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	835,011	G→C	21.6%	A1157P (GCA→CCA) ‡	narG →	nitrate reductase 1, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	835,011	0	G	C	21.6%	256.2 / 65.0	125	A1157P (GCA→CCA) ‡	narG	nitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand): ref base G (44/54); new base C (16/11); total (60/65)
Fisher's exact test for biased strand distribution p-value = 2.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

Only 100 of 125 total aligned reads displayed.

GACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAA  >  minE/834942‑835079

gACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGc                                                                     <  1:3507533/71‑1 (MQ=255)

     gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                                  <  1:234117/69‑1 (MQ=255)

     gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                                  <  1:4852113/69‑1 (MQ=255)

     gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                                  <  1:4414455/69‑1 (MQ=255)

     gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                                  <  1:1166388/69‑1 (MQ=255)

     gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                                  <  1:3777645/69‑1 (MQ=255)

     gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGa                                                                >  1:3396998/1‑71 (MQ=255)

         gAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGAc                                                            >  1:2012149/1‑71 (MQ=255)

          aaGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGAc                                                            <  1:388643/70‑1 (MQ=255)

           aGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGa                                                             >  1:1540180/1‑68 (MQ=255)

           aGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                                                          <  1:114199/71‑1 (MQ=255)

           aGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                                                          <  1:5112215/71‑1 (MQ=255)

            gtattCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCa                                                          >  1:4559720/4‑70 (MQ=255)

            gTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                                                         >  1:277424/1‑71 (MQ=255)

            gTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                                                         >  1:1337076/1‑71 (MQ=255)

            gTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                                                         >  1:4671006/1‑71 (MQ=255)

            gTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                                                         >  1:4921961/1‑71 (MQ=255)

               ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                                  <  1:3374290/59‑1 (MQ=255)

               ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                                  <  1:828517/59‑1 (MQ=255)

               ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatgat                                                      >  1:1140239/1‑71 (MQ=255)

                 cAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGAt                                                               >  1:783057/1‑60 (MQ=255)

                 cAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGAt                                                               >  1:1074713/1‑60 (MQ=255)

                    cAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAcc                                                 <  1:3832943/71‑1 (MQ=255)

                     gccAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCa                                                >  1:1251324/3‑71 (MQ=255)

                      ccAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAc                                               >  1:4609626/2‑71 (MQ=255)

                        aaCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgc                                             >  1:906405/1‑71 (MQ=255)

                        aaCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgc                                             >  1:828027/1‑71 (MQ=255)

                         aCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAg                                                                   <  1:3711934/48‑1 (MQ=255)

                         aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTat                                                  >  1:1890195/1‑64 (MQ=255)

                         aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTat                                                  >  1:2962100/1‑64 (MQ=255)

                         aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTat                                                  >  1:2708417/1‑64 (MQ=255)

                         aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgcc                                            >  1:3788152/1‑70 (MQ=255)

                           ggTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgcg                                            >  1:4350576/1‑69 (MQ=255)

                            gTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAg                                         <  1:1291937/71‑1 (MQ=255)

                             tGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAgg                                        <  1:859508/71‑1 (MQ=255)

                               cgctGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGaa                                      <  1:412202/69‑1 (MQ=255)

                                tctGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGc                                                                     <  1:5557475/39‑1 (MQ=255)

                                 ctGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                    >  1:447976/1‑71 (MQ=255)

                                  tGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTTCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                    >  1:4915988/1‑70 (MQ=255)

                                   gACTGCCCGTGCGGTTGTCAGGCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTa                                  >  1:4388736/1‑71 (MQ=255)

                                   gACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTa                                  >  1:2540680/1‑71 (MQ=255)

                                    aCTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAt                                 >  1:91440/1‑71 (MQ=255)

                                      tGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatgatg                                                     <  1:1829981/49‑1 (MQ=255)

                                        cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCg                               <  1:661469/69‑1 (MQ=255)

                                        cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                             <  1:4116101/71‑1 (MQ=255)

                                        cccGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAttat                              <  1:3019946/70‑4 (MQ=255)

                                        cccGCGCGGTGGTCAACCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAttat                              >  1:45183/1‑67 (MQ=255)

                                         ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                   <  1:1621651/64‑1 (MQ=255)

                                         ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                   <  1:3707454/64‑1 (MQ=255)

