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
A8 F28 I1 R1 182 57.1 1926220 99.1% 1908884 138.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,906,596 (A)7→8 intergenic (‑29/+257) bglG ← / ← phoU transcriptional antiterminator BglG/negative regulator of the pho regulon

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,906,5891.A98.0% 173.8 / ‑3.4 50intergenic (‑22/+264)bglG/phoUtranscriptional antiterminator BglG/negative regulator of the pho regulon
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base A (24/25);  total (24/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.27e-01

TTCGCCAGCGCGTTTTTGAAAGCCAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAAC‑AAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAATTAATTTAATTGCGTGCAGA  >  NC_000913/3906451‑3906722
                                                                                                                                           |                                                                                                                                     
ttCGCCAGCGCGTTTTTGAAAGCCAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAAC‑a                                                                                                                                      >  1:89986/1‑140 (MQ=255)
   gCCAGCGCGTTTTTGAAAGCCAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAAC‑aaaa                                                                                                                                   <  2:317414/140‑1 (MQ=255)
      aGCGCGTTTTTGAAAGCCAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAAC‑aaaaaaa                                                                                                                                >  2:275934/1‑140 (MQ=255)
      aGCGCGTTTTTGAAAGCCAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAAC‑aaaaaaa                                                                                                                                >  2:144015/1‑140 (MQ=255)
        cgcgTTTTTGAAAGCCAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAAC‑aaaaaaaac                                                                                                                              <  2:513814/140‑3 (MQ=255)
        cgcgTTTTTGAAAGCCAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAAC‑aaaaaaaac                                                                                                                              <  2:6207/140‑3 (MQ=255)
          cgTTTTTGAAAGCCAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAAC‑AAAAAAAaccc                                                                                                                            <  1:274661/140‑2 (MQ=255)
             ttttGAAAGCCAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGAc                                                                                                                          <  2:826059/140‑1 (MQ=255)
               ttGAAAGCCAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACtt                                                                                                                        <  2:876208/140‑1 (MQ=255)
                       cAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATGATCTATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTa                                                                                                                <  2:667964/140‑1 (MQ=255)
                       cAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTa                                                                                                                <  1:275934/140‑1 (MQ=255)
                       cAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTa                                                                                                                <  1:144015/140‑1 (MQ=255)
                       cAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTa                                                                                                                <  1:127825/140‑1 (MQ=255)
                       cAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTa                                                                                                                <  1:789157/140‑1 (MQ=255)
                           tCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATtct                                                                                                            <  2:47786/140‑1 (MQ=255)
                              gcgcCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTg                                                                                                         <  2:869821/140‑1 (MQ=255)
                                gcCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGt                                                                                                       >  2:366342/1‑140 (MQ=255)
                                            cTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGttt                                                                                           <  2:538520/140‑1 (MQ=255)
                                                     gCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGa                                                                                  >  1:75510/1‑140 (MQ=255)
                                                      cTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGaa                                                                                 <  2:75510/140‑1 (MQ=255)
                                                       tGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAAt                                                                                >  1:331643/1‑140 (MQ=255)
                                                        gTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATg                                                                               <  1:403116/140‑1 (MQ=255)
                                                        gTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATg                                                                               <  1:366342/140‑1 (MQ=255)
                                                                 caATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACaa                                                                      >  1:377773/1‑140 (MQ=255)
                                                                   aTAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATc                                                                    <  2:377773/140‑1 (MQ=255)
                                                                       ccaccaCAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGt                                                                >  1:520822/1‑140 (MQ=255)
                                                                           cacaACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCAtt                                                            >  1:770536/1‑140 (MQ=255)
                                                                           cacaACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCAtt                                                            >  2:90211/1‑140 (MQ=255)
                                                                                caTTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATttatta                                                       >  1:777531/1‑140 (MQ=255)
                                                                                 attattGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTaa                                                      >  2:82953/1‑140 (MQ=255)
                                                                                  ttattGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAAt                                                     >  1:349375/1‑140 (MQ=255)
                                                                                       gttgAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGttt                                                <  2:144658/140‑1 (MQ=255)
                                                                                        ttgAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGtttt                                               >  1:710645/1‑140 (MQ=255)
                                                                                        atgAGCATTTTGGTGATTTGCATGTTCCTATCAAGGACGTTTTTTATAAAC‑ACAAAAACCCGACTTCACCAGTCTTCCCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGttttt                                              >  2:403464/2‑140 (MQ=255)
                                                                                          gagaATTTTGGTGATTTGCATGTTCATAGCAAGGGCCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTta                                             >  2:852289/1‑140 (MQ=255)
                                                                                           agaATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTtat                                            >  2:467652/1‑140 (MQ=255)
                                                                                              aTTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAAc                                         <  2:252817/140‑1 (MQ=255)
                                                                                               ttttGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACg                                        >  1:780548/1‑140 (MQ=255)
                                                                                                tttGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGa                                       <  2:540194/140‑1 (MQ=255)
                                                                                                       aTTTGCATGTTCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCa                                >  2:707230/1‑140 (MQ=255)
                                                                                                                ttCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGaa                       <  2:228727/140‑1 (MQ=255)
                                                                                                                ttCATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGaa                       <  2:520822/140‑1 (MQ=255)
                                                                                                                  cATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAaat                     >  1:248065/1‑140 (MQ=255)
                                                                                                                  cATAGCAAGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAaat                     >  1:10358/1‑140 (MQ=255)
                                                                                                                         aGGACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAAttaattta              >  1:526116/1‑140 (MQ=255)
                                                                                                                          ggACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGGCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAAttaatttaa             >  2:658157/1‑140 (MQ=255)
                                                                                                                          ggACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGaa                       >  1:811661/1‑130 (MQ=255)
                                                                                                                          ggACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGaa                       <  2:811661/130‑1 (MQ=255)
                                                                                                                          ggACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAAttaatttaa             >  2:628792/1‑140 (MQ=255)
                                                                                                                          ggACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAAttaatttaa             >  1:881471/1‑140 (MQ=255)
                                                                                                                           gACCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAAttaatttaat            >  1:738807/1‑140 (MQ=255)
                                                                                                                            aCCTTTTTTATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAATtaatttaatt           <  2:738807/140‑1 (MQ=255)
                                                                                                                                tttttATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAATTAATTTAATTGCGt       <  1:707230/140‑1 (MQ=255)
                                                                                                                                 ttttATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAATTAATTTAATTGCGTg      >  1:306877/1‑140 (MQ=255)
                                                                                                                                   ttATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAATTAATTTAATTGCGTGCa    <  1:628792/140‑1 (MQ=255)
                                                                                                                                   ttATAAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAATTAATTTAATTGCGTGCa    <  2:490810/140‑1 (MQ=255)
                                                                                                                                     ataAACAAAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAATTAATTTAATTGCGTGCaga  <  1:107573/140‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                     
TTCGCCAGCGCGTTTTTGAAAGCCAATTCCGCGCCCCATGACGACTTTTTCCCGCTGTTGATCATCAATAACCACCACAACATTATTGTTGAGAATTTTGGTGATTTGCATGTTCATAGCAAGGACCTTTTTTATAAAC‑AAAAAAACCCGACTTCACCAGTATTCTCTGGTTATGTCAGGTTTTGCCTGCGAATGCAGTAACAATCCAGTCATTTATTAATGGTTTTTATAACGAACATCCAGGTTCGGAAATTAATTTAATTGCGTGCAGA  >  NC_000913/3906451‑3906722

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A