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 F3 I0 R1 41 86.6 4450826 94.1% 4188227 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,804,090 G→A 26.8% G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,804,0900GA26.8% 306.8 / 124.4 168G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (57/66);  new base A (25/20);  total (82/86)
Fisher's exact test for biased strand distribution p-value = 3.02e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 173 total aligned reads displayed.

CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCT  >  minE/1804023‑1804159
                                                                   |                                                                     
  cGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                  >  1:1808152/1‑71 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                                   <  1:272269/69‑1 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                                   <  1:2691755/69‑1 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 >  1:3648979/1‑71 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 <  1:2467416/71‑1 (MQ=255)
      tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 >  1:4417280/1‑68 (MQ=255)
      tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 >  1:1830462/1‑68 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGAc                                                            >  1:1679128/1‑71 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                            >  1:465396/1‑71 (MQ=255)
         gcatgcaCATGCAAAGCAAGCTGCTGGAGAACCTCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                            <  1:3958674/70‑1 (MQ=255)
          catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                          <  1:1055082/71‑1 (MQ=255)
          catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                          <  1:1513938/71‑1 (MQ=255)
             gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                               >  1:2834563/1‑63 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      <  1:958728/71‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                      <  1:2860039/71‑1 (MQ=255)
               acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      >  1:3846402/1‑70 (MQ=255)
               acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                     <  1:523299/71‑1 (MQ=255)
                  tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                  >  1:1707910/1‑71 (MQ=255)
                      aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGt                                              >  1:639100/1‑71 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      <  1:2750965/62‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                             >  1:1308454/1‑71 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                             <  1:1686741/71‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                            >  1:2257067/1‑56 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                            >  1:1068935/1‑56 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                    <  1:2888653/47‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                             <  1:2438963/70‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                             <  1:2698213/70‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                            <  1:823958/71‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                            <  1:3968131/71‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                            <  1:2137945/71‑1 (MQ=255)
                         caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                           >  1:1261862/1‑71 (MQ=255)
                         caagcTGCTGGAGAAACGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTCTTTATGGCGTTg                                            >  1:4286689/1‑70 (MQ=255)
                          aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                  >  1:3195468/1‑47 (MQ=255)
                          aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                  >  1:3105117/1‑47 (MQ=255)
                          aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                                   >  1:2189644/1‑46 (MQ=255)
                           agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      <  1:3581441/58‑1 (MQ=255)
                             ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                            >  1:1718924/1‑66 (MQ=255)
                             ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                           >  1:209495/1‑67 (MQ=255)
                             ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                           >  1:2445372/1‑67 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                           >  1:3328380/1‑64 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                           >  1:1890926/1‑64 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                   >  1:2023818/1‑55 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                   >  1:3737518/1‑55 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 <  1:2689425/39‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 <  1:2989535/39‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 <  1:2351802/39‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 <  1:1938307/39‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   >  1:1726225/1‑69 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 <  1:3882767/71‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 <  1:427275/71‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                             >  1:1277700/1‑43 (MQ=255)
                                    agaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACTCTgg                                  <  1:3928262/69‑1 (MQ=255)
                                    agaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                               <  1:4148463/40‑1 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgag                                                              <  1:340726/39‑1 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      <  1:886376/63‑1 (MQ=255)
                                       aCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             <  1:2526438/71‑1 (MQ=255)
                                        ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGTAGtctc                            <  1:5842/71‑1 (MQ=255)
                                        ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                            <  1:1010830/71‑1 (MQ=255)
                                        ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             <  1:1534780/70‑1 (MQ=255)
                                        ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             >  1:4230084/1‑70 (MQ=255)
                                         cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                           <  1:3437663/71‑1 (MQ=255)
                                          gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             >  1:1057135/1‑68 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                          >  1:2603242/1‑70 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   <  1:1015667/59‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:3190063/71‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                         >  1:2229692/1‑69 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:3671489/71‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:2301716/71‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                     <  1:2093112/40‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      <  1:3521134/55‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      <  1:2280504/55‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                      <  1:3354845/71‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                      <  1:3362269/71‑1 (MQ=255)
                                               aaaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                     >  1:2754123/1‑71 (MQ=255)
                                               aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                  >  1:1468861/1‑58 (MQ=255)
                                               aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 >  1:691782/1‑59 (MQ=255)
                                               aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 >  1:1750136/1‑59 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                                 >  1:4281305/1‑40 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                  >  1:15770/1‑71 (MQ=255)
                                                   tGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                           <  1:90323/61‑1 (MQ=255)
                                                   tGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                  >  1:1119611/1‑70 (MQ=255)
                                                   tGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTATCAGGAAAACca                  >  1:3942295/1‑70 (MQ=255)
                                                     cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                         >  1:1401646/1‑61 (MQ=255)
                                                     cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg               <  1:4039951/71‑1 (MQ=255)
                                                      tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                            <  1:763257/41‑1 (MQ=255)
                                                      tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                           >  1:2540948/1‑42 (MQ=255)
                                                      tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:4114311/62‑1 (MQ=255)
                                                      tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:4109190/62‑1 (MQ=255)
                                                       gAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                    >  1:242209/1‑48 (MQ=255)
                                                        aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                     >  1:2782393/1‑62 (MQ=255)
                                                        aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                     >  1:3500184/1‑62 (MQ=255)
                                                        aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt            <  1:2185706/71‑1 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGt              <  1:1627603/69‑1 (MQ=255)
                                                          ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTc          <  1:4012635/71‑1 (MQ=255)
                                                            cTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAg        <  1:1465526/71‑1 (MQ=255)
                                                             tCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa         <  1:4304194/69‑1 (MQ=255)
                                                               aGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTc          <  1:1082367/66‑1 (MQ=255)
                                                                  ggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTc   >  1:3832348/1‑70 (MQ=255)
                                                                   gATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             >  1:2118068/1‑43 (MQ=255)
                                                                   gATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCt  >  1:1858703/1‑70 (MQ=255)
                                                                   |                                                                     
CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCT  >  minE/1804023‑1804159

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A