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
A6 F21 I0 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,093,658 T→C 52.7% T907A (ACA→GCA)  ydiJ ← predicted FAD‑linked oxidoreductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,093,6580TC52.7% 11.9 / 133.3 93T907A (ACA→GCA) ydiJpredicted FAD‑linked oxidoreductase
Reads supporting (aligned to +/- strand):  ref base T (22/22);  new base C (21/28);  total (43/50)
Fisher's exact test for biased strand distribution p-value = 5.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.51e-01

CGCACCCGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCCATTCATTCGCCAGTAAGACGTTAAACT  >  minE/1093593‑1093720
                                                                 |                                                              
cgcACCCGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCa                                                           >  1:3499268/1‑71 (MQ=255)
 gcACCCGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCAc                                                          >  1:1682694/1‑71 (MQ=255)
 gcACCCGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCAc                                                          >  1:1854504/1‑71 (MQ=255)
  cACCCGGCAAGGCGGTAACTTCGGTACAGTGCCCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACt                                                         >  1:924720/1‑71 (MQ=255)
  cACCCGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTTACCGCTGACTGTAGCCACt                                                         >  1:2401327/1‑71 (MQ=255)
    cccGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTgg                                                       >  1:646728/1‑71 (MQ=255)
    cccGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTgg                                                       >  1:3554191/1‑71 (MQ=255)
    cccGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTgg                                                       <  1:3042745/71‑1 (MQ=255)
    cccGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTgg                                                       <  1:53968/71‑1 (MQ=255)
    cccGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTgg                                                       <  1:275793/71‑1 (MQ=255)
     ccGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGt                                                                <  1:2943608/61‑1 (MQ=255)
     ccGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGt                                                                <  1:539479/61‑1 (MQ=255)
      cGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCt                                                     <  1:3021782/71‑1 (MQ=255)
      cGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCt                                                     <  1:550087/71‑1 (MQ=255)
      cGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCt                                                     <  1:284715/71‑1 (MQ=255)
       ggCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAg                                                              >  1:179864/1‑61 (MQ=255)
       ggCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAg                                                              >  1:2775884/1‑61 (MQ=255)
       ggCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAg                                                              >  1:949416/1‑61 (MQ=255)
        gCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCtgt                                                   <  1:3548979/71‑1 (MQ=255)
        gCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCtgt                                                   <  1:1092311/71‑1 (MQ=255)
        gCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCtgt                                                   <  1:3492234/71‑1 (MQ=255)
        gCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCtgt                                                   <  1:458541/71‑1 (MQ=255)
        gCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCtgt                                                   <  1:2066801/71‑1 (MQ=255)
         cAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCtgt                                                   >  1:1526821/1‑70 (MQ=255)
           aGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGAc                                                <  1:2858743/71‑1 (MQ=255)
           aGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGcc                                                            >  1:3713919/1‑59 (MQ=255)
           aGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGAc                                                >  1:2345153/1‑71 (MQ=255)
           aGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGAc                                                >  1:878084/1‑71 (MQ=255)
           aGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGAc                                                >  1:1487992/1‑71 (MQ=255)
            ggCGGTAACTTCGGTACAGTGACCAAAGGAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACt                                               <  1:2437398/71‑1 (MQ=255)
            ggCGGTAACTTCGGTACAGTGACCAAAGGAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACt                                               <  1:2441714/71‑1 (MQ=255)
            ggCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCtg                                                    >  1:1456122/1‑66 (MQ=255)
             gCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTc                                              <  1:1306207/71‑1 (MQ=255)
             gCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTc                                              <  1:2749618/71‑1 (MQ=255)
               ggTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCa                                                           >  1:2223586/1‑56 (MQ=255)
               ggTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCtgt                                                   <  1:1797570/64‑1 (MQ=255)
               ggTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCt                                                     <  1:2698588/62‑1 (MQ=255)
               ggTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCaa                                            <  1:1825447/71‑1 (MQ=255)
               ggTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCaa                                            <  1:836511/71‑1 (MQ=255)
               ggTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCaa                                            <  1:1168209/71‑1 (MQ=255)
               ggTAACTTCGGAACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCt                                                     <  1:1940356/62‑1 (MQ=255)
                 tAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCtg                                                    >  1:1221790/1‑61 (MQ=255)
                 tAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCtgt                                                   >  1:417939/1‑62 (MQ=255)
                 tAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCtgt                                                   >  1:1348116/1‑62 (MQ=255)
                 tAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGa                                                 >  1:1056185/1‑64 (MQ=255)
                 tAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGa                                                 >  1:1478216/1‑64 (MQ=255)
                 tAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGt                                          >  1:705104/1‑71 (MQ=255)
