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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 385,816 T→C 36.8% H342H (CAT→CAC)  cstA → carbon starvation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE385,8160TC36.8% 75.1 / 91.9 95H342H (CAT→CAC) cstAcarbon starvation protein
Reads supporting (aligned to +/- strand):  ref base T (30/30);  new base C (23/12);  total (53/42)
Fisher's exact test for biased strand distribution p-value = 1.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

GACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGCTTTATCGGCTAC  >  minE/385753‑385885
                                                               |                                                                     
gACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTg                                                                 <  1:4515735/70‑1 (MQ=255)
gACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTg                                                                 <  1:1045122/70‑1 (MQ=255)
    ggTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAtctc                                                            <  1:5356668/71‑1 (MQ=255)
     gTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATctct                                                           <  1:3691129/71‑1 (MQ=255)
      tAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtctt                                                          <  1:4003777/71‑1 (MQ=255)
      tAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtctt                                                          <  1:3370116/71‑1 (MQ=255)
       aaCCTGTTCGCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtcttc                                                         >  1:3309006/1‑71 (MQ=255)
       aaCCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTg                                                                 >  1:1059454/1‑63 (MQ=255)
       aaCCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtcttc                                                         >  1:5359783/1‑71 (MQ=255)
          cTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTgg                                                      <  1:4010256/71‑1 (MQ=255)
          cTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTgg                                                      <  1:3770457/71‑1 (MQ=255)
          cTGTTCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGAt                                                               >  1:3604457/1‑62 (MQ=255)
          cTGTTCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCgg                                                      >  1:344535/1‑71 (MQ=255)
          cTGTTCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCgg                                                      >  1:3630361/1‑71 (MQ=255)
           tGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTgg                                                      >  1:316871/1‑70 (MQ=255)
           tGTTCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCtcttccg                                                       <  1:379824/69‑3 (MQ=255)
           tGTTCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCgg                                                      >  1:3299243/1‑70 (MQ=255)
             ttCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTAc                                                   >  1:2880985/1‑71 (MQ=255)
              tcgcGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGAc                                                   >  1:2441857/4‑70 (MQ=255)
                ccGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCAc                                                <  1:5355415/71‑1 (MQ=255)
                  gTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGc                                              >  1:4703036/1‑71 (MQ=255)
                  gTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGc                                              >  1:201029/1‑71 (MQ=255)
                  gTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGc                                              >  1:5588902/1‑71 (MQ=255)
                   ttCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGcc                                             <  1:168692/71‑1 (MQ=255)
                   ttCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGcc                                             <  1:3677951/71‑1 (MQ=255)
                    tCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCtcttc                                                         >  1:2926318/1‑58 (MQ=255)
                     ccTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGa                                                                >  1:3575214/1‑50 (MQ=255)
                      cTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAt                                                               >  1:1272292/1‑50 (MQ=255)
                      cTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAt                                                               >  1:577523/1‑50 (MQ=255)
                      cTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAt                                                               >  1:1213713/1‑50 (MQ=255)
                      cTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAt                                                               >  1:4105061/1‑50 (MQ=255)
                      cTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGccaa                                           <  1:345194/70‑3 (MQ=255)
                      cTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGccaa                                           <  1:2874781/70‑3 (MQ=255)
                       tGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtcttct                                                        <  1:2502230/56‑1 (MQ=255)
                         tttATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATctct                                                           <  1:1289056/51‑1 (MQ=255)
                         tttATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                                        <  1:1576820/70‑1 (MQ=255)
                         tttATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                                        <  1:1661703/70‑1 (MQ=255)
                         tttATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                                        <  1:5116961/70‑1 (MQ=255)
                             tCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTAcga                                                 <  1:2420229/57‑3 (MQ=255)
                               aCCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTgg                                  >  1:3700686/1‑70 (MQ=255)
                               aCCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGc                                 >  1:4549970/1‑71 (MQ=255)
                               aCCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGc                                 >  1:2658140/1‑71 (MQ=255)
                               aCCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGc                                 >  1:5469831/1‑71 (MQ=255)
                                ccATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTAcga                                                 <  1:1188041/54‑3 (MQ=255)
                                ccATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGct                                <  1:3375521/71‑2 (MQ=255)
                                   tCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTgg                                  <  1:4625930/66‑1 (MQ=255)
