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 R2 230 93.6 4701257 96.3% 4527310 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,963,081 G→A 20.4% A92V (GCG→GTG)  yjjI ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,963,0810GA20.4% 197.5 / 42.5 93A92V (GCG→GTG) yjjIconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (44/30);  new base A (6/13);  total (50/43)
Fisher's exact test for biased strand distribution p-value = 3.95e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01

Only 100 of 102 total aligned reads displayed.

TCGATGTGACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGTAAGACATAGCGC  >  minE/2963013‑2963149
                                                                    |                                                                    
tCGATGTGACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTcgcg                                                                    >  1:1335659/1‑71 (MQ=255)
 cGATGTGACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCgcgc                                                                   >  1:2006339/1‑71 (MQ=255)
 cGATGTGACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCgcgc                                                                   >  1:745560/1‑71 (MQ=255)
  gATGTGACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCgcgc                                                                   >  1:2575719/1‑70 (MQ=255)
  gATGTGACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCgcgc                                                                   <  1:1477250/70‑1 (MQ=255)
  gATGTGACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGcc                                                                  >  1:3853388/1‑71 (MQ=255)
  gATGTGACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGcc                                                                  >  1:1462926/1‑71 (MQ=255)
   aTGTGACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTcg                                                                      <  1:3661624/66‑1 (MQ=255)
   aTGTGACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCt                                                                 <  1:236193/71‑1 (MQ=255)
    tgtgACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCtt                                                                >  1:1510348/1‑71 (MQ=255)
     gtgACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtc                                                               >  1:4165098/1‑71 (MQ=255)
     gtgACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtc                                                               >  1:3925189/1‑71 (MQ=255)
      tgACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCACGCCTtc                                                               <  1:3636570/70‑1 (MQ=255)
         ccGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCACGCCTtccagc                                                           >  1:1627725/1‑71 (MQ=255)
         ccGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCACGCCTtccagc                                                           >  1:2546770/1‑71 (MQ=255)
         accaCGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCACGCCTtccagc                                                           <  1:1813774/68‑1 (MQ=255)
          cGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtccagct                                                          >  1:4612923/1‑71 (MQ=255)
            aCGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtccagctc                                                         >  1:3836030/1‑70 (MQ=255)
                 aCGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCa                                                   >  1:231562/1‑71 (MQ=255)
                  cGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtccagctc                                                         >  1:1937219/1‑64 (MQ=255)
                  cGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCAt                                                  <  1:4243305/71‑1 (MQ=255)
                   gtggtgGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCAtt                                                 <  1:1356695/71‑1 (MQ=255)
                    tggtggTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAATATCTTTCGCGCCTtccagc                                                           >  1:3342410/1‑60 (MQ=255)
                    tggtggTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtccagctcc                                                        <  1:3132618/63‑1 (MQ=255)
                    tggtggTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCAtt                                                 >  1:3959597/1‑70 (MQ=255)
                    tggtggTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTc                                                >  1:4613432/1‑71 (MQ=255)
                     ggtggtAAAGAATGGTCAGCAGAGAGAGTGCGTCATCATGATCTTTCACGCCTTCCAGCTCCAGCCATTCg                                               >  1:2971380/1‑71 (MQ=255)
                        ggtAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGaa                                            >  1:2543239/1‑71 (MQ=255)
                         gtAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAAc                                           >  1:1417160/1‑71 (MQ=255)
                         gtAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAAc                                           <  1:51635/71‑1 (MQ=255)
                          tAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAAcc                                          <  1:1995941/71‑1 (MQ=255)
                           aaaGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCgcgc                                                                   >  1:257395/1‑45 (MQ=255)
                           aaaGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtccagctcca                                                       >  1:2261439/1‑57 (MQ=255)
                            aaGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTcgc                                                                     >  1:3044591/1‑42 (MQ=255)
                            aaGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtccagctcca                                                       <  1:500461/56‑1 (MQ=255)
                            aaGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGt                                        <  1:4387479/71‑1 (MQ=255)
                            aaGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGt                                        >  1:851537/1‑71 (MQ=255)
                             aGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGtt                                       <  1:212843/71‑1 (MQ=255)
                              gAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtccagctccagc                                                     >  1:1216561/1‑56 (MQ=255)
                              gAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGtt                                       >  1:4086021/1‑70 (MQ=255)
                               aaTGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtc                                                               <  1:712952/45‑1 (MQ=255)
                                aTGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCGTGCCAtt                                                 <  1:4646502/58‑1 (MQ=255)
                                 tGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTcgcg                                                                    >  1:3971759/1‑38 (MQ=255)
                                 tGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtccag                                                            <  1:3111019/46‑1 (MQ=255)
                                      agcagAGAGAGTGCGTCATCAAGATCTTTCGCGCCTtcc                                                              >  1:1976878/1‑39 (MQ=255)
                                      agcagAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGaaa                              <  1:3028589/71‑1 (MQ=255)
                                      agcagAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGaaa                              <  1:2120713/71‑1 (MQ=255)
                                      agcagAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGaa                               >  1:1741680/1‑70 (MQ=255)
                                      agcagAGAGAGTGCGTCATCAAGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGaa                               <  1:3914742/70‑1 (MQ=255)
