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
A2 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,026,348 T→C 50.9% E175G (GAG→GGG)  malI ← DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,026,3480TC50.9% 1.4 / 87.4 59E175G (GAG→GGG) malIDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base T (19/10);  new base C (18/12);  total (37/22)
Fisher's exact test for biased strand distribution p-value = 7.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGTTAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGATAAC  >  minE/1026283‑1026411
                                                                 |                                                               
gggTTAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGt                                                             >  1:3583634/1‑70 (MQ=255)
  gTTAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaa                                                          >  1:271981/1‑71 (MQ=255)
      aTGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTcaacaa                                                       <  1:1961596/70‑1 (MQ=255)
      aTGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTcaacaa                                                       <  1:1290582/70‑1 (MQ=255)
       tGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                         <  1:4210461/67‑1 (MQ=255)
       tGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCaacaac                                                      <  1:2487733/70‑1 (MQ=255)
        gAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCaacaac                                                      <  1:1440574/69‑1 (MQ=255)
        gAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCaacaac                                                      <  1:3131168/69‑1 (MQ=255)
                ttGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCt                                            >  1:3787400/1‑71 (MQ=255)
                ttGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGACCCGTCAACAACTGTGCAGCCt                                            >  1:824013/1‑71 (MQ=255)
                 tGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTg                                           >  1:4020312/1‑71 (MQ=255)
                 tGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTCCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTg                                           >  1:3151506/1‑71 (MQ=255)
                     cTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCaacaac                                                      >  1:1627740/1‑56 (MQ=255)
                     cTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCaacaac                                                      >  1:2064429/1‑56 (MQ=255)
                     cTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCaacaac                                                      >  1:238474/1‑56 (MQ=255)
                     cTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCaacaac                                                      >  1:2423676/1‑56 (MQ=255)
                       cccAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCAtgtt                                     >  1:3076593/1‑71 (MQ=255)
                       cccAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCAtgtt                                     >  1:2816903/1‑71 (MQ=255)
                       cccAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCAtgtt                                     >  1:2525853/1‑71 (MQ=255)
                        ccagccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCAtgttg                                    >  1:3873300/1‑71 (MQ=255)
                        ccagccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCAtgttg                                    >  1:2996312/1‑71 (MQ=255)
                        ccagccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCAtgttg                                    >  1:3012473/1‑71 (MQ=255)
                        ccagccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCAtgttg                                    >  1:2714990/1‑71 (MQ=255)
                        ccagccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCAtgttg                                    >  1:2734446/1‑71 (MQ=255)
                        ccagccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCAtgttg                                    >  1:926497/1‑71 (MQ=255)
                        ccagccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCAtgttg                                    >  1:1634613/1‑71 (MQ=255)
                         cagccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCAtgttgt                                   >  1:1195425/1‑71 (MQ=255)
                         cagccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCAtgttgt                                   <  1:3923287/71‑1 (MQ=255)
                                gCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCAtgtt                                     <  1:2453813/62‑1 (MQ=255)
                                gCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCAtgtt                                     <  1:3118746/62‑1 (MQ=255)
                                gCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCAtgtt                                     <  1:3127952/62‑1 (MQ=255)
                                 cGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGa                           <  1:1882858/71‑1 (MQ=255)
                                     ccGCTGATGCCCATTGCGAATGAGATGCTCCGTcaa                                                          >  1:3796020/1‑36 (MQ=255)
                                     ccGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCg                       >  1:783762/1‑71 (MQ=255)
                                      cGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCg                       >  1:1011440/1‑70 (MQ=255)
                                      cGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCg                       >  1:3268913/1‑70 (MQ=255)
                                      cGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCg                       <  1:866351/70‑1 (MQ=255)
                                      cGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCg                       <  1:2911882/70‑1 (MQ=255)
                                      cGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCg                       >  1:4017126/1‑70 (MQ=255)
                                        cTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACt                                                     >  1:3122063/1‑38 (MQ=255)
                                        cTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACt                                                     >  1:3471943/1‑38 (MQ=255)
                                                 aTTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAAcatcat           >  1:835874/1‑71 (MQ=255)
                                                 aTTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAAcatcat           >  1:978809/1‑71 (MQ=255)
                                                 aTTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAAcatcat           >  1:3677138/1‑71 (MQ=255)
                                                 aTTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAAcatcat           >  1:2532058/1‑71 (MQ=255)
                                                 aTTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAAcatcat           >  1:2418300/1‑71 (MQ=255)
                                                  ttGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAAcatcat           >  1:597268/1‑70 (MQ=255)
                                                  ttGCGAATGAGATGCCCCGTCAACAACTGTGCAGc                                              <  1:2858441/35‑1 (MQ=255)
                                                  ttGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCAtgtt                                     <  1:630991/44‑1 (MQ=255)
                                                    gCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACatcatc          >  1:2512426/1‑69 (MQ=255)
                                                     cGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAg       <  1:2821196/71‑1 (MQ=255)
                                                     cGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAg       <  1:857092/71‑1 (MQ=255)
                                                     cGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAg       <  1:2372203/71‑1 (MQ=255)
                                                     cGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAg       <  1:1219397/71‑1 (MQ=255)
                                                       aaTGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGAt     <  1:2513739/71‑1 (MQ=255)
                                                       aaTGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGAt     <  1:4086059/71‑1 (MQ=255)
                                                       aaTGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGAt     <  1:1060264/71‑1 (MQ=255)
                                                          gagaTGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCg                            >  1:3853379/1‑45 (MQ=255)
                                                          gagaTGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGATAAc  >  1:3876262/1‑71 (MQ=255)
                                                                 |                                                               
GGGTTAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGATAAC  >  minE/1026283‑1026411

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