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
A1 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 4,268,686 C→T L261L (CTG→TTG)  dnaB → replicative DNA helicase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,268,6860CT99.1% 341.6 / ‑4.4 108L261L (CTG→TTG) dnaBreplicative DNA helicase
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (59/48);  total (60/48)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

Only 100 of 108 total aligned reads displayed.

CAACATTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGCTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTGGCGTCGCTGTCGCGCGTTGAC  >  W3110S.gb/4268618‑4268745
                                                                    |                                                           
caacaTTTGCGATGAACCTCGTCGAAAACTCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:3576219/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:3630425/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           <  1:2575008/71‑1 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           <  1:2725940/71‑1 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:2407898/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           <  1:2395716/71‑1 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:4103570/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           <  1:206802/71‑1 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           <  1:2051049/71‑1 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           <  1:4079613/71‑1 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:486572/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           <  1:186928/71‑1 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:3079256/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:4014880/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:1280140/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:802821/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:390044/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:3848904/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:1529435/1‑71 (MQ=255)
caacaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:140029/1‑71 (MQ=255)
caaaaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:2381256/1‑71 (MQ=255)
  acaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:1683684/1‑69 (MQ=255)
  acaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:1607459/1‑69 (MQ=255)
  acaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:3593637/1‑69 (MQ=255)
  acaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:1581304/1‑69 (MQ=255)
  acaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:2265389/1‑69 (MQ=255)
  acaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:2231080/1‑69 (MQ=255)
  acaTTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           >  1:2216453/1‑69 (MQ=255)
     tttGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGAt                                                      <  1:2162429/71‑1 (MQ=255)
     tttGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGAt                                                      <  1:305552/71‑1 (MQ=255)
            tGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           <  1:1718095/59‑1 (MQ=255)
                    gtcgAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTgg                                                          >  1:2388422/1‑52 (MQ=255)
                    gtcgAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGga                                                         >  1:57417/1‑53 (MQ=255)
                    gtcgAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGga                                                         >  1:2423440/1‑53 (MQ=255)
                    gtcgAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGga                                                         >  1:3302546/1‑53 (MQ=255)
                    gtcgAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGga                                                         >  1:217798/1‑53 (MQ=255)
                     tcgAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTg                                                           <  1:3028366/50‑1 (MQ=255)
                       gAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCa                                     <  1:2853782/70‑1 (MQ=255)
                       gAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCa                                     <  1:2423364/70‑1 (MQ=255)
                       gAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCa                                     <  1:1199647/70‑1 (MQ=255)
                       gAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAAAAGATCa                                     <  1:1563/70‑1 (MQ=255)
                        aaaaCGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGAt                                                      <  1:537355/52‑1 (MQ=255)
                          aaCGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCatgat                                 >  1:2292198/1‑71 (MQ=255)
                          aaCGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCatgat                                 >  1:1956432/1‑71 (MQ=255)
                              cggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGt                             <  1:3044977/71‑1 (MQ=255)
                              cggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGt                             <  1:2735106/71‑1 (MQ=255)
                              cggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGt                             <  1:3698987/71‑1 (MQ=255)
                              cggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGt                             <  1:2192800/71‑1 (MQ=255)
                              cggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGt                             <  1:911465/71‑1 (MQ=255)
                              cggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGt                             <  1:1852456/71‑1 (MQ=255)
                              cggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGt                             <  1:1832977/71‑1 (MQ=255)
                              cggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGt                             <  1:670233/71‑1 (MQ=255)
                              cggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGt                             <  1:623541/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAAGCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:2530527/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGTTGCGtt                            <  1:18809/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:2570211/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:945081/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:1227619/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:3722476/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:1692771/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:3325757/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:4052334/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:1698439/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:1851752/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:4567/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:447052/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:4122632/71‑1 (MQ=255)
                               ggcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGt                             <  1:1117029/70‑1 (MQ=255)
                                gcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:452004/70‑1 (MQ=255)
                                gcgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:57949/70‑1 (MQ=255)
                                 cgATGTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:575443/69‑1 (MQ=255)
                                     gTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTgg                      >  1:725941/1‑71 (MQ=255)
                                     gTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTgg                      >  1:1233747/1‑71 (MQ=255)
                                     gTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTgg                      >  1:2009787/1‑71 (MQ=255)
                                     gTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTgg                      >  1:4137424/1‑71 (MQ=255)
                                     gTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTgg                      >  1:2655816/1‑71 (MQ=255)
                                     gTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTgg                      >  1:2824335/1‑71 (MQ=255)
                                     gTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTgg                      >  1:2947938/1‑71 (MQ=255)
                                     gTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTgg                      >  1:645020/1‑71 (MQ=255)
                                     gTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTgg                      >  1:685986/1‑71 (MQ=255)
                                     gTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTg                       >  1:3378390/1‑70 (MQ=255)
                                     gTTGCAGGATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGAGTTCTCTgg                      >  1:3318246/1‑71 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGaa                                            >  1:524837/1‑42 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTtctc                         >  1:1578256/1‑61 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTtctc                         >  1:1393658/1‑61 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTtctc                         >  1:1352376/1‑61 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTtctc                         >  1:789322/1‑61 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTtctc                         >  1:46562/1‑61 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTtctc                         >  1:232659/1‑61 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTtctc                         >  1:4127741/1‑61 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTtctc                         >  1:3351595/1‑61 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTtctc                         >  1:3934730/1‑61 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTtctc                         >  1:336113/1‑61 (MQ=255)
                                            gATAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTtctc                         >  1:3745093/1‑61 (MQ=255)
                                             aTAAACCGGTACTTATCTTCTCGCTGGAGATGCCATCAGAACAGATCATGATGCGTtct                          >  1:2048252/1‑59 (MQ=255)
                                              tAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTGGCGTCGCTGt             >  1:3659677/1‑71 (MQ=255)
                                              tAAACCGGTACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTGGCGTCGCTGt             >  1:1096695/1‑71 (MQ=255)
                                                      tACTTATCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGtt                            <  1:2034373/48‑1 (MQ=255)
                                                           aTCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTGGCGTCGCTGTCGCGCGTTGAc  >  1:1636020/1‑69 (MQ=255)
                                                           aTCTTCTCGTTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTGGCGTCGCTGTCGCGCGTTGAc  >  1:3453734/1‑69 (MQ=255)
                                                                    |                                                           
CAACATTTGCGATGAACCTCGTCGAAAACGCGGCGATGTTGCAGGATAAACCGGTACTTATCTTCTCGCTGGAGATGCCATCAGAACAGATCATGATGCGTTCTCTGGCGTCGCTGTCGCGCGTTGAC  >  W3110S.gb/4268618‑4268745

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