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 2,103,973 A→G 26.6% intergenic (‑221/‑28) agaR ← / → kbaZ DNA‑binding transcriptional dual regulator/tagatose 6‑phosphate aldolase 1, kbaZ subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,103,9730AG26.6% 110.9 / 40.6 101intergenic (‑221/‑28)agaR/kbaZDNA‑binding transcriptional dual regulator/tagatose 6‑phosphate aldolase 1, kbaZ subunit
Reads supporting (aligned to +/- strand):  ref base A (29/45);  new base G (10/17);  total (39/62)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.37e-01

Only 100 of 101 total aligned reads displayed.

ATCTTTCGTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGTGAGACAGCACA  >  minE/2103909‑2104034
                                                                |                                                             
aTCTTTCGTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGc                                                           <  1:10301/69‑1 (MQ=255)
aTCTTTCGTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGc                                                           >  1:2796364/1‑69 (MQ=255)
aTCTTTCGTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGc                                                           >  1:2412112/1‑69 (MQ=255)
aTCTTTCGTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGc                                                           >  1:2107175/1‑69 (MQ=255)
aTCTTTCGTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGc                                                           >  1:1713183/1‑69 (MQ=255)
       gTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTaa                                                      <  1:548122/67‑1 (MQ=255)
       gTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTaa                                                      <  1:505169/67‑1 (MQ=255)
       gTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTaa                                                      <  1:365325/67‑1 (MQ=255)
       gTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTaa                                                      <  1:2283374/67‑1 (MQ=255)
       gTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTaa                                                      <  1:226723/67‑1 (MQ=255)
       gTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTa                                                       <  1:895758/66‑1 (MQ=255)
       gTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTa                                                       <  1:3322051/66‑1 (MQ=255)
       gTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTa                                                       <  1:2658146/66‑1 (MQ=255)
       gTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTa                                                       <  1:2485657/66‑1 (MQ=255)
       gTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTa                                                       <  1:2235449/66‑1 (MQ=255)
        ttttatttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTaa                                                      <  1:3088780/66‑1 (MQ=255)
        ttttatttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTa                                                       <  1:2712858/65‑1 (MQ=255)
         tttatttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTg                                                  <  1:1610025/69‑1 (MQ=255)
            atttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATGTCGCAGTAATCTg                                                  >  1:1813031/1‑66 (MQ=255)
            atttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATGTCGCAGTAATCTGAAc                                               >  1:1843005/1‑69 (MQ=255)
            atttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATGTCGCAGTAATCTGAAc                                               >  1:216492/1‑69 (MQ=255)
            atttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATGTCGCAGTAATCTGAAc                                               >  1:2473651/1‑69 (MQ=255)
            atttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATGTCGCAGTAATCTGAAc                                               >  1:2109597/1‑69 (MQ=255)
            atttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATGTCGCAGTAATCTGAAc                                               >  1:636533/1‑69 (MQ=255)
            atttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATGTCGCAGTAATCTGAAc                                               >  1:3088070/1‑69 (MQ=255)
            atttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATGTCGCAGTAATCTGAAc                                               >  1:3099514/1‑69 (MQ=255)
            atttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATGTCGCAGTAATCTGAAc                                               >  1:3259349/1‑69 (MQ=255)
            atttttatCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATGTCGCAGTAATCTGAAc                                               >  1:1665640/1‑69 (MQ=255)
                    ctcACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGagag                                        <  1:1775848/68‑1 (MQ=255)
                    ctcACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGagag                                        <  1:2117834/68‑1 (MQ=255)
                     tcACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGagag                                        <  1:2260889/67‑1 (MQ=255)
                           tGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTa                                                       <  1:3080285/46‑1 (MQ=255)
                           tGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGa                                <  1:3133266/69‑1 (MQ=255)
                                    aTCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTg                                                  <  1:1628543/42‑1 (MQ=255)
                                    aTCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTg                                                  <  1:623560/42‑1 (MQ=255)
                                    aTCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTg                                                  <  1:1057310/42‑1 (MQ=255)
                                     tCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCt                         >  1:1821138/1‑66 (MQ=255)
                                     tCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCt                         >  1:2851656/1‑66 (MQ=255)
                                     tCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCt                         >  1:1042804/1‑66 (MQ=255)
                                     tCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCt                         >  1:3377138/1‑66 (MQ=255)
                                     tCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCt                         >  1:109529/1‑66 (MQ=255)
