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 1,938,229 T→C 32.7% L261L (TTA→TTG)  xerD ← site‑specific tyrosine recombinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,938,2290TC32.7% 101.4 / 67.9 125L261L (TTA→TTG) xerDsite‑specific tyrosine recombinase
Reads supporting (aligned to +/- strand):  ref base T (54/30);  new base C (14/27);  total (68/57)
Fisher's exact test for biased strand distribution p-value = 2.10e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.07e-01

Only 100 of 125 total aligned reads displayed.

CGTATAAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGT  >  minE/1938172‑1938286
                                                         |                                                         
cGTATAAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCAcc                                                >  1:1570067/1‑69 (MQ=255)
cGTATAAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCAcc                                                >  1:2203503/1‑69 (MQ=255)
cGTATAAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCAcc                                                >  1:2210052/1‑69 (MQ=255)
cGTATAAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCAcc                                                >  1:2836886/1‑69 (MQ=255)
cGTATAAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCAcc                                                >  1:13634/1‑69 (MQ=255)
cGTATAAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCAcc                                                >  1:732377/1‑69 (MQ=255)
cGTATAAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCAcc                                                >  1:92644/1‑69 (MQ=255)
cGTATAAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCAcc                                                >  1:807064/1‑69 (MQ=255)
cGTATAAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCAc                                                 >  1:908433/1‑68 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGa                                            >  1:736507/1‑69 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGa                                            >  1:2088949/1‑69 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGa                                            >  1:1078529/1‑69 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGa                                            >  1:2313202/1‑69 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGa                                            >  1:2647486/1‑69 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGa                                            >  1:2732975/1‑69 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGa                                            >  1:2826969/1‑69 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGa                                            >  1:1853113/1‑69 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGa                                            >  1:2842972/1‑69 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGa                                            >  1:73955/1‑69 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGa                                            >  1:1554602/1‑69 (MQ=255)
    taAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCAGCACCATGa                                            >  1:2076515/1‑69 (MQ=255)
      aaTTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGAt                                           >  1:3421139/1‑68 (MQ=255)
      aaTTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGAt                                           >  1:2865060/1‑68 (MQ=255)
            cGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTtaata                                     <  1:3247830/68‑1 (MQ=255)
            cGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTtaata                                     <  1:3046135/68‑1 (MQ=255)
            cGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTtaata                                     <  1:698280/68‑1 (MQ=255)
            cGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTtaata                                     <  1:3160934/68‑1 (MQ=255)
            cGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTtaata                                     <  1:1234869/68‑1 (MQ=255)
              tggtggAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAAt                                  <  1:108278/69‑1 (MQ=255)
              tggtggAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAAt                                  <  1:1852875/69‑1 (MQ=255)
              tggtggAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAAt                                  <  1:3229210/69‑1 (MQ=255)
               ggtggAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATg                                 <  1:357488/69‑1 (MQ=255)
                          cGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAg                      >  1:283882/1‑69 (MQ=255)
                          cGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAg                      >  1:3431638/1‑69 (MQ=255)
                          cGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAg                      >  1:2568357/1‑69 (MQ=255)
                          cGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAg                      >  1:428605/1‑69 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACTCa             <  1:502807/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:2184208/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:904251/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:862896/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:82827/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:1140483/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:1222736/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:599293/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:1353057/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:1422129/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:3383325/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:3339364/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:3314084/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:2997469/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:2992552/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:295012/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:1704433/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:1792729/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:2032157/69‑1 (MQ=255)
                                   ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa             <  1:2462475/69‑1 (MQ=255)
                                      gTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          <  1:1990500/69‑1 (MQ=255)
                                      gTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          <  1:1971454/69‑1 (MQ=255)
                                         gCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACAt       >  1:1703390/1‑69 (MQ=255)
                                         gCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACAt       >  1:1646881/1‑69 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                 >  1:1319464/1‑54 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                 >  1:465949/1‑54 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                 >  1:486450/1‑54 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                 >  1:523821/1‑54 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                 >  1:1239542/1‑54 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                 >  1:3223931/1‑54 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                 >  1:2383447/1‑54 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                 >  1:807148/1‑54 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          <  1:666335/61‑1 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          <  1:1176957/61‑1 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          <  1:1991035/61‑1 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          <  1:808725/61‑1 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          <  1:2063796/61‑1 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          <  1:2112318/61‑1 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          >  1:1059824/1‑61 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          <  1:2915340/61‑1 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          >  1:102379/1‑61 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          >  1:1360913/1‑61 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          <  1:3138009/61‑1 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          >  1:1691544/1‑61 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca          >  1:1565183/1‑61 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTAGCAAAAGCGTGa                 >  1:1157842/1‑54 (MQ=255)
                                              tGCACCACGCGTAAATCCGCACCATGATTTAATAAAAGAGTGGCAAAAg                      >  1:1127597/1‑49 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:690640/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:2116239/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:3026316/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:3171997/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:449692/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:669749/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:3267203/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:1861574/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:588904/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:3335642/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:2787190/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:476440/1‑69 (MQ=255)
                                              tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt  >  1:292392/1‑69 (MQ=255)
                                                  ccacGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGt  <  1:3193060/65‑1 (MQ=255)
                                                  ccacGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGt  <  1:1711552/65‑1 (MQ=255)
                                                  ccacGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGt  <  1:747935/65‑1 (MQ=255)
                                                        gTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTCACGCAaca          <  1:2644274/51‑1 (MQ=255)
                                                         |                                                         
CGTATAAATTTGCGTGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGT  >  minE/1938172‑1938286

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A