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	2,571,357	C→A	26.6%	intergenic (+125/‑1654)	yibH → / → ysaB	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,571,357	0	C	A	26.6%	296.5 / 80.4	146	intergenic (+125/‑1654)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (33/74); new base A (21/18); total (54/92)
Fisher's exact test for biased strand distribution p-value = 1.27e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.12e-01

Only 100 of 151 total aligned reads displayed.

TATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGAT  >  minE/2571289‑2571427

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

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

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

        cATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGa                                                              >  1:2016698/1‑71 (MQ=255)

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

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

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

                 tgatgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGAtttctt                                                        <  1:4252406/69‑1 (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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

                              tttAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                              <  1:5480766/67‑1 (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‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc                                        >  1:2674080/1‑71 (MQ=255)

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

                                tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc                                        >  1:3672754/1‑71 (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‑GGATGAGTGTGCTCTCATTGGATTTTTTATc                                                     >  1:4038816/1‑52 (MQ=255)

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

                                     ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt                                          <  1:1716614/63‑1 (MQ=255)

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

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

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

                                     ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                   <  1:1175257/70‑1 (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‑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‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt                                            <  1:4167997/57‑1 (MQ=255)

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

                                            tGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                              <  1:4295897/53‑1 (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)

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

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

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

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

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

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

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

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

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

                                                          t‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtc                <  1:3932380/69‑1 (MQ=255)

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

                                                             gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt                                >  1:2566562/1‑51 (MQ=255)

                                                             gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt                                >  1:1469927/1‑51 (MQ=255)

                                                             gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt                                >  1:1823475/1‑51 (MQ=255)

                                                             gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtc                <  1:5436525/67‑1 (MQ=255)

                                                             gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCgaga            <  1:5619635/71‑1 (MQ=255)

                                                             gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCgag             <  1:3413843/70‑1 (MQ=255)

                                                             gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCga              <  1:4358569/69‑1 (MQ=255)

                                                             gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCga              <  1:4149641/69‑1 (MQ=255)

                                                             gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCga              <  1:2161337/69‑1 (MQ=255)

                                                             gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGACGCAGGATGAGACTATACATCGTCgag             <  1:3829152/70‑1 (MQ=255)

                                                               tGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACa                     <  1:1392556/60‑1 (MQ=255)

                                                                gAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCg         >  1:463623/1‑71 (MQ=255)

                                                                gAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCg         >  1:1537116/1‑71 (MQ=255)

                                                                 gctgtgATCTCATTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTgagaa           >  1:1551697/3‑67 (MQ=255)

                                                                 aGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCg         <  1:1820505/70‑1 (MQ=255)

                                                                  gtgtGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCa       <  1:227182/71‑1 (MQ=255)

                                                                     tgCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                   <  1:886221/40‑1 (MQ=255)

                                                                     tgCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                   <  1:3201858/40‑1 (MQ=255)

                                                                     tgCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                   <  1:5117893/40‑1 (MQ=255)

                                                                     tgCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatg    <  1:1268388/71‑1 (MQ=255)

                                                                     tgCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatg    <  1:3810209/71‑1 (MQ=255)

                                                                     tgCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAat     <  1:4984534/70‑1 (MQ=255)

                                                                      gCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCgag             <  1:417316/61‑1 (MQ=255)

                                                                       ctctCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatgat  <  1:151787/71‑1 (MQ=255)

TATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGAT  >  minE/2571289‑2571427

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A