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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 310,164 C→T 47.5% L903L (CTG→CTA)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE310,1640CT47.5% ‑0.0 / 31.4 40L903L (CTG→CTA) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (17/4);  new base T (5/14);  total (22/18)
Fisher's exact test for biased strand distribution p-value = 1.16e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01

TCATTGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGAATCGACCAGCTCTCGTACAGCGCCGCCA  >  minE/310102‑310210
                                                              |                                              
tCATTGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATa                                          >  1:1238437/1‑69 (MQ=255)
tCATTGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATa                                          >  1:559166/1‑69 (MQ=255)
tCATTGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATa                                          >  1:3158245/1‑69 (MQ=255)
tCATTGGTCAGGCCACGGAAGGTGGCAGC‑‑‑CAACGCACCGATAACCCCCAGCGGAACGACCAGCATaa                                         >  1:967860/1‑67 (MQ=37)
   ttGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:3206244/69‑1 (MQ=255)
    tGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:1168322/68‑1 (MQ=255)
    tGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:679186/68‑1 (MQ=255)
    tGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:673985/68‑1 (MQ=255)
    tGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:3203777/68‑1 (MQ=255)
    tGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:3051728/68‑1 (MQ=255)
    tGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:3027354/68‑1 (MQ=255)
    tGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:295080/68‑1 (MQ=255)
    tGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:2719557/68‑1 (MQ=255)
    tGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:1506616/68‑1 (MQ=255)
    tGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:198675/68‑1 (MQ=255)
    tGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:2149644/68‑1 (MQ=255)
     ggTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:171404/67‑1 (MQ=255)
     ggTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACgg                                      >  1:683741/1‑68 (MQ=255)
       tCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACg                                       <  1:3074968/65‑1 (MQ=255)
        cAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGaa                                  >  1:2464692/1‑69 (MQ=255)
        cAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGaa                                  >  1:90525/1‑69 (MQ=255)
        cAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGaa                                  >  1:904266/1‑69 (MQ=255)
        cAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGaa                                  >  1:2055742/1‑69 (MQ=255)
           gCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACGGAGAACgg                               >  1:3232436/1‑69 (MQ=255)
           gCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACGGAGAACgg                               >  1:3331191/1‑69 (MQ=255)
           gCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACGGAGAACgg                               >  1:1219060/1‑69 (MQ=255)
           gCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACTAGCATAACGGAGAACgg                               >  1:1014404/1‑69 (MQ=255)
           gCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCACCAGCGGAACGACTAGCATAACGGAGAACgg                               >  1:2990478/1‑69 (MQ=255)
            ccACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGa                              >  1:1458125/1‑69 (MQ=255)
            ccACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGa                              >  1:1741860/1‑69 (MQ=255)
            ccACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGa                              <  1:2114293/69‑1 (MQ=255)
            ccACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGa                              <  1:2510255/69‑1 (MQ=255)
             cACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGa                              <  1:1799798/68‑1 (MQ=255)
                      tGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGAATCGACCAGc                    >  1:3147406/1‑69 (MQ=255)
                      tGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGAATCGACCAGc                    >  1:556363/1‑69 (MQ=255)
                       ggCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGAATCGACCAGct                   <  1:847059/69‑1 (MQ=255)
                                         gATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGAATCGACCAGCTCTCGTACAGCGCCGCCa  >  1:309231/1‑68 (MQ=255)
                                         gATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGAATCGACCAGCTCTCGTACAGCGCCGCCa  >  1:1451410/1‑68 (MQ=255)
                                         gATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGAATCGACCAGCTCTCGTACAGCGCCGCCa  >  1:2819440/1‑68 (MQ=255)
                                         gATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGAATCGACCAGCTCTCGTACAGCGCCCCCa  >  1:2244634/1‑68 (MQ=255)
                                                              |                                              
TCATTGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGAATCGACCAGCTCTCGTACAGCGCCGCCA  >  minE/310102‑310210

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A