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 1,502,847 A→T 79.3% intergenic (‑220/‑700) lrhA ← / → yfbQ DNA‑binding transcriptional repressor/predicted aminotransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,502,8470AT79.3% 227.1 / 54.1 106intergenic (‑220/‑700)lrhA/yfbQDNA‑binding transcriptional repressor/predicted aminotransferase
Reads supporting (aligned to +/- strand):  ref base A (13/9);  new base T (44/40);  total (57/49)
Fisher's exact test for biased strand distribution p-value = 6.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 107 total aligned reads displayed.

ACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCAC  >  minE/1502779‑1502914
                                                                    |                                                                   
acaTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTa                                                                   >  1:679040/1‑71 (MQ=255)
 caTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTa                                                                   <  1:2027626/70‑1 (MQ=255)
 caTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTa                                                                   <  1:4137097/70‑1 (MQ=255)
 caTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTa                                                                   <  1:3630623/70‑1 (MQ=255)
  aTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTact                                                                 >  1:1957182/1‑71 (MQ=255)
  aTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTact                                                                 >  1:204538/1‑71 (MQ=255)
  aTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATact                                                                 >  1:5044726/1‑71 (MQ=255)
   ttGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTact                                                                 >  1:4032057/1‑70 (MQ=255)
   ttGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTact                                                                 >  1:5043036/1‑70 (MQ=255)
   ttGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATact                                                                 >  1:2955841/1‑70 (MQ=255)
        ccGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTactcactc                                                            <  1:5127489/70‑1 (MQ=255)
        ccGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCActct                                                           >  1:2415717/1‑71 (MQ=255)
        ccGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATACCTATTAAGTTACTCActct                                                           >  1:4829466/1‑71 (MQ=255)
         cGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCtt                                                          <  1:3084535/71‑1 (MQ=255)
         cGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCtt                                                          <  1:4074900/71‑1 (MQ=255)
         cGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCtt                                                          <  1:4313250/71‑1 (MQ=255)
           ttATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCtttt                                                        >  1:2136659/1‑71 (MQ=255)
           ttATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCttt                                                         >  1:656500/1‑70 (MQ=255)
           ttATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCtttt                                                        >  1:673031/1‑71 (MQ=255)
            tataATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTc                                                       >  1:2548806/1‑71 (MQ=255)
             ataATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTc                                                       <  1:1378624/70‑1 (MQ=255)
             ataATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTc                                                       >  1:433649/1‑70 (MQ=255)
              taATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTa                                                     <  1:2128412/71‑1 (MQ=255)
                   ccTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTactcactc                                                            <  1:2199723/59‑1 (MQ=255)
                    cTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATg                                               <  1:4301082/71‑1 (MQ=255)
                     tGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTAt                                                <  1:5322005/69‑1 (MQ=255)
                     tGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGa                                              >  1:3402163/1‑71 (MQ=255)
                      gAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGa                                              >  1:2364368/1‑70 (MQ=255)
                       aaGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGa                                              <  1:1823152/69‑1 (MQ=255)
                         gTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCActct                                                           >  1:3925618/1‑54 (MQ=255)
                          tAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgc                                         <  1:3066638/71‑1 (MQ=255)
                           aGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgcg                                        >  1:736860/1‑71 (MQ=255)
                            gATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgcg                                        >  1:3795479/1‑70 (MQ=255)
                            gATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgc                                         >  1:2609518/1‑69 (MQ=255)
                             aTCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTactcac                                                              <  1:4806461/47‑1 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCgtg                                    >  1:4145412/1‑71 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCgtg                                    >  1:5126153/1‑71 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCgt                                     >  1:664600/1‑70 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCgtgt                                   >  1:2676908/1‑71 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCgtgt                                   >  1:3041311/1‑71 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCgtg                                    <  1:5072121/70‑1 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCt                                                      <  1:282627/52‑1 (MQ=255)
                                    aaTATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGt                               <  1:2138397/71‑1 (MQ=255)
                                      tatatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACa                                            <  1:5251125/56‑1 (MQ=255)
                                      tatatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGta                              >  1:586575/1‑70 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACAt                                           >  1:1416639/1‑55 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACAt                                           >  1:3762275/1‑55 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaa                           <  1:1399324/71‑1 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtata                            >  1:210774/1‑70 (MQ=255)
