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 R2 251 90.0 5200563 86.9% 4519289 59.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,502,847 A→T 11.3% 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
*minE1,502,8470AT11.3% 345.0 / 30.1 124intergenic (‑220/‑700)lrhA/yfbQDNA‑binding transcriptional repressor/predicted aminotransferase
Reads supporting (aligned to +/- strand):  ref base A (66/44);  new base T (11/3);  total (77/47)
Fisher's exact test for biased strand distribution p-value = 2.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 126 total aligned reads displayed.

ACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCACTC  >  minE/1502779‑1502916
                                                                    |                                                                     
acaTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATa                                                                     >  1:2861202/1‑71 (MQ=255)
  aTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATact                                                                   >  1:4948488/1‑71 (MQ=255)
  aTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATac                                                                    >  1:3370557/1‑70 (MQ=255)
    tGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGTGATCGCATATCTATTAAGATactca                                                                 >  1:1100574/1‑71 (MQ=255)
     gTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATactcac                                                                >  1:3717391/1‑71 (MQ=255)
     gTTCCGTTA‑AATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATactcac                                                                >  1:4547263/1‑70 (MQ=255)
         cGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCtt                                                            <  1:473930/71‑1 (MQ=255)
                aTGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAtt                                                     <  1:610655/71‑1 (MQ=255)
                   ccTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTAt                                                  >  1:2247657/1‑71 (MQ=255)
                   ccTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTAt                                                  >  1:4741269/1‑71 (MQ=255)
                   ccTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTAt                                                  >  1:781397/1‑71 (MQ=255)
                    cTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATg                                                 <  1:412094/71‑1 (MQ=255)
                    cTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATg                                                 <  1:4107708/71‑1 (MQ=255)
                    cTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATg                                                 <  1:284655/71‑1 (MQ=255)
                    cTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATg                                                 <  1:2898052/71‑1 (MQ=255)
                       aaGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATg                                                 >  1:2119521/1‑68 (MQ=255)
                           aGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgcg                                          >  1:2813319/1‑71 (MQ=255)
                           aGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgcg                                          >  1:2007884/1‑71 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAttt                                                    >  1:1836228/1‑57 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCgtg                                      >  1:4461254/1‑71 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCgtg                                      >  1:2939543/1‑71 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCgtg                                      >  1:2513753/1‑71 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:114770/1‑62 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCgtgt                                     <  1:2726393/71‑1 (MQ=255)
                                  aGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGttt                                   >  1:274067/1‑71 (MQ=255)
                                  aGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGtt                                    >  1:3051861/1‑70 (MQ=255)
                                  aGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGtt                                    >  1:1386502/1‑70 (MQ=255)
                                   gAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTg                                  >  1:3220247/1‑71 (MQ=255)
                                    aaTATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTg                                  >  1:629332/1‑70 (MQ=255)
                                      tatatCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCgtg                                      >  1:1889324/1‑64 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtata                              <  1:3922006/70‑1 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtata                              <  1:3941302/70‑1 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaa                             <  1:2716937/71‑1 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaa                             <  1:4061823/71‑1 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaa                             <  1:4266059/71‑1 (MQ=255)
                                          tCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtata                              <  1:4169925/68‑1 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGATACTCACTCtttt                                                          >  1:488567/1‑36 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGATACTCACTCtttt                                                          >  1:2957128/1‑36 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGATACTCACTCtttt                                                          >  1:3460665/1‑36 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                        <  1:5155979/70‑1 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                        >  1:2156230/1‑70 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                        >  1:2975857/1‑70 (MQ=255)
                                              cAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                        <  1:4258330/70‑1 (MQ=255)
                                               aGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAt                                                      >  1:4801888/1‑39 (MQ=255)
                                               aGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAt                                                      >  1:127738/1‑39 (MQ=255)
                                               aGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAt                                                      >  1:4119264/1‑39 (MQ=255)
                                               aGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAt                                                      >  1:4167373/1‑39 (MQ=255)
                                               aGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAt                                                      >  1:4208741/1‑39 (MQ=255)
                                               aGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAt                                                      >  1:2067072/1‑39 (MQ=255)
                                               aGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAt                                                      >  1:4259196/1‑39 (MQ=255)
                                               aGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAt                                                      >  1:2412719/1‑39 (MQ=255)
                                               aGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAt                                                      >  1:4594530/1‑39 (MQ=255)
                                                gtgATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                        <  1:3226469/66‑1 (MQ=255)
                                                  gATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:4397775/71‑1 (MQ=255)
                                                    tCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:64566/69‑1 (MQ=255)
                                                    tCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:3255415/69‑1 (MQ=255)
                                                    tCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:4433796/69‑1 (MQ=255)
                                                    tCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:2131011/69‑1 (MQ=255)
                                                    tCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 <  1:4609749/71‑1 (MQ=255)
                                                       cATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTc              <  1:3003792/71‑1 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGAc                                               >  1:3937967/1‑37 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:427746/1‑38 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:4822713/1‑38 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:4189548/1‑38 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:805626/1‑38 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:1279010/1‑38 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:1405407/1‑38 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:1726286/1‑38 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:3240481/1‑38 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:3238972/1‑38 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:2738190/1‑38 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTcc             <  1:155835/71‑1 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTcc             >  1:2315667/1‑71 (MQ=255)
                                                        atatCTATTAAGATAATCACTCTTTTCTATTTATGACa                                              >  1:3664324/1‑38 (MQ=255)
                                                         tatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtata                              <  1:3306558/53‑1 (MQ=255)
                                                         tatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtata                              <  1:4724256/53‑1 (MQ=255)
                                                         tatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:3750160/64‑1 (MQ=255)
                                                         tatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:2030388/64‑1 (MQ=255)
                                                           tCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:3501960/1‑64 (MQ=255)
                                                           tCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:3121955/1‑64 (MQ=255)
                                                           tCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:3049350/1‑64 (MQ=255)
                                                           tCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTg          >  1:3685582/1‑71 (MQ=255)
                                                            cTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:1003641/1‑63 (MQ=255)
                                                            cTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:4952864/1‑63 (MQ=255)
                                                            cTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:34094/1‑63 (MQ=255)
                                                            cTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:178610/1‑63 (MQ=255)
                                                            cTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:4625421/1‑63 (MQ=255)
                                                            cTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:2359335/1‑63 (MQ=255)
                                                             tATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:119524/60‑1 (MQ=255)
                                                               ttAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:3020697/1‑60 (MQ=255)
                                                               ttAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTc       <  1:139581/70‑1 (MQ=255)
                                                               ttAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTc       <  1:110230/70‑1 (MQ=255)
                                                               ttAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTc       <  1:2892974/70‑1 (MQ=255)
                                                                tAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                        <  1:3023144/52‑1 (MQ=255)
                                                                tAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                        <  1:2447884/52‑1 (MQ=255)
                                                                 aaGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:552898/1‑58 (MQ=255)
                                                                 aaGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:1293445/1‑58 (MQ=255)
                                                                 aaGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGa                 >  1:3976847/1‑58 (MQ=255)
                                                                  aGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaa                      >  1:1367235/1‑52 (MQ=255)
                                                                   gATACTCACTATTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCActc  <  1:2309932/71‑1 (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