                                            tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                                                          <  1:2461041/38‑1 (MQ=255)

                                            tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                                                          <  1:2566865/38‑1 (MQ=255)

                                            tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTa                                                   >  1:641543/1‑45 (MQ=255)

                                            tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTa                                                   >  1:293482/1‑45 (MQ=255)

                                            tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                             <  1:2860641/67‑1 (MQ=255)

                                            tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                             <  1:679706/67‑1 (MQ=255)

                                            tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcc                         >  1:2168996/1‑71 (MQ=255)

                                             gCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcct                        >  1:1216563/1‑71 (MQ=255)

                                              cGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctg                       >  1:3045363/1‑71 (MQ=255)

                                              cGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctg                       >  1:4223642/1‑71 (MQ=255)

                                                gTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAc                                                  <  1:4478773/42‑1 (MQ=255)

                                                 ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctgcct                    <  1:2602551/71‑1 (MQ=255)

                                                 ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctgcct                    <  1:1044911/71‑1 (MQ=255)

                                                 ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctgcct                    <  1:3365965/71‑1 (MQ=255)

                                                   gTCAGCCAGCGTGTTCCGGCAGGGATGACCatgatg                                                     >  1:1405320/1‑36 (MQ=255)

                                                   gTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                    >  1:1033878/1‑53 (MQ=255)

                                                   gTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTgg                  >  1:4585703/1‑71 (MQ=255)

                                                   gTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCa                                          <  1:2518405/47‑1 (MQ=16)

                                                   gTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCa                                          <  1:3277177/47‑1 (MQ=16)

                                                     cagccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGtt                >  1:4710332/1‑71 (MQ=255)

                                                     cagccaacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAgg                                        >  1:2456129/1‑47 (MQ=16)

                                                     cagccaacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACgc                                   >  1:5210683/1‑51 (MQ=16)

                                                      agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc               >  1:832669/1‑71 (MQ=255)

                                                      agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc               >  1:839341/1‑71 (MQ=255)

                                                      agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc               >  1:2082186/1‑71 (MQ=255)

                                                      agccaacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTc               >  1:3183756/1‑71 (MQ=255)

                                                       gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                            <  1:2997136/57‑1 (MQ=255)

                                                       gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                            <  1:4065311/57‑1 (MQ=255)

                                                       gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                            <  1:5384197/57‑1 (MQ=255)

                                                        ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg             <  1:4492449/71‑1 (MQ=255)

                                                        ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg             <  1:641250/71‑1 (MQ=255)

                                                        ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGCTTCgg             <  1:2188890/71‑1 (MQ=255)

                                                          agcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa            >  1:1111952/1‑70 (MQ=255)

                                                          agcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa            <  1:5320507/70‑1 (MQ=255)

                                                          aacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCg              <  1:1771948/66‑1 (MQ=255)

                                                           acGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGaa                                      >  1:4853511/2‑43 (MQ=12)

                                                            cGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg             <  1:5510869/67‑1 (MQ=255)

                                                            cGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg             <  1:3043868/67‑1 (MQ=255)

                                                            cGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg             <  1:2805172/67‑1 (MQ=255)

                                                             gtgtACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCGGaagta        <  1:4552860/71‑4 (MQ=255)

                                                             gtgtACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCGGaagt         >  1:540723/1‑68 (MQ=255)

                                                              tgtTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGt                              <  1:5269924/48‑1 (MQ=255)

                                                              tgtTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGt                              <  1:4029514/48‑1 (MQ=255)

                                                                ttCCGGCAGGGATGACCATGATGTACCACGCGCAg                                         >  1:5210523/1‑35 (MQ=255)

                                                                ttCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa            <  1:3109862/64‑1 (MQ=255)

                                                                ttCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAcc     >  1:3714975/1‑71 (MQ=255)

                                                                  ccGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGaaa          >  1:5110952/1‑64 (MQ=255)

                                                                  ccGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAccc    >  1:1956105/1‑70 (MQ=255)

                                                                  ccGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAccc    >  1:1409111/1‑70 (MQ=255)

                                                                   cGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCaa  <  1:100192/71‑1 (MQ=255)

                                                                   cGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCa   <  1:2256105/70‑1 (MQ=255)

GACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAA  >  minE/834942‑835079

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