                                      agcagAGAGAGTGCGTCATCAAGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGaa                               <  1:1021572/70‑1 (MQ=255)
                                       gcagAGAGAGTGCGTCATCAAGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGaa                               <  1:3236657/69‑1 (MQ=255)
                                        cagAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAAc                            <  1:479153/71‑1 (MQ=255)
                                        cagAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAAc                            <  1:4189372/71‑1 (MQ=255)
                                        cagAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAAc                            <  1:2436419/71‑1 (MQ=255)
                                         agagagagTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAAc                            <  1:2490326/70‑1 (MQ=255)
                                         agagagagTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCAATTCGGAACCGTTCGCCAGAAAACg                           >  1:3699337/1‑71 (MQ=255)
                                          gagagagTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGtt                                       >  1:3107487/1‑58 (MQ=255)
                                             agagTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCg                       >  1:3097057/1‑71 (MQ=255)
                                             agagTGCGACATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGaa                                            >  1:2420877/1‑50 (MQ=255)
                                              gagTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGt                      <  1:4640047/71‑1 (MQ=255)
                                               agTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTa                     <  1:12408/71‑1 (MQ=255)
                                               agTGCGTCATCAAGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTa                     <  1:2521398/71‑1 (MQ=255)
                                               agTGCGTCATCAAGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTa                     <  1:793094/71‑1 (MQ=255)
                                                 tGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGa                                             <  1:1912678/45‑1 (MQ=255)
                                                   cGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGt                      >  1:3066841/1‑66 (MQ=255)
                                                   cGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCg                 >  1:4648978/1‑71 (MQ=255)
                                                   cGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCg                 >  1:877572/1‑71 (MQ=255)
                                                   cGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCg                 >  1:904190/1‑71 (MQ=255)
                                                   cGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCg                 >  1:1546386/1‑71 (MQ=255)
                                                   cGTCATCAAGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATc                  <  1:1770099/70‑1 (MQ=255)
                                                   cGTCATCAAGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATc                  <  1:2955811/70‑1 (MQ=255)
                                                     tcatcaAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCggg               >  1:3970240/1‑71 (MQ=255)
                                                       atcaAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCgg                                              >  1:4259086/1‑38 (MQ=255)
                                                       atcaAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGt              <  1:1048056/70‑1 (MQ=255)
                                                       atcaAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGt              >  1:489101/1‑70 (MQ=255)
                                                       atcaAGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGt              <  1:109120/70‑1 (MQ=255)
                                                       atcaAGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGt              <  1:4145892/70‑1 (MQ=255)
                                                       atcaAGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGt              >  1:524921/1‑70 (MQ=255)
                                                        tcaAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGaa                               <  1:3864665/52‑1 (MQ=255)
                                                        tcaAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGt              >  1:3837039/1‑69 (MQ=255)
                                                         caAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGt              >  1:2403744/1‑68 (MQ=255)
                                                         caAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGt              >  1:1155938/1‑68 (MQ=255)
                                                         caAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGt              >  1:3272021/1‑68 (MQ=255)
                                                          aaGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAAc                                           >  1:1083832/1‑38 (MQ=255)
                                                          aaGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGaa                               >  1:3998015/1‑50 (MQ=255)
                                                          aaGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGaa                               <  1:76228/50‑1 (MQ=255)
                                                          aaGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGaa                               <  1:70668/50‑1 (MQ=255)
                                                          aaGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGt                      <  1:2833965/59‑1 (MQ=255)
                                                          aaGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGTAAGa          >  1:538139/1‑71 (MQ=255)
                                                          aaGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGTAAGa          <  1:826754/71‑1 (MQ=255)
                                                          aaGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGTAAGa          <  1:3480245/71‑1 (MQ=255)
                                                          aaGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGTAAGa          <  1:2433099/71‑1 (MQ=255)
                                                          aaGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGaa                                            >  1:169190/1‑37 (MQ=255)
                                                          aaGATCTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATAGGGTAAg           <  1:2042016/70‑1 (MQ=255)
                                                           aGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGaa                               <  1:3016332/49‑1 (MQ=255)
                                                              tCTTTCGCGCCTTCCAGCTCCAGCCATTCGGATCCGTTCGCCAg                                 >  1:4029259/1‑44 (MQ=255)
                                                               cTTTCACGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGTAAGACATAg     >  1:1896283/1‑71 (MQ=255)
                                                                tttCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGTAAGACATAg     >  1:1618211/1‑70 (MQ=255)
                                                                 ttCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGTAAGACa        >  1:2102725/1‑66 (MQ=255)
                                                                  tCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGTAAGACATAgcgc  >  1:541971/1‑71 (MQ=255)
                                                                    |                                                                    
TCGATGTGACCGACGGTACGTGGTGGTAAAGAATGGTCAGCAGAGAGAGTGCGTCATCAAGATCTTTCGCGCCTTCCAGCTCCAGCCATTCGGAACCGTTCGCCAGAAAACGGGCGTAATCGGGTAAGACATAGCGC  >  minE/2963013‑2963149

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