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 2,684,679 A→G 61.7% L56L (TTA→TTG)  ompR → DNA‑binding response regulator in two‑component regulatory system with EnvZ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,684,6790AG61.7% 65.1 / 72.1 112L56L (TTA→TTG) ompRDNA‑binding response regulator in two‑component regulatory system with EnvZ
Reads supporting (aligned to +/- strand):  ref base A (21/22);  new base G (19/50);  total (40/72)
Fisher's exact test for biased strand distribution p-value = 2.68e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 112 total aligned reads displayed.

TAATGCAGAACAGATGGATCGCCTGCTGACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCAGAGCAACCCGATGCCG  >  minE/2684616‑2684745
                                                               |                                                                  
tAATGCAGAACAGATGGATCGCCTGCTGACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGtt                                                               <  1:2069840/69‑1 (MQ=255)
tAATGCAGAACAGATGGATCGCCTGCTGACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGtt                                                               <  1:2283688/69‑1 (MQ=255)
tAATGCAGAACAGATGGATCGCCTGCTGACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGt                                                                <  1:1078651/68‑1 (MQ=255)
 aaTGCAGAACAGATGGATCGCCTGCTGACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGTTa                                                              <  1:1707948/69‑1 (MQ=255)
 aaTGCAGAACAGATGGATCGCCTGCTGACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGTTa                                                              <  1:2347491/69‑1 (MQ=255)
 aaTGCAGAACAGATGGATCGCCTGCTGACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGTTa                                                              <  1:2586843/69‑1 (MQ=255)
 aaTGCAGAACAGATGGATCGCCTGCTGACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGTTa                                                              <  1:1173171/69‑1 (MQ=255)
          cAGATGGATCGCCTGCTGACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGTTACCTGGTGaa                                                     <  1:1003992/69‑1 (MQ=255)
              tGGATCGCCTGCTGACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGTTACCTGGTGAAGATg                                                 <  1:762005/69‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:1791959/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:5062/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:956499/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:1818685/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:1944807/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:939115/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:2080187/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:2083072/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:878479/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:2316886/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:251669/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:2554485/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:676388/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:666454/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:2691110/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:272480/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:274969/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:2994851/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:1528245/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:120672/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:1464981/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:1157340/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:1103101/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:148396/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:1487089/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:1539776/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:1788778/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTCACCTgg                                                         <  1:696282/52‑1 (MQ=255)
                       tgctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGTTACCTGGTGAAGATGGCTTGTCGa                                        <  1:628149/69‑1 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGt                                                                >  1:2732913/1‑43 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:3183214/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:531471/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:3244749/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:3146021/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:2905633/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:3258699/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:3413942/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:3434648/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:612860/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:1968801/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:2011663/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:2188632/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:1922437/1‑57 (MQ=255)
                         ctgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGAt                                                  >  1:1466913/1‑57 (MQ=255)
                          tgACTCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:794566/49‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:2831032/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:3159964/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:1055542/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:3079290/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:662127/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:2964365/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:1621794/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:3269881/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:2765269/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:3398473/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:700906/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:445318/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:112777/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:1173089/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:1199542/68‑1 (MQ=255)
                              tCGTGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:2539183/68‑1 (MQ=255)
                              tCGGGAATCTTTCCATCTTATGGTACTGGATTTGATGTTACCTGGTGAAGATGGCTTGTCGATTTGcc                                  <  1:2618493/68‑1 (MQ=255)
                                  gAATCTTTCCATCTTATGGTACTGGATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGAc                               <  1:1887306/67‑1 (MQ=255)
                                  gAATCTTTCCATCTTATGGTACTGGATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGAc                               <  1:815456/67‑1 (MQ=255)
                                  gAATCTTTCCATCTTATGGTACTGGATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGAc                               <  1:289896/67‑1 (MQ=255)
                                  gAATCTTTCCATCTTATGGTACTGGATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGAc                               <  1:1057854/67‑1 (MQ=255)
                                   aaTCTTTCCATCTTATGGTACTGGATTTGATGTTACCTgg                                                         <  1:2942124/40‑1 (MQ=255)
                                       tttCCATCTTATGGTACTGGATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCtt                          >  1:2715667/1‑67 (MQ=255)
                                               ttATGGTACTGGATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCag                 >  1:677632/1‑68 (MQ=255)
                                               ttATGGTACTGGATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCag                 >  1:653919/1‑68 (MQ=255)
                                               ttATGGTACTGGATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCag                 >  1:1171637/1‑68 (MQ=255)
                                                         ggATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCAGAGCAAccc         <  1:1059038/66‑1 (MQ=255)
                                                         ggATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCAGAGCAAccc         <  1:1023229/66‑1 (MQ=255)
                                                         ggATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCAGAGCAAccc         <  1:1153710/66‑1 (MQ=255)
                                                         ggATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCAGAGCAAccc         <  1:2709842/66‑1 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGcc   >  1:3223631/1‑69 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGcc   >  1:1689602/1‑69 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGcc   >  1:105140/1‑69 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGcc   >  1:801609/1‑69 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGcc   >  1:2206735/1‑69 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGcc   >  1:2332585/1‑69 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGcc   >  1:7511/1‑69 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGcc   >  1:2449802/1‑69 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGcc   >  1:2804955/1‑69 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGcc   >  1:3113178/1‑69 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGc    >  1:640525/1‑68 (MQ=255)
                                                            tttAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTTAGAGCAACCCGATGc    >  1:359446/1‑68 (MQ=255)
                                                              tAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCAGAGCAAc           >  1:2391678/1‑59 (MQ=255)
                                                              tAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCAGAGCAACCCGATGCCg  >  1:1213822/1‑68 (MQ=255)
                                                              tAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCAGAGCAACCCGATGCCg  >  1:1999296/1‑68 (MQ=255)
                                                              tAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCAGAGCAACCCGATGCCg  >  1:1886317/1‑68 (MQ=255)
                                                               |                                                                  
TAATGCAGAACAGATGGATCGCCTGCTGACTCGTGAATCTTTCCATCTTATGGTACTGGATTTAATGTTACCTGGTGAAGATGGCTTGTCGATTTGCCGACGTCTTCGTAGTCAGAGCAACCCGATGCCG  >  minE/2684616‑2684745

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