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 832,349 T→C 24.6% T269T (ACT→ACC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE832,3490TC24.6% 171.6 / 57.8 103T269T (ACT→ACC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (43/34);  new base C (15/10);  total (59/44)
Fisher's exact test for biased strand distribution p-value = 8.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 103 total aligned reads displayed.

CAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCAAACTGTGC  >  minE/832283‑832418
                                                                  |                                                                     
cAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGa                                                                     <  1:4799217/69‑1 (MQ=255)
cAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGa                                                                     <  1:650272/69‑1 (MQ=255)
 aGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGt                                                                  <  1:4962118/71‑1 (MQ=255)
      cctcatcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGt                                                              >  1:3551809/3‑70 (MQ=255)
      catcatCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACgc                                                              <  1:4611402/70‑2 (MQ=255)
      catcatCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGt                                                              >  1:2484509/1‑70 (MQ=255)
       atcatcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTa                                                            >  1:656725/1‑71 (MQ=255)
         catcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTAc                                                           >  1:4222716/1‑70 (MQ=255)
         catcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTAc                                                           >  1:5535609/1‑70 (MQ=255)
          atcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACa                                                          >  1:4172383/1‑70 (MQ=255)
          atcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACaa                                                         <  1:2475442/71‑1 (MQ=255)
          atcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACa                                                          >  1:3839864/1‑70 (MQ=255)
          atcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACa                                                          >  1:2794444/1‑70 (MQ=255)
          atcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACa                                                          >  1:1620070/1‑70 (MQ=255)
           tcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACAGAAGTACGCTACaaa                                                        >  1:2735956/1‑71 (MQ=255)
           tcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACaaa                                                        <  1:3325938/71‑1 (MQ=255)
            cGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAg                                                       >  1:1353362/1‑71 (MQ=255)
             gCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAg                                                       <  1:2757397/70‑1 (MQ=255)
             gCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAg                                                       <  1:5040542/70‑1 (MQ=255)
                  ggggTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCActa                                                 <  1:2941623/71‑3 (MQ=255)
                  ggggTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCActa                                                 <  1:3623406/71‑3 (MQ=255)
                   gggTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTaa                                                <  1:5529506/71‑1 (MQ=255)
                   gggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaa                                                <  1:243501/71‑1 (MQ=255)
                   gggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaa                                                <  1:3847510/71‑1 (MQ=255)
                   gggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaa                                                <  1:1378252/71‑1 (MQ=255)
                    ggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaaa                                               <  1:2029313/71‑1 (MQ=255)
                      tctaaCGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAAc                                             <  1:5613126/68‑1 (MQ=255)
                       cAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAgg                                                      >  1:113967/1‑61 (MQ=255)
                        aaaCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGaa                                                                    >  1:1881890/1‑46 (MQ=255)
                        aaaCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAgg                                                      <  1:3776140/60‑1 (MQ=255)
                        aaaCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTg                                           >  1:3052503/1‑71 (MQ=255)
                         aaCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaaa                                               <  1:1482629/66‑1 (MQ=255)
                          aCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGtc                                         <  1:3143133/71‑2 (MQ=255)
                          aCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGt                                          <  1:164303/70‑1 (MQ=255)
                          aCGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAg                                                                   >  1:2466735/1‑45 (MQ=255)
                          aCGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAg                                                                   >  1:464371/1‑45 (MQ=255)
                          aCGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAAc                                             >  1:1477693/1‑67 (MQ=255)
                           cGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAAc                                             >  1:270907/1‑66 (MQ=255)
                           cGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTg                                        >  1:824326/1‑71 (MQ=255)
                            gTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTg                                        >  1:1725713/1‑70 (MQ=255)
                            gTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTg                                        >  1:2942999/1‑70 (MQ=255)
                            gTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGc                                       >  1:654801/1‑71 (MQ=255)
                            gTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGc                                       >  1:2328699/1‑71 (MQ=255)
                             tGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGcc                                      >  1:350784/1‑71 (MQ=255)
                              gCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCg                                     >  1:2668483/1‑71 (MQ=255)
                               ccGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGt                                    <  1:5044771/71‑1 (MQ=255)
                               ccGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGt                                    <  1:2411531/71‑1 (MQ=255)
                                   aGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACaaa                                                        >  1:5423738/1‑47 (MQ=255)
                                      cgcgTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCa                             <  1:568557/71‑1 (MQ=255)
                                      cacgTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTaa                                                >  1:2967376/3‑52 (MQ=255)
