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 2,326,771 A→G 36.3% E179E (GAA→GAG)  cpxR → DNA‑binding response regulator in two‑component regulatory system with CpxA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,326,7710AG36.3% 51.9 / 54.0 88E179E (GAA→GAG) cpxRDNA‑binding response regulator in two‑component regulatory system with CpxA
Reads supporting (aligned to +/- strand):  ref base A (25/31);  new base G (5/27);  total (30/58)
Fisher's exact test for biased strand distribution p-value = 9.40e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.91e-01

Only 100 of 104 total aligned reads displayed.

TTAACCGGTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGATATGCACATT  >  minE/2326703‑2326837
                                                                    |                                                                  
ttAACCGGTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGaa                                                                    <  1:57328/69‑1 (MQ=255)
ttAACCGGTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGaa                                                                    <  1:2920494/69‑1 (MQ=255)
ttAACCGGTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGaa                                                                    <  1:444546/69‑1 (MQ=255)
ttAACCGGTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGaa                                                                    <  1:2415410/69‑1 (MQ=255)
ttAACCGGTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGaa                                                                    <  1:2306138/69‑1 (MQ=255)
ttAACCGGTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGaa                                                                    <  1:2301370/69‑1 (MQ=255)
ttAACCGGTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGaa                                                                    <  1:213812/69‑1 (MQ=255)
ttAACCGGTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGaa                                                                    <  1:1562926/69‑1 (MQ=255)
ttAACCGGTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGaa                                                                    <  1:1171099/69‑1 (MQ=255)
      ggTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTa                                                              <  1:2383876/69‑1 (MQ=255)
      ggTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTa                                                              <  1:825290/69‑1 (MQ=255)
      ggTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTa                                                              <  1:813523/69‑1 (MQ=255)
      ggTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTa                                                              <  1:3135327/69‑1 (MQ=255)
      ggTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTa                                                              <  1:1044450/69‑1 (MQ=255)
      ggTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTa                                                              <  1:2634273/69‑1 (MQ=255)
      ggTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTa                                                              <  1:3400870/69‑1 (MQ=255)
      ggTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTa                                                              <  1:1689032/69‑1 (MQ=255)
      ggTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGGTTCCCGTGAGCATTTa                                                              <  1:1202869/69‑1 (MQ=255)
      ggTACTGAGTTTACCCTGCTCTATTTCCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTa                                                              <  1:3107657/69‑1 (MQ=255)
        tACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTa                                                              <  1:84930/67‑1 (MQ=255)
          cTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGcc                                                          >  1:2361162/1‑69 (MQ=255)
               tttACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGaa                                                     >  1:1308173/1‑69 (MQ=255)
               tttACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGaa                                                     >  1:1417882/1‑69 (MQ=255)
               tttACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGaa                                                     >  1:1527732/1‑69 (MQ=255)
                 tACCCTGCTCTATTTGCTGGGACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:1295560/62‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:1746602/62‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:1784647/62‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:857598/62‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:2936990/62‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:1130858/62‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:3312062/62‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:657828/62‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:864108/62‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:2660711/62‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:2842216/62‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGCCAGGAAgt                                                   >  1:1739191/1‑69 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGCCAGGAAgt                                                   >  1:2905464/1‑69 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGCCAGGAAgt                                                   >  1:481259/1‑69 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGCCAGGAAgt                                                   >  1:1908608/1‑69 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGCCAGGAAgt                                                   >  1:1850367/1‑69 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAgt                                                   >  1:2014413/1‑69 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAgt                                                   <  1:2191013/69‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAgt                                                   >  1:1849651/1‑69 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAgt                                                   >  1:279831/1‑69 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAgt                                                   >  1:57699/1‑69 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGT‑AGCATTTAAGcc                                                          <  1:2105794/61‑1 (MQ=255)
                 tACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGT‑AGCATTTAAGcc                                                          <  1:2101847/61‑1 (MQ=255)
                 tACCCTGATCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAGCATTTAAGcc                                                          <  1:181988/62‑1 (MQ=255)
                     cTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACAt                                                                 >  1:2774429/1‑51 (MQ=255)
                     cTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGtt                                                >  1:2526568/1‑68 (MQ=255)
                     cTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTg                                               >  1:530222/1‑69 (MQ=255)
                     cTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTg                                               >  1:1264763/1‑69 (MQ=255)
                     cTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTg                                               >  1:2053975/1‑69 (MQ=255)
                     cTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTg                                               >  1:1621520/1‑69 (MQ=255)
                             tttGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACg                                       >  1:2268556/1‑69 (MQ=255)
                             tttGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACg                                       >  1:3221478/1‑69 (MQ=255)
                             tttGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACg                                       >  1:1384984/1‑69 (MQ=255)
                             tttGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACg                                       >  1:2997418/1‑69 (MQ=255)
                             tttGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACg                                       >  1:2034361/1‑69 (MQ=255)
                             tttGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACg                                       >  1:3348611/1‑69 (MQ=255)
                             tttGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACg                                       >  1:3293225/1‑69 (MQ=255)
                             tttGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACg                                       >  1:2278274/1‑69 (MQ=255)
                                         gCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAgt                                                   <  1:1840776/45‑1 (MQ=255)
                                              tGGGTCAGGTGGTTTCCCGTTAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTc                          <  1:2120100/65‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTTGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:3074119/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGTCCGCGCTATTGa            <  1:2621353/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:3410110/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:364618/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            >  1:535899/1‑69 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:2607898/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:592221/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:858284/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:323299/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:956368/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:279713/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:1471612/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:1611925/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:1735872/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            >  1:3221218/1‑69 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:2147074/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:2469868/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:1432644/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:2740879/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:279803/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:1421602/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:1412376/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:1388491/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            >  1:125649/1‑69 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:1095165/69‑1 (MQ=255)
                                                        ggtTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:3070245/69‑1 (MQ=255)
                                                        gggttCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGa            <  1:2031302/66‑1 (MQ=255)
                                                           ttCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGata          <  1:2840887/68‑1 (MQ=255)
                                                           ttCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGata          <  1:332227/68‑1 (MQ=255)
                                                                   aaCATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGATATGCACAtt  >  1:737750/1‑68 (MQ=255)
                                                                   aaCATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGATATGCACAtt  >  1:263262/1‑68 (MQ=255)
                                                                   aaCATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGATATGCACAtt  >  1:3003297/1‑68 (MQ=255)
                                                                   aaCATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGATATGCACAtt  >  1:3312572/1‑68 (MQ=255)
                                                                   aaCATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGATATGCACAtt  >  1:3037044/1‑68 (MQ=255)
                                                                   aaCATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGATATGCACAtt  >  1:929842/1‑68 (MQ=255)
                                                                   aaCATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGATATGCACAtt  >  1:1087783/1‑68 (MQ=255)
                                                                    |                                                                  
TTAACCGGTACTGAGTTTACCCTGCTCTATTTGCTGGCACAGCATCTGGGTCAGGTGGTTTCCCGTGAACATTTAAGCCAGGAAGTGTTGGGCAAACGCCTGACGCCTTTCGACCGCGCTATTGATATGCACATT  >  minE/2326703‑2326837

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