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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,045,839 T→A 32.7% intergenic (+601/+194) yqiK → / ← rfaE conserved hypothetical protein/fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,045,8390TA32.7% 219.8 / 100.6 110intergenic (+601/+194)yqiK/rfaEconserved hypothetical protein/fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase
Reads supporting (aligned to +/- strand):  ref base T (34/40);  new base A (17/19);  total (51/59)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

Only 100 of 117 total aligned reads displayed.

GCTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTT  >  minE/2045772‑2045908
                                                                    |                                                                     
gcTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGta                                                                      >  1:5442407/1‑69 (MQ=255)
 cTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGtata                                                                    <  1:1887124/70‑1 (MQ=255)
    atcaACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGtat                                                                     <  1:2333700/66‑1 (MQ=255)
    atcaACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg                                                                 >  1:3343442/1‑70 (MQ=255)
    atcaACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAg                                                                  <  1:5466060/69‑1 (MQ=255)
     tcaACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGaa                                                               <  1:2717963/71‑1 (MQ=255)
       aacaaTCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAg                                                             >  1:5640262/1‑71 (MQ=255)
       aacaaTCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAg                                                             >  1:2466718/1‑71 (MQ=255)
        ctaaTCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGaaa                                                              <  1:4132819/67‑1 (MQ=255)
                  ggCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg                                                                 <  1:4051813/56‑1 (MQ=255)
                  ggCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg                                                                 <  1:346786/56‑1 (MQ=255)
                  ggCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg                                                                 <  1:2562837/56‑1 (MQ=255)
                   gcagcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg                                                                 <  1:165441/55‑1 (MQ=255)
                   gcagcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGa                                                                <  1:733399/56‑1 (MQ=255)
                    cagcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAg                                                >  1:830053/1‑71 (MQ=255)
                     agcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTa                                                        <  1:2531398/62‑1 (MQ=255)
                     agcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTa                                                        <  1:4329956/62‑1 (MQ=255)
                      gcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg                                                                 <  1:4661619/52‑1 (MQ=255)
                      gcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAgg                                                            <  1:3000704/57‑1 (MQ=255)
                      gcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTatg                                                      >  1:4328361/1‑63 (MQ=255)
                        aaGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGt                                                          >  1:781119/1‑57 (MQ=255)
                         aGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTc                                             <  1:657273/69‑1 (MQ=255)
                           gggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGTCCTTGTATAAGGAAAGGGTTa                                                        <  1:1977594/56‑1 (MQ=255)
                           acgCTGAAACGGGAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGt                                           >  1:303292/3‑70 (MQ=0)
                            ggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGtat                                                                     <  1:57129/42‑1 (MQ=255)
                            ggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtcat                                        >  1:5627124/1‑71 (MQ=255)
                            ggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtcat                                        >  1:3187602/1‑71 (MQ=255)
                            cgCTGAAACGGGAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGtca                                         <  1:1786500/70‑1 (MQ=1)
                              cTGAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGaaa                                                              >  1:3653992/1‑47 (MQ=14)
                              cTGAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatg                                                      <  1:144998/55‑1 (MQ=14)
                              cTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATaa                                                                   >  1:442617/1‑42 (MQ=255)
                                gAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGaa                                                               >  1:1492151/1‑44 (MQ=14)
                                gAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACtcat                                        >  1:1889915/1‑67 (MQ=14)
                                gAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACtcat                                        >  1:1896669/1‑67 (MQ=14)
                                gAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGtt                                                         <  1:1190765/50‑1 (MQ=255)
                                 aaaCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                                    <  1:3787364/54‑1 (MQ=14)
                                 aaaCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcatcg                                   <  1:565443/71‑3 (MQ=11)
                                 aaaCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATAc                                   >  1:4899675/1‑71 (MQ=255)
                                   aCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCAtgatga                                                  >  1:3633700/1‑54 (MQ=14)
                                   aCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCAtgatga                                                  >  1:3590871/1‑54 (MQ=14)
                                      ggAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                                    <  1:2622584/49‑1 (MQ=14)
                                      ggAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTCATCATCGTGgtg                              >  1:1155474/1‑70 (MQ=2)
                                      ggAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgtt                              >  1:3793091/1‑71 (MQ=255)
                                       gAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgt                               >  1:3680797/1‑70 (MQ=11)
                                       gAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTCATCATCGTGgtgc                             >  1:3332284/1‑69 (MQ=2)
                                       gAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttg                             <  1:2081641/71‑1 (MQ=255)
                                        aaaGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTCATCATCGTGgtgc                             >  1:3132334/1‑68 (MQ=2)
                                          aGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGt                                                          <  1:3505689/40‑1 (MQ=0)
