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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,572,705 C→T 32.8% intergenic (+1473/‑306) yibH → / → ysaB hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,572,7050CT32.8% 84.1 / 58.5 70intergenic (+1473/‑306)yibH/ysaBhypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (27/20);  new base T (15/8);  total (42/28)
Fisher's exact test for biased strand distribution p-value = 6.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01

TAAACAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAG  >  minE/2572635‑2572774
                                                                      |                                                                     
taAACAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCac                                                                       >  1:980038/1‑71 (MQ=255)
taAACAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCac                                                                       >  1:3397725/1‑71 (MQ=255)
  aaCAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacc                                                                      >  1:1646607/1‑70 (MQ=255)
    cAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacctac                                                                   >  1:130073/1‑71 (MQ=255)
    cAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacctac                                                                   >  1:1423098/1‑71 (MQ=255)
        tGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacctacc                                                                  <  1:2517164/68‑1 (MQ=255)
         ggCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacct                                                                     >  1:2613601/1‑64 (MQ=255)
          gCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                               >  1:3664811/1‑69 (MQ=255)
           cTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacc                                                                      >  1:481953/1‑61 (MQ=255)
           cTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTACAg                                                            >  1:3191069/1‑71 (MQ=255)
              aTCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGccc                                                         <  1:2666618/71‑1 (MQ=255)
              aTCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGcc                                                          >  1:1950598/1‑70 (MQ=255)
              aTCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGc                                                           >  1:3826998/1‑69 (MQ=255)
                cccAACGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCac                                                                       >  1:579912/1‑55 (MQ=255)
                 ccAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGcc                                                          >  1:3596932/1‑67 (MQ=255)
                 ccAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCaa                                                       <  1:3388852/70‑1 (MQ=255)
                 ccAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                      >  1:2056839/1‑71 (MQ=255)
                   aaGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                    >  1:2024191/1‑71 (MQ=255)
                    aGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacct                                                                     <  1:724619/53‑1 (MQ=255)
                    aGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                    >  1:89579/1‑70 (MQ=255)
                       ggATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                               <  1:1730317/56‑1 (MQ=255)
                       ggATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                               <  1:2108127/56‑1 (MQ=255)
                          tCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                    <  1:783807/64‑1 (MQ=255)
                            gATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacctac                                                                   <  1:3612179/47‑1 (MQ=255)
                                ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                      >  1:3748041/1‑56 (MQ=255)
                                ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                        >  1:2295665/1‑70 (MQ=255)
                                  aGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGa                                            <  1:2194973/64‑1 (MQ=255)
                                   gAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                        <  1:1563705/67‑1 (MQ=255)
                                    aaaTCGGGTTCAACGGATACTGATAAAAATTCCac                                                                       >  1:1409401/1‑35 (MQ=255)
                                     aaccGGATTCAGCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATAcc                                  >  1:3568319/4‑71 (MQ=255)
                                     aaTCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAcc                                  >  1:347736/1‑71 (MQ=255)
                                         ggattCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGccc                              >  1:1572421/4‑71 (MQ=255)
                                          ggTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGtt                                       >  1:779276/1‑61 (MQ=255)
                                          gattCAGCGGATACGCATACAGACTCCATCCCCCCACCAGCCCTATCGGGTCCTGAGTGATATACCGcccc                             >  1:1313014/3‑71 (MQ=255)
                                           attCAACGGATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATACCGCCCct                            <  1:590119/70‑1 (MQ=255)
                                           attCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAAt                                                      <  1:3099794/44‑1 (MQ=255)
                                           attCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAAt                                                      <  1:2179628/44‑1 (MQ=255)
                                           attCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAAt                                                      <  1:57599/44‑1 (MQ=255)
                                           attCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAAt                                                      <  1:1586647/44‑1 (MQ=255)
                                               agcGGATACGCATACAGACTCCATCCCCCCTCCAGCCCTATCGGGTCCTGAGTGATATACCGCCCctgca                         <  1:2009461/68‑2 (MQ=255)
                                                aCGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCg                                                    >  1:2323779/1‑42 (MQ=255)
