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 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 405,935 T→G 36.4% Q118P (CAG→CCG)  ybeA ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE405,9350TG36.4% 1.5 / 25.9 22Q118P (CAG→CCG) ybeAconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (9/5);  new base G (6/2);  total (15/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

GACTCTCTGCGACCAGCACGCGAACCAGCGGATGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGC  >  minE/405870‑406001
                                                                 |                                                                  
gACTCTCTGCGACCAGCACGCGAACCAGCGGATGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCt                                                                 >  1:2242945/1‑69 (MQ=255)
            ccAGCACGCGAACCAGCGGATGGGGGAGGGTAAGCCCCGACAGCGACCAGCTCGGCTCAGCCGCCGCTTTa                                                   <  1:3116815/71‑1 (MQ=255)
              aGCACGCGAACCAGCGGATGGTGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTa                                                   >  1:3876984/1‑69 (MQ=255)
               gCACGCGAACCAGCGGATGGGGGAGGGTAAGCGCCGACAGAGACCAGCTCTGCTCAGCCGCCGCTTTAcag                                                >  1:1513961/1‑71 (MQ=255)
                              gATGGGTGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCt                                 <  1:372281/71‑1 (MQ=255)
                                tGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCtt                                >  1:4064500/1‑70 (MQ=255)
                                tGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCtt                                >  1:2378948/1‑70 (MQ=255)
                                tGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCtt                                >  1:2595762/1‑70 (MQ=255)
                                  ggggAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAg                             >  1:3824203/1‑71 (MQ=255)
                                  ggggAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAg                             >  1:2642460/1‑71 (MQ=255)
                                        ggTAAGCGCCGACAGCGACCAGCTCGGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGc                       >  1:3734960/1‑71 (MQ=255)
                                           aaGCGCCGACAGCGACCAGCTCGGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCaa                    >  1:1327752/1‑71 (MQ=255)
                                           aaGCGCCGACAGCGACCAGCTCGGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCaa                    >  1:3225300/1‑71 (MQ=255)
                                                ccGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAg                <  1:999914/70‑1 (MQ=255)
                                                 cGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTa              <  1:3707298/71‑1 (MQ=255)
                                                     aGCGACCAGCTCGGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGa            >  1:2496241/1‑69 (MQ=255)
                                                     aGCGACCAGCTCGGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGa            >  1:223371/1‑69 (MQ=255)
                                                     aGCGACCAGCTCGGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGa            >  1:760208/1‑69 (MQ=255)
                                                     aGCGACCAGCTCGGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACt          <  1:1233238/71‑1 (MQ=255)
                                                      gCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACt          >  1:3501742/1‑70 (MQ=255)
                                                           cAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGcc                      <  1:594413/53‑1 (MQ=255)
                                                             gCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTcgc  <  1:1288524/71‑1 (MQ=255)
                                                                 |                                                                  
GACTCTCTGCGACCAGCACGCGAACCAGCGGATGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGC  >  minE/405870‑406001

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