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 1,015,784 G→T 22.4% D95E (GAC→GAA)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,7840GT22.4% 208.6 / 37.6 89D95E (GAC→GAA) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base G (49/20);  new base T (11/9);  total (60/29)
Fisher's exact test for biased strand distribution p-value = 1.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGT  >  minE/1015716‑1015854
                                                                    |                                                                      
ccTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTc                                                                      >  1:851234/1‑71 (MQ=255)
ccTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTc                                                                      <  1:2657598/71‑1 (MQ=255)
  ttttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                                                     >  1:1028860/1‑70 (MQ=255)
  ttttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                                                     >  1:2546137/1‑70 (MQ=255)
  ttttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                                                     >  1:150716/1‑70 (MQ=255)
   tttttACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCg                                                                     >  1:657737/1‑69 (MQ=255)
   tttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                                                     >  1:4703573/1‑69 (MQ=255)
   tttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                                                     >  1:4065337/1‑69 (MQ=255)
   tttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                                                     >  1:2910695/1‑69 (MQ=255)
    ttttACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAg                                                                  >  1:5225673/1‑71 (MQ=255)
     tttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGt                                                                 >  1:1643407/1‑71 (MQ=255)
      ttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGt                                                                 <  1:2777173/70‑1 (MQ=255)
             caaTAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAgg                                                         <  1:1928952/71‑1 (MQ=255)
              aataatCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAgg                                                         >  1:3286898/1‑70 (MQ=255)
                taatCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAAt                                                      >  1:2007616/1‑71 (MQ=255)
                  atCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTg                                                    <  1:3132523/71‑1 (MQ=255)
                  atCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTg                                                    <  1:791435/71‑1 (MQ=255)
                          gCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCca                                            >  1:4192488/1‑71 (MQ=255)
                           ccGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCcac                                           >  1:998317/1‑71 (MQ=255)
                             ggTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCcac                                           >  1:1102281/1‑69 (MQ=255)
                               tATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACata                                        <  1:3301211/70‑1 (MQ=255)
                                aTCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATAtt                                      >  1:5109385/1‑71 (MQ=255)
                                aTCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATAtt                                      >  1:3329695/1‑71 (MQ=255)
                                 tCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCcacg                                          <  1:5676077/66‑2 (MQ=255)
                                 tCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACgtac                                       <  1:4853166/69‑2 (MQ=255)
                                 tCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGc                                                   <  1:1596908/57‑1 (MQ=255)
                                 tCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCca                                            <  1:1046048/64‑1 (MQ=255)
                                 tCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATAtt                                      >  1:542707/1‑70 (MQ=255)
                                 tCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATAtt                                      >  1:4150612/1‑70 (MQ=255)
                                   cTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTa                                    <  1:3355582/70‑1 (MQ=255)
                                   cTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTAt                                   >  1:1937606/1‑71 (MQ=255)
                                   cTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTAt                                   >  1:3885883/1‑71 (MQ=255)
                                    tggcAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTc                                  >  1:3719848/4‑71 (MQ=255)
                                     gACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTg                                                    >  1:3165474/1‑52 (MQ=255)
                                     gACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCa                                                  >  1:4388660/1‑54 (MQ=255)
                                     gACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCa                                                  >  1:2935923/1‑54 (MQ=255)
                                     gACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCa                                                  >  1:4178052/1‑54 (MQ=255)
                                      gcAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTcgt                                >  1:198594/2‑69 (MQ=255)
                                      gcAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTcg                                 <  1:3760770/69‑2 (MQ=255)
                                      aCAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATc                                  <  1:1445599/69‑1 (MQ=255)
                                      aCAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAt                                >  1:1035501/1‑71 (MQ=255)
                                      aCAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAt                                >  1:4058642/1‑71 (MQ=255)
                                       cAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAtt                               >  1:5096043/1‑71 (MQ=255)
                                       cAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAtt                               <  1:4048499/71‑1 (MQ=255)
                                          gtcggCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGTTTTc                            <  1:184778/68‑1 (MQ=255)
                                           tcggCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGTTTTCg                           <  1:800685/69‑1 (MQ=255)
