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	1,933,324	G→T	27.6%	T373T (ACC→ACA)	lysS ←	lysine tRNA synthetase, constitutive

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,933,324	0	G	T	27.6%	272.7 / 80.5	141	T373T (ACC→ACA)	lysS	lysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand): ref base G (54/48); new base T (18/21); total (72/69)
Fisher's exact test for biased strand distribution p-value = 5.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.04e-01

Only 100 of 152 total aligned reads displayed.

TTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAATTGCTTTCG  >  minE/1933255‑1933391

ttCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCgg                                                                    >  1:746224/1‑71 (MQ=255)

ttCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCgg                                                                    >  1:659157/1‑71 (MQ=255)

ttCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGAGCTTCTGCCACTTCTTCGAAGATCTCgg                                                                    >  1:2016147/1‑71 (MQ=255)

  cTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGt                                                                   >  1:1264060/1‑70 (MQ=255)

  cTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGt                                                                   <  1:5263079/70‑1 (MQ=255)

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

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

     ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                                                                <  1:5251145/70‑1 (MQ=255)

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

      cGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGAcaa                                                              <  1:3572823/71‑3 (MQ=255)

      cGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                              <  1:688790/71‑1 (MQ=255)

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

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

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

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

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

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

               cgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTcc                                                       >  1:4073074/2‑69 (MQ=255)

               aGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCa                                                     <  1:3773351/71‑1 (MQ=255)

                 taataaAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCaac                                                   <  1:2622100/71‑3 (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)

                   aTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc                                                 >  1:5092796/1‑71 (MQ=255)

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

                    tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                              <  1:3930688/57‑1 (MQ=255)

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

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

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

                      aaGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAccc                                                >  1:1942019/1‑69 (MQ=255)

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

                          tCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                              >  1:3669043/1‑51 (MQ=255)

                           tggCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGcttt                                         >  1:2315922/2‑69 (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)

                                gAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGtga                                                                 >  1:4453235/1‑40 (MQ=25)

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

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

                                 aaTCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctcta                                   >  1:1322916/1‑69 (MQ=255)

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

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

                                   tCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                              <  1:2143698/42‑1 (MQ=255)

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

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

                                   tCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTTCTCTAcc                                 >  1:4148008/1‑70 (MQ=255)

                                    cAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGccc                                                      >  1:3603968/1‑49 (MQ=255)

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

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

                                    cAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctc                                     >  1:135385/1‑66 (MQ=255)

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

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

                                     aGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTTCTCTAccgt                               <  1:3852109/71‑4 (MQ=255)

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

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

                                        tgtgCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCa                                                     <  1:1279444/46‑1 (MQ=19)

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

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

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

                                         gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc                                                 >  1:1714676/1‑49 (MQ=255)

                                         gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCtcttc                                       >  1:4011272/1‑59 (MQ=255)

                                         gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATg                           >  1:2393523/1‑71 (MQ=255)

                                         gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATg                           >  1:2899991/1‑71 (MQ=255)

                                          tgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATg                           >  1:1089477/1‑70 (MQ=255)

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

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

                                            cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCtcttc                                       >  1:4239722/1‑56 (MQ=255)

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

                                            cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGcc                         >  1:1875216/1‑70 (MQ=255)

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

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

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

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

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

                                               cTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGa                       <  1:2313055/69‑1 (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              >  1:2793419/1‑70 (MQ=255)

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

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

                                                         ttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGAt                            <  1:2489382/54‑1 (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)

                                                              aGATCTCGGTAACGATACGGCCCAGACCCCAGCtctt                                        >  1:2710813/1‑37 (MQ=255)

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

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

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

                                                                     ggTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAATTGCTTTCg  >  1:2012272/1‑68 (MQ=255)

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

                                                                     ggTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAATTGCTTTCg  >  1:3711795/1‑68 (MQ=255)

TTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAATTGCTTTCG  >  minE/1933255‑1933391

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