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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,045,853 T→C 22.1% intergenic (+615/+180) yqiK → / ← rfaE conserved hypothetical protein/fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,045,8530TC22.1% 258.2 / 62.5 122intergenic (+615/+180)yqiK/rfaEconserved hypothetical protein/fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase
Reads supporting (aligned to +/- strand):  ref base T (46/49);  new base C (12/15);  total (58/64)
Fisher's exact test for biased strand distribution p-value = 8.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.71e-01

Only 100 of 124 total aligned reads displayed.

CAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTAACAACTCAT  >  minE/2045792‑2045921
                                                              |                                                                    
cagcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAg                                                             >  1:830053/1‑71 (MQ=255)
 agcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTa                                                                     <  1:2531398/62‑1 (MQ=255)
 agcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTa                                                                     <  1:4329956/62‑1 (MQ=255)
  gcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTatg                                                                   >  1:4328361/1‑63 (MQ=255)
     aGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTa                                                                     >  1:3736880/1‑58 (MQ=255)
     aGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTc                                                          <  1:657273/69‑1 (MQ=255)
       gggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGTCCTTGTATAAGGAAAGGGTTa                                                                     <  1:1977594/56‑1 (MQ=255)
        ggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtcat                                                     >  1:5627124/1‑71 (MQ=255)
        ggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtcat                                                     >  1:552372/1‑71 (MQ=255)
        ggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtcat                                                     >  1:3187602/1‑71 (MQ=255)
        cgCTGAAACGGGAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGtca                                                      <  1:1786500/70‑1 (MQ=1)
          cTGAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatg                                                                   <  1:144998/55‑1 (MQ=14)
            gAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACtcat                                                     >  1:1896669/1‑67 (MQ=14)
            gAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACtcat                                                     >  1:1889915/1‑67 (MQ=14)
            gAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGtt                                                                      <  1:1190765/50‑1 (MQ=255)
             aaaCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                                                 <  1:3787364/54‑1 (MQ=14)
             aaaCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                                                 <  1:4403377/54‑1 (MQ=14)
             aaaCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcatcg                                                <  1:565443/71‑3 (MQ=11)
             aaaCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATAc                                                >  1:4899675/1‑71 (MQ=255)
              aaCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAg                                                             >  1:3535738/1‑57 (MQ=255)
               aCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCAtgatga                                                               >  1:3590871/1‑54 (MQ=14)
               aCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAATGAAAGGGTTATGATGAAGCTCGt                                                        <  1:5193989/61‑1 (MQ=255)
                  ggAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                                                 <  1:2622584/49‑1 (MQ=14)
                  ggAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTCATCATCGTGgtg                                           >  1:1155474/1‑70 (MQ=2)
                   gAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgt                                            >  1:3680797/1‑70 (MQ=11)
                   gAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTCATCATCGTGgtgc                                          >  1:3332284/1‑69 (MQ=2)
                         cccTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACt                                               <  1:1253870/60‑1 (MQ=255)
                          tcTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgtg                                           <  1:3123410/63‑2 (MQ=11)
                          ccTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttgt                                    >  1:3907027/1‑70 (MQ=255)
                           cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtc                                                       <  1:1663603/50‑1 (MQ=255)
                           cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtc                                                       <  1:3373786/50‑1 (MQ=255)
                           cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTa                                  <  1:4919004/71‑1 (MQ=255)
                            tCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCat                                                                    <  1:128161/36‑1 (MQ=12)
                            tCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCat                                                                    <  1:2965762/36‑1 (MQ=12)
                             cccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCtac                                                         >  1:74665/1‑44 (MQ=9)
                             cccGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGc                                                            >  1:3127908/1‑43 (MQ=255)
                              ccGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgtga                                          >  1:3161910/1‑59 (MQ=2)
                              ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatga                                                                  >  1:5472944/1‑36 (MQ=12)
                              ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatga                                                                  >  1:1660542/1‑36 (MQ=12)
                              ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat                                                  <  1:213885/52‑1 (MQ=9)
                              ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat                                                  <  1:2184869/52‑1 (MQ=9)
                              ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat                                                  <  1:3118384/52‑1 (MQ=9)
                              ccGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttgt                                    <  1:2337461/66‑1 (MQ=255)
                               cGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                                                 <  1:3931266/36‑1 (MQ=9)
                               cGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                                                 <  1:3598393/36‑1 (MQ=9)
                               cGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATa                                                 >  1:1020149/1‑52 (MQ=255)
                               cGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTg                                              <  1:2294832/55‑1 (MQ=255)
                                gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATa                                                 >  1:525181/1‑51 (MQ=255)