                                                aCGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCagcagc                       >  1:1705092/1‑71 (MQ=255)
                                                aCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCCtgcagc                       >  1:3842904/1‑71 (MQ=255)
                                                aCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCtgctgc                       >  1:1264693/1‑71 (MQ=255)
                                                 cGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCg                      >  1:971589/1‑71 (MQ=255)
                                                  ggATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGCCCCTGCAGCgg                     >  1:3260527/1‑71 (MQ=255)
                                                   gATACTGATAAAAATTCCACCTACCTTCCAGCCCa                                                        <  1:1823575/35‑1 (MQ=255)
                                                   gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTTTTATACCGCCCCTGCTGCGGt                    <  1:2939456/71‑1 (MQ=255)
                                                   gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGt                    <  1:3895595/71‑1 (MQ=255)
                                                   gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGt                    <  1:858554/71‑1 (MQ=255)
                                                    aTACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgggt                   >  1:2302654/1‑69 (MQ=255)
                                                    aTACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCt                                              <  1:1972586/44‑1 (MQ=255)
                                                    aTACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCt                                              <  1:3918603/44‑1 (MQ=255)
                                                    aTACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCgg                     >  1:95052/1‑69 (MQ=255)
                                                     tACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGcc                                               >  1:1034159/1‑42 (MQ=255)
                                                     tACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTa                  <  1:1229746/71‑1 (MQ=255)
                                                      aCTGATAAAAATTCCATCCCCCTTTCAGCCCAATCgg                                                   >  1:1441278/1‑37 (MQ=25)
                                                      aCTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                        <  1:558483/48‑1 (MQ=255)
                                                       cTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAgtga                                        <  1:77414/47‑2 (MQ=255)
                                                       cTGATAAAAATTCCACCTACCTTCCAGCCCAATCgg                                                   >  1:1514680/1‑36 (MQ=255)
                                                       cTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                    <  1:1019278/35‑1 (MQ=255)
                                                        tGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGAtata                                    >  1:2244817/1‑50 (MQ=255)
                                                        tGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATAc                                   >  1:609916/1‑51 (MQ=255)
                                                        tGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCTCCCctgc                          <  1:1437110/60‑1 (MQ=255)
                                                        tGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGtt                                       >  1:1270654/1‑47 (MQ=255)
                                                        tGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                      >  1:2116853/1‑48 (MQ=255)
                                                        tGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                      >  1:230084/1‑48 (MQ=255)
                                                         gATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCt                                              >  1:228892/1‑39 (MQ=16)
                                                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAg                                           >  1:1450907/1‑41 (MQ=255)
                                                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt             <  1:420021/71‑1 (MQ=255)
                                                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt             <  1:2991903/71‑1 (MQ=255)
                                                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGt              >  1:1480502/1‑70 (MQ=255)
                                                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGt              <  1:2367022/70‑1 (MQ=255)
                                                           tAAAAATTCCATCCCCCTT‑CAGCCCAATCGGATCCTGAGTGAta                                      >  1:1796954/1‑44 (MQ=255)
                                                            aaaaaTTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAAt                >  1:1951617/1‑66 (MQ=255)
                                                            aaaaaTTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTAc           >  1:18002/1‑71 (MQ=255)
                                                             aaaaTTCCATCCCCCCTTCAGCCCAATCGGATCCTGAgtga                                        >  1:1701010/1‑40 (MQ=255)
                                                              aaaTTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTAcc          >  1:1885943/1‑70 (MQ=255)
                                                                aTTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGa        >  1:1505057/1‑70 (MQ=255)
                                                                 ttCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgctg                        <  1:2546707/53‑1 (MQ=255)
                                                                   ccACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt             >  1:462565/1‑62 (MQ=255)
                                                                   ccACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt             >  1:3575229/1‑62 (MQ=255)
                                                                     acctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAg  <  1:1701539/71‑1 (MQ=255)
                                                                      |                                                                     
TAAACAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAG  >  minE/2572635‑2572774

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