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 1,772,441 G→A 47.4% G105G (GGC→GGT)  tyrA ← fused chorismate mutase T and prephenate dehydrogenase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,772,4410GA47.4% 3.9 / 50.1 62G105G (GGC→GGT) tyrAfused chorismate mutase T and prephenate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base G (29/3);  new base A (17/12);  total (46/16)
Fisher's exact test for biased strand distribution p-value = 6.36e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAATCCGCACCTGATAACCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGA  >  minE/1772374‑1772506
                                                                   |                                                                 
gAATCCGCACCTGATAACCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGaccgccaccg                                                                   >  1:2360466/1‑68 (MQ=255)
gAATCCGCACCTGATAACCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGaccgccaccg                                                                   >  1:931308/1‑68 (MQ=255)
gAATCCGCACCTGATAACCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGaccgccaccg                                                                   >  1:462626/1‑68 (MQ=255)
gAATCCGCACCTGATAACCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGaccgccaccg                                                                   >  1:1286851/1‑68 (MQ=255)
gAATCCGCACCTGATAACCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGaccgccaccg                                                                   >  1:111596/1‑68 (MQ=255)
       cACCTGATAACCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGAt                                                           <  1:295677/69‑1 (MQ=255)
       cACCTGATAACCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGAt                                                           <  1:2117046/69‑1 (MQ=255)
       cACCTGATAACCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGAt                                                           <  1:2663115/69‑1 (MQ=255)
               aaCCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCg                                                   >  1:2062973/1‑69 (MQ=255)
               aaCCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCg                                                   >  1:221164/1‑69 (MQ=255)
               aaCCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCg                                                   >  1:2654365/1‑69 (MQ=255)
               aaCCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCg                                                   >  1:663132/1‑69 (MQ=255)
               aaCCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCg                                                   >  1:2827060/1‑69 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAacc                                                       >  1:1119693/1‑45 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAacc                                                       >  1:2869859/1‑45 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAacc                                                       >  1:918375/1‑45 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAacc                                                       >  1:864050/1‑45 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAacc                                                       >  1:1243702/1‑45 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAacc                                                       >  1:2948559/1‑45 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt                               >  1:1483091/1‑69 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt                               >  1:447387/1‑69 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt                               >  1:1519772/1‑69 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt                               >  1:1638920/1‑69 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt                               >  1:3250301/1‑69 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt                               >  1:2288347/1‑69 (MQ=255)
                                   ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt                               >  1:1825571/1‑69 (MQ=255)
                                          aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:2985776/66‑1 (MQ=255)
                                          aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:2230251/66‑1 (MQ=255)
                                          aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:320310/66‑1 (MQ=255)
                                          aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:3101652/66‑1 (MQ=255)
                                          aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:3048140/66‑1 (MQ=255)
                                          aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:2934321/66‑1 (MQ=255)
                                          aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:604311/66‑1 (MQ=255)
                                          aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:3283072/66‑1 (MQ=255)
                                          aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:1437001/66‑1 (MQ=255)
                                          aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:3325458/66‑1 (MQ=255)
                                          aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:1691392/66‑1 (MQ=255)
                                           cAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTaaa                       >  1:2500988/1‑69 (MQ=255)
                                           cAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTaaa                       >  1:689157/1‑69 (MQ=255)
                                           cAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTaaa                       >  1:3207910/1‑69 (MQ=255)
                                           cAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTaaa                       >  1:2251576/1‑69 (MQ=255)
                                           cAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTaaa                       >  1:1968670/1‑69 (MQ=255)
                                           cAGACGTCCCATCTGACCGCCACCTCCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:467429/65‑1 (MQ=255)
                                           cAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt                           <  1:160625/65‑1 (MQ=255)
                                                gTCCCATCTGACCGCCCCCACCGACGATAACCACCGGGCGCAGTGCCGGACAAAg                                >  1:293356/1‑55 (MQ=255)
                                                gTCCCATCTGACCGCCACCGCCGACGATATCCCCCGGACGCAGTGACGGACAAAGTGTTTTAAATCCt                   >  1:3322194/1‑68 (MQ=255)
                                                gTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTg                                          >  1:2979957/1‑45 (MQ=255)
                                                gTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCtt                  >  1:1426030/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCtt                  >  1:2043645/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTCACCGACAAAg                                >  1:2729880/1‑55 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:1066031/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:1139743/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:472808/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:3139814/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:3317455/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:3252035/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:2729556/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:1187600/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:1355197/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:1450815/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:1453420/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:1764543/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:1700192/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:1512809/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:2759034/1‑69 (MQ=255)
                                                gTCCCATCTGACCGCCACCACCGACGATAACCAACGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt                  >  1:249395/1‑69 (MQ=255)
                                                        tGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGtt           >  1:1115328/1‑68 (MQ=255)
                                                              ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg    <  1:1492463/69‑1 (MQ=255)
                                                              ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg    <  1:1212789/69‑1 (MQ=255)
                                                              ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg    <  1:46402/69‑1 (MQ=255)
                                                              ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg    <  1:199141/69‑1 (MQ=255)
                                                              ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg    <  1:2117597/69‑1 (MQ=255)
                                                              ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg    <  1:2328144/69‑1 (MQ=255)
                                                              ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg    <  1:1024337/69‑1 (MQ=255)
                                                                   gccgACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTgg   >  1:1255177/1‑65 (MQ=255)
                                                                   gccgACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGa  >  1:1163903/1‑66 (MQ=255)
                                                                   gccgACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGa  >  1:1161377/1‑66 (MQ=255)
                                                                   gccgACGATAACCACCGGACGCAGTGACGCACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGa  >  1:2438299/1‑66 (MQ=255)
                                                                   |                                                                 
GAATCCGCACCTGATAACCCGAGAGGGTCAGCATCTTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGA  >  minE/1772374‑1772506

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