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 1,336,522 G→A 54.3% T133T (ACC→ACT)  gmd ← GDP‑D‑mannose dehydratase, NAD(P)‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,336,5220GA54.3% 7.5 / 57.6 70T133T (ACC→ACT) gmdGDP‑D‑mannose dehydratase, NAD(P)‑binding
Reads supporting (aligned to +/- strand):  ref base G (22/10);  new base A (13/25);  total (35/35)
Fisher's exact test for biased strand distribution p-value = 7.84e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.21e-01

CGCGGGTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGCCTCC  >  minE/1336460‑1336579
                                                              |                                                         
cgcgGGTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGaa                                                     >  1:401164/1‑69 (MQ=255)
cgcgGGTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGaa                                                     >  1:1510018/1‑69 (MQ=255)
cgcgGGTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGaa                                                     >  1:843180/1‑69 (MQ=255)
   gggTAGAACGGCGTGGTCTC‑‑TCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:3087840/69‑1 (MQ=255)
     gTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:98572/69‑1 (MQ=255)
     gTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:561376/69‑1 (MQ=255)
     gTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:2141339/69‑1 (MQ=255)
     gTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:1598256/69‑1 (MQ=255)
     gTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:154838/69‑1 (MQ=255)
     gTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:883562/69‑1 (MQ=255)
     gTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:111895/69‑1 (MQ=255)
     gTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:908440/69‑1 (MQ=255)
      tAGAACGGCGTTGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:2314412/68‑1 (MQ=255)
      tAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:1372668/68‑1 (MQ=255)
      tAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:2535005/68‑1 (MQ=255)
      tAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:709343/68‑1 (MQ=255)
      tAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:324092/68‑1 (MQ=255)
      tAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:1333200/68‑1 (MQ=255)
       aGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:1821269/67‑1 (MQ=255)
                         tCTGCGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTg                                                <  1:2338226/49‑1 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCa                         >  1:3207854/1‑68 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAg                        >  1:3394482/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAg                        >  1:3413038/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAg                        >  1:343573/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAg                        >  1:916488/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAg                        >  1:2610666/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAg                        >  1:1386301/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAg                        >  1:541717/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAg                        >  1:2098260/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAg                        >  1:618168/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAg                        >  1:1268126/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAg                        >  1:818721/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTATTTTCCAg                        >  1:2670077/1‑69 (MQ=255)
                             cGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGa                                      <  1:522220/55‑1 (MQ=255)
                             cGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGa                                      <  1:604137/55‑1 (MQ=255)
                             cGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGa                                      <  1:621964/55‑1 (MQ=255)
                             cGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGa                                      <  1:3275044/55‑1 (MQ=255)
                             cGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGa                                      <  1:2973951/55‑1 (MQ=255)
                             cGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGa                                      <  1:1066147/55‑1 (MQ=255)
                             cGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGa                                      <  1:2617225/55‑1 (MQ=255)
                             cGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGa                                      <  1:1804268/55‑1 (MQ=255)
                             cGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGa                                      <  1:2718904/55‑1 (MQ=255)
                             cGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGa                                      <  1:262926/55‑1 (MQ=255)
                                    tCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCcagacaga                   >  1:143084/1‑67 (MQ=255)
                                    tCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGa                   >  1:2096032/1‑67 (MQ=255)
                                    tCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGa                   >  1:18335/1‑67 (MQ=255)
                                    tCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGa                   >  1:2296820/1‑67 (MQ=255)
                                    tCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGa                   >  1:699259/1‑67 (MQ=255)
                                    tCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGa                   >  1:3292932/1‑67 (MQ=255)
                                    tCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGa                   >  1:3264417/1‑67 (MQ=255)
                                    tCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGa                   >  1:3150901/1‑67 (MQ=255)
                                            cAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAGACCGAGGAAGCGGAt         <  1:712933/69‑1 (MQ=255)
                                            cAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAGACCGAGGAAGCGGAt         <  1:709020/69‑1 (MQ=255)
                                            cAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAGACCGAGGAAGCGGAt         <  1:1235791/69‑1 (MQ=255)
                                            cAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAGACCGAGGAAGCGGAt         <  1:3027138/69‑1 (MQ=255)
                                            cAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAGACCGAGGAAGCGGAt         <  1:1047191/69‑1 (MQ=255)
                                            cAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAGACCGAGGAAGCGGAt         <  1:450914/69‑1 (MQ=255)
                                            cAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAGACCGAGGAAGCGGAt         <  1:3231928/69‑1 (MQ=255)
                                            cAGACCGTACAGTTCAGAAGTAGAAGCCTGATAGAAACGGGTTTTCTTTTCCAGACCGAGGAAGCGGAt         <  1:2981961/69‑1 (MQ=255)
                                                 cATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGcc     >  1:2244345/1‑68 (MQ=255)
                                                 cATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGcc     >  1:252337/1‑68 (MQ=255)
                                                 cATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGcc     >  1:2621648/1‑68 (MQ=255)
                                                 cATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGcc     >  1:734163/1‑68 (MQ=255)
                                                 cATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGcc     >  1:1374276/1‑68 (MQ=255)
                                                     cAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGCCTcc  >  1:2159270/1‑67 (MQ=255)
                                                     cAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGCCTcc  >  1:2784155/1‑67 (MQ=255)
                                                     cAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGCCTcc  >  1:1346965/1‑67 (MQ=255)
                                                     cAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGCCTcc  >  1:1042796/1‑67 (MQ=255)
                                                     cAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGCCTcc  >  1:939734/1‑67 (MQ=255)
                                                         tCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGc      >  1:355324/1‑59 (MQ=255)
                                                              |                                                         
CGCGGGTAGAACGGCGTGGTCTCTTTCTGCGGAATTTCCTGCACCAGACCATACAGTTCAGAGGTGGAAGCCTGATAGAAACGAGTTTTCTTTTCCAGACCGAGGAAGCGGATCGCCTCC  >  minE/1336460‑1336579

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