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	2,571,345	T→G	23.5%	intergenic (+113/‑1666)	yibH → / → ysaB	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,571,345	0	T	G	23.5%	205.4 / 96.6	145	intergenic (+113/‑1666)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (46/65); new base G (20/14); total (66/79)
Fisher's exact test for biased strand distribution p-value = 8.08e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.99e-01

Only 100 of 150 total aligned reads displayed.

AATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTC  >  minE/2571276‑2571413

aaTTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     >  1:2212674/1‑71 (MQ=255)

 attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     <  1:4483016/70‑1 (MQ=255)

 attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     <  1:4295718/70‑1 (MQ=255)

 attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     <  1:1810774/70‑1 (MQ=255)

   tattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGAt                                                                  >  1:1101002/1‑71 (MQ=255)

    attTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGAt                                                                  >  1:2151432/1‑70 (MQ=255)

     tttttGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGAt                                                                  >  1:3723745/1‑69 (MQ=255)

          gCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGtgtg                                                           >  1:764500/1‑71 (MQ=255)

             tatTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGctc                                                        >  1:2722097/1‑71 (MQ=255)

              atTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     <  1:3553326/57‑1 (MQ=255)

              atTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGa                                                                   >  1:4371958/1‑59 (MQ=255)

              atTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGa                                                                   >  1:4377557/1‑59 (MQ=255)

              atTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGctct                                                       >  1:4021442/1‑71 (MQ=255)

              atTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGctct                                                       >  1:5669681/1‑71 (MQ=255)

               ttACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCtctc                                                      <  1:2285486/71‑1 (MQ=255)

                  cTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑gca                                                                   >  1:5408570/1‑53 (MQ=255)

                   ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     <  1:692641/52‑1 (MQ=255)

                   ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     <  1:5198668/52‑1 (MQ=255)

                   ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     <  1:1216093/52‑1 (MQ=255)

                   ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATg                                                                 <  1:5365132/56‑1 (MQ=255)

                     cATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGa                                                                <  1:1926925/55‑1 (MQ=255)

                       ttAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGAtt                                              >  1:4836689/1‑71 (MQ=255)

                        tAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGTAtt                                              <  1:225473/70‑1 (MQ=255)

                            ttCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGa                                                                >  1:4025417/1‑48 (MQ=255)

                              tgatgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGAtttctt                                          <  1:4252406/69‑1 (MQ=255)

                              tgatgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTC‑t                                                                       <  1:4702250/40‑1 (MQ=12)

                              tgatgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTC‑T‑gg                                                                    <  1:4008848/42‑1 (MQ=16)

                              cGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑t                                                                       >  1:4491163/1‑40 (MQ=255)

                               gatgatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATcc                                      <  1:1022779/71‑1 (MQ=255)

                                atgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATc                                       >  1:3425292/1‑71 (MQ=255)

                                atgatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCAtt                                                   <  1:1042987/57‑1 (MQ=255)

                                  gatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATcc                                      <  1:3671395/68‑1 (MQ=255)

                                  gatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTc                                   >  1:3264253/1‑71 (MQ=255)

                                   atTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGa                                                                   >  1:3172798/1‑38 (MQ=255)

                                   atTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCtctc                                                      <  1:2802838/51‑1 (MQ=255)

                                   atTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTc                                   <  1:2984344/70‑1 (MQ=255)

                                    ttttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGtgtg                                                           <  1:720328/45‑1 (MQ=255)

                                    ttttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGtgtg                                                           <  1:1745162/45‑1 (MQ=255)

                                    ttttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCtt                                 <  1:119029/71‑1 (MQ=255)

                                    ttttc‑CTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCt                                  >  1:1490904/1‑71 (MQ=255)

                                     tttc‑CTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCt                                  >  1:1847902/1‑70 (MQ=255)

                                      ttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTg                                <  1:4212067/70‑1 (MQ=255)

                                      ttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑CGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGt                               >  1:5527992/1‑71 (MQ=255)

                                        tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                <  1:2353435/68‑1 (MQ=255)

                                        tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                <  1:4726710/68‑1 (MQ=255)

                                        tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                <  1:327799/68‑1 (MQ=255)

                                        tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                <  1:2989061/68‑1 (MQ=255)

                                        tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                <  1:529762/68‑1 (MQ=255)

                                        tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                <  1:5635651/68‑1 (MQ=255)

                                        tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                <  1:2033084/68‑1 (MQ=255)

