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 2,562,718 C→G 10.2% G453G (GGG→GGC)  lldP ← L‑lactate permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,562,7180CG10.2% 166.0 / 7.9 62G453G (GGG→GGC) lldPL‑lactate permease
Reads supporting (aligned to +/- strand):  ref base C (28/27);  new base G (4/2);  total (33/29)
Fisher's exact test for biased strand distribution p-value = 6.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.48e-01

CGGTGGCTTGCAGCGCGGCGAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGT  >  minE/2562657‑2562787
                                                             |                                                                     
cGGTGGCTTGCAGCGCGGCGAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCccagcca                                                               <  1:2200930/70‑1 (MQ=255)
      cTTGCAGCGCGGCGAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCAAGCCAGCCGAgg                                                        <  1:1715006/71‑1 (MQ=255)
       ttGCAGCGCGGCGAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCccag                                                                  <  1:1569462/60‑1 (MQ=255)
       ttGCAGCGCGGCGAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAgg                                                        >  1:1927720/1‑70 (MQ=255)
         gCAGCGCGGCGAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCccag                                                                  >  1:1131862/1‑58 (MQ=255)
         gCAGCGCGGCGAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCccag                                                                  >  1:619563/1‑58 (MQ=255)
            gcgcGGCGAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGc                                                  <  1:1087162/71‑1 (MQ=255)
             cgcgGCGAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCccagccag                                                              >  1:3417283/1‑58 (MQ=255)
                ggcgAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATAccc                                                                      >  1:3138321/1‑47 (MQ=255)
                 gcgAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGagaa                                             <  1:1758913/71‑1 (MQ=255)
                    aaCAGGGCGTTAGAGGAGGTGTCCGAGCCGGTAAGGAATACGCCCAGCCAGCCGAGAAACggt                                                  >  1:1096630/1‑62 (MQ=255)
                    aaCAGGGCGTTAGAGGAGGTGTCCGAGCCGGTAAGGAATACGCCCAGCCAGCCGAGAAACgg                                                   >  1:2521122/1‑62 (MQ=255)
                    aaCAGGGCGTTAGAGGAGGTGTCCGAGCCGGTAAGGAATACGCCCAGCCAGCCGAGAAACGGTGagaag                                            <  1:83398/69‑1 (MQ=255)
                      cAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCccagcc                                                                >  1:988312/1‑47 (MQ=255)
                      cAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCccagcc                                                                >  1:866392/1‑47 (MQ=255)
                      cAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGagaa                                             >  1:3873898/1‑66 (MQ=255)
                      cAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGagaa                                             >  1:3869225/1‑66 (MQ=255)
                        gggCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGaa                                                      >  1:3295031/1‑55 (MQ=255)
                         ggCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGa                                     <  1:1327871/71‑1 (MQ=255)
                         ggCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGa                                     <  1:124496/71‑1 (MQ=255)
                           cGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAATGTGAAt                                   <  1:505031/71‑1 (MQ=255)
                           cGTTAGAGGAGGTGTCCGAGCCGGTAAGGAATACGCCCAGCCAGCCGAGAAACGGTGAGAAGAACGGGaa                                    >  1:3290278/1‑70 (MQ=255)
                             ttAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGa                                     <  1:1370431/67‑1 (MQ=255)
                             ttAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAAt                                   <  1:2929700/69‑1 (MQ=255)
                             ttAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGc                                 <  1:2770260/71‑1 (MQ=255)
                              tAGAGGAGGTGTCCGAGCCGGTAAGGAATACGCCCAGCCAGCCGAGAAACGGTGAGAAGAACGGGaacat                                 >  1:1457708/1‑67 (MQ=255)
                               aGATGAGGTATCCGACCCGGTCAGGAATACCCccagcca                                                               >  1:606549/1‑39 (MQ=255)
                               aGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCa                                <  1:850830/70‑1 (MQ=255)
                               aGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCAt                               >  1:3828736/1‑71 (MQ=255)
                                gATGAGGTATCCGACCCGGTCAGGAATACCCccagccag                                                              <  1:3538920/39‑1 (MQ=255)
                                gATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCAt                               <  1:995191/70‑1 (MQ=255)
                                 aggAGGTGTCCGAGCCGGTAAGGAATACGCCCAGCCAGCCGAGAAACg                                                    <  1:1772796/46‑1 (MQ=19)
                                 aTGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGa                             >  1:1929560/1‑71 (MQ=255)
                                 aTGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGa                             >  1:3147750/1‑71 (MQ=255)
                                  tGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGa                                                       >  1:2189709/1‑44 (MQ=255)
                                   gAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCgag                                               <  1:1882487/51‑1 (MQ=255)
                                   gAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCgag                                               <  1:3308563/51‑1 (MQ=255)
                                   gAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGAcc                           >  1:618523/1‑71 (MQ=255)
                                    aGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCg                          <  1:2615893/71‑1 (MQ=255)
                                     ggTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAgg                                        >  1:1576350/1‑56 (MQ=255)
                                     ggTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCgg                         <  1:1222223/71‑1 (MQ=255)
                                       tATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGgtg                       <  1:721815/71‑1 (MQ=255)
                                        aTCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATg                              <  1:2799648/63‑1 (MQ=255)
                                        aTCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGgtgt                      >  1:3640938/1‑71 (MQ=255)
                                         tCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGagaaga                                           >  1:1271012/1‑49 (MQ=255)
                                         tCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATg                              <  1:1101573/62‑1 (MQ=255)
                                          ccGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCAt                               >  1:3584682/1‑60 (MQ=255)
                                            gACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTgcgc                  <  1:1735141/71‑1 (MQ=255)
                                             aCCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTgcgc                  >  1:154673/1‑70 (MQ=255)
                                              cccGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCa                <  1:2371450/71‑1 (MQ=255)
                                              cccGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCa                <  1:2318651/71‑1 (MQ=255)
                                                 ggTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGt              >  1:974396/1‑70 (MQ=255)
                                                 ggTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGTg             >  1:1907396/1‑71 (MQ=255)
                                                       gAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTg                                      <  1:1736152/40‑1 (MQ=255)
                                                       gAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTg                                      <  1:3160904/40‑1 (MQ=255)
                                                       gAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCTGTGTGCGCCAGTGCCAgcg       >  1:2761252/1‑71 (MQ=255)
                                                       gAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGTGCCAgcg       >  1:1748500/1‑71 (MQ=255)
                                                        aaTACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGTGCCAgcgc      >  1:3154040/1‑71 (MQ=255)
                                                         aTACTCCCAGCCAGCCGAGAAACGGTGAgaagaac                                         >  1:332702/1‑34 (MQ=25)
                                                         aTACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGTGCCAgcgc      >  1:1022546/1‑70 (MQ=255)
                                                         aTACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGTGCCAgcgc      >  1:1247580/1‑70 (MQ=255)
                                                          tACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGTGCCAgcgc      >  1:2790105/1‑69 (MQ=255)
                                                          tACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCa    <  1:925556/71‑1 (MQ=255)
                                                            cccccAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGt              <  1:2733568/59‑1 (MQ=255)
                                                            cccccAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAgt  <  1:2901893/71‑1 (MQ=255)
                                                             ccccAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAAt                                   <  1:1279357/37‑1 (MQ=255)
                                                             |                                                                     
CGGTGGCTTGCAGCGCGGCGAACAGGGCGTTAGATGAGGTATCCGACCCGGTCAGGAATACCCCCAGCCAGCCGAGGAACGGCGAGAAGAAGGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGT  >  minE/2562657‑2562787

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