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 1,590,071 G→A 40.8% G75G (GGC→GGT)  pdxK ← pyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,590,0710GA40.8% 41.1 / 66.5 96G75G (GGC→GGT) pdxKpyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase
Reads supporting (aligned to +/- strand):  ref base G (29/27);  new base A (12/27);  total (41/55)
Fisher's exact test for biased strand distribution p-value = 5.80e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCATATAGCCCGTGGTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATAATGCGGCGTATTGCTC  >  minE/1590003‑1590134
                                                                    |                                                               
cccATATAGCCCGTGGTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAg                                                                 >  1:718447/1‑69 (MQ=255)
     ataGCCCGTGGTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGc                                                             >  1:1308877/1‑68 (MQ=255)
       aGCCCGTGGTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTaa                                                          >  1:2832334/1‑69 (MQ=255)
       aGCCCGTGGTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTaa                                                          >  1:693597/1‑69 (MQ=255)
               gTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCg                                                  >  1:940240/1‑69 (MQ=255)
               gTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCg                                                  >  1:3307935/1‑69 (MQ=255)
               gTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCg                                                  >  1:2862595/1‑69 (MQ=255)
               gTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCg                                                  >  1:1325507/1‑69 (MQ=255)
               gTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCg                                                  >  1:2679437/1‑69 (MQ=255)
               gTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCg                                                  >  1:739370/1‑69 (MQ=255)
               gTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCg                                                  >  1:1157352/1‑69 (MQ=255)
               gTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCg                                                  >  1:936270/1‑69 (MQ=255)
                     gCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGa                                            <  1:205076/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATCACCGCTAAACCATTCATCCGGAATCg                                        <  1:3253561/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:2735139/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:2525872/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:2040955/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:1942535/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:3396005/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:3350807/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:180379/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:3372381/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:411321/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:49836/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:570861/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:1234588/69‑1 (MQ=255)
                         gAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCg                                        <  1:1123255/69‑1 (MQ=255)
                            gTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGcac                                     <  1:1974240/69‑1 (MQ=255)
                             ttGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGcac                                     <  1:1286986/68‑1 (MQ=255)
                               ggCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGcc                                                               >  1:620128/1‑40 (MQ=255)
                               ggCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGcaccac                                  >  1:3362132/1‑69 (MQ=255)
                               ggCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGcaccac                                  >  1:972221/1‑69 (MQ=255)
                               ggCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGcaccac                                  >  1:451187/1‑69 (MQ=255)
                               ggCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGcaccac                                  >  1:2469435/1‑69 (MQ=255)
                               ggCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGcaccac                                  >  1:2142722/1‑69 (MQ=255)
                               ggCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGcaccac                                  >  1:1624632/1‑69 (MQ=255)
                               ggCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGcacca                                   >  1:2468622/1‑68 (MQ=255)
                                      cgcaTCACGCTCCTGAAGCGCACGCAAATATCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGaa                           <  1:581957/69‑1 (MQ=255)
                                      cgcaTCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGaa                           <  1:3129572/69‑1 (MQ=255)
                                      cgcaTCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGaa                           <  1:3205867/69‑1 (MQ=255)
                                      cgcaTCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGaa                           <  1:545643/69‑1 (MQ=255)
                                      cgcaTCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGaa                           <  1:3248479/69‑1 (MQ=255)
                                      cgcaTCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGaa                           <  1:1936201/69‑1 (MQ=255)
                                      cgcaTCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGaa                           <  1:2565291/69‑1 (MQ=255)
                                       gcaTCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGaaa                          >  1:3007021/1‑69 (MQ=255)
                                       gcaTCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGaaa                          >  1:2220403/1‑69 (MQ=255)
                                       gcaTCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGaaa                          >  1:1805243/1‑69 (MQ=255)
                                       gcaTCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGaaa                          >  1:1489420/1‑69 (MQ=255)
