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 252,572 A→G 59.7% H530R (CAT→CGT)  malZ → maltodextrin glucosidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE252,5720AG59.7% 45.0 / 67.9 99H530R (CAT→CGT) malZmaltodextrin glucosidase
Reads supporting (aligned to +/- strand):  ref base A (32/8);  new base G (19/40);  total (51/48)
Fisher's exact test for biased strand distribution p-value = 4.25e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.11e-01

TACGGCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCCGCGTGCTGAATCAGC  >  minE/252507‑252637
                                                                 |                                                                 
tACGGCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATgg                                                                >  1:1562220/1‑69 (MQ=255)
tACGGCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATgg                                                                >  1:2576878/1‑69 (MQ=255)
tACGGCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATgg                                                                >  1:1398658/1‑69 (MQ=255)
tACGGCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATgg                                                                >  1:2490856/1‑69 (MQ=255)
  cGGCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcg                                                              >  1:3017812/1‑69 (MQ=255)
  cGGCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcg                                                              >  1:2485216/1‑69 (MQ=255)
  cGGCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcg                                                              <  1:299191/69‑1 (MQ=255)
  cGGCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcg                                                              >  1:3154953/1‑69 (MQ=255)
    gCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcggc                                                            >  1:1711662/1‑69 (MQ=255)
    gCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcggc                                                            >  1:2010498/1‑69 (MQ=255)
    gCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcggc                                                            >  1:1367298/1‑69 (MQ=255)
    gCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcggc                                                            >  1:832853/1‑69 (MQ=255)
    gCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcggc                                                            >  1:464509/1‑69 (MQ=255)
    gCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcggc                                                            >  1:87045/1‑69 (MQ=255)
    gCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcggc                                                            >  1:3117341/1‑69 (MQ=255)
    gCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcggc                                                            >  1:1125018/1‑69 (MQ=255)
    gCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATggcgg                                                             >  1:3041790/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTggcggc                                                            >  1:3249120/1‑67 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTgg                                                                >  1:263061/1‑63 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:331678/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:2442256/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:2394072/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:649614/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:1940176/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:3171573/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:2282454/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:3085536/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:1529389/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:2726916/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:2804174/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:1428314/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:282264/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:2954152/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:1311457/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:1219385/1‑68 (MQ=255)
      gTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCt                                                           >  1:1212644/1‑68 (MQ=255)
            cgcgCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCTGTCAgg                                                     <  1:2697389/68‑1 (MQ=255)
            cgcgCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCTGTCAgg                                                     <  1:2760026/68‑1 (MQ=255)
            cgcgCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCTGTCAgg                                                     <  1:3281756/68‑1 (MQ=255)
            cgcgCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCTGTCAgg                                                     <  1:136173/68‑1 (MQ=255)
            cgcgCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCTGTCAgg                                                     <  1:2165796/68‑1 (MQ=255)
            cgcgCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCATCGTGGCGGCTGTCAgg                                                     <  1:1037326/68‑1 (MQ=255)
                   tACCAGCGAATGATTGCGCTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCTGTCAgg                                                     <  1:911256/61‑1 (MQ=255)
                            aTGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGAt                                    <  1:1136010/69‑1 (MQ=255)
                            aTGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGAt                                    <  1:2449032/69‑1 (MQ=255)
                            aTGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGAt                                    <  1:1350938/69‑1 (MQ=255)
                            aTGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGAt                                    <  1:1928150/69‑1 (MQ=255)
                            aTGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGAt                                    <  1:1239780/69‑1 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCt                                                 >  1:3360673/1‑55 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTAt                                             >  1:622308/1‑59 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATa                                   >  1:2002061/1‑69 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATa                                   >  1:2878361/1‑69 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATa                                   >  1:136085/1‑69 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATa                                   >  1:1381314/1‑69 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATa                                   >  1:1437742/1‑69 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATa                                   >  1:737284/1‑69 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATa                                   >  1:638694/1‑69 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATa                                   >  1:3022539/1‑69 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATa                                   >  1:2125692/1‑69 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATa                                   >  1:338559/1‑69 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGATGTCAGGTGCTGTATGCGGAAGATa                                   >  1:174774/1‑69 (MQ=255)
                             tGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGAGGCTGTCAGGTGCTGTATGCGGAAGATa                                   >  1:2068317/1‑69 (MQ=255)
                                  gcgcTGCGTAAGAAAGGTCAGGCGTTGCGTCGTGGCGGCTGTCAgg                                                     <  1:745542/46‑1 (MQ=37)
                                               aaggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATG‑GGAAGATAACGTGGTGGTATTTGTCcg                <  1:1508607/66‑1 (MQ=255)
                                                aggTCAGGGGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:1654220/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTTTCcg                <  1:2331030/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:3371777/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:700520/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:880735/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:386415/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:3318480/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:915398/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:3078997/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:1350901/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:1540640/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:1823731/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:1978800/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:1077937/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:2072933/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:2094012/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:211663/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:2125562/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:2129619/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:2271610/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:2410734/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:2411073/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:247696/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:2496216/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:2553904/67‑1 (MQ=255)
                                                aggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:2589292/67‑1 (MQ=255)
                                                 ggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:506328/67‑1 (MQ=255)
                                                 ggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:3299765/67‑1 (MQ=255)
                                                 ggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:2829291/67‑1 (MQ=255)
                                                 ggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:1434395/67‑1 (MQ=255)
                                                 ggTCAGGCGTTGCGTCGTGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCcg                <  1:1176493/67‑1 (MQ=255)
                                                        cgcTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCCGCGTGCTGa        <  1:2995311/69‑1 (MQ=255)
                                                         gcTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTAATTGTCCGCGTGCTGa        <  1:642084/68‑1 (MQ=255)
                                                              gTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCCGCGTGCTGAATCAGc  >  1:1180197/1‑69 (MQ=255)
                                                              gTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCCGCGTGCTGAATCAGc  >  1:1059440/1‑69 (MQ=255)
                                                                 |                                                                 
TACGGCGTTATTCGCGCTGTACCAGCGAATGATTGCGCTGCGTAAGAAAAGTCAGGCGCTACGTCATGGCGGCTGTCAGGTGCTGTATGCGGAAGATAACGTGGTGGTATTTGTCCGCGTGCTGAATCAGC  >  minE/252507‑252637

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A