                                gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt                             <  1:4698006/71‑1 (MQ=255)
                                gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGt                              >  1:5507266/1‑70 (MQ=255)
                                 aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgt                                            >  1:1201610/1‑55 (MQ=255)
                                 aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt                             >  1:3440667/1‑70 (MQ=255)
                                 aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTa                            <  1:1849759/71‑1 (MQ=255)
                                  agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTgg                                             >  1:4303137/1‑53 (MQ=255)
                                  agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTgg                                             >  1:3598080/1‑53 (MQ=255)
                                  agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTaa                           <  1:4262499/71‑1 (MQ=255)
                                  agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTaa                           <  1:1283014/71‑1 (MQ=255)
                                   gaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAg                          >  1:5332259/1‑71 (MQ=255)
                                      g‑gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttg                                     <  1:5080620/57‑1 (MQ=255)
                                      g‑gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttg                                     <  1:3400364/57‑1 (MQ=255)
                                        gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttg                                     <  1:4397732/56‑1 (MQ=255)
                                          gCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTccc                    <  1:2279448/71‑1 (MQ=255)
                                          gCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTccc                    <  1:2599328/71‑1 (MQ=255)
                                           ccTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTg                                              <  1:5123806/44‑1 (MQ=255)
                                            cTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGa                  >  1:4961894/1‑71 (MQ=255)
                                            cTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGa                  >  1:5610479/1‑71 (MQ=255)
                                            cTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGa                  >  1:2174414/1‑71 (MQ=255)
                                               gTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTa                                  >  1:3449558/1‑52 (MQ=255)
                                               gTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACt                                >  1:2513298/1‑54 (MQ=255)
                                               gTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACt                <  1:2989076/70‑1 (MQ=255)
                                               gTATAAGGAAAGGGTTATGATGAAGCTCGTCAACATACTg                                              >  1:4741596/1‑40 (MQ=255)
                                                tataAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGttt                       <  1:2037146/62‑1 (MQ=255)
                                                tataAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACtt               <  1:2360843/70‑1 (MQ=255)
                                                tataAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACtt               <  1:4805201/70‑1 (MQ=255)
                                                 ataAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTAc             >  1:3781916/1‑71 (MQ=255)
                                                 ataAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgt                                            <  1:177545/40‑1 (MQ=255)
                                                 ataAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgt                                            <  1:4983593/40‑1 (MQ=255)
                                                  taAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTAc             >  1:3135905/1‑70 (MQ=255)
                                                  taAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACt            <  1:4184059/71‑1 (MQ=255)
                                                  taAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgtga                                          <  1:2103245/41‑3 (MQ=14)
                                                  taAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgtga                                          <  1:1334239/41‑3 (MQ=14)
                                                   aaGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACt            >  1:1233939/1‑70 (MQ=255)
                                                    aGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTaa                           >  1:385031/1‑54 (MQ=255)
                                                    aGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTaa                           >  1:486568/1‑54 (MQ=255)
                                                    aGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTaa                           >  1:315198/1‑54 (MQ=255)
                                                      gAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGa                  <  1:3086171/61‑1 (MQ=255)
                                                       aaaGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTaacaa       >  1:1408650/1‑71 (MQ=255)
                                                       aaaGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTaacaa       <  1:1078939/71‑1 (MQ=255)
                                                        aaGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTGCTGTTAAGTTTCCCGACTTACTaacaa       >  1:777201/1‑70 (MQ=255)
                                                        aaGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGttt                       >  1:1940289/1‑54 (MQ=255)
                                                        aaGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGtt                        >  1:5557866/1‑53 (MQ=255)
                                                         aGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTAACAACt     <  1:1435832/71‑1 (MQ=255)
                                                         aGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTAACAACt     <  1:4297176/71‑1 (MQ=255)
                                                          gggTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGa                  >  1:4734498/1‑57 (MQ=255)
                                                           ggTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTaacaa       >  1:2129616/1‑67 (MQ=255)
                                                            gTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTAACAACtcat  <  1:1968655/71‑1 (MQ=255)
                                                            gTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTAACAACtcat  <  1:1948681/71‑1 (MQ=255)
                                                            gTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTAACAACtcat  <  1:2787557/71‑1 (MQ=255)
                                                            gTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTAACAACtcat  <  1:2724373/71‑1 (MQ=255)
                                                              tATGATGACGAGCTTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTAACAACtcat  <  1:4135275/69‑1 (MQ=25)
                                                              |                                                                    
CAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTTACTAACAACTCAT  >  minE/2045792‑2045921

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