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 1,014,818 A→G 25.8% H417H (CAT→CAC)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,014,8180AG25.8% 146.9 / 53.5 89H417H (CAT→CAC) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base A (40/26);  new base G (13/10);  total (53/36)
Fisher's exact test for biased strand distribution p-value = 8.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGTGAGCAATAT  >  minE/1014749‑1014888
                                                                     |                                                                      
ggTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGgat                                                                       <  1:2927941/71‑1 (MQ=255)
 gTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGgatg                                                                      <  1:1281739/71‑1 (MQ=255)
       gggCCAAGTGAACCTGATGGATAACCGGCAGGGGTTTTCGCCGGACCCGCGTAGTAGATCGGGTGATCttt                                                                >  1:2622623/1‑71 (MQ=255)
       gggCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCtt                                                                 >  1:82283/1‑70 (MQ=255)
        ggCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCttt                                                                <  1:3307703/70‑1 (MQ=255)
        ggCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCttt                                                                <  1:549856/70‑1 (MQ=255)
           cAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATg                                                            <  1:5629680/71‑1 (MQ=255)
            aaGTGAACCTGATGGATAACCGGCAGGGGTTTTCGCCGGACCCGCGTAGTAGATCGGGTGATCTTTGATg                                                            >  1:2722137/1‑70 (MQ=255)
            aaGTGAACCTGATGGATAACCGGCAGGGGTTTTCGCCGGACCCGCGTAGTAGATCGGGTGATCTTTGATg                                                            >  1:2967144/1‑70 (MQ=255)
            aaGAGAACGGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATc                                                                   <  1:961661/63‑1 (MQ=255)
              gagaACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGga                                                                        >  1:4586304/1‑56 (MQ=255)
              gagaACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTAc                                                         >  1:47173/1‑71 (MQ=255)
               agaACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCttt                                                                <  1:770335/63‑1 (MQ=255)
                gaACCTGATGGATAACCGGCAGGGGTTTTCGCCGGACCCGCGTAGTAGATCGGGTGATCTTTGATGTACTg                                                       >  1:5638293/1‑71 (MQ=255)
                 aaCCTGATGGATAACCGGCAGGGGTTTTCGCCGGACCCGCGTAGTAGATCGGGTGATCTTTg                                                               <  1:4151197/62‑1 (MQ=255)
                     ggAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGa                                                              >  1:590103/1‑59 (MQ=255)
                     ggAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGa                                                              >  1:86848/1‑59 (MQ=255)
                      gAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAg                                                 >  1:808093/1‑71 (MQ=255)
                             aaCCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGgatga                                                                     >  1:314085/1‑44 (MQ=255)
                             aaCCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCg                                                     >  1:5326622/1‑60 (MQ=255)
                             aaCCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCg                                                     >  1:3455482/1‑60 (MQ=255)
                              aCCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGa                                                              >  1:1864890/1‑50 (MQ=255)
                              aCCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCa                                          >  1:5414016/1‑70 (MQ=255)
                              aCCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCa                                          >  1:3814459/1‑70 (MQ=255)
                              aCCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCAc                                         >  1:101591/1‑71 (MQ=255)
                               ccTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCAcc                                        >  1:4527079/1‑71 (MQ=255)
                                  tCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCtt                                                                 >  1:549322/1‑43 (MQ=255)
                                  tCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCAcc                                        >  1:2011655/1‑68 (MQ=255)
                                  tCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGt                                      >  1:3026398/1‑70 (MQ=255)
                                    cGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGccc                                              <  1:2412323/60‑1 (MQ=255)
                                       ggTTTTCGCCGGACCCGCGTAGTAGATCGGGTGATc                                                                   <  1:2039985/35‑1 (MQ=25)
                                         ttttGGCCGGACGCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTatccatc                              >  1:4626157/1‑71 (MQ=255)
                                         ttttGGCCGGACCCGCGTAGTAAATCGGATGATCTTTg                                                               <  1:235991/38‑1 (MQ=255)
                                         ttttGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGt                                      <  1:1013865/63‑1 (MQ=255)
                                         ttttGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTatccatc                              >  1:3414559/1‑71 (MQ=255)
                                         ttttCGCCGGACCCGCGTAGTAGATCGGGTGATCTTTGATGTACTGCg                                                     <  1:2721111/48‑1 (MQ=37)
                                           ttGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGAt                                                             >  1:1479560/1‑38 (MQ=255)
                                           ttGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGAt                                                             >  1:3959589/1‑38 (MQ=255)
                                           ttGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTg                                                       >  1:2857754/1‑44 (MQ=255)
                                           ttGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTatcca                                >  1:4590974/1‑67 (MQ=255)
                                           ttGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCg                            >  1:1345685/1‑71 (MQ=255)
                                           ttGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCg                            >  1:1742759/1‑71 (MQ=255)
                                           ttGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCg                            >  1:2099960/1‑71 (MQ=255)
                                           ttGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCg                            >  1:3490139/1‑71 (MQ=255)
                                            tcgCCGGACCCGCGTAGTAGATCGGGTGATCTTTGATGTa                                                          >  1:271588/3‑40 (MQ=255)
                                            tcgCCGGACCCGCGTAGTAGATCGGGTGATCTTTGATGTa                                                          >  1:2205042/3‑40 (MQ=255)
                                            tcgCCGGACCCGCGTAGTAGATCGGGTGATCTTTGATGTa                                                          >  1:2171060/3‑40 (MQ=255)
                                             ggCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGc                           <  1:5612886/70‑1 (MQ=255)