                                        tccTTTAATATCCAGCATGTTAAGAAGTTC‑TGGGATAGCTGTAATCTCATTAGATTTCTCATCCGTCTTg                                <  1:4254032/68‑1 (MQ=255)

                                        tccTTTAATATCCAGCATGTTAAGAAGTTC‑TGGGATAGCTGTAATCTCATTAGATTTCTCATCCGTCTTg                                <  1:1522883/68‑1 (MQ=255)

                                        tccTTTAATATCCAGCATGTTAAGAAGTTC‑TGGGATAGCTGTAATCTCATTAGATTTCTCATCCGTCTTg                                <  1:4309757/68‑1 (MQ=255)

                                          cTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt                              <  1:5031128/69‑1 (MQ=255)

                                          cTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc                             <  1:116806/71‑1 (MQ=255)

                                          cTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc                             >  1:4842888/1‑71 (MQ=255)

                                           tttAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTc                             <  1:475903/69‑1 (MQ=255)

                                             tAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGGTCTGcc                         >  1:5014420/1‑71 (MQ=255)

                                             tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTa                                         >  1:4814237/1‑56 (MQ=255)

                                             tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTa                                         >  1:2221760/1‑56 (MQ=255)

                                             tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTgt                          >  1:5697330/1‑70 (MQ=255)

                                             tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc                          >  1:5528958/1‑71 (MQ=255)

                                             tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc                          >  1:2674080/1‑71 (MQ=255)

                                             tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc                          >  1:2356605/1‑71 (MQ=255)

                                             tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc                          >  1:4743825/1‑71 (MQ=255)

                                              aaTATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt                            <  1:2164482/67‑1 (MQ=255)

                                              aaTATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTgat                              >  1:3672967/1‑64 (MQ=255)

                                               atatTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCg                        <  1:1877765/70‑1 (MQ=255)

                                                  ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATc                                       >  1:5095556/1‑52 (MQ=255)

                                                  ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt                            <  1:2512567/63‑1 (MQ=255)

                                                  ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt                            <  1:1611576/63‑1 (MQ=255)

                                                  ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAgt                    <  1:5305193/71‑2 (MQ=255)

                                                  ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                     <  1:3328060/70‑1 (MQ=255)

                                                    cATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt                  >  1:2803109/1‑71 (MQ=255)

                                                     agcaTGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc                             >  1:1731674/4‑60 (MQ=255)

                                                     agcaTGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc                             >  1:5207379/4‑60 (MQ=255)

                                                     aTTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt                  <  1:3930766/70‑1 (MQ=255)

                                                     aTTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATg                 <  1:4985725/71‑1 (MQ=255)

                                                     aTTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTATATCCGTCTTGTTCTGCCGCAGGAt                  <  1:5026670/70‑1 (MQ=255)

                                                      ttATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTa                                         <  1:398453/46‑1 (MQ=255)

                                                      ttATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt                              <  1:127074/57‑1 (MQ=255)

                                                      ttATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt                              <  1:4167997/57‑1 (MQ=255)

                                                         tGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                <  1:380857/53‑1 (MQ=255)

                                                         tGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                <  1:4290170/53‑1 (MQ=255)

                                                           ttAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATcc                                      <  1:4938778/44‑1 (MQ=255)

                                                           ttAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACta           <  1:1616543/71‑1 (MQ=255)

                                                           ttAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACt            <  1:1536982/70‑1 (MQ=255)

                                                           ttAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACt            <  1:596909/70‑1 (MQ=255)

                                                           ttAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACt            <  1:3411049/70‑1 (MQ=255)

                                                            taataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTa                                         >  1:414453/1‑40 (MQ=255)

                                                            taataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCt                                  >  1:479064/1‑47 (MQ=255)

                                                            taataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt                            >  1:3661204/1‑53 (MQ=255)

                                                            taataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACta           >  1:4223154/1‑70 (MQ=255)

                                                              ataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACtata         >  1:2060905/1‑70 (MQ=255)

                                                              ataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACtata         <  1:4326404/70‑1 (MQ=255)

                                                                aaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATga                >  1:246516/1‑61 (MQ=255)

                                                                  gTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTc                             <  1:1266936/46‑1 (MQ=255)

                                                                  gTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGAc             <  1:153790/62‑1 (MQ=255)

                                                                     c‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtc  <  1:3511341/70‑1 (MQ=255)

                                                                       t‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtc  <  1:774512/69‑1 (MQ=255)

AATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTC  >  minE/2571276‑2571413

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