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 1,015,697 A→G 29.1% G124G (GGT→GGC)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,6970AG29.1% 71.6 / 37.3 56G124G (GGT→GGC) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base A (22/17);  new base G (5/11);  total (28/28)
Fisher's exact test for biased strand distribution p-value = 1.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.30e-01

GTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGA  >  minE/1015631‑1015766
                                                                  |                                                                     
gTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCgg                                                                   >  1:1569488/1‑71 (MQ=255)
    cgcAGGTTATCTTCGATATAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCa                                                               <  1:2678046/71‑1 (MQ=255)
      cAGGTTATCTTCGATATAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCaca                                                             >  1:5239332/1‑69 (MQ=255)
      cAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATa                                                             >  1:707321/1‑71 (MQ=255)
        ggttATCTTCGATATAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCacac                                                            >  1:2203505/3‑70 (MQ=255)
         aTTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTcc                                                                <  1:141177/65‑1 (MQ=255)
           tATCTTCGATATAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACgcgc                                                        >  1:2326450/1‑71 (MQ=255)
             tCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTg                                                      >  1:3654795/1‑71 (MQ=255)
              cTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATcaccaccac                                                                      <  1:2301525/54‑1 (MQ=255)
                  gATATAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCtt                                                 <  1:1704682/71‑1 (MQ=255)
                  gATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCAt                                                              >  1:1070353/1‑58 (MQ=255)
                   atatAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCttt                                                <  1:1357801/71‑1 (MQ=255)
                   atatAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCttt                                                <  1:1647556/71‑1 (MQ=255)
                   atatAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCttt                                                <  1:2118962/71‑1 (MQ=255)
                    tataGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCttt                                                <  1:1981250/70‑1 (MQ=255)
                     ataAGTGTTATAGACACCGCGCGCCAGCGCCGCTCCATCACCACCACCGGTCCATACACGCTGCCCttttt                                              >  1:4085079/1‑71 (MQ=255)
                      taAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCa                                                               <  1:4237096/53‑1 (MQ=255)
                        aGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTAc                                           >  1:2649153/1‑71 (MQ=255)
                         gtgtTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCTTTTTTAcc                                          <  1:5075048/71‑1 (MQ=255)
                              ataGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACcaaca                                      >  1:5127351/1‑70 (MQ=255)
                               taGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACcaacaa                                     >  1:2528372/1‑70 (MQ=255)
                               taGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACcaacaa                                     >  1:3402511/1‑70 (MQ=255)
                               taGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACaat                                    <  1:4727397/71‑1 (MQ=255)
                                 gACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACaataa                                  >  1:3811583/1‑71 (MQ=255)
                                  acacCGCGCGCCAGCGCCGCTTCATCACCACCCCCGGTCCATACCCGCTGCCCTTTTTTACCAACaataat                                 >  1:520643/1‑71 (MQ=255)
                                   cacCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATc                                <  1:3447993/71‑1 (MQ=255)
                                    acCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATcg                               <  1:2695996/71‑1 (MQ=255)
                                     ccGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATcgc                              >  1:3982361/1‑71 (MQ=255)
                                      cgcgcgCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATcg                               <  1:3658047/69‑1 (MQ=255)
                                       gcgcgcCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCgg                            >  1:232508/1‑71 (MQ=255)
                                        cgcgcCAGCGCCGCTTCATCACCACCACCGGTCCATa                                                             >  1:435346/1‑37 (MQ=255)
                                        cgcgcCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCttttt                                              >  1:5052715/1‑52 (MQ=255)
                                           gcCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGccc                                                   <  1:3002665/44‑1 (MQ=255)
                                            ccAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGccc                                                   <  1:4759638/43‑1 (MQ=255)
                                              aGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCgg                      >  1:1551041/1‑70 (MQ=255)
                                                cgccgcTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTAt                   >  1:4722473/1‑71 (MQ=255)
                                                 gccgcTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACaat                                    >  1:5430502/1‑53 (MQ=255)
                                                 gccgcTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACaat                                    >  1:1775721/1‑53 (MQ=255)
                                                 gccgcTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATc                                >  1:4629508/1‑57 (MQ=255)
                                                  ccgcTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATc                  <  1:1063355/70‑1 (MQ=255)
                                                   cgcTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCt                <  1:3896823/71‑1 (MQ=255)
                                                   cgcTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCt                <  1:3515801/71‑1 (MQ=255)
                                                    tcTTCATCACCGCCGCCGGTCCACACGCGCTGGCCTTTTTTACcgac                                       >  1:1429097/2‑47 (MQ=16)
                                                     cTTCATCACCACCACCGGTCCATACACGCTGCCCtt                                                 <  1:623383/36‑1 (MQ=255)
                                                     cTTCATCACCACCACCGGTCCATACACGCTGCCCtt                                                 <  1:5502752/36‑1 (MQ=255)
                                                     cTTCATCACCACCACCGGTCCATACACGCTGCCCtt                                                 <  1:5361848/36‑1 (MQ=255)
                                                      ttCATCACCGCCGCCGGTCCACACGCGCTGGCCTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTg               <  1:1524142/69‑1 (MQ=255)
                                                       tcatcaCCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCgg                      <  1:237579/61‑1 (MQ=255)
                                                        catcaCCGCCGCCGGTCCACACGCGCTGGCCTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTggc             <  1:2661484/69‑3 (MQ=255)
                                                        catcaCCGCCGCCGGTCCACACGCGCTGGCCTTTTTTACCGACGATGATCGAGGTGCCGGTATCCTgtc             <  1:2363479/69‑3 (MQ=255)
                                                         atcaCCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCgg                            >  1:2489002/1‑53 (MQ=255)
                                                         atcaCCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGa              >  1:3467340/1‑67 (MQ=255)
                                                         atcaCCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGa              >  1:5142457/1‑67 (MQ=255)
                                                         atcaCCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAgg          <  1:770359/71‑1 (MQ=255)
                                                          tcaCCGCCGCCGGTCCACACGCGCTGGCCTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGt         <  1:243615/71‑1 (MQ=255)
                                                          tcaCCGCCGCCGGTCCACACGCGCTGGCCTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGt         >  1:4035952/1‑71 (MQ=255)
                                                          tcaCCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGa              <  1:646429/66‑1 (MQ=255)
                                                            accaccaccGGTCCATACACGCTGCCCTTTTTTACCAACaataat                                 >  1:4356031/1‑45 (MQ=255)
                                                            accaccaccGGTCCATACACGCTGCCCTTTTTTACCAACAATAATcg                               >  1:1572158/1‑47 (MQ=255)
                                                             ccaccaccGGTCCATACACGCTGCCCTTTTTTACCAACaata                                   <  1:431388/42‑1 (MQ=255)
                                                             ccaccaccGGTCCATACACGCTGCCCTTTTTTACCAACAATAATc                                <  1:1340906/45‑1 (MQ=255)
                                                                ccaccGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAg   <  1:1060718/71‑1 (MQ=255)
                                                                 caccGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGa  <  1:304152/71‑1 (MQ=255)
                                                                 caccGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGa  <  1:3155127/71‑1 (MQ=255)
                                                                  |                                                                     
GTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGA  >  minE/1015631‑1015766

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