                                               ccGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGctct                        <  1:3958427/71‑1 (MQ=255)
                                               ccGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGctct                        <  1:4025183/71‑1 (MQ=255)
                                                cGGACCCGCGTAGTAGATCGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCGGCGTCAATCAGCTCtt                       <  1:386899/71‑1 (MQ=255)
                                                cGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCtt                       <  1:5068988/71‑1 (MQ=255)
                                                 ggACCCGCGTAGTAGATCGGGTGATCTTTGATGTACTGCGGAAgt                                                <  1:3704952/45‑2 (MQ=25)
                                                 ggACCCGCGTAGTAGATCGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCGGCGTCAATCAGCTCttt                      <  1:4819662/71‑1 (MQ=255)
                                                 ggACCCGCGTAGTAAATCGGATGATCTTTGATGTAc                                                         >  1:1338504/1‑36 (MQ=255)
                                                    cccGCGTAGTAGATCGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCGGCGTCAATCAGCTCTTTCAg                   >  1:488525/1‑71 (MQ=255)
                                                    cccGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAg                   >  1:4683493/1‑71 (MQ=255)
                                                    cccGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAg                   <  1:2653573/71‑1 (MQ=255)
                                                       gcgTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGttt                <  1:4713331/71‑1 (MQ=255)
                                                          tagtaAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTc                     <  1:5550914/63‑1 (MQ=255)
                                                          tagtaAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTc                     <  1:855344/63‑1 (MQ=255)
                                                            gtaGATCGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCggc                                     >  1:2740048/1‑43 (MQ=12)
                                                            gtaGATCGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCggc                                     >  1:1577843/1‑43 (MQ=12)
                                                            gtaGATCGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCggc                                     >  1:1971180/1‑43 (MQ=12)
                                                            gtaGATCGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCGGCGTCAATCAGCTCTTTCAGCTTGGCGt           >  1:591435/1‑71 (MQ=255)
                                                            gtaGATCGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCGGCGTCAATCAGCTCTTTCAGCTTGGCGt           <  1:159008/71‑1 (MQ=255)
                                                            gtaAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGctct                        <  1:669181/58‑1 (MQ=255)
                                                            gtaAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGctct                        <  1:2701980/58‑1 (MQ=255)
                                                            gtaAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAg                   >  1:4561844/1‑63 (MQ=255)
                                                             taAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGt           <  1:5614760/70‑1 (MQ=255)
                                                              aaaTCGGATGATCTTTGATGTACTGCGGCAGCCCt                                             >  1:3967715/1‑35 (MQ=255)
                                                              aaaTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCAc                                         <  1:1106746/39‑1 (MQ=255)
                                                               aaTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGt                                      >  1:2009132/1‑41 (MQ=255)
                                                               aaTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGt                                      >  1:2718549/1‑41 (MQ=255)
                                                               aaTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGt                                      >  1:4673677/1‑41 (MQ=255)
                                                               aaTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGt           >  1:2767455/1‑68 (MQ=255)
                                                               aaTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGTGAg        >  1:5363902/1‑71 (MQ=255)
                                                               aaTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGTGAg        <  1:2528025/71‑1 (MQ=255)
                                                               aaTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGTGAg        <  1:3039072/71‑1 (MQ=255)
                                                               aaTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGTGAg        >  1:3063084/1‑71 (MQ=255)
                                                               aaTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGTGAg        >  1:4459167/1‑71 (MQ=255)
                                                                aTCGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCGGCGTCAATCAGCTCTTTCAGCTTgg              <  1:571955/64‑1 (MQ=255)
                                                                aTCGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCGGCGTCAATCAGCTCTTTCAGCTTgg              <  1:1891405/64‑1 (MQ=255)
                                                                aTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCg                                       >  1:2794645/1‑39 (MQ=255)
                                                                aTCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCg                                       >  1:2889820/1‑39 (MQ=255)
                                                                 tCGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCGGCGTCAATCAGCTCTTTCAGCTTGGCGTGTGCa      <  1:2257829/71‑1 (MQ=255)
                                                                 tCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCtt                       <  1:5657746/54‑1 (MQ=255)
                                                                 tCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTgg              <  1:5341876/63‑1 (MQ=255)
                                                                  cGGGTGATCTTTGATGTACTGCGGAAGTTCTTTACCGGCGTCAATCAGCTCTTTCAGCTTGGCGTGTGCaa     >  1:76916/1‑71 (MQ=255)
                                                                   ggATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAg                   >  1:4045622/1‑56 (MQ=255)
                                                                   ggATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAg                   >  1:3956383/1‑56 (MQ=255)
                                                                   ggATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGTGAGCaa     <  1:2865223/70‑1 (MQ=255)
                                                                   ggATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGTGAGCAat    <  1:5541178/71‑1 (MQ=255)
                                                                     atgatCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGttt                <  1:1704753/57‑1 (MQ=255)
                                                                     atgatCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGTGAGCAatat  <  1:584630/71‑1 (MQ=255)
                                                                     atgatCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGTGAGCAatat  <  1:401998/71‑1 (MQ=255)
                                                                     |                                                                      
GGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTACTGCGGCAGCCCTTCACCGTTATCCATCCGCTCTTTCAGTTTGGCGTGAGCAATAT  >  minE/1014749‑1014888

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