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
A6 F21 I0 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,605,853 T→C 46.1% V14V (GTT→GTC)  yhiO → predicted universal stress (ethanol tolerance) protein B

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,605,8530TC46.1% 18.6 / 144.2 102V14V (GTT→GTC) yhiOpredicted universal stress (ethanol tolerance) protein B
Reads supporting (aligned to +/- strand):  ref base T (35/20);  new base C (35/12);  total (70/32)
Fisher's exact test for biased strand distribution p-value = 2.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-01

Only 100 of 108 total aligned reads displayed.

CGCGGGCAGGTCGCCGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGCGTAACTGCGATC  >  minE/2605786‑2605923
                                                                   |                                                                      
cgcgGGCAGGTCGCCGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTg                                                                      >  1:1470556/1‑70 (MQ=255)
   gggCAGGTCGCCGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCAtt                                                                  <  1:1147724/71‑1 (MQ=255)
    ggCAGGTCGCCGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTACGTGTCGTCTGCATTg                                                                 <  1:1612935/71‑1 (MQ=255)
       aGGTCGCCGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGtt                                                               <  1:1877216/70‑1 (MQ=255)
       aGGTCGCCGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGtt                                                               >  1:808079/1‑70 (MQ=255)
         gTCGCCGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGt                                                                <  1:2700510/67‑1 (MQ=255)
            gCCGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATg                                                         >  1:3368339/1‑71 (MQ=255)
            gCCGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACAt                                                          <  1:3288583/70‑1 (MQ=255)
            gCCGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACAt                                                          <  1:3681382/70‑1 (MQ=255)
             ccGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTa                                                              <  1:2848461/65‑1 (MQ=255)
             ccGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTa                                                              <  1:440826/65‑1 (MQ=255)
             ccGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTCGCATTGTTa                                                              <  1:3394982/65‑1 (MQ=255)
                gggAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGgcgc                                                     >  1:324377/1‑71 (MQ=255)
                gggAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGgcgc                                                     <  1:1870114/71‑1 (MQ=255)
                   aggaggTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGgcgcgc                                                   >  1:1525632/1‑70 (MQ=255)
                    ggaggTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTa                                                 >  1:1898725/1‑71 (MQ=255)
                     gaggTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTg                                                                      <  1:15810/49‑1 (MQ=255)
                     gaggTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTg                                                                      <  1:1721369/49‑1 (MQ=255)
                     gaggTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCt                                                  <  1:3461400/69‑1 (MQ=255)
                      aggTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTg                                                                      <  1:1205264/48‑1 (MQ=255)
                       ggTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCa                                                                    >  1:2284074/1‑49 (MQ=255)
                        gTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTtc                                             >  1:2989919/1‑71 (MQ=255)
                          aTGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTtct                                            >  1:1358611/1‑70 (MQ=255)
                          aTGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTtct                                            >  1:701902/1‑70 (MQ=255)
                           tGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTtctc                                           >  1:1340638/1‑70 (MQ=255)
                           tGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCtca                                          >  1:3310111/1‑71 (MQ=255)
                           tGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTAATTCtca                                          >  1:2219452/1‑71 (MQ=255)
                            gATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAAc                                                            >  1:253755/1‑52 (MQ=255)
                            gATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAAc                                                            >  1:2134100/1‑52 (MQ=255)
                            gATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAAc                                                            >  1:2833686/1‑52 (MQ=255)
                            gATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAAc                                                            >  1:462225/1‑52 (MQ=255)
                            gATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACAt                                                          >  1:648609/1‑54 (MQ=255)
                             aTAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCtcatc                                        <  1:814567/71‑1 (MQ=255)
                             aTAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCtcat                                         <  1:1244758/70‑1 (MQ=255)
                             aTAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTAt                                                >  1:3555416/1‑63 (MQ=255)
                             aTAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTAt                                                >  1:3716190/1‑63 (MQ=255)
                                aGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCtcatca                                       >  1:2295193/1‑69 (MQ=255)
                                aGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCAc                                      >  1:2039110/1‑70 (MQ=255)
                                aGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCAc                                      >  1:1546409/1‑70 (MQ=255)
                                aGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCAc                                      >  1:16042/1‑70 (MQ=255)
                                aGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCAc                                      >  1:2320639/1‑70 (MQ=255)
                                 gCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTa                                                              >  1:2877440/1‑45 (MQ=255)
                                 gCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTa                                                              >  1:3359112/1‑45 (MQ=255)
                                 gCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTa                                                              >  1:2629011/1‑45 (MQ=255)
                                 gCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTaa                                                             >  1:2031222/1‑46 (MQ=255)
                                 gCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTAtt                                               >  1:2324422/1‑60 (MQ=255)
                                 gCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTa                                    >  1:974795/1‑71 (MQ=255)
                                 gCACCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTa                                    >  1:2346962/1‑71 (MQ=255)
                                   aCCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTAcg                                  <  1:1081287/71‑1 (MQ=255)
