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	1,933,327	A→G	24.6%	V372V (GTT→GTC)	lysS ←	lysine tRNA synthetase, constitutive

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,933,327	0	A	G	24.6%	250.4 / 85.4	146	V372V (GTT→GTC)	lysS	lysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand): ref base A (56/54); new base G (16/20); total (72/74)
Fisher's exact test for biased strand distribution p-value = 5.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 146 total aligned reads displayed.

CCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAATTGCTTTCGCAGAG  >  minE/1933260‑1933396

ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                                                                     <  1:4175604/70‑1 (MQ=255)

ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                                                                     <  1:3331715/70‑1 (MQ=255)

ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                                                                     <  1:5257695/70‑1 (MQ=255)

ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                                                                     <  1:2198002/70‑1 (MQ=255)

 cGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGAcaa                                                                   <  1:3931061/71‑3 (MQ=255)

 cGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGAcaa                                                                   <  1:1224416/71‑3 (MQ=255)

  ggATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAAt                                                                  <  1:2151697/71‑1 (MQ=255)

  ggATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGAt                                                                  <  1:4125749/71‑1 (MQ=255)

    atatTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATAc                                                                >  1:2914735/1‑71 (MQ=255)

    atatTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATAc                                                                <  1:1503976/71‑1 (MQ=255)

    atatTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATAc                                                                >  1:5397678/1‑71 (MQ=255)

       ttCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGAt                                                                  <  1:3361860/66‑1 (MQ=255)

       ttCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGAt                                                                  <  1:248214/66‑1 (MQ=255)

        tCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGcc                                                            >  1:3587386/1‑71 (MQ=255)

         ccgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTcc                                                            >  1:228746/3‑70 (MQ=255)

         cAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGcc                                                            >  1:1606530/1‑70 (MQ=255)

          cgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTccc                                                           <  1:5349380/69‑1 (MQ=255)

             aaTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGa                                                        <  1:3029277/70‑1 (MQ=255)

             aaTGAAGCTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAc                                                       >  1:3738040/1‑71 (MQ=255)

              aTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc                                                      >  1:3130815/1‑71 (MQ=255)

              aTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc                                                      >  1:2666226/1‑71 (MQ=255)

               tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                                   <  1:171847/57‑1 (MQ=255)

               tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                                   <  1:1088435/57‑1 (MQ=255)

               tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGcc                                                            <  1:3814991/64‑1 (MQ=255)

                 aaGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATa                                                                 >  1:2208617/1‑57 (MQ=255)

                 aaGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATa                                                                 >  1:450541/1‑57 (MQ=255)

                 aaGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATa                                                                 >  1:4037722/1‑57 (MQ=255)

                 aaGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCa                                                          >  1:25551/1‑64 (MQ=255)

                 aaGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAccc                                                     >  1:5525834/1‑69 (MQ=255)

                  aGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAg                                                  <  1:375750/71‑1 (MQ=255)

                      tggCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGcttt                                              >  1:2315922/2‑69 (MQ=255)

                       ggCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAc                                                       <  1:4098982/61‑1 (MQ=255)

                       ggCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAc                                                       <  1:2444210/61‑1 (MQ=255)

                       ggCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAc                                                       <  1:58183/61‑1 (MQ=255)

                       ggCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGctct                                              <  1:3906577/70‑1 (MQ=255)

                       ggCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCa                                                   >  1:3610316/1‑65 (MQ=255)

                       ggCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCa                                                   >  1:1904783/1‑65 (MQ=255)

                        gCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                                   <  1:3830996/48‑1 (MQ=255)

                          tGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAAt                                                                  <  1:3573310/47‑1 (MQ=25)

                           gAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGcttt                                              >  1:3166104/1‑64 (MQ=255)

                            aaTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcccc                                                    >  1:1300250/1‑59 (MQ=255)

                            aaTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTtctc                                          <  1:3421519/69‑1 (MQ=255)

                            aaTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCa                                         <  1:3710205/70‑1 (MQ=255)

                            aaTCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctc                                          <  1:1853951/69‑1 (MQ=255)

                            aaTCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctc                                          <  1:2721236/69‑1 (MQ=255)

                            aaTCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctc                                          <  1:1493536/69‑1 (MQ=255)

                             aTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc                                                      <  1:3894561/56‑1 (MQ=255)

                             aTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTtctc                                          <  1:4173209/68‑1 (MQ=255)

                              tCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                                   <  1:215251/42‑1 (MQ=255)

                              tCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcccc                                                    >  1:4681172/1‑57 (MQ=255)

                              tCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGAcaa                                                                   <  1:4724694/42‑3 (MQ=21)

                               cAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                                   <  1:2003497/41‑1 (MQ=255)