                                           tcggCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGTTTTCg                           <  1:4983230/69‑1 (MQ=255)
                                             ggCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGc                          <  1:1965448/70‑1 (MQ=255)
                                             ggCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCt                         >  1:3020013/1‑71 (MQ=255)
                                               cAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTgg                       >  1:389951/1‑71 (MQ=255)
                                               cAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTgg                       >  1:1444056/1‑71 (MQ=255)
                                                aGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGc                      >  1:2746248/1‑71 (MQ=255)
                                                 gAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGcc                     >  1:4096225/1‑71 (MQ=255)
                                                 gAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGcc                     >  1:4326027/1‑71 (MQ=255)
                                                 gAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGcc                     >  1:321512/1‑71 (MQ=255)
                                                 gAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGcc                     >  1:978119/1‑71 (MQ=255)
                                                 gAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGc                      >  1:334766/1‑70 (MQ=255)
                                                  aaCGCCTTTCGCCGCGATGTCGGAGTTACGCAGGaa                                                       <  1:2351181/36‑1 (MQ=255)
                                                  aaCGCCTTTCGCCGCGATGTCGGAGTTACGCAGGaa                                                       <  1:2324461/36‑1 (MQ=255)
                                                  aaCGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCt                    <  1:2604459/71‑1 (MQ=255)
                                                   aCGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGTTTTCGCt                         >  1:3612019/1‑65 (MQ=255)
                                                   aCGCCTTTCGCCGCGATGTCGGAGTTACGCAGGaa                                                       <  1:2073473/35‑1 (MQ=255)
                                                    cGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAAt                                                      >  1:3904525/1‑35 (MQ=255)
                                                    cGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAAt                                                      >  1:1969188/1‑35 (MQ=255)
                                                    cGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTcc                  >  1:2402841/1‑71 (MQ=255)
                                                    cGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTcc                  >  1:4245253/1‑71 (MQ=255)
                                                     gCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGtttt                             <  1:4648872/59‑1 (MQ=255)
                                                      ccTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGTTTTCGCTGGCTTctg                 >  1:3510957/1‑68 (MQ=255)
                                                        tttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTc                            <  1:1010751/57‑1 (MQ=255)
                                                        tttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTc                            <  1:1200733/57‑1 (MQ=255)
                                                         ttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCcaca                                          >  1:1340184/1‑42 (MQ=255)
                                                         ttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCcaca                                          >  1:1137746/1‑42 (MQ=255)
                                                         ttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGt              >  1:2318724/1‑70 (MQ=255)
                                                         ttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTACGGGt              >  1:5195157/1‑70 (MQ=255)
                                                          tCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGc                          >  1:2722800/1‑57 (MQ=255)
                                                          tCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGc                          >  1:3601394/1‑57 (MQ=255)
                                                          tCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGc                          >  1:3277650/1‑57 (MQ=255)
                                                              cgcgATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACg          >  1:5304385/1‑69 (MQ=255)
                                                              cgcgATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACg          >  1:5350317/1‑69 (MQ=255)
                                                              cgcgATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACg          >  1:53878/1‑69 (MQ=255)
                                                               gcgATTTCGGAGTTTCTTAAGAATTGCAGCGCCACgtac                                       >  1:3582023/1‑38 (MQ=12)
                                                               gcgATTTCGGAGTTTCTTAAGAATTGCAGCGCCACgtac                                       >  1:134986/1‑38 (MQ=12)
                                                               gcgATTTCGGAGTTTCTTAAGAATTGCAGCGCCACgtac                                       >  1:3307507/1‑38 (MQ=12)
                                                                cgATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGa      <  1:3181149/71‑1 (MQ=255)
                                                                 gATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAtt                               <  1:3794902/45‑1 (MQ=255)
                                                                  aTGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAtttt                             >  1:3358815/1‑46 (MQ=255)
                                                                  aTGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAt                                <  1:1164286/43‑1 (MQ=255)
                                                                   tGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCgg                >  1:4340196/1‑58 (MQ=255)
                                                                   tGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATg   <  1:5305721/71‑1 (MQ=255)
                                                                    gTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGc         >  1:3968666/1‑64 (MQ=255)
                                                                    gTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGt  >  1:780844/1‑71 (MQ=255)
                                                                    gTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGt  >  1:1802020/1‑71 (MQ=255)
                                                                    |                                                                      
CCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGT  >  minE/1015716‑1015854

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A