                                   aCCGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTAcg                                  >  1:158967/1‑71 (MQ=255)
                                     cGTCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTtc                                             <  1:3651385/58‑1 (MQ=255)
                                       tCGCATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTAcgcgcg                              <  1:42022/71‑1 (MQ=255)
                                         gCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCgtt                            <  1:896012/71‑1 (MQ=255)
                                          cATTATTTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCgttg                           <  1:1865793/71‑1 (MQ=255)
                                           attattTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGgc                                                       >  1:2036946/1‑42 (MQ=255)
                                           attattTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCtcatca                                       >  1:2285371/1‑58 (MQ=255)
                                           attattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCtcatca                                       >  1:1957946/1‑58 (MQ=255)
                                           attattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCgttg                           <  1:1760194/70‑1 (MQ=255)
                                            ttattTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCgttgtt                         <  1:1886544/71‑1 (MQ=255)
                                            ttattTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCgttgtt                         <  1:574882/71‑1 (MQ=255)
                                            ttattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTAcgcgc                               >  1:3690183/1‑65 (MQ=255)
                                            ttattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTAcgcgc                               >  1:1635450/1‑65 (MQ=255)
                                            ttattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTAcgcgc                               >  1:3524811/1‑65 (MQ=255)
                                            ttattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTAcgcgc                               >  1:1254832/1‑65 (MQ=255)
                                            ttattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTAcgcgc                               >  1:528311/1‑65 (MQ=255)
                                            ttattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTAcgcgc                               >  1:1090425/1‑65 (MQ=255)
                                            ttattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTAcgcgc                               >  1:2827175/1‑65 (MQ=255)
                                            ttattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCgttgt                          >  1:904532/1‑70 (MQ=255)
                                            ttattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCgttgt                          >  1:3409702/1‑70 (MQ=255)
                                             tattTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCgttgt                          >  1:1108395/1‑69 (MQ=255)
                                             tattTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCgttgt                          >  1:840442/1‑69 (MQ=255)
                                             tattTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTTCGCGCgttg                           <  1:3497916/68‑1 (MQ=255)
                                              attTTGGGCTTTATGTGTCGTCTGCATTGTTAACAt                                                          >  1:2358139/1‑36 (MQ=255)
                                              attTTGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTAcgcgc                               >  1:2868375/1‑63 (MQ=255)
                                               ttttGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGt                      <  1:3550998/71‑1 (MQ=255)
                                               ttttGGGCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGt                      <  1:2932892/71‑1 (MQ=255)
                                                tttGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTg                     >  1:1891592/1‑71 (MQ=255)
                                                tttGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTg                     >  1:2409647/1‑71 (MQ=255)
                                                tttGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTg                     >  1:1107060/1‑71 (MQ=255)
                                                 ttGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTAttt                                              >  1:147518/1‑45 (MQ=255)
                                                 ttGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTAttt                                              >  1:1119422/1‑45 (MQ=255)
                                                 ttGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTAttt                                              >  1:2520978/1‑45 (MQ=255)
                                                    ggCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTAttt                                              <  1:2058299/42‑1 (MQ=255)
                                                     gCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTAt                                                >  1:3387178/1‑39 (MQ=255)
                                                     gCTTTATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACt                <  1:1641491/71‑1 (MQ=255)
                                                       tttATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGc              >  1:1907494/1‑71 (MQ=255)
                                                       tttATGTGTCGTCTGCATTGTTAACATGGCGCGGTAATTCtcat                                         >  1:28590/1‑44 (MQ=37)
                                                       tttATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGc              >  1:2203002/1‑71 (MQ=255)
                                                       tttATGTGTCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGc              >  1:3649368/1‑71 (MQ=255)
                                                         tATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAg                       >  1:1058339/1‑60 (MQ=255)
                                                          aTGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGCGt            <  1:2405071/70‑1 (MQ=255)
                                                            gtgtCGTCTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGc              >  1:1418736/1‑66 (MQ=255)
                                                              gtcgtcTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGc              >  1:668552/1‑64 (MQ=255)
                                                              gtcgtcTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGc              >  1:2542427/1‑64 (MQ=255)
                                                              gtcgtcTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGc              >  1:417967/1‑64 (MQ=255)
                                                               tCGTCTGCATTGTTAACATGGCGCGCTATTTCtca                                          >  1:3386439/1‑35 (MQ=255)
                                                               tCGTCTGCATTGTTAACATGGCGCGCTATTTCtca                                          >  1:441874/1‑35 (MQ=255)
                                                               tCGTCTGCATTGTTAACATGGCGCGCTATTTCtca                                          >  1:969351/1‑35 (MQ=255)
                                                                   ttGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGCGTAACTGCGATc  >  1:324842/1‑71 (MQ=255)
                                                                   ttGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGCGTAACTGCGATc  >  1:2341626/1‑71 (MQ=255)
                                                                   |                                                                      
CGCGGGCAGGTCGCCGGGGAGGAGGTATGATAAGCACCGTCGCATTATTTTGGGCTTTATGTGTCGTTTGCATTGTTAACATGGCGCGCTATTTCTCATCACTACGCGCGTTGTTAGTGGTACTGCGTAACTGCGATC  >  minE/2605786‑2605923

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A