                               cAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGccc                                                           >  1:155765/1‑49 (MQ=255)

                               cAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCaa                                        >  1:1590314/1‑68 (MQ=255)

                               cAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctc                                          >  1:50082/1‑66 (MQ=255)

                                aGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGcc                                                            <  1:133440/47‑1 (MQ=255)

                                aGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGt                                     <  1:2902844/70‑1 (MQ=255)

                                aGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTg                                    >  1:4659103/1‑71 (MQ=255)

                                aGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTg                                    <  1:2546909/71‑1 (MQ=255)

                                   tgtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGAt                                 <  1:5369291/71‑1 (MQ=255)

                                   tgtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGAt                                 <  1:5632467/71‑1 (MQ=255)

                                   tgtgCTTCTGCCACTTCATCAAAGATCTCTGTAACAATACGTCCCa                                                          <  1:4562239/46‑1 (MQ=25)

                                    gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATa                                                                 >  1:471681/1‑38 (MQ=255)

                                    gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATa                                                                 >  1:662941/1‑38 (MQ=255)

                                    gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCa                                                          >  1:1040531/1‑45 (MQ=255)

                                     tgCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTTCTCTAcc                                      <  1:3678908/64‑2 (MQ=255)

                                      gCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCa                                         <  1:3461882/60‑1 (MQ=255)

                                       cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTgg                                   >  1:347108/1‑65 (MQ=255)

                                       cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGcc                              >  1:2069040/1‑70 (MQ=255)

                                       cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGcc                              >  1:3481753/1‑70 (MQ=255)

                                       cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGcc                              >  1:1034932/1‑70 (MQ=255)

                                         tCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCa                                                          >  1:3955280/1‑40 (MQ=255)

                                         tCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCa                                                          >  1:1984331/1‑40 (MQ=255)

                                         tCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCa                                                          >  1:2966395/1‑40 (MQ=255)

                                          cTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGCCCCCAGCtcttc                                            >  1:2372027/1‑53 (MQ=255)

                                            gCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTtctc                                          >  1:3801942/1‑53 (MQ=255)

                                               aCTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCtctt                                             >  1:5169978/1‑47 (MQ=255)

                                                cttcttCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGAtt                      >  1:5553026/1‑69 (MQ=255)

                                                cttcttCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGAtt                      >  1:548779/1‑69 (MQ=255)

                                                  tcttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAg                   >  1:296842/1‑70 (MQ=255)

                                                  tcttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAg                   >  1:2793419/1‑70 (MQ=255)

                                                   cttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGc                  <  1:697422/70‑1 (MQ=255)

                                                   cttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGc                  <  1:3662298/70‑1 (MQ=255)

                                                   cttcGAAGATCTAGGTAACGATACTGCCAAGACCCCAGct                                                >  1:4581491/1‑40 (MQ=255)

                                                    ttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGAt                                 <  1:1923287/54‑1 (MQ=255)

                                                    ttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGAt                       <  1:1316710/64‑1 (MQ=255)

                                                     tcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGAt                       <  1:2928213/63‑1 (MQ=255)

                                                     tcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAAt               >  1:693485/1‑71 (MQ=255)

                                                     tcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAAt               >  1:1137033/1‑71 (MQ=255)

                                                      cGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAg                   >  1:3270839/1‑66 (MQ=255)

                                                        aaGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTTCTCTACCGTAATACCGATAGATTCAGCTAATGc            <  1:5280438/71‑1 (MQ=255)

                                                          gATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAATTGCtt          <  1:4023790/71‑1 (MQ=255)

                                                           aTCTCTGTGACAATACGTCCCAACCCCCAGCTTTTCTCTACCGTAATACCGATAGATTCAGCTAATGCtt          >  1:2622580/1‑70 (MQ=255)

                                                             ctctGTGACAATACGTCCCAACCCCCAGCTTTTCTCTACCGTAATACCGATAGATTCAGCTAATGCttta        >  1:2088103/1‑69 (MQ=255)

                                                                ggTAACGATACGGCCCAGACCCCAGCTCTTCTCaa                                        <  1:5103850/35‑1 (MQ=255)

                                                                ggTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAATTGCTTTc        <  1:1343296/67‑1 (MQ=255)

                                                                ggTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAATTGCTTTc        <  1:476645/67‑1 (MQ=255)

                                                                ggTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAATTGCTTTCg       <  1:4826876/68‑1 (MQ=255)

                                                                  tAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTg                                    <  1:4947452/37‑1 (MQ=255)

                                                                  tAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAATTGCTTTCGCagag  >  1:3408136/1‑71 (MQ=255)

CCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAATTGCTTTCGCAGAG  >  minE/1933260‑1933396

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