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 2,665,363 G→A 24.6% R883R (CGC→CGT)  malT ← DNA‑binding transcriptional activator, maltotriose‑ATP‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,665,3630GA24.6% 139.3 / 37.5 109R883R (CGC→CGT) malTDNA‑binding transcriptional activator, maltotriose‑ATP‑binding
Reads supporting (aligned to +/- strand):  ref base G (64/18);  new base A (3/24);  total (67/42)
Fisher's exact test for biased strand distribution p-value = 6.28e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.18e-01

Only 100 of 110 total aligned reads displayed.

CGGCTAAACTTACACGCCGTACCCCATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGATGGTGGTTGCCGCGACT  >  minE/2665297‑2665429
                                                                  |                                                                  
cGGCTAAACTTACACGCCGTACCCCATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGc                                                                   <  1:1649391/68‑1 (MQ=255)
cGGCTAAACTTACACGCCGTACCCCATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGc                                                                   <  1:1024902/68‑1 (MQ=255)
cGGCTAAACTTACACGCCGTACCCCATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGc                                                                   <  1:2129656/68‑1 (MQ=255)
cGGCTAAACTTACACGCCGTACCCCATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGc                                                                   <  1:2782936/68‑1 (MQ=255)
cGGCTAAACTTACACGCCGTACCCCATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGc                                                                   <  1:570839/68‑1 (MQ=255)
cGGCTAAACTTACACGCCGTACCCCATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGc                                                                   <  1:725851/68‑1 (MQ=255)
cGGCTAAACTTACACGCCGTACCCCATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGc                                                                   <  1:1144880/68‑1 (MQ=255)
cGGCTAAACTTACACGCCGTACCCCATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGc                                                                   <  1:890079/68‑1 (MQ=255)
  gCTAAACTCATACCCCATATCCCATCATCTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACgg                                                                 <  1:491976/68‑2 (MQ=255)
  gCTAAACTCATACCCCATATCCCATCATCTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACgg                                                                 <  1:1945723/68‑2 (MQ=255)
  gCTAAACTCATACCCCATATCCCATCATCTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACgg                                                                 <  1:1932438/68‑2 (MQ=255)
  gCTAAACTCATACCCCATATCCCATCATCTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACgg                                                                 <  1:1704605/68‑2 (MQ=255)
  gCTAAACTCATACCCCATATCCCATCATCTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACgg                                                                 <  1:3302439/68‑2 (MQ=255)
  gCTAAACTCATACCCCATATCCCATCATCTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACgg                                                                 <  1:2379452/68‑2 (MQ=255)
  gCTAAACTCATACCCCATATCCCATCATCTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACgg                                                                 <  1:1791215/68‑2 (MQ=255)
  gCTAAACTCATACCCCATATCCCATCATCTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACgg                                                                 <  1:1048767/68‑2 (MQ=255)
  gCTAAACTCATACCCCATATCCCATCATCTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACgg                                                                 <  1:762517/68‑2 (MQ=255)
                     ccccATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCt                                              >  1:2871536/1‑68 (MQ=255)
                     ccccATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCt                                              >  1:1842754/1‑68 (MQ=255)
                     ccccATCATCTTCAGCAATTGCTGGGCGTGTTGTACAGCATCCTGGCGATGGGCCACGCCGAGTTTCt                                              >  1:1445987/1‑68 (MQ=255)
                         atcatcTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTa                                          <  1:2948262/68‑1 (MQ=255)
                         atcatcTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTa                                          <  1:2811563/68‑1 (MQ=255)
                         atcatcTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTa                                          <  1:1600158/68‑1 (MQ=255)
                         atcatcTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTa                                          <  1:1554729/68‑1 (MQ=255)
                         atcatcTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTa                                          <  1:1545065/68‑1 (MQ=255)
                         atcatcTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTa                                          <  1:2460325/68‑1 (MQ=255)
                         atcatcTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTa                                          <  1:443434/68‑1 (MQ=255)
                         atcatcTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTa                                          <  1:1452124/68‑1 (MQ=255)
                         atcatcTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTa                                          <  1:1319307/68‑1 (MQ=255)
                         atcatcTTCAGCAGTTTCTGCGCGTGTTGTACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTa                                          <  1:1269250/68‑1 (MQ=255)
                          tcatcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACa                                        <  1:2526082/69‑1 (MQ=255)
                          tcatcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACa                                        <  1:2232645/69‑1 (MQ=255)
                          tcatcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACa                                        <  1:1878680/69‑1 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTTGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:784675/1‑69 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:3354110/1‑69 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:1321206/1‑69 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:1126223/1‑69 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:1446456/1‑69 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:2412783/1‑69 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:3376257/1‑69 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:1096322/1‑69 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:2795603/1‑69 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:1915510/1‑69 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:1769356/1‑69 (MQ=255)
                            atcTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGa                                      >  1:1816850/1‑69 (MQ=255)
                              cTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCCCGCCGAGTTTCTGATACAGAtt                                    >  1:3065816/1‑69 (MQ=255)
                              cTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGAtt                                    >  1:3324128/1‑69 (MQ=255)
