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 2,135,716 A→T 22.4% T205T (ACT→ACA)  pnp ← polynucleotide phosphorylase/polyadenylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,135,7160AT22.4% 138.6 / 33.9 80T205T (ACT→ACA) pnppolynucleotide phosphorylase/polyadenylase
Reads supporting (aligned to +/- strand):  ref base A (32/30);  new base T (15/3);  total (47/33)
Fisher's exact test for biased strand distribution p-value = 2.77e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCCCAGCATCTGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAGTACGT  >  minE/2135651‑2135780
                                                                 |                                                                
gcgcCCAGCATCTGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGt                                                                <  1:227829/68‑1 (MQ=255)
gcgcCCAGCATCTGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGt                                                                <  1:2238992/68‑1 (MQ=255)
 cgcCCAGCATCTGGTCTTCGCGCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGt                                                                <  1:2786980/67‑1 (MQ=255)
      aGCATCTGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATAAGTACAGCGGCTTCAGTACCGGc                                                          <  1:1090809/68‑1 (MQ=255)
          tCTGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAG‑GGCTTCAGTACCGGCaacaac                                                    <  1:2101238/69‑1 (MQ=255)
           cTGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCaacaac                                                    <  1:458258/69‑1 (MQ=255)
            tGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGcaaca                                                      >  1:345902/1‑66 (MQ=255)
            tGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGcaaca                                                      >  1:568113/1‑66 (MQ=255)
            tGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGcaaca                                                      >  1:3398630/1‑66 (MQ=255)
            tGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGcaaca                                                      >  1:2224610/1‑66 (MQ=255)
            tGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGcaaca                                                      >  1:2697839/1‑66 (MQ=255)
            tGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGcaaca                                                      >  1:3056189/1‑66 (MQ=255)
            tGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGcaaca                                                      >  1:1980256/1‑66 (MQ=255)
            tGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTGCAGTACCGGcaaca                                                      >  1:2785607/1‑66 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:2779791/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:474034/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:2685172/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:2560602/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:2552519/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:2179941/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:2208102/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:1710142/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:1672569/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:2830261/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:2959204/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:3105071/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:3331035/57‑1 (MQ=255)
                          cagTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAg                                                 <  1:1223391/57‑1 (MQ=255)
                               gAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGctctct                                 >  1:1549850/1‑68 (MQ=255)
                                     cAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCt                          >  1:1056027/1‑69 (MQ=255)
                                     cAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCt                          >  1:3149275/1‑69 (MQ=255)
                                     cAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCt                          >  1:3323665/1‑69 (MQ=255)
                                     cAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCt                          >  1:2439493/1‑69 (MQ=255)
                                     cAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCt                          >  1:606833/1‑69 (MQ=255)
                                     cAGATTCAACCATCAGCGCGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                           >  1:3412704/1‑67 (MQ=255)
                                     cAGATTCAACCATCAGCACGGCAGCTTCTGTACCg                                                            >  1:2688870/1‑35 (MQ=19)
                                     cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                           >  1:733553/1‑67 (MQ=255)
                                     cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                           >  1:1869535/1‑67 (MQ=255)
                                     cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                           >  1:3053334/1‑67 (MQ=255)
                                     cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                           >  1:1533707/1‑67 (MQ=255)
                                     cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                           >  1:2049678/1‑67 (MQ=255)
                                     cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                           >  1:1221387/1‑67 (MQ=255)
                                     cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                           >  1:1480017/1‑67 (MQ=255)
                                     cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                           >  1:959368/1‑67 (MQ=255)
                                     cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                           >  1:386978/1‑67 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:3085583/1‑68 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:1461641/1‑68 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:3280371/1‑68 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:1200139/1‑68 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:156297/1‑68 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:1683121/1‑68 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:1601358/1‑68 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:584514/1‑68 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:2723163/1‑68 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:1927721/1‑68 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:2089714/1‑68 (MQ=255)
                                          tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                      >  1:1025391/1‑68 (MQ=255)
                                                     tACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCggg            >  1:2489553/1‑67 (MQ=255)
                                                     tACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCggg            >  1:1402851/1‑67 (MQ=255)
                                                     tACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGATTGCTCTCTTTCAGCTCGTCCTGAGTCgg             >  1:2985779/1‑66 (MQ=255)
                                                      aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc         <  1:509243/69‑1 (MQ=255)
                                                      aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc         <  1:353479/69‑1 (MQ=255)
                                                      aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc         <  1:1380444/69‑1 (MQ=255)
                                                      aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc         <  1:2602134/69‑1 (MQ=255)
                                                      aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc         <  1:2133808/69‑1 (MQ=255)
                                                      aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc         <  1:2510639/69‑1 (MQ=255)
                                                       cAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGtt          >  1:609463/1‑67 (MQ=255)
                                                       cAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc         >  1:2996831/1‑68 (MQ=255)
                                                       cAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc         >  1:2253520/1‑68 (MQ=255)
                                                         gcagCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAg       <  1:2853806/65‑1 (MQ=255)
                                                         gcagCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAg       <  1:1610732/65‑1 (MQ=255)
                                                          cagCTTCTGTACCCGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAg       <  1:1189672/65‑1 (MQ=255)
                                                           agCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCg              >  1:247428/2‑59 (MQ=255)
                                                           agCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAgta     >  1:2452657/2‑68 (MQ=255)
                                                           agCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAgta     >  1:639637/2‑68 (MQ=255)
                                                           agCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAgta     >  1:2486931/2‑68 (MQ=255)
                                                            gCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAgtacg   <  1:1070261/69‑1 (MQ=255)
                                                            gCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAgtacg   <  1:998097/69‑1 (MQ=255)
                                                             cTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAgtacgt  <  1:1347906/69‑1 (MQ=255)
                                                             cTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAgtacgt  <  1:978676/69‑1 (MQ=255)
                                                                 |                                                                
GCGCCCAGCATCTGGTCTTCGCTCAGCAGTTGAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAGTACGT  >  minE/2135651‑2135780

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