                                   tCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaac                             >  1:1952477/1‑71 (MQ=255)
                                   tCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaac                             >  1:5309445/1‑71 (MQ=255)
                                    cGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaat                             >  1:1707696/1‑69 (MQ=255)
                                     gCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatg                            >  1:5027682/1‑68 (MQ=255)
                                     gCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatg                            <  1:5170441/70‑3 (MQ=255)
                                     gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg                            <  1:133727/70‑1 (MQ=255)
                                     gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg                            <  1:3113432/70‑1 (MQ=255)
                                     gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg                            <  1:2474919/70‑1 (MQ=255)
                                     gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg                            <  1:2238044/70‑1 (MQ=255)
                                     gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg                            <  1:4227084/70‑1 (MQ=255)
                                     gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcg                                >  1:3418768/1‑66 (MQ=255)
                                      ccTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatga                           >  1:4632422/1‑70 (MQ=255)
                                      ccTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatga                           >  1:1528704/1‑70 (MQ=255)
                                       cTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAg                         >  1:2125439/1‑71 (MQ=255)
                                          tgGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatgaaacc                       <  1:89464/70‑4 (MQ=255)
                                          tgGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatgaaacc                       >  1:950498/1‑67 (MQ=255)
                                          tgGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGct                                <  1:1943278/61‑2 (MQ=255)
                                          tgGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                                        >  1:3948685/1‑53 (MQ=255)
                                          tgGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                                        >  1:2359027/1‑53 (MQ=255)
                                          tgGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                                        >  1:2217885/1‑53 (MQ=255)
                                          tgGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                                        >  1:5612503/1‑53 (MQ=255)
                                          tgGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                                        >  1:4199975/1‑53 (MQ=255)
                                           ggCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATg                                      >  1:4360710/1‑54 (MQ=255)
                                           ggCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATg                                      >  1:5336243/1‑54 (MQ=255)
                                           ggCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATg                                      >  1:2834309/1‑54 (MQ=255)
                                           ggCGCGGTGTCTGGCTTCCATGCGCTGATCTCTT‑AGGGACCACGCCGAAGATg                                      >  1:2771463/1‑53 (MQ=255)
                                            gtgcgGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaa                              >  1:36651/3‑61 (MQ=255)
                                            gtgcgGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaa                              >  1:5412112/3‑61 (MQ=255)
                                            gtgcgGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaa                              >  1:3497235/3‑61 (MQ=255)
                                            gtgcgGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGc                                 >  1:3204708/3‑58 (MQ=255)
                                                  tgtCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg                            <  1:4439594/57‑1 (MQ=255)
                                                  tgtCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg                            <  1:2946652/57‑1 (MQ=255)
                                                  tgtCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGc              <  1:510735/71‑1 (MQ=255)
                                                    tCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg                            <  1:1964989/55‑1 (MQ=255)
                                                    tCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGCtt            >  1:4033926/1‑71 (MQ=255)
                                                    tCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGCtt            <  1:3530569/71‑1 (MQ=255)
                                                    tCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaat                             <  1:256970/54‑2 (MQ=255)
                                                      tGGCTTCCCTGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGCTTTa          >  1:4829790/1‑71 (MQ=255)
                                                      tGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGCTTTa          >  1:383174/1‑71 (MQ=255)
                                                      tGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatgaaac                        >  1:3451681/1‑55 (MQ=255)
                                                        tcTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGAGAACGAAGGGCAGGCGTGATTTATc        >  1:1509315/2‑71 (MQ=255)
                                                        gCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGCttt           <  1:2768365/68‑1 (MQ=255)
                                                        gCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGCttt           <  1:4386772/68‑1 (MQ=255)
                                                        gCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGCTTTATc        >  1:889385/1‑71 (MQ=255)
                                                        gCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaa                              >  1:3400887/1‑49 (MQ=255)
                                                            ccATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg                            <  1:4855209/47‑1 (MQ=255)
                                                             cATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGCTTTATCGGCTa   <  1:385124/71‑1 (MQ=255)
                                                             cATGCGCTGATCTCTTCTGGGACCACGCAGAAGATGCTGGCGAACGAAGGGCAGGc                  >  1:4279267/1‑56 (MQ=255)
                                                              aTGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGCTTTATCGGCTAc  <  1:5662606/71‑1 (MQ=255)
                                                               |                                                                     
GACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGGCAGGCGTGCTTTATCGGCTAC  >  minE/385753‑385885

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