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 2,584,463 T→C 45.6% K938K (AAA→AAG)  mdtF ← multidrug transporter, RpoS‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,584,4630TC45.6% 17.9 / 107.2 125K938K (AAA→AAG) mdtFmultidrug transporter, RpoS‑dependent
Reads supporting (aligned to +/- strand):  ref base T (41/27);  new base C (25/32);  total (66/59)
Fisher's exact test for biased strand distribution p-value = 7.47e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 126 total aligned reads displayed.

TCGGCGTTTTCCCTTCTTTCTGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGAAGTAGACGTCATTACTTAAGCCG  >  minE/2584402‑2584526
                                                             |                                                               
tCGGCGTTTTCCCTTCTTTCTGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTTGCg                                                           >  1:2394299/1‑68 (MQ=255)
tCGGCGTTTTCCCTTCTTTCTGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCg                                                           >  1:2421951/1‑68 (MQ=255)
tCGGCGTTTTCCCTTCTTTCTGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCg                                                           >  1:153168/1‑68 (MQ=255)
  ggCGTTTTCCCTTCTTTCTGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGtttt                                                                >  1:1907931/1‑61 (MQ=255)
  ggCGTTTTCCCTTCTTTCTGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGaa                                                        >  1:627169/1‑69 (MQ=255)
  ggCGTTTTCCCTTCTTTCTGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGaa                                                        >  1:1860496/1‑69 (MQ=255)
  ggCGTTTTCCCTTCTTTCTGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGaa                                                        >  1:3409692/1‑69 (MQ=255)
  ggCGTTTTCCCTTCTTTCTGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGaa                                                        >  1:2556190/1‑69 (MQ=255)
          cccTTCTTTCTGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGa                                                 <  1:550845/68‑1 (MQ=255)
                 ttctGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATtgtggt                                          <  1:546047/68‑1 (MQ=255)
                 ttctGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATggtggt                                          <  1:1197770/68‑1 (MQ=255)
                 ttctGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATggtggt                                          <  1:2762904/68‑1 (MQ=255)
                 ttctGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATggtggt                                          <  1:2217468/68‑1 (MQ=255)
                 ttctGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATggtggt                                          <  1:2661412/68‑1 (MQ=255)
                 ttctGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATggtggt                                          <  1:1840395/68‑1 (MQ=255)
                 ttctGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATggtggt                                          <  1:1677203/68‑1 (MQ=255)
                 ttctGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATggtggt                                          <  1:560552/68‑1 (MQ=255)
                 ttctGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATggtggt                                          <  1:91318/68‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAg                                       >  1:2251621/1‑68 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAg                                       >  1:2168353/1‑68 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAg                                       >  1:2299987/1‑68 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:2299275/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:2266911/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:2750083/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:856274/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:2167620/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:2159306/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:2130785/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:2909145/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:2956137/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:655674/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:3061234/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:2471164/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:146149/67‑1 (MQ=255)
                    tGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:548092/67‑1 (MQ=255)
                     gCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:2639836/66‑1 (MQ=255)
                     gCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCa                                        <  1:95315/66‑1 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                >  1:2825106/1‑69 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                >  1:2980840/1‑69 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                >  1:1195314/1‑69 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                <  1:595148/69‑1 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                >  1:608970/1‑69 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                >  1:2423189/1‑69 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                <  1:866908/69‑1 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                >  1:869598/1‑69 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                >  1:1554235/1‑69 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                >  1:1929826/1‑69 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                <  1:1217988/69‑1 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                <  1:122783/69‑1 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                <  1:1779344/69‑1 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                >  1:2359962/1‑69 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                >  1:1759061/1‑69 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacca                                >  1:1868152/1‑69 (MQ=255)
                          atcTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaacc                                 >  1:1363941/1‑68 (MQ=255)
                            ctcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGCAaaccaa                               <  1:3095650/68‑1 (MQ=255)
                            ctcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGCAaaccaa                               <  1:1993092/68‑1 (MQ=255)
                            ctcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGCAaaccaa                               <  1:2773/68‑1 (MQ=255)
                            ctcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGCAaaccaa                               <  1:2302886/68‑1 (MQ=255)
                            ctcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGCAaaccaa                               <  1:804742/68‑1 (MQ=255)
                            ctcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGCAaaccaa                               <  1:2355955/68‑1 (MQ=255)
                             tcAACTGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:2734709/1‑60 (MQ=39)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaaccaacc                             >  1:3069032/1‑69 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaaccaacc                             >  1:876545/1‑69 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaaccaacc                             >  1:2365622/1‑69 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAaaccaacc                             >  1:2467488/1‑69 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAg                                                      >  1:393480/1‑44 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:674789/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:1686729/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:1623004/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:1434477/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:1340761/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:1113702/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:674909/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:768270/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:1233880/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:2369148/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:3298815/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:2546726/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:2525836/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:251114/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:2218104/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:2796744/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:2072670/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:2898509/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:2034996/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:3209740/1‑60 (MQ=255)
                             tcAACGGCAAATTCGACAATCAGGATGGCGTTCTTGGCGGAAAGCCCGATGGTGGTCAGc                                      >  1:2497296/1‑60 (MQ=255)
                                 cGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTggg                         <  1:180032/69‑2 (MQ=255)
                                 cGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGa                         <  1:3037158/69‑1 (MQ=255)
                                 cGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGa                         <  1:2821466/69‑1 (MQ=255)
                                 cGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGa                         <  1:361462/69‑1 (MQ=255)
                                 cGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGa                         <  1:2732298/69‑1 (MQ=255)
                                 cGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGa                         <  1:704586/69‑1 (MQ=255)
                                 cGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGa                         <  1:1238537/69‑1 (MQ=255)
                                          cGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGAAGTAGACGt                <  1:2426115/69‑1 (MQ=255)
                                             cAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGAAGTAGACGTCAt             <  1:3338610/69‑1 (MQ=255)
                                                 cAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGAAGTAGACGTCATTAc          >  1:2245525/1‑68 (MQ=255)
                                                        gCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGAAGTAGACGTCATTACTTAAGCcg  >  1:2649697/1‑69 (MQ=255)
                                                        gCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGAAGTAGACGTCATTACTTAAGCcg  >  1:3252173/1‑69 (MQ=255)
                                                        gCGTTCTTGGCGGAAAGCCCGATGGTGGGCAGCAaaccaa                               <  1:2640285/40‑1 (MQ=38)
                                                             |                                                               
TCGGCGTTTTCCCTTCTTTCTGCATCATCTCAACGGCAAATTCGACAATCAGGATGGCGTTTTTGGCGGAAAGCCCGATGGTGGTCAGCAAACCAACCTGGAAGTAGACGTCATTACTTAAGCCG  >  minE/2584402‑2584526

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