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 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,804,090 G→A 73.5% G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,804,0900GA73.5% 366.2 / 158.0 226G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (30/30);  new base A (77/89);  total (107/119)
Fisher's exact test for biased strand distribution p-value = 6.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.72e-01

Only 100 of 237 total aligned reads displayed.

CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCT  >  minE/1804023‑1804159
                                                                   |                                                                     
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 <  1:2926668/71‑1 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                 <  1:1416111/71‑1 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                               <  1:466372/68‑1 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGGGAc                                                            >  1:63680/1‑71 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                            >  1:1025638/1‑71 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                            >  1:1326646/1‑71 (MQ=255)
             gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                       >  1:3628158/1‑71 (MQ=255)
             gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                       >  1:2341715/1‑71 (MQ=255)
             gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                       >  1:3449978/1‑71 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      >  1:484053/1‑71 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                      <  1:3738642/71‑1 (MQ=255)
               acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                     <  1:1474735/71‑1 (MQ=255)
                 atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                   <  1:1689083/71‑1 (MQ=255)
                 atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                      <  1:1049088/68‑1 (MQ=255)
                    caATGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                <  1:3163636/71‑1 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 >  1:3817638/1‑54 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                    <  1:3785147/67‑1 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                >  1:770014/1‑71 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                >  1:3294911/1‑71 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                >  1:1898245/1‑71 (MQ=255)
                     aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                               <  1:2947046/71‑1 (MQ=255)
                     aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                               <  1:340125/71‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATg                                                  >  1:1715303/1‑66 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                             >  1:3687724/1‑71 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGt                                              <  1:3240375/70‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             >  1:2510873/1‑71 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             >  1:1795647/1‑71 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             <  1:1272073/71‑1 (MQ=255)
                         caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                  >  1:2604994/1‑48 (MQ=255)
                         caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                           >  1:3031006/1‑71 (MQ=255)
                           agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                          >  1:3722639/1‑70 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                     <  1:3488577/58‑1 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             <  1:3091602/66‑1 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             <  1:136343/66‑1 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                        >  1:1945979/1‑71 (MQ=255)
                              tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                     >  1:581252/1‑40 (MQ=255)
                              tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                     >  1:1250192/1‑40 (MQ=255)
                                ctgGAGAACCTCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                     <  1:346060/70‑1 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      <  1:891809/69‑1 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      <  1:1192785/69‑1 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                     <  1:1099286/70‑1 (MQ=255)
                                  ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   >  1:3863059/1‑70 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                  <  1:722652/70‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   <  1:1600037/69‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   <  1:3676425/69‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   <  1:335995/69‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   <  1:2190440/69‑1 (MQ=255)
                                     gaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                               >  1:2826758/1‑71 (MQ=255)
                                     gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                               >  1:3518327/1‑71 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                     <  1:3044631/48‑1 (MQ=255)
                                       aCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      >  1:3368517/1‑46 (MQ=255)
                                       aCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             <  1:2549057/71‑1 (MQ=255)
                                         cGCAATAAAATGCTGAAGGCTCAGGGGATTAAGGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                           <  1:2616567/71‑1 (MQ=255)
                                         cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             >  1:2421678/1‑69 (MQ=255)
                                         cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             >  1:39969/1‑69 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             <  1:2235240/67‑1 (MQ=255)
                                            aaTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                         >  1:1322546/1‑70 (MQ=255)
                                            aaTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                        <  1:543528/71‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:656175/71‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                              >  1:432097/1‑64 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:23309/71‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:167354/71‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                      <  1:2319649/39‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                          <  1:2802437/51‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             <  1:212676/64‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                      <  1:525080/71‑1 (MQ=255)
                                               aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                       >  1:2150226/1‑53 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:62899/68‑1 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                <  1:2069733/43‑1 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                          <  1:3919786/49‑1 (MQ=255)
                                                 aaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 >  1:2912820/1‑57 (MQ=255)
                                                 aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 >  1:3578287/1‑57 (MQ=255)
                                                 aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 >  1:1627675/1‑57 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                           >  1:2482212/1‑46 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                        >  1:1647039/1‑49 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                        >  1:2895377/1‑49 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                  <  1:2360972/71‑1 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                  >  1:1537174/1‑71 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                  <  1:3005546/71‑1 (MQ=255)
                                                   tGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                           >  1:2692587/1‑61 (MQ=255)
                                                   tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 >  1:2366138/1‑55 (MQ=255)
                                                   tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 >  1:2902862/1‑55 (MQ=255)
                                                   tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac                 <  1:1163960/71‑1 (MQ=255)
                                                    gCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                  <  1:2523750/53‑1 (MQ=255)
                                                     cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg               <  1:3617300/71‑1 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                            >  1:2089811/1‑39 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                          >  1:1129749/1‑57 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt            <  1:2576990/71‑1 (MQ=255)
                                                         aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                           <  1:276220/39‑1 (MQ=255)
                                                         aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt           <  1:852246/71‑1 (MQ=255)
                                                         aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt           >  1:1239298/1‑71 (MQ=255)
                                                          ggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                            >  1:1923600/1‑53 (MQ=255)
                                                           gCTCAGGGAATTAACGAGCCGTTGTTTATGGCGTTGa                                           >  1:3847591/1‑37 (MQ=37)
                                                            cTCAGGGGATTAACGAGACGTTCTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt           <  1:149915/68‑1 (MQ=255)
                                                             tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGc       >  1:2276341/1‑71 (MQ=255)
                                                               aGGGGATTAACGAGACGTTGTTTATGGCGTTGAtt                                         <  1:3647395/35‑1 (MQ=255)
                                                               aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGc       <  1:1452441/69‑1 (MQ=255)
                                                                ggggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                      >  1:3338779/1‑53 (MQ=255)
                                                                ggggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                        >  1:1383340/1‑51 (MQ=255)
                                                                  ggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTc   >  1:75545/1‑70 (MQ=255)
                                                                   |                                                                     
CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCT  >  minE/1804023‑1804159

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