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
A42 F60 I1 R1 20 78.9 2679734 98.6% 2642217 138.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,396,152 G→C S26T (AGT→ACT)  insH‑4 → IS5 transposase and trans‑activator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,396,1520GC100.0% 19.3 / NA 8S26T (AGT→ACT) insH‑4IS5 transposase and trans‑activator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (6/2);  total (6/2)

GGAAGGAAGTAGCAACATTAGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAG  >  NC_000913/1396019‑1396177
                                                                                                                                     |                         
ggaaggaaGTAGCAACATTAGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCACTAAgcg                     >  1:1022317/1‑140 (MQ=255)
ggaaggaaGTAGCAACATTAGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCACTAAgcg                     >  1:67853/1‑140 (MQ=255)
ggaaggaaGTAGCAACATTAGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCACTAAgcg                     >  2:303181/1‑140 (MQ=255)
          aGCAACATTAGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCACTAAGCGCCGTCAGAcc           >  2:127472/1‑140 (MQ=38)
          aGCAACATTAGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCACTAAGCGCCGTCAGAcc           >  2:954602/1‑140 (MQ=38)
               cATTAGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCACTAAGCGCCGTCAGACCCGaaa      <  2:1022317/140‑1 (MQ=16)
               cATTAGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCACTAAGCGCCGTCAGACCCGaaa      <  2:21218/140‑1 (MQ=16)
                   aGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCACTAAGCGCCGTCAGACCCGAAAagag  >  2:605644/1‑140 (MQ=11)
                                                                                                                                     |                         
GGAAGGAAGTAGCAACATTAGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAG  >  NC_000913/1396019‑1396177

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A