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 478,602 T→C 74.7% A230A (GCT→GCC)  cydA → cytochrome d terminal oxidase, subunit I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE478,6020TC74.7% 131.0 / 37.7 106A230A (GCT→GCC) cydAcytochrome d terminal oxidase, subunit I
Reads supporting (aligned to +/- strand):  ref base T (17/10);  new base C (32/47);  total (49/57)
Fisher's exact test for biased strand distribution p-value = 4.82e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

Only 100 of 126 total aligned reads displayed.

CTGAAAGGTCGTGACTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAACCA  >  minE/478534‑478666
                                                                    |                                                                
cTGAAAGGTCGTGACTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGgctgct                                                                  <  1:1937818/69‑1 (MQ=255)
cTGAAAGGTCGTGACTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGgctgct                                                                  <  1:2115141/69‑1 (MQ=255)
 tGAAAGGTCGTGACTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGgctgct                                                                  <  1:2846362/68‑1 (MQ=255)
     aGGTCGTGACTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTtct                                                             >  1:1811849/1‑69 (MQ=255)
     aGGTCGTGACTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTtct                                                             >  1:2252596/1‑69 (MQ=255)
     aGGTCGTGACTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTtc                                                              >  1:828692/1‑68 (MQ=255)
        tCGTGACTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTtctgtc                                                          >  1:151190/1‑69 (MQ=255)
             aCTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTa                                                     <  1:774476/69‑1 (MQ=255)
             aCTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTa                                                     <  1:1434013/69‑1 (MQ=255)
               ttcgccttcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTAt                                                    <  1:714565/68‑1 (MQ=255)
                   ccttcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGt                                                 <  1:925613/67‑1 (MQ=255)
                     ttcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCt                                              >  1:1980815/1‑68 (MQ=255)
                     ttcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTg                                             >  1:2442258/1‑69 (MQ=255)
                     ttcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTg                                             >  1:1548116/1‑69 (MQ=255)
                     ttcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTg                                             >  1:1359194/1‑69 (MQ=255)
                     ttcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTg                                             >  1:838979/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:1991501/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:1097682/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:2602612/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:288198/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:2587868/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:3163334/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:2893727/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:1618964/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:1111013/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:883092/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:3257809/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:1534583/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTGATTGTTCTgg                                            >  1:1436768/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTAGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:1587932/1‑69 (MQ=255)
                      tcgcTAAACGCTCCTTTGCTAACGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTgg                                            >  1:1422538/1‑69 (MQ=255)
                       cgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTgg                                            >  1:1179457/1‑68 (MQ=255)
                       cgcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTgg                                            >  1:2613747/1‑68 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:469931/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:988783/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:2541254/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:2839860/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:712184/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:465106/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:2873721/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:3375210/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:2610991/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:2893856/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:3018542/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:3022519/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:2407247/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:1802691/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:1874118/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:1569507/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:1421683/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:1410191/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:2347620/54‑1 (MQ=255)
                        gcTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCCGTtctgtct                                                         <  1:2392598/54‑1 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGa                         <  1:1439744/68‑1 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGa                         <  1:1547072/68‑1 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGa                         <  1:2989560/68‑1 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGa                         <  1:1761522/68‑1 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGaa                        >  1:1113311/1‑69 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGaa                        >  1:612798/1‑69 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGaa                        >  1:3376522/1‑69 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGaa                        >  1:152759/1‑69 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGaa                        >  1:2428658/1‑69 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGaa                        >  1:3174648/1‑69 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGaa                        >  1:2110612/1‑69 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGaa                        >  1:2766124/1‑69 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGaa                        >  1:2770303/1‑69 (MQ=255)
                                          aTCGCTGCCAGCTTCGGTATGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGaa                        >  1:2333805/1‑69 (MQ=255)
                                             gCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATg                     >  1:558973/1‑69 (MQ=255)
                                             gCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATg                     >  1:3354256/1‑69 (MQ=255)
                                                            aTGGCTGCTGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGaa       >  1:2255900/1‑68 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTTTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:1402170/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGTGTGATGAATCCGGCTACGAAATGGGCg                 <  1:3276618/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:2635581/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:264390/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:562561/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:394888/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:1478547/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:1494239/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:400544/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:1099478/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:2911052/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:3284899/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:3208988/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:2830736/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:3082041/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:1698164/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:1708048/57‑1 (MQ=255)
                                                             tGGCTGCCGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTAAGAAATGGGCg                 <  1:2136762/57‑1 (MQ=255)
                                                               gctgctGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAAc    >  1:2893952/1‑68 (MQ=255)
                                                               gctgctGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAAc    >  1:852341/1‑68 (MQ=255)
                                                               gctgctGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAAc    >  1:1223779/1‑68 (MQ=255)
                                                               gctgctGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAAc    >  1:2940789/1‑68 (MQ=255)
                                                               gctgctGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAAc    >  1:753410/1‑68 (MQ=255)
                                                               gctgctGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAAc    >  1:710148/1‑68 (MQ=255)
                                                               gctgctGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAAc    >  1:594701/1‑68 (MQ=255)
                                                               gctgctGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAAc    >  1:3351782/1‑68 (MQ=255)
                                                               gctgccGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCg                 <  1:1968320/55‑1 (MQ=255)
                                                                  gctgTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAACCa  >  1:209972/1‑67 (MQ=255)
                                                                  gctgTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAACCa  >  1:1140306/1‑67 (MQ=255)
                                                                  gctgTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAACCa  >  1:2718789/1‑67 (MQ=255)
                                                                    |                                                                
CTGAAAGGTCGTGACTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTGTTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAACCA  >  minE/478534‑478666

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