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 2,469,733 C→T 52.0% L239L (CTG→TTG)  atpD → F1 sector of membrane‑bound ATP synthase, beta subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,469,7330CT52.0% ‑0.4 / 90.5 100L239L (CTG→TTG) atpDF1 sector of membrane‑bound ATP synthase, beta subunit
Reads supporting (aligned to +/- strand):  ref base C (17/31);  new base T (13/39);  total (30/70)
Fisher's exact test for biased strand distribution p-value = 2.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.77e-01

Only 100 of 101 total aligned reads displayed.

GCTCTGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTGGGCCG  >  minE/2469679‑2469800
                                                      |                                                                   
gCTCTGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGac                                                       >  1:88449/1‑69 (MQ=255)
gCTCTGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGac                                                       >  1:745191/1‑69 (MQ=255)
gCTCTGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGac                                                       >  1:3361608/1‑69 (MQ=255)
gCTCTGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGac                                                       >  1:1502763/1‑69 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaac                                                    >  1:1717562/1‑69 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaac                                                    <  1:981960/69‑1 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaac                                                    <  1:3044856/69‑1 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaac                                                    >  1:641180/1‑69 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaac                                                    <  1:1334634/69‑1 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaac                                                    >  1:549957/1‑69 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaac                                                    >  1:240338/1‑69 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaac                                                    >  1:3280125/1‑69 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaac                                                    <  1:1403505/69‑1 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaac                                                    >  1:3333934/1‑69 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaac                                                    >  1:3329624/1‑69 (MQ=255)
   ctGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGacaa                                                     >  1:2583950/1‑68 (MQ=255)
        cGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCt                                                <  1:375680/68‑1 (MQ=255)
                    ggCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCt                                   >  1:1985016/1‑69 (MQ=255)
                    ggCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCt                                   >  1:1767826/1‑69 (MQ=255)
                     gCTGAGAAATTCCGTGACGAATGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:2979075/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:2334185/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:2739489/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:2000559/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:2732760/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:1054856/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:3277840/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:543997/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:682411/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:985662/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:1162189/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:171194/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:1998157/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:1337454/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:1891726/69‑1 (MQ=255)
                     gCTGAGAAATTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:1863660/69‑1 (MQ=255)
                           aaaTTCCGTGACGAATGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:3261/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:465869/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:1621892/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:2945464/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:2868553/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:1181971/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:1545250/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:3315120/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:2628350/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:244651/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:2438349/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:2397592/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:2007580/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:2459902/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:1150013/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:2130365/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:982531/68‑1 (MQ=255)
                           aaaTTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTCACAACATCTATCGTTACACCCTGGCCgg                             <  1:2322310/68‑1 (MQ=255)
                            aaTTCGGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:2225012/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCGTg                                  <  1:3240632/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:601387/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:1356444/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:3108674/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:795524/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:1403040/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:661617/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:131296/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:3076378/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:90831/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:2866633/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:1066713/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:931549/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:944802/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:178380/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:2739091/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:2661365/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:1872394/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:1990866/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:975968/62‑1 (MQ=255)
                            aaTTCCGTGACGAAGGTCGTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTg                                  <  1:2137895/62‑1 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTAcc                         >  1:665089/1‑52 (MQ=37)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:3195414/1‑69 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:1289022/1‑69 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:8883/1‑69 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:3215826/1‑69 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:2004553/1‑69 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:2101761/1‑69 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:2286865/1‑69 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:2295692/1‑69 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:1559150/1‑69 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:1500287/1‑69 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:358878/1‑69 (MQ=255)
                                              gTGACGTATTGCTGTTCGTCGATAACATCTATCGTTACACCCTGGCCGGTACCGAAGTATCCGCActgc         >  1:1364900/1‑69 (MQ=255)
                                                 aCGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTgg      >  1:3222360/1‑69 (MQ=255)
                                                 aCGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTgg      >  1:2978763/1‑69 (MQ=255)
                                                 aCGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTgg      >  1:552004/1‑69 (MQ=255)
                                                     tCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTGGGcct  <  1:516584/69‑2 (MQ=255)
                                                     tCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTGGGCCg  <  1:648357/69‑1 (MQ=255)
                                                     tCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTGGGCCg  <  1:1481642/69‑1 (MQ=255)
                                                     tCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTGGGCCg  <  1:3182365/69‑1 (MQ=255)
                                                     tCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTGGGCCg  <  1:3081260/69‑1 (MQ=255)
                                                     tCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTGGGCCg  <  1:2980224/69‑1 (MQ=255)
                                                     tCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTGGGCCg  <  1:2836560/69‑1 (MQ=255)
                                                     tCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTGGGCCg  <  1:491387/69‑1 (MQ=255)
                                                      ctgctgTTCGTTGACAACATCTATCGTTACACCCTGGCCgg                             <  1:284579/41‑1 (MQ=255)
                                                      |                                                                   
GCTCTGACCGGTCTGACCATGGCTGAGAAATTCCGTGACGAAGGTCGTGACGTTCTGCTGTTCGTTGACAACATCTATCGTTACACCCTGGCCGGTACGGAAGTATCCGCACTGCTGGGCCG  >  minE/2469679‑2469800

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