                                            ttCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTAt                                                <  1:4183287/46‑1 (MQ=255)
                                            ttCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTAt                                                <  1:2776415/46‑1 (MQ=255)
                                             tCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTa                                                 >  1:5070670/1‑44 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGta                              >  1:5609358/1‑62 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                      >  1:3278167/1‑70 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                      <  1:3654242/70‑1 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                      <  1:4622202/70‑1 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgt                       >  1:5271181/1‑69 (MQ=255)
                                               aGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaa                    <  1:1035516/71‑1 (MQ=255)
                                               aGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaa                    <  1:4707674/71‑1 (MQ=255)
                                               aGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaa                    <  1:1200642/71‑1 (MQ=255)
                                                gggATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaat                   <  1:2512015/71‑1 (MQ=255)
                                                 ggATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtata                            <  1:393534/61‑1 (MQ=255)
                                                 ggATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtata                            <  1:1745828/61‑1 (MQ=255)
                                                  gATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                 <  1:4612543/71‑1 (MQ=255)
                                                   aTCGCATATCTATTAAGTTACTCACTCTTTTCTAtt                                                   >  1:5002403/1‑36 (MQ=255)
                                                   aTCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaa                          >  1:783328/1‑61 (MQ=255)
                                                      gCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAg              <  1:106663/70‑1 (MQ=255)
                                                      gCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGt             >  1:5462280/1‑71 (MQ=255)
                                                      gCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGt             >  1:1140723/1‑71 (MQ=255)
                                                        atatCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTcc           <  1:4437583/71‑1 (MQ=255)
                                                         tatCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaat                         <  1:4356670/56‑1 (MQ=255)
                                                         tatCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCt          <  1:1118158/71‑1 (MQ=255)
                                                         tatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaa                    <  1:3622974/61‑1 (MQ=255)
                                                         tatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaa                    <  1:3260581/61‑1 (MQ=255)
                                                          atCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaat                   <  1:108381/61‑1 (MQ=255)
                                                          atCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaat                   <  1:699857/61‑1 (MQ=255)
                                                          atCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaat                   <  1:3032185/61‑1 (MQ=255)
                                                          atCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCtt         >  1:3101377/1‑71 (MQ=255)
                                                          atCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCt          <  1:1878400/70‑1 (MQ=255)
                                                           tCTATTAAGTTACTCCCTCTTTTCTATTTATGACATGCGCGTGTTTGt                               >  1:1270238/1‑48 (MQ=255)
                                                           tCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTg                                >  1:5605748/1‑47 (MQ=255)
                                                           tCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGt                               >  1:5691474/1‑48 (MQ=255)
                                                           tCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaat                   >  1:4625501/1‑60 (MQ=255)
                                                           tCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaa                    >  1:4392262/1‑59 (MQ=255)
                                                           tCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaa                    >  1:4041565/1‑59 (MQ=255)
                                                           tCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaa                    >  1:4664024/1‑59 (MQ=255)
                                                           tCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTg        >  1:5343288/1‑71 (MQ=255)
                                                            cTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCt          <  1:2120628/68‑1 (MQ=255)
                                                               ttAAGTTACTCACTCTTTTCTATTTATGACATTCGCGTGTTTGTATAAATGTAAATGTGa               >  1:5605045/1‑60 (MQ=255)
                                                               ttAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa               >  1:1889717/1‑60 (MQ=255)
                                                               ttAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa               >  1:3010775/1‑60 (MQ=255)
                                                               ttAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTc     <  1:23599/70‑1 (MQ=255)
                                                               ttAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTc     >  1:4311204/1‑70 (MQ=255)
                                                               ttAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTc     <  1:3902110/70‑1 (MQ=255)
                                                                tAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCa   >  1:2642597/1‑71 (MQ=255)
                                                                 aaGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCa   <  1:337816/70‑1 (MQ=255)
                                                                 aaGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCAc  >  1:3595788/1‑71 (MQ=255)
                                                                 aaGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCAc  >  1:3852191/1‑71 (MQ=255)
                                                                 aaGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTg                                >  1:4622929/1‑41 (MQ=255)
                                                                    aTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                      <  1:1786311/48‑1 (MQ=255)
                                                                    |                                                                   
ACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCAC  >  minE/1502779‑1502914

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