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	2,571,384	T→A	23.3%	intergenic (+152/‑1627)	yibH → / → ysaB	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,571,384	0	T	A	23.3%	332.0 / 102.3	168	intergenic (+152/‑1627)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (48/80); new base A (26/13); total (75/93)
Fisher's exact test for biased strand distribution p-value = 1.68e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 177 total aligned reads displayed.

TTTCTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTTCCTCCTGCGACG  >  minE/2571314‑2571452

tttCTTTAATATTCATTATGTTAATAAGTTC‑TCGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGt                                                                      >  1:5527992/1‑71 (MQ=255)

  tCTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt                                                                     <  1:5695919/70‑1 (MQ=255)

   cTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt                                                                   >  1:4191709/1‑71 (MQ=255)

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

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

      tAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGcc                                                                >  1:109743/1‑71 (MQ=255)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

                              c‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtc                                         <  1:5004618/70‑1 (MQ=255)

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

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

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

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

                                  gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCga                                       <  1:666272/69‑1 (MQ=255)

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

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

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

                                    tGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACa                                              <  1:3179875/60‑1 (MQ=255)

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

                                     gAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCg                                  >  1:3667859/1‑71 (MQ=255)

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

                                      aGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATga                                                       <  1:1982580/49‑1 (MQ=255)

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

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

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

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

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

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

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

                                          tgCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatg                             <  1:4960781/71‑1 (MQ=255)

                                           gCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCgag                                      <  1:4165716/61‑1 (MQ=255)

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

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

                                            atctcATTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACg                                  <  1:1855778/63‑1 (MQ=255)

                                            atctcATTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACg                                  <  1:4993226/63‑1 (MQ=255)

                                             tctcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACtata                                                >  1:814179/1‑49 (MQ=255)

                                              ctcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                                            <  1:1266480/36‑1 (MQ=255)

                                              ctcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                                            <  1:1470732/36‑1 (MQ=255)

                                              ctcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                                            <  1:398488/36‑1 (MQ=255)

                                              ctcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                                            <  1:1381712/36‑1 (MQ=255)

                                              ctcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATga                                                       >  1:3864690/1‑41 (MQ=255)

                                              ctcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATga                                                       >  1:2578423/1‑41 (MQ=255)

                                              ctcATTAGATTTCTCATCCGTCTTGATCTGTCCGATGACCAGACTGTGCATTGTTGAGAACGCACtaatga                         >  1:2317238/1‑71 (MQ=255)

                                               tcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAAtgatga                         >  1:4314960/1‑70 (MQ=255)

                                               tcATTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCacta                             <  1:4315466/66‑4 (MQ=255)

                                                cATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACtata                                                >  1:510010/1‑46 (MQ=255)

                                                cATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatgatg                          <  1:1937277/68‑1 (MQ=255)

                                                cATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGata                       >  1:2811266/1‑71 (MQ=255)

                                                cATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGata                       >  1:1951030/1‑71 (MQ=255)

                                                 aTTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAAtgatga                         <  1:3581123/68‑1 (MQ=255)

                                                 aTTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTgagaa                                    >  1:1460628/1‑56 (MQ=255)

                                                 aTTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCActaatg                          <  1:4527043/67‑1 (MQ=255)

                                                 aTTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCACTAATGacat                      >  1:1715371/1‑71 (MQ=255)

                                                 aTTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCACTAATGacat                      >  1:2753796/1‑71 (MQ=255)

                                                  ttGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATga                                                       <  1:4703125/37‑1 (MQ=255)

                                                  ttGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCa                                <  1:1107040/60‑1 (MQ=255)

                                                  ttGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAat                              <  1:5173566/62‑1 (MQ=255)

                                                    ggATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatgat                           <  1:5399116/63‑1 (MQ=255)

                                                    ggATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatga                            >  1:4112445/1‑62 (MQ=255)

                                                    ggATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAg                   >  1:4664338/1‑71 (MQ=255)

                                                    ggATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTTTGCATTGTTGAGAACGCACTAATGACATGa                    <  1:5040939/70‑1 (MQ=255)

                                                    ggATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCACTAATGACATGa                    <  1:947627/70‑1 (MQ=255)

                                                    ggATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCACTAATGACATGa                    <  1:1182047/70‑1 (MQ=255)

                                                     gATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAgt                  >  1:383292/1‑71 (MQ=255)

                                                     gATTTCTTATCCGTCTTGATCTGTCCGATGACCAGACTGTGCATTGTTGAGAACGCACTAATGACATGaat                  >  1:3122013/1‑69 (MQ=255)

                                                       ttttttATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATg                     <  1:2994731/66‑1 (MQ=255)

                                                       tttcttATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCa                                >  1:4599096/1‑55 (MQ=255)

                                                        tttttATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtcg                                        <  1:1363715/46‑1 (MQ=255)

                                                        tttttATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGc                                 <  1:4813418/53‑1 (MQ=255)

                                                        tttttATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatgatg                          >  1:2172702/1‑60 (MQ=255)

                                                          tttATCGGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCaa                               >  1:731348/1‑53 (MQ=255)

                                                          tttATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTtc             >  1:2823603/1‑71 (MQ=255)

                                                            tATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTtcc            <  1:2406726/70‑1 (MQ=255)

                                                              tCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAAtgatga                         <  1:3553576/55‑1 (MQ=255)

                                                              tCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAAtgatga                         <  1:1538276/55‑1 (MQ=255)

                                                              tCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTtcctcc         >  1:2529112/1‑71 (MQ=255)

                                                                cGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTTcctcct        <  1:5342248/70‑1 (MQ=255)

                                                                cGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTTCCTCCTg       >  1:3330444/1‑71 (MQ=255)

                                                                cGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTTCCTCCTg       >  1:5491644/1‑71 (MQ=255)

                                                                  tCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTTCCTCCTg       <  1:5372862/69‑1 (MQ=255)

                                                                    ttGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTTCCTCCTGCGAc   >  1:1955615/1‑71 (MQ=255)

                                                                    ttGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTTCCTCCTGCGAc   >  1:1260997/1‑71 (MQ=255)

                                                                    ttGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCG‑AATGATGATATGAGTTGTTCCTCCTGCGACg  >  1:1619006/1‑71 (MQ=255)

                                                                    ttGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCG‑AATGATGATATGAGTTGTTCCTCCTGCGACg  >  1:1625714/1‑71 (MQ=255)

                                                                       ttCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAAtgatga                         >  1:3234548/1‑46 (MQ=255)

                                                                       ttCTGCCCCAGGATGAGACTATACATCGTCGAGATCGCAAtgatga                         >  1:4292406/1‑46 (MQ=255)

TTTCTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTTCCTCCTGCGACG  >  minE/2571314‑2571452

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A