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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,266,736 G→A 39.1% intergenic (+57/+5) tyrP → / ← yecA tyrosine transporter/conserved metal‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,266,7360GA39.1% 42.9 / 48.9 79intergenic (+57/+5)tyrP/yecAtyrosine transporter/conserved metal‑binding protein
Reads supporting (aligned to +/- strand):  ref base G (24/24);  new base A (12/19);  total (36/43)
Fisher's exact test for biased strand distribution p-value = 3.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGTGGGGTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCACGGGCAAGG  >  minE/1266669‑1266791
                                                                   |                                                       
aaGTGGGGTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGc                                                        <  1:103328/69‑1 (MQ=255)
aaGTGGGGTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGc                                                        <  1:650777/69‑1 (MQ=255)
aaGTGGGGTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGc                                                        <  1:562807/69‑1 (MQ=255)
aaGTGGGGTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGc                                                        <  1:3228035/69‑1 (MQ=255)
aaGTGGGGTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGc                                                        <  1:3219335/69‑1 (MQ=255)
aaGTGGGGTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGc                                                        <  1:299558/69‑1 (MQ=255)
aaGTGGGGTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGc                                                        <  1:2431630/69‑1 (MQ=255)
aaGTGGGGTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGc                                                        <  1:2356947/69‑1 (MQ=255)
aaGTGGGGTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGc                                                        <  1:2132371/69‑1 (MQ=255)
    ggggTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCctc                                                     >  1:966110/1‑68 (MQ=255)
    ggggTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCctc                                                     >  1:76256/1‑68 (MQ=255)
    ggggTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCctc                                                     >  1:374775/1‑68 (MQ=255)
    ggggTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCctc                                                     >  1:1576139/1‑68 (MQ=255)
    ggggTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCctc                                                     >  1:1425681/1‑68 (MQ=255)
     gggTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCtt                                                   <  1:3430604/69‑1 (MQ=255)
        tGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCtt                                                   <  1:3078441/66‑1 (MQ=255)
         gATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTaa                                                 >  1:1517710/1‑67 (MQ=255)
         gATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTaa                                                 >  1:3070261/1‑67 (MQ=255)
         gATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTaa                                                 >  1:2033512/1‑67 (MQ=255)
         gATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTaa                                                 >  1:1204668/1‑67 (MQ=255)
         gATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTa                                                  >  1:2247027/1‑66 (MQ=255)
            cAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgca                                             >  1:1622416/1‑68 (MQ=255)
            cAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgca                                             >  1:3330402/1‑68 (MQ=255)
            cAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgca                                             >  1:191901/1‑68 (MQ=255)
            cAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgca                                             >  1:2758344/1‑68 (MQ=255)
               aTAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgcaggc                                          >  1:1013900/1‑68 (MQ=255)
               aTAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgcaggc                                          >  1:3225773/1‑68 (MQ=255)
               aTAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgcaggc                                          >  1:3052989/1‑68 (MQ=255)
               aTAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgcaggc                                          >  1:1087635/1‑68 (MQ=255)
                tAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgcaggcag                                        <  1:1947056/69‑1 (MQ=255)
                tAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgcaggcag                                        <  1:2987968/69‑1 (MQ=255)
                tAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgcaggcag                                        <  1:3082476/69‑1 (MQ=255)
                tAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgcaggcag                                        <  1:594689/69‑1 (MQ=255)
                tAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgcaggcag                                        <  1:2535725/69‑1 (MQ=255)
                tAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCCCTTAATgcaggcag                                        <  1:321875/69‑1 (MQ=255)
                   ccTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCAc                                     >  1:228766/1‑69 (MQ=255)
                   ccTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCAc                                     >  1:3317673/1‑69 (MQ=255)
                       aaaTTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATgcaggcag                                        <  1:1274716/62‑1 (MQ=255)
                                  tGGGTGCCAGAATTAACGCTGGCACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCtt                       >  1:1508689/1‑68 (MQ=255)
                                  tGGGTGCCAGAATTAACGCTGACACCCAATGTGACCTCTTAAt                                                >  1:2883203/1‑43 (MQ=38)
                                  tGGGTGCCAGAATTAACGCTGACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCtt                       >  1:2508302/1‑68 (MQ=255)
                                  tGGGTGCCAGAATTAACGCTGACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCtt                       >  1:3325995/1‑68 (MQ=255)
                                  tGGGTGCCAGAATTAACGCTGACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCtt                       >  1:1229540/1‑68 (MQ=255)
                                  tGGGTGCCAGAATTAACGCTGACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCtt                       >  1:3341517/1‑68 (MQ=255)
                                  tGGGTGCCAGAATTAACGCTGACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCtt                       >  1:1869944/1‑68 (MQ=255)
                                  tGGGTGCCAGAATTAACGCTGACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCtt                       >  1:2390789/1‑68 (MQ=255)
                                  tGGGTGCCAGAATTAACGCTGACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCtt                       >  1:2370968/1‑68 (MQ=255)
                                  tGGGTGCCAGAATTAACGCTGACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCtt                       >  1:2948058/1‑68 (MQ=255)
                                  tGGGTGCCAGAATTAACGCTGACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCtt                       >  1:2275866/1‑68 (MQ=255)
                                  tGGGTGCCAGAATTAACGCTGACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCtt                       >  1:1275565/1‑68 (MQ=255)
                                          aGAATTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTAc               <  1:2298912/68‑1 (MQ=255)
                                          aGAATTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTAc               <  1:2131197/68‑1 (MQ=255)
                                          aGAATTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTAc               <  1:1086818/68‑1 (MQ=255)
                                          aGAATTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTAc               <  1:2464634/68‑1 (MQ=255)
                                          aGAATTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTAc               <  1:1392801/68‑1 (MQ=255)
                                             aTTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTAccacg           >  1:2245356/1‑66 (MQ=255)
                                             aTTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           >  1:2993251/1‑69 (MQ=255)
                                             aTTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           >  1:2783186/1‑69 (MQ=255)
                                             aTTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           >  1:2579462/1‑69 (MQ=255)
                                                      gACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCACGGGCAAgg  <  1:2827329/69‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:437006/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:874082/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:493270/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:411586/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:942084/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:354208/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:2888914/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:3427939/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:3257770/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:1261488/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:3040508/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:1560159/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:2722019/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:2707889/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:2685053/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:2217228/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:1741677/60‑1 (MQ=255)
                                                      gACACCCAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:1572719/60‑1 (MQ=255)
                                                      gACACACAATGTGACCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCa           <  1:1947576/60‑1 (MQ=255)
                                                                   |                                                       
AAGTGGGGTGATCAGATAGCCTCAAATTCCTTATTGGGTGCCAGAATTAACGCTGACACCCAATTTGGCCTCTTAATGCAGGCAGCACTGCTTAAATTTCTTACCACTACCGCACGGGCAAGG  >  minE/1266669‑1266791

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