                                     tCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCt                         >  1:1489849/1‑66 (MQ=255)
                                     tCAACTGAAACAAAACGAAAGATTAAAATCGCAGTAATCTGAACTGGAGACGAAAGTGa                                >  1:2828610/1‑59 (MQ=255)
                                      cAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGAc                      >  1:1626172/1‑68 (MQ=255)
                                      cAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGAc                      >  1:1405270/1‑68 (MQ=255)
                                      cAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGAc                      >  1:2666853/1‑68 (MQ=255)
                                       aaCTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACa                     >  1:2120162/1‑68 (MQ=255)
                                           gAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAAt                <  1:2113233/69‑1 (MQ=255)
                                           gAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAAt                <  1:1129018/69‑1 (MQ=255)
                                           gAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAAt                <  1:428800/69‑1 (MQ=255)
                                           gAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAAt                <  1:3082352/69‑1 (MQ=255)
                                           gAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAAt                <  1:1296346/69‑1 (MQ=255)
                                           gAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAAt                <  1:828775/69‑1 (MQ=255)
                                           gAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTCACAGAAAt                <  1:405094/69‑1 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAg                                   >  1:2652903/1‑48 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGaaa                 >  1:2550901/1‑66 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGAAATg               >  1:3318424/1‑68 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGAAATg               >  1:1925025/1‑68 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGAAATg               >  1:855663/1‑68 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGAAATg               >  1:863459/1‑68 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGAAATg               >  1:274795/1‑68 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGAAATg               >  1:1581709/1‑68 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGAAATg               >  1:2629987/1‑68 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGAAATg               >  1:544669/1‑68 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGAAATg               >  1:81524/1‑68 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGAAATg               >  1:364888/1‑68 (MQ=255)
                                             aaCAAAACGAAAGATTAATATCGCAGTAATCGGAACTGGAGAGGCAAGTGAAACATCTGACAGAAATg               >  1:1499408/1‑68 (MQ=255)
                                              aCAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATg               <  1:3278962/67‑1 (MQ=255)
                                              aCAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATg               <  1:2250933/67‑1 (MQ=255)
                                              aCAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATg               <  1:834923/67‑1 (MQ=255)
                                              aCAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATg               <  1:1390433/67‑1 (MQ=255)
                                              aCAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGt             <  1:3129498/69‑1 (MQ=255)
                                              aCAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGt             <  1:2000258/69‑1 (MQ=255)
                                              aCAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGt             <  1:678456/69‑1 (MQ=255)
                                              aCAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGt             <  1:682364/69‑1 (MQ=255)
                                              aCAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGt             <  1:362874/69‑1 (MQ=255)
                                              aCAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGt             <  1:2432733/69‑1 (MQ=255)
                                              aCAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGt             <  1:392353/69‑1 (MQ=255)
                                               cAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGt             <  1:2994852/68‑1 (MQ=255)
                                                aaaaCGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGTga           <  1:2562034/69‑1 (MQ=255)
                                                 aaaCGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGTga           <  1:1356194/68‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTTGAGAGGAAAGTGAAACATCTGa                       <  1:589089/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:683162/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:815648/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:1017040/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:362911/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:3341640/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:3334556/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:2854106/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:280758/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:1167746/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:2485805/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:2064321/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:2053313/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:1822569/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:1704920/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGa                       <  1:1677422/50‑1 (MQ=255)
                                                       aaGATTAATGTCGCAGTAATCTGAACTGGACAGGAAAGTGAAACATCTGa                       <  1:2259303/50‑1 (MQ=255)
                                                         gATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAGCATCTGACAGAAATGGTGAGACAGcaca  <  1:2672048/69‑1 (MQ=255)
                                                         gATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGTGAGACAGcaca  <  1:2862496/69‑1 (MQ=255)
                                                                |                                                             
ATCTTTCGTTTTATTTTTATCTCACCATGACGCAGTATCAACTGAAACAAAACGAAAGATTAATATCGCAGTAATCTGAACTGGAGAGGAAAGTGAAACATCTGACAGAAATGGTGAGACAGCACA  >  minE/2103909‑2104034

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