                                             cccTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACt                                  <  1:1253870/60‑1 (MQ=255)
                                              tcTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgtg                              <  1:3123410/63‑2 (MQ=11)
                                              ccTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttgt                       >  1:3907027/1‑70 (MQ=255)
                                               cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtc                                          <  1:1663603/50‑1 (MQ=255)
                                               cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtc                                          <  1:3373786/50‑1 (MQ=255)
                                               cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTa                     <  1:4919004/71‑1 (MQ=255)
                                                tCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCat                                                       <  1:128161/36‑1 (MQ=12)
                                                tCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCat                                                       <  1:1943990/36‑1 (MQ=12)
                                                tCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCat                                                       <  1:2965762/36‑1 (MQ=12)
                                                 cccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCtac                                            >  1:74665/1‑44 (MQ=9)
                                                  ccGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgtga                             >  1:3161910/1‑59 (MQ=2)
                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatga                                                     >  1:5472944/1‑36 (MQ=12)
                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatga                                                     >  1:4550644/1‑36 (MQ=12)
                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatga                                                     >  1:1660542/1‑36 (MQ=12)
                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat                                     <  1:3479904/52‑1 (MQ=9)
                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat                                     <  1:3118384/52‑1 (MQ=9)
                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat                                     <  1:213885/52‑1 (MQ=9)
                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat                                     <  1:2184869/52‑1 (MQ=9)
                                                  ccGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttgt                       <  1:2337461/66‑1 (MQ=255)
                                                   cGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                                    <  1:3598393/36‑1 (MQ=9)
                                                   cGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                                    <  1:2218638/36‑1 (MQ=9)
                                                   cGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                                    <  1:3931266/36‑1 (MQ=9)
                                                   cGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATa                                    >  1:1020149/1‑52 (MQ=255)
                                                   cGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTg                                 <  1:2294832/55‑1 (MQ=255)
                                                    gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATa                                    >  1:525181/1‑51 (MQ=255)
                                                    gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt                <  1:4307788/71‑1 (MQ=255)
                                                    gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt                <  1:4698006/71‑1 (MQ=255)
                                                    gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGt                 >  1:5507266/1‑70 (MQ=255)
                                                     aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgt                               >  1:1201610/1‑55 (MQ=255)
                                                     aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt                >  1:3440667/1‑70 (MQ=255)
                                                     aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTa               <  1:2702621/71‑1 (MQ=255)
                                                     aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTa               <  1:1849759/71‑1 (MQ=255)
                                                      agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTgg                                >  1:3598080/1‑53 (MQ=255)
                                                      agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTgg                                >  1:4303137/1‑53 (MQ=255)
                                                      agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTaa              <  1:4262499/71‑1 (MQ=255)
                                                       gaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAg             >  1:5332259/1‑71 (MQ=255)
                                                          g‑gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttg                        <  1:5080620/57‑1 (MQ=255)
                                                            gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttg                        <  1:4397732/56‑1 (MQ=255)
                                                            gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTaa              <  1:2402884/66‑1 (MQ=255)
                                                            gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTaa              <  1:5556436/66‑1 (MQ=255)
                                                              gCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTccc       <  1:2279448/71‑1 (MQ=255)
                                                              gCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTccc       <  1:2599328/71‑1 (MQ=255)
                                                               ccTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTg                                 <  1:5123806/44‑1 (MQ=255)
                                                                cTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGa     >  1:5610479/1‑71 (MQ=255)
                                                                cTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGa     >  1:2174414/1‑71 (MQ=255)
                                                                cTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGa     >  1:4961894/1‑71 (MQ=255)
                                                                   gTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTa                     >  1:3449558/1‑52 (MQ=255)
                                                                   gTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACt   <  1:2989076/70‑1 (MQ=255)
                                                                   gTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACt   >  1:5045282/1‑70 (MQ=255)
                                                                   gTATAAGGAAAGGGTTATGATGAAGCTCGTCAACATACTg                                 >  1:4741596/1‑40 (MQ=255)
                                                                    tataAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACtt  <  1:4805201/70‑1 (MQ=255)
                                                                    tataAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACtt  <  1:2360843/70‑1 (MQ=255)
                                                                    |                                                                     
GCTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGACTT  >  minE/2045772‑2045908

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