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	2,571,344:1	+A	24.1%	intergenic (+112/‑1667)	yibH → / → ysaB	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,571,344	1	.	A	24.1%	302.4 / 165.9	141	intergenic (+112/‑1667)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base . (45/62); new base A (20/14); total (65/76)
Fisher's exact test for biased strand distribution p-value = 1.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

Only 100 of 155 total aligned reads displayed.

CTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTC  >  minE/2571274‑2571413

   attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     >  1:3597404/1‑70 (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                                                                  >  1:2657581/1‑70 (MQ=255)

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

             cATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGtgtg                                                           <  1:4267138/70‑1 (MQ=255)

               tatTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGctc                                                        >  1:2352113/1‑71 (MQ=255)

                atTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     <  1:3364244/57‑1 (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‑GGATGAGTGTGctct                                                       >  1:4021442/1‑71 (MQ=255)

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

                    cTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTTTGTTAATAAGTTc                                                                         <  1:687733/51‑1 (MQ=255)

                    cTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTc                                                                         <  1:4607018/51‑1 (MQ=255)

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

                     ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     <  1:284437/52‑1 (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‑GGATGAGTGTGCTCTCATTGGa                                                >  1:2016698/1‑71 (MQ=255)

                        aTTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGAt                                               <  1:327776/71‑1 (MQ=255)

                         ttAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGAtt                                              >  1:598891/1‑71 (MQ=255)

                           aGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGAttt                                             <  1:2451652/70‑1 (MQ=255)

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

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

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

                                cGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTc                                                                         <  1:4416152/39‑1 (MQ=255)

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

                                cGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑t                                                                       >  1:3069491/1‑40 (MQ=255)

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

                                  atgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTc                                                                         <  1:3842416/38‑1 (MQ=12)

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

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

                                    gatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     >  1:4875433/1‑37 (MQ=255)

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

                                    gatTTTA‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTc                                   >  1:734041/1‑71 (MQ=255)

                                    gatATTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                                     >  1:5530527/1‑37 (MQ=255)

                                     tttttc‑CTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTc                                   >  1:5093691/2‑71 (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‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCtt                                 <  1:119029/71‑1 (MQ=255)

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

                                       tttc‑CTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCtt                                 >  1:2110719/1‑71 (MQ=255)

                                        ttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTg                                <  1:3487164/70‑1 (MQ=255)

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

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

                                         ttccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCtt                                 <  1:1754179/67‑1 (MQ=255)

                                         tt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTa                                         >  1:2233766/1‑60 (MQ=255)

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

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

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

                                          tccTTTAATATCCAGCATGTTAAGAAGTTC‑TGGGATAGCTGTAATCTCATTAGATTTCTCATCCGTCTTg                                <  1:2759612/68‑1 (MQ=255)

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

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

                                          t‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt                              <  1:5695919/70‑1 (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‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGcc                         >  1:837254/1‑71 (MQ=255)

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

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

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

                                               tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCt                            >  1:3759709/1‑69 (MQ=255)

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

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

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

                                               tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc                          >  1:3672754/1‑71 (MQ=255)

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

                                                aaTATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTgat                              >  1:2205858/1‑64 (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                            <  1:1716614/63‑1 (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)

                                                    ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                     <  1:1864496/70‑1 (MQ=255)

                                                      cATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt                  >  1:1549294/1‑71 (MQ=255)

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

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

                                                       aTTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATcc                                      >  1:482338/1‑50 (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)

                                                           tGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGAc             <  1:4784700/71‑1 (MQ=255)

                                                           tGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                <  1:4295897/53‑1 (MQ=255)

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

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

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

                                                              taataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTg                           >  1:4514969/1‑54 (MQ=255)

                                                              taataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTg                           >  1:4344942/1‑54 (MQ=255)

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

                                                                ataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCg                                     <  1:4732441/42‑1 (MQ=255)

                                                                ataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGt                               <  1:4440026/48‑1 (MQ=255)

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

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

CTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTC  >  minE/2571274‑2571413

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