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
A17 F3 I1 R1 15 66.3 2212468 93.9% 2077507 141.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 3,560,455 +G intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA3,560,4551.G98.0% 153.2 / ‑3.0 49intergenic (‑2/+1)glpR/glpRpseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base G (24/24);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01

ATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGT  >  NC_000913_3_pae_tpiA/3560311‑3560591
                                                                                                                                                  |                                                                                                                                        
atatCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGcgcag                                                                                                                                       <  2:722544/149‑5 (MQ=255)
     gATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCa                                                                                                                                  >  1:480212/1‑149 (MQ=255)
     gATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCa                                                                                                                                  >  1:879740/1‑149 (MQ=255)
     gATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGAAACCCGCGAGTGCTACGGGATATCTGTCGAGCTGGAAGGCAGCGCCGCCCCGCCATGA‑TGGCGCAGGATCa                                                                                                                                  <  1:539729/149‑1 (MQ=255)
      aTAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAg                                                                                                                                 >  1:1052147/1‑149 (MQ=255)
      aTAAACAGCGGCGAGCCATTGGGGATTTGCTCCGCCCCTTTGCGGTGGTTTCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAg                                                                                                                                 <  1:583171/149‑1 (MQ=255)
       tAAACAGCGTCGAGCCGTTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAgg                                                                                                                                <  2:440833/149‑1 (MQ=255)
         aaCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGGGGGCGGAGCGCTCTTTTTCTCCGGTCTGGGTGGGCTTGCGCTCGTGCCACGGCGTGCTTACCGAACTGGAAGGCAACGCCCGACCACCCCGA‑TGGCGCACGATCAGGtt                                                                                                                              >  2:562356/1‑149 (MQ=255)
             gCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGc                                                                                                                          <  2:573087/149‑1 (MQ=255)
                tCGAGCCATTGGGGATTTGCTCCGCGACTTTGCGGGCGATGTGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGTAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTcc                                                                                                                       <  1:999006/149‑1 (MQ=255)
                tCGAGCCAGTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCTAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTcc                                                                                                                       <  1:722363/149‑1 (MQ=255)
                gcGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTcc                                                                                                                       <  2:204457/148‑1 (MQ=255)
                        ttGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTc                                                                                                               >  2:994468/1‑149 (MQ=255)
                              aTTTGCGCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACGGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAg                                                                                                         <  1:973172/149‑1 (MQ=255)
                                  gCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCCCCGCCAGCCCCTTGAGGTcg                                                                                                     >  2:348811/1‑149 (MQ=255)
                                    tCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGCTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcgcg                                                                                                   >  1:212522/1‑149 (MQ=255)
                                     ccgccgCTTTGCGGGCGGTGCGCTGTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAGCTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcgg                                                                                                  <  2:905458/149‑1 (MQ=255)
                                     ccGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcgg                                                                                                  <  1:922175/149‑1 (MQ=255)
                                        ccACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGa                                                                                               >  2:629628/1‑149 (MQ=255)
                                          aCTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAAt                                                                                             <  1:66432/149‑1 (MQ=255)
                                                 gggCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCCCCATGA‑TGGCGCACGATCAGGTTTTGCTCCGCCCGCTCATTCAGGTCCCGGCGAATAGTCTGc                                                                                      >  2:891648/1‑149 (MQ=255)
                                                            tctTTTTCTTCGGTCTGGGTGGCCGTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGga                                                                           >  1:958062/1‑149 (MQ=255)
                                                             ctTGTTCTTCGGTCTGGGTTGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGgag                                                                          >  2:932838/1‑149 (MQ=255)
                                                                tttCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGaaa                                                                       <  2:480212/149‑1 (MQ=255)
                                                                tttCTTCGGGCTGGGTGGCCGTGCGATCGGGCCACGGCTTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCAATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGaaa                                                                       <  1:456103/149‑1 (MQ=255)
                                                                  ttttcGGTCTGGGTGGCCTTGGCATCGTGCCAAGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGTTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATg                                                                     <  2:757924/147‑1 (MQ=255)
                                                                   cttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGc                                                                    <  1:897974/149‑1 (MQ=255)
                                                                    ttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGct                                                                   >  2:174436/1‑149 (MQ=255)
                                                                        gtttGGGTGGTCGTGCGAGCGTGCCACGGCGTGTTAACCGAACTGGGAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAc                                                               <  2:469811/146‑1 (MQ=255)
                                                                        gTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGATCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAc                                                               >  1:484723/1‑149 (MQ=255)
                                                                            gggTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGc                                                           >  1:711520/1‑149 (MQ=255)
                                                                                  ccTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCg                                                     >  2:428188/1‑149 (MQ=255)
                                                                                            gTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCCGCATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGACCTCCCAGCTCTTCGGTACTGACAt                                           >  2:81852/1‑149 (MQ=255)
                                                                                              gCCACGGCGTGTTAACCGAACGGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATaa                                         <  1:238138/149‑1 (MQ=255)
                                                                                               ccACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAc                                        >  2:871476/1‑149 (MQ=255)
                                                                                               ccACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAc                                        >  1:781264/1‑149 (MQ=255)
                                                                                               ccACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTCACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAc                                        >  2:870587/1‑149 (MQ=255)
                                                                                                cACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAcc                                       <  2:879740/149‑1 (MQ=255)
                                                                                                      gtgtTAACCGAACGGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgctg                                 <  1:629628/149‑1 (MQ=255)
                                                                                                                   tGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCg                    >  1:773395/1‑149 (MQ=255)
                                                                                                                    ggAAGGCAGCGCCGGACCGCCAGGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGa                   <  2:733958/149‑1 (MQ=255)
                                                                                                                         gCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACt                                                <  2:484854/115‑1 (MQ=255)
                                                                                                                         gCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACt                                                >  1:484854/1‑115 (MQ=255)
                                                                                                                           aGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCAGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATAcc            >  2:696976/1‑149 (MQ=255)
                                                                                                                            gcgcCGGCCCGCCAGGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCg           <  2:576535/149‑1 (MQ=255)
                                                                                                                              gccgcACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACAGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTCCTGTTTAACCAGTTCGATAATACCGtt         <  2:981548/149‑1 (MQ=255)
                                                                                                                                cgcACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTtgt       <  1:741127/149‑1 (MQ=255)
                                                                                                                                   aCCGCCATGAGTGCG‑CAGGATTAGTTTTTGCTCCGCCAGGTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGAc    <  2:36753/149‑1 (MQ=255)
                                                                                                                                     cGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTAAcat  >  1:801012/1‑147 (MQ=255)
                                                                                                                                     cGCCATGA‑TGGCGCAGGATCAAGTTTAGCACCGCACGCCCAGCGAGGACGCGGCGAATGGTCTGCGGACTGACGGAGAAAAGCTCTACCAGCTCTTCGGTACTGACCTCACCCTGCTCTTTAAACAGTTCCATACTACCCTTGTGAccc  >  2:517584/1‑147 (MQ=255)
                                                                                                                                                  |                                                                                                                                        
ATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGT  >  NC_000913_3_pae_tpiA/3560311‑3560591

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A