                                       gcaTCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGaaa                          >  1:1347083/1‑69 (MQ=255)
                                       gcaTCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGaaa                          >  1:2374664/1‑69 (MQ=255)
                                       gcaTCACGCTCCTGAAGCGCACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGaaa                          >  1:597825/1‑69 (MQ=255)
                                         aTCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAgt                        <  1:2761192/69‑1 (MQ=255)
                                          tCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAgt                        <  1:2858801/68‑1 (MQ=255)
                                              gCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCAt                   <  1:524024/69‑1 (MQ=255)
                                              gCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCAt                   <  1:3027338/69‑1 (MQ=255)
                                              gCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCAt                   <  1:2314038/69‑1 (MQ=255)
                                              gCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCAt                   <  1:2281472/69‑1 (MQ=255)
                                              gCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCAt                   <  1:2303401/69‑1 (MQ=255)
                                                tCCTGAAGCTCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATaa                 <  1:1125295/69‑1 (MQ=255)
                                                tCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATaa                 <  1:410238/69‑1 (MQ=255)
                                                tCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATaa                 <  1:1752532/69‑1 (MQ=255)
                                                tCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATaa                 <  1:2381838/69‑1 (MQ=255)
                                                tCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCAACGTAGAAAGTGTCATaa                 <  1:2568761/69‑1 (MQ=255)
                                                tCCTGAAGCCCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATaa                 <  1:300790/69‑1 (MQ=255)
                                                  cTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGt                               >  1:2806934/1‑53 (MQ=255)
                                                  cTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATAATg               >  1:1180762/1‑69 (MQ=255)
                                                  cTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATAATg               >  1:2367478/1‑69 (MQ=255)
                                                  cTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATAATg               >  1:404913/1‑69 (MQ=255)
                                                    gAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGca                                      >  1:2883566/1‑44 (MQ=255)
                                                    gAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAA‑‑GTCATAATgcgg            >  1:698913/1‑68 (MQ=255)
                                                    gAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAA‑‑GTCATAATgcgg            >  1:637649/1‑68 (MQ=255)
                                                    gAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAA‑‑GTCATAATgcgg            >  1:3250381/1‑68 (MQ=255)
                                                    gAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAA‑‑GTCATAATgcgg            >  1:1373091/1‑68 (MQ=255)
                                                    gAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAA‑‑GTCATAATgcag            >  1:2163351/1‑66 (MQ=255)
                                                       gcgcACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggcg          <  1:834034/69‑1 (MQ=255)
                                                       gcgcACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggcg          <  1:2985413/69‑1 (MQ=255)
                                                       gcgcACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggcg          <  1:2523878/69‑1 (MQ=255)
                                                       gcgcACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggcg          <  1:406293/69‑1 (MQ=255)
                                                       gcgcACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggcg          <  1:1976209/69‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:1275348/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:1066073/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:1092916/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:2929788/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:2136067/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:3100644/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:2604187/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:1852060/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:2243778/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:2452382/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:3389179/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:1456990/68‑1 (MQ=255)
                                                       gcgcACGCAAATAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATgcggc           <  1:421934/68‑1 (MQ=255)
                                                               aaaTAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATGCGGCGTATTGCTc  >  1:1261198/1‑69 (MQ=255)
                                                               aaaTAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATGCGGCGTATTGCTc  >  1:1227825/1‑69 (MQ=255)
                                                               aaaTAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATGCGGCGTATTGCTc  >  1:3073775/1‑69 (MQ=255)
                                                               aaaTAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATGCGGCGTATTGCTc  >  1:936291/1‑69 (MQ=255)
                                                               aaaTAACCGCTAAACCATTCATCCGGAATCGCACCACCGTAGAAAGTGTCATAATGCGGCGTATTGCTc  >  1:251964/1‑69 (MQ=255)
                                                                    |                                                               
CCCATATAGCCCGTGGTTACAGCACGAAGTTGGCGCAGCGCATCACGCTCCTGAAGCGCACGCAAATAGCCGCTAAACCATTCGTCCGGAATCGCACCACCGTAGAAAGTGTCATAATGCGGCGTATTGCTC  >  minE/1590003‑1590134

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