTGTAAATTTACTTTGAAATGGAGGAATAAGTAAGTTATAAACGCGGGCTa                                                              >  1:235604/1‑141 (MQ=255)
                                                                          aaCTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAg                                                  >  1:193984/1‑141 (MQ=255)
                                                                               ccACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTGATCTCGTTATAGAATcg                                             >  1:145211/1‑140 (MQ=255)
                                                                                   ccGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTa                                         >  1:152441/1‑141 (MQ=255)
                                                                                        tCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTATGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGAGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGATATAGAATCCATTAAaata                                    <  1:325346/141‑1 (MQ=255)
                                                                                         cAATATTTCTCGCTGCACCGAAGAATGCTTTTCGTTTGTGTATAGATGCAGGATCTAAACCAGCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAaataa                                   >  1:359287/1‑141 (MQ=255)
                                                                                                      tGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTcccc                      <  1:12475/141‑1 (MQ=255)
                                                                                                                   gCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAATTTCTACTaaa         <  1:277148/141‑1 (MQ=255)
                                                                                                                          gTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAATTTCTACTAAACGCTTTg  <  1:216264/141‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                   
TCCTTTAAATTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTAAAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAATTTCTACTAAACGCTTTG  >  USA300TCH1516_ALE/2236725‑2236987

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A