                              cTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGAtt                                    >  1:2525510/1‑69 (MQ=255)
                              cTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGAtt                                    >  1:2520122/1‑69 (MQ=255)
                              cTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGAtt                                    >  1:2267119/1‑69 (MQ=255)
                              cTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGAtt                                    >  1:922779/1‑69 (MQ=255)
                              cTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGAtt                                    >  1:1865261/1‑69 (MQ=255)
                              cTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGAtt                                    >  1:2075353/1‑69 (MQ=255)
                              cTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGAtt                                    >  1:1082973/1‑69 (MQ=255)
                                    cAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGa                               <  1:2159399/68‑1 (MQ=255)
                                    cAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGa                               <  1:2751506/68‑1 (MQ=255)
                                    cAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGa                               <  1:1972457/68‑1 (MQ=255)
                                        tGCTGGGCGTGTTTTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGc                          >  1:1540702/1‑69 (MQ=255)
                                        tGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATTCAGATTGCGGATATGc                          >  1:816707/1‑69 (MQ=255)
                                        tGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGc                          >  1:2032703/1‑69 (MQ=255)
                                        tGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGc                          >  1:1760018/1‑69 (MQ=255)
                                        tGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGc                          >  1:3200593/1‑69 (MQ=255)
                                        tGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGc                          >  1:2949824/1‑69 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGGCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:2688065/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:1336694/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:1377208/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:640852/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:672781/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:1458633/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:1259403/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:1258624/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:801460/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:1886445/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:2859115/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCg                                 >  1:1134525/1‑61 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCg                         >  1:1317318/1‑69 (MQ=255)
                                         gCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCg                         >  1:2780871/1‑69 (MQ=255)
                                               cGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGtttt                     <  1:1896313/67‑1 (MQ=255)
                                                   ttgtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggt               >  1:887447/1‑69 (MQ=255)
                                                   ttgtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggt               >  1:525951/1‑69 (MQ=255)
                                                   ttgtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggt               >  1:2307154/1‑69 (MQ=255)
                                                   ttgtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggt               >  1:94673/1‑69 (MQ=255)
                                                   ttgtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggt               >  1:3416688/1‑69 (MQ=255)
                                                   ttgtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggt               >  1:2655076/1‑69 (MQ=255)
                                                   ttgtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggt               >  1:1955532/1‑69 (MQ=255)
                                                   ttgtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggt               >  1:3027345/1‑69 (MQ=255)
                                                   ttgtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggt               >  1:1833354/1‑69 (MQ=255)
                                                   ttgtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggt               >  1:3314104/1‑69 (MQ=255)
                                                   ttgtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggt               >  1:1631487/1‑69 (MQ=255)
                                                     gtACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTACAGATTGCGGATATGCGTCTTGAtggtgg             >  1:2053725/1‑69 (MQ=255)
                                                     gtACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTACAGATTGCGGATATGCGTCTTGAtggtgg             >  1:932243/1‑69 (MQ=255)
                                                     gtACCGCGGCCTGACGGTGGGCGACACCGAGTTTTTGGTACAGATTGCGGATATGCGTCTTGAtggtgg             >  1:2157443/1‑69 (MQ=255)
                                                     gtACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGAtggtg              <  1:1497569/68‑1 (MQ=255)
                                                          gCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATTCGTTTTGATGGTGGTTGcc        >  1:713171/1‑69 (MQ=255)
                                                          gCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATTCGTTTTGATGGTGGTTGcc        >  1:709264/1‑69 (MQ=255)
                                                          gCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGATGGTGGTTGcc        >  1:88386/1‑69 (MQ=255)
                                                           cATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGATGGTGGTTGcc        >  1:1924159/1‑68 (MQ=255)
                                                             tCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGATGGTGGTTGCcgcg     <  1:3187749/69‑1 (MQ=255)
                                                             tCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGATGGTGGTTGCcgcg     <  1:435308/69‑1 (MQ=255)
                                                                  gCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGATGGTGGTTGCCGCGACt  >  1:3355075/1‑67 (MQ=255)
                                                                  |                                                                  
CGGCTAAACTTACACGCCGTACCCCATCATCTTCAGCAATTGCTGGGCGTGTTGTACCGCATCCTGGCGATGGGCCACGCCGAGTTTCTGATACAGATTGCGGATATGCGTTTTGATGGTGGTTGCCGCGACT  >  minE/2665297‑2665429

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A