                 tAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGt                                          >  1:3507889/1‑71 (MQ=255)
                 tAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGt                                          <  1:1779332/71‑1 (MQ=255)
                 tAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGt                                          <  1:3290471/71‑1 (MQ=255)
                  aaCTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGt                                          >  1:3073242/1‑70 (MQ=255)
                  aaCTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTg                                         >  1:2873590/1‑71 (MQ=255)
                  aaCTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTg                                         >  1:1633644/1‑71 (MQ=255)
                  aaCTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGc                                                      <  1:690507/58‑1 (MQ=255)
                   aCTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTgc                                        >  1:1255375/1‑71 (MQ=255)
                   aCTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTg                                         <  1:2456049/70‑1 (MQ=255)
                       cGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTgcgc                                      <  1:3195873/69‑1 (MQ=255)
                       cGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCtt                                    >  1:2679260/1‑71 (MQ=255)
                       cGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCtt                                    >  1:3007930/1‑71 (MQ=255)
                       cGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCtt                                    >  1:2808910/1‑71 (MQ=255)
                        ggTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGt                                          >  1:86141/1‑64 (MQ=255)
                        ggTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCtt                                    <  1:662527/70‑1 (MQ=255)
                          tACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTgcc                                 <  1:2557272/71‑1 (MQ=255)
                          tACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTgcc                                 <  1:578392/71‑1 (MQ=255)
                            cAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGc                                                             >  1:263373/1‑41 (MQ=255)
                            cAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTgccag                               <  1:2793740/71‑1 (MQ=255)
                            cAGTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTgccag                               >  1:2481987/1‑71 (MQ=255)
                              gTGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTgccagcc                             <  1:1099725/71‑1 (MQ=255)
                               tGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTgcc                                 <  1:262492/66‑1 (MQ=255)
                               tGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTgcc                                 <  1:2578898/66‑1 (MQ=255)
                               tGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTc                                              <  1:3453743/53‑1 (MQ=255)
                               tGACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTgccagcca                            >  1:1306451/1‑71 (MQ=255)
                                gACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCcat                           >  1:3363365/1‑71 (MQ=255)
                                gACCAAAGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTc                                              <  1:3446419/52‑1 (MQ=255)
                                 aCCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTgccag                               >  1:332984/1‑66 (MQ=255)
                                    aaaGAAATACCATGATTCACCGCTGACTGTAGCCa                                                           >  1:50020/1‑35 (MQ=255)
                                    aaaGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCcattcat                       <  1:2220099/71‑1 (MQ=255)
                                      aGAAATACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCCattcattc                     >  1:2955569/1‑71 (MQ=255)
                                        aaaTACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCCATTCATTCGc                   >  1:1928655/1‑71 (MQ=255)
                                         aaTACCATGATTCACCGCTGACTGTAGCCACTGGCtgt                                                   >  1:1422405/1‑38 (MQ=255)
                                         aaTACCATGATTCACCGCTGACTGTAGCCACTGGCtgt                                                   >  1:1253288/1‑38 (MQ=255)
                                         aaTACCATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCCATTCATTCGc                   <  1:892244/70‑1 (MQ=255)
                                            aCCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCcattcat                       <  1:1294880/63‑1 (MQ=255)
                                            aCCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCcattcat                       <  1:362163/63‑1 (MQ=255)
                                            aCCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCcattcat                       <  1:2205129/63‑1 (MQ=255)
                                            aCCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCcattcat                       <  1:2932882/63‑1 (MQ=255)
                                            aCCATGATTCACCGCTGACTCTAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCcattcat                       <  1:1040325/63‑1 (MQ=255)
                                             ccATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCCATTCATTCGCCAGt               <  1:305357/70‑1 (MQ=255)
                                              cATGATTCACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTgcc                                 <  1:830990/51‑1 (MQ=255)
                                                tGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCCATTCATTCGCCAGTAAGa           <  1:366495/71‑1 (MQ=255)
                                                  aTTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCCATTCATTCGCCAGTAAGAc          <  1:1326824/70‑1 (MQ=255)
                                                     cACCGCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCCATTCATTCGCCAGTAAGACGtt       >  1:896829/1‑70 (MQ=255)
                                                      aCCGCTGACTGTAGCCACTGGCTGTGACTCAAGTgcgc                                      <  1:688468/38‑1 (MQ=255)
                                                         gCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTgcc                                 <  1:3039137/40‑1 (MQ=255)
                                                         gCTGACTGCAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCCATTCATTCGCCAGTAAGACGTTAAACt  <  1:3556624/71‑1 (MQ=255)
                                                                 |                                                              
CGCACCCGGCAAGGCGGTAACTTCGGTACAGTGACCAAAGAAATACCATGATTCACCGCTGACTGTAGCCACTGGCTGTGACTCAAGTGCGCTTGCCAGCCATTCATTCGCCAGTAAGACGTTAAACT  >  minE/1093593‑1093720

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