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 1,015,814 A→G 15.2% Y85Y (TAT→TAC)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,8140AG15.2% 211.8 / 27.6 92Y85Y (TAT→TAC) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base A (54/24);  new base G (4/10);  total (58/34)
Fisher's exact test for biased strand distribution p-value = 6.00e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01

Only 100 of 106 total aligned reads displayed.

TATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGC  >  minE/1015747‑1015876
                                                                   |                                                              
tATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACata                                                              <  1:3301211/70‑1 (MQ=255)
 aTCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATAtt                                                            >  1:3329695/1‑71 (MQ=255)
 aTCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATAtt                                                            >  1:5109385/1‑71 (MQ=255)
  tCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACgtac                                                             <  1:4853166/69‑2 (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)
       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                                                     <  1:4048499/71‑1 (MQ=255)
        cAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAtt                                                     >  1:5096043/1‑71 (MQ=255)
           gtcggCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGTTTTc                                                  <  1:184778/68‑1 (MQ=255)
            tcggCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGTTTTCg                                                 <  1:4983230/69‑1 (MQ=255)
            tcggCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGTTTTCg                                                 <  1:800685/69‑1 (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                                           >  1:321512/1‑71 (MQ=255)
                  gAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGc                                            >  1:334766/1‑70 (MQ=255)
                   aaCGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCt                                          <  1:2604459/71‑1 (MQ=255)
                    aCGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGTTTTCGCt                                               >  1:3612019/1‑65 (MQ=255)
                     cGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTcc                                        >  1:4245253/1‑71 (MQ=255)
                     cGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTcc                                        >  1:2402841/1‑71 (MQ=255)
                      gCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGtttt                                                   <  1:4648872/59‑1 (MQ=255)
                       ccTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGTTTTCGCTGGCTTctg                                       >  1:3510957/1‑68 (MQ=255)
                         tttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTc                                                  <  1:1200733/57‑1 (MQ=255)
                         tttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTc                                                  <  1:1010751/57‑1 (MQ=255)
                          ttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCcaca                                                                >  1:1137746/1‑42 (MQ=255)
                          ttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCcaca                                                                >  1:1340184/1‑42 (MQ=255)
                          ttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGt                                    >  1:2318724/1‑70 (MQ=255)
                           tCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGc                                                >  1:3601394/1‑57 (MQ=255)
                           tCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGc                                                >  1:3277650/1‑57 (MQ=255)
                           tCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGc                                                >  1:2722800/1‑57 (MQ=255)
                               cgcgATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACg                                >  1:5304385/1‑69 (MQ=255)
                               cgcgATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACg                                >  1:5350317/1‑69 (MQ=255)
                               cgcgATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACg                                >  1:53878/1‑69 (MQ=255)
                                gcgATTTCGGAGTTTCTTAAGAATTGCAGCGCCACgtac                                                             >  1:3307507/1‑38 (MQ=12)
                                gcgATTTCGGAGTTTCTTAAGAATTGCAGCGCCACgtac                                                             >  1:134986/1‑38 (MQ=12)
                                  gATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAtt                                                     <  1:3794902/45‑1 (MQ=255)
                                   atttCGGAGTTTCTTAAGAATTGCAGCGCCACGTACTTGTCGTTTTCGCTGGCTTCTGGATCGTGAAGAAt                          <  1:5408500/68‑1 (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)
                                        ggAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGc                                            >  1:3472034/1‑48 (MQ=255)
                                        ggAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGc                                            >  1:4184880/1‑48 (MQ=255)
                                            ttACGCAGGAATTGCAGCGCCACATATTTATCATTTTc                                                  <  1:1534111/38‑1 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCg                                                 >  1:806016/1‑37 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCg                                                 >  1:3437760/1‑37 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCg                                                 >  1:3471870/1‑37 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGc                                                >  1:3403599/1‑38 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGc                                                >  1:1129622/1‑38 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCttg                                             >  1:507482/1‑39 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCt                                               >  1:1777286/1‑39 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCt                                               >  1:5571374/1‑39 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCg                                       >  1:1514323/1‑47 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCg                                       >  1:1097490/1‑47 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCg                                       >  1:3334255/1‑47 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCg                                       >  1:5484388/1‑47 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCg                                       >  1:3739970/1‑47 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCAcc                <  1:429491/70‑1 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCAc                 >  1:1528072/1‑69 (MQ=255)
                                              aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCt               >  1:5421536/1‑71 (MQ=255)
                                               cGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGTTCACGCAGAATg                         <  1:3467043/60‑1 (MQ=255)
                                               cGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAGTg                         <  1:2447274/60‑1 (MQ=255)
                                               cGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATg                         <  1:4853194/60‑1 (MQ=255)
                                                  aagAATTGCAGCGCCACGTACTTGTCGTTTTCGCTGGCTTCTGGATCGTGAAGAATAGCCGCAACCtgt             <  1:4656579/67‑1 (MQ=255)
                                                  aGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCtgttg           <  1:4675294/71‑1 (MQ=255)
                                                   ggAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCtgttgt          >  1:4422276/1‑71 (MQ=255)
                                                   ggAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCtgttgt          >  1:4551879/1‑71 (MQ=255)
                                                    gAATTGCAGCGCCACGTACTTGTCGTTTTCGCTGGCTTCTGGATCGTGAAGAATAGCCGCAACCtgtttct         <  1:5373429/71‑4 (MQ=255)
                                                    gAATTGCAGCGCCACGTACTTGTCGTTTTCGCTGGCTTCTGGATCGTGAAGAATAGCCGCAACCtgtttct         <  1:454642/71‑4 (MQ=255)
                                                    gAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTgttgtt         <  1:3149309/71‑1 (MQ=255)
                                                    gAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTgttgtt         <  1:1863648/71‑1 (MQ=255)
                                                     aaTTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGaa                           >  1:1826152/1‑52 (MQ=255)
                                                     aaTTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGttgttg        <  1:1931121/71‑1 (MQ=255)
                                                       ttGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGt                        <  1:4871374/53‑1 (MQ=255)
                                                       ttGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGt                        <  1:1562051/53‑1 (MQ=255)
                                                       ttGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTgttgtt         <  1:5392302/68‑1 (MQ=255)
                                                         gCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTgc    >  1:875784/1‑71 (MQ=255)
                                                          cAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTgcg   <  1:396762/71‑1 (MQ=255)
                                                           aGCGCCACGTACTTGTCGTTTTCGCTGGCTTCTGGATCGTGAAGAATAGCCGCAACCTGTTTCTGGTgtgc  <  1:5010150/71‑1 (MQ=255)
                                                                cacaTATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCtgtt            <  1:3193465/56‑1 (MQ=255)
                                                                 acaTATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTgg       <  1:4727920/60‑1 (MQ=255)
                                                                   atatTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGcc                   <  1:4517514/46‑1 (MQ=255)
                                                                   atatTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCtgttgt          <  1:5620737/55‑1 (MQ=255)
                                                                   atatTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGt      >  1:1850817/1‑59 (MQ=255)
                                                                   atatTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGt      >  1:1200501/1‑59 (MQ=255)
                                                                   atatTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTg     >  1:2582099/1‑60 (MQ=255)
                                                                   |                                                              
TATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGC  >  minE/1015747‑1015876

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