                                       gcgTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCacac                               >  1:4665990/1‑68 (MQ=255)
                                         gTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTg                                           >  1:482381/1‑54 (MQ=255)
                                         gTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGt                                    <  1:4666541/61‑1 (MQ=255)
                                          tACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACa                                                          <  1:2496207/38‑1 (MQ=255)
                                            cgccGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAACCATCGCCATTACCCCTGACTa                        >  1:1199696/3‑70 (MQ=255)
                                            ccccGGATGCTCACTTCTTTACTGAAGTGCGTTACa                                                          >  1:2666763/1‑36 (MQ=255)
                                            ccccGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAAc                                             <  1:3603495/49‑1 (MQ=255)
                                            ccccGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAAc                                             <  1:1543223/49‑1 (MQ=255)
                                              ccGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAAcca                                           >  1:5219047/1‑47 (MQ=255)
                                               cGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAACCATCGCCATTACCCCTGACTActct                    >  1:3479817/1‑71 (MQ=255)
                                               cGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAACCATCGCCATTACCCCTGACTActct                    >  1:2756726/1‑71 (MQ=255)
                                               cGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAACCATCGCCATTACCCCTGACTActc                     >  1:259288/1‑68 (MQ=255)
                                                ggATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGt                                    <  1:4998232/54‑1 (MQ=255)
                                                ggATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGt                                    <  1:284573/54‑1 (MQ=255)
                                                ggATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGc                     >  1:1864301/1‑69 (MQ=255)
                                                ggACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAACCATCGCCATTACCCCTGACTACTCTg                   <  1:2691524/71‑1 (MQ=255)
                                                ggACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAACCATCGCCATTACCCCTGACTACTCTg                   <  1:5512562/71‑1 (MQ=255)
                                                 gATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTg                   >  1:689125/1‑70 (MQ=255)
                                                  aTGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGaa                 <  1:4310725/71‑1 (MQ=255)
                                                   tGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGaaa                <  1:2307398/71‑1 (MQ=255)
                                                   tGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGaa                 >  1:3174580/1‑70 (MQ=255)
                                                    gCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaaa                                               <  1:4119077/39‑1 (MQ=255)
                                                    gCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAAc                                             <  1:1698369/41‑1 (MQ=255)
                                                     cTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTca                                  >  1:5423924/1‑51 (MQ=255)
                                                     cTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTca                                  >  1:5139528/1‑51 (MQ=255)
                                                     cTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTca                                  >  1:3486655/1‑51 (MQ=255)
                                                      tCACTTCTTTACTGAAGTGCGTTAGAAAGGGACCAAAAc                                             >  1:5014385/1‑39 (MQ=255)
                                                      tCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTg                                           >  1:3764434/1‑41 (MQ=255)
                                                      tCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTg                                           >  1:4794281/1‑41 (MQ=255)
                                                      tCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTg                                           >  1:2005069/1‑41 (MQ=255)
                                                      tCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCg             >  1:3303168/1‑71 (MQ=255)
                                                       cACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTa                        <  1:3966909/59‑1 (MQ=255)
                                                       cACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTa                        <  1:5307474/59‑1 (MQ=255)
                                                       cACTTCTTTACCGAAGTACGCTACAAAGGCACTaaaa                                              >  1:5687904/1‑37 (MQ=16)
                                                        aCTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGa                           >  1:5292437/1‑55 (MQ=255)
                                                        aCTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGc            >  1:2640918/1‑70 (MQ=255)
                                                        aCTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGc            >  1:2624974/1‑70 (MQ=255)
                                                         cttcttTACTGAAGTGCGTTACAAAGGGACCAAAAc                                             >  1:4810934/1‑36 (MQ=255)
                                                          ttcttTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGcc                                      <  1:2940867/42‑1 (MQ=255)
                                                           tcttTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCaaa        >  1:2717180/1‑71 (MQ=255)
                                                            cttTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCAAAc       >  1:270543/1‑71 (MQ=255)
                                                            cttTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCAAAc       >  1:3395995/1‑71 (MQ=255)
                                                            cttTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCAAAc       >  1:1454583/1‑71 (MQ=255)
                                                            cttTACTGAAGTGCGTTACAAAGGGACAAAAACTGTTGCCGTCACACCAGACTACGCTGAAATc              >  1:3524381/1‑64 (MQ=255)
                                                               tACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCAAACtg     <  1:2003354/70‑1 (MQ=255)
                                                                aCTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCaa         <  1:4275270/65‑1 (MQ=255)
                                                                aCTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCAAACtgtg   >  1:5422094/1‑71 (MQ=255)
                                                                aCTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCAAACtgtg   >  1:2901675/1‑71 (MQ=255)
                                                                aCTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCAAACtgt    >  1:88103/1‑70 (MQ=255)
                                                                 cTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCAAACTGTGc  <  1:5286533/71‑1 (MQ=255)
                                                                  |                                                                     
CAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCAGACTACGCTGAAATCGCCAAACTGTGC  >  minE/832283‑832418

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