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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,502,847 A→T 30.3% 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
*minE1,502,8470AT30.3% 114.3 / 64.4 79intergenic (‑220/‑700)lrhA/yfbQDNA‑binding transcriptional repressor/predicted aminotransferase
Reads supporting (aligned to +/- strand):  ref base A (33/22);  new base T (7/17);  total (40/39)
Fisher's exact test for biased strand distribution p-value = 1.50e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

ACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCACTC  >  minE/1502779‑1502916
                                                                    |                                                                     
acaTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGa                                                                       >  1:289745/1‑69 (MQ=255)
acaTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGa                                                                       <  1:3553573/69‑1 (MQ=255)
acaTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGa                                                                       <  1:1207438/69‑1 (MQ=255)
acaTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTa                                                                     >  1:232643/1‑71 (MQ=255)
acaTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATa                                                                     >  1:3928135/1‑71 (MQ=255)
 caTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATac                                                                    <  1:80754/71‑1 (MQ=255)
    tGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATactca                                                                 >  1:1753845/1‑71 (MQ=255)
     gTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATactca                                                                 >  1:470890/1‑70 (MQ=255)
      ttCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTactcac                                                                <  1:2195507/70‑1 (MQ=255)
      ttCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTactcac                                                                <  1:2190586/70‑1 (MQ=255)
         cGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCtt                                                            <  1:667546/71‑1 (MQ=255)
            tataATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTc                                                         >  1:327660/1‑71 (MQ=255)
              taATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTa                                                       <  1:3678179/71‑1 (MQ=255)
               aaTGCCTGAAGTAGATCACATAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTa                                                       >  1:972086/1‑70 (MQ=255)
                aTGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAtt                                                     >  1:4006738/1‑71 (MQ=255)
                 tGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAttt                                                    <  1:1479797/71‑1 (MQ=255)
                   ccTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGa                                                                       <  1:2801676/50‑1 (MQ=255)
                   ccTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGa                                                                       <  1:357314/50‑1 (MQ=255)
                   ccTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTAt                                                  <  1:1891547/71‑1 (MQ=255)
                   ccTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTAt                                                  <  1:2256550/71‑1 (MQ=255)
                    cTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATg                                                 <  1:393690/71‑1 (MQ=255)
                         gTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATg                                            >  1:1120549/1‑71 (MQ=255)
                          tAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATgc                                           <  1:1177764/71‑1 (MQ=255)
                           aGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATa                                                                     >  1:744015/1‑44 (MQ=255)
                              tCACAGAATATATCTTCAGGGATCGCATATCTATTAAGa                                                                       >  1:3180621/1‑39 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGa                                                                       >  1:1558923/1‑38 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATg                                                 <  1:1661775/60‑1 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGa                                                >  1:3954124/1‑61 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:3737155/1‑63 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCgtg                                      >  1:518056/1‑71 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCgtg                                      >  1:442687/1‑71 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCgtg                                      >  1:2624598/1‑71 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGATactcac                                                                >  1:3735528/1‑44 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATgcgc                                         >  1:2089670/1‑67 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGTGCgtgt                                     <  1:534625/71‑1 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCgtgt                                     <  1:1033378/71‑1 (MQ=255)
                                 caGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGtt                                    <  1:2028625/71‑1 (MQ=255)
                                  aGAATATATCTTCAGGGATCGCATATCTATTAAGa                                                                       <  1:1048539/35‑1 (MQ=255)
                                   gAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTg                                  >  1:3687517/1‑71 (MQ=255)
                                   gAATATATCTTCAGGGATCGCATATCTATTAAGATa                                                                     >  1:418793/1‑36 (MQ=255)
                                    aaTATATCTTCAGGGATCGCATATCTATTAAGATactca                                                                 >  1:2637748/1‑39 (MQ=255)
                                    aaTATATCTTCAGGGATCGCATATCTATTAAGATa                                                                     >  1:3779668/1‑35 (MQ=255)
                                    aaTATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGAc                                               >  1:2334241/1‑57 (MQ=255)
                                    aaTATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTg                                  >  1:3976279/1‑70 (MQ=255)
                                      tatatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTg                                  <  1:3832181/68‑1 (MQ=255)
                                      tatatCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGa                                                <  1:2803059/54‑1 (MQ=255)
                                      tatatCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGta                                >  1:1913642/1‑70 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtata                              <  1:103527/70‑1 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtata                              <  1:1084488/70‑1 (MQ=255)
                                         atCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaa                            >  1:2010214/1‑71 (MQ=255)
                                           cTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGttt                                   >  1:2029763/1‑62 (MQ=255)
                                            ttCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGa                                                >  1:298842/1‑48 (MQ=255)
                                             tCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgt                         >  1:2466573/1‑70 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                        <  1:3672308/70‑1 (MQ=255)
                                                  gATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:1865258/71‑1 (MQ=255)
                                                  gATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:435687/71‑1 (MQ=255)
                                                  gATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   >  1:1182717/1‑71 (MQ=255)
                                                   aTCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGa                                                <  1:1260385/41‑1 (MQ=255)
                                                   aTCGCATATCTATTAAGATACTCACTCTTTTCTAtt                                                     <  1:2597608/36‑1 (MQ=255)
                                                    tCGCATATCTATTAAGTTACTCACTCTTTTCTATTTAt                                                  <  1:3726942/38‑1 (MQ=255)
                                                    tCGCATATCTATTAAGTTACTCACTCTTTTCTATTTAt                                                  <  1:942233/38‑1 (MQ=255)
                                                    tCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 <  1:3441999/71‑1 (MQ=255)
                                                     cGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGttt                                   >  1:3783208/1‑52 (MQ=255)
                                                      gCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGt               >  1:1534383/1‑71 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTcc             >  1:380226/1‑71 (MQ=255)
                                                         tatCTATTAAGTTACTCACTCTTTTCTATTTATGa                                                <  1:3556977/35‑1 (MQ=255)
                                                         tatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCt            <  1:2217414/71‑1 (MQ=255)
                                                          atCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:443005/63‑1 (MQ=255)
                                                          atCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:305259/1‑65 (MQ=255)
                                                           tCTATTAAGTTACTCACTCTTTTCTATTTATGAGTTGCGCGTGTTTGTAtaaatgtaaat                     <  1:1487086/60‑1 (MQ=255)
                                                           tCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCtt           <  1:2324556/70‑1 (MQ=255)
                                                           tCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCt            <  1:2546470/69‑1 (MQ=255)
                                                            cTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTg          >  1:1910663/1‑70 (MQ=255)
                                                             tATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaat                     >  1:2448598/1‑58 (MQ=255)
                                                               ttAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTg          <  1:3628725/67‑1 (MQ=255)
                                                               ttAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTc       <  1:3350805/70‑1 (MQ=255)
                                                               ttAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtat                               <  1:2595586/46‑1 (MQ=255)
                                                               ttAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGta                                >  1:2505197/1‑45 (MQ=255)
                                                               ttAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaa                            >  1:2635033/1‑49 (MQ=255)
                                                               ttAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAg                <  1:2558355/61‑1 (MQ=255)
                                                               ttAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTc       <  1:3049178/70‑1 (MQ=255)
                                                                 aaGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaa                            >  1:2970932/1‑47 (MQ=255)
                                                                 aaGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTc       >  1:2758474/1‑68 (MQ=255)
                                                                 aaGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCAc    >  1:3388546/1‑71 (MQ=255)
                                                                 aaGATACTCACTCTTTTCTATTTATGACATGCCCGTGTTTCTAtaa                             >  1:2449939/1‑46 (MQ=255)
                                                                  aGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCAc    <  1:3816204/70‑1 (MQ=255)
                                                                   gATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCActc  <  1:3955546/71‑1 (MQ=255)
                                                                    |                                                                     
ACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCACTC  >  minE/1502779‑1502916

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A