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 834,974 T→G 8.3% A1144A (GCT→GCG)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE834,9740TG 8.3% 175.8 / 9.4 74A1144A (GCT→GCG) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (21/46);  new base G (2/4);  total (23/51)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGA  >  minE/834904‑835042
                                                                      |                                                                    
gTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAATAGCAACGGTGct                                                                      >  1:64183/1‑71 (MQ=255)
gTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGct                                                                      >  1:1741899/1‑71 (MQ=255)
 tGAAGCCGATGCCAAAGATCTGTGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctc                                                                     <  1:394803/71‑1 (MQ=255)
   aaGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctct                                                                    >  1:506076/1‑70 (MQ=255)
   aaGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctct                                                                    >  1:930899/1‑70 (MQ=255)
   aaGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctct                                                                    <  1:3112857/70‑1 (MQ=255)
   aaGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctc                                                                     >  1:506077/1‑69 (MQ=255)
    aGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTTGATTGAAGTCTTCAACAGCAACGGTGCTCTGa                                                                  <  1:285491/71‑1 (MQ=255)
    aGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGa                                                                  <  1:2811445/71‑1 (MQ=255)
      ccGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACt                                                                <  1:1281711/71‑1 (MQ=255)
       cGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTg                                                               >  1:3517072/1‑71 (MQ=255)
        gATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTg                                                               >  1:207762/1‑70 (MQ=255)
        gATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGc                                                              <  1:3276774/71‑1 (MQ=255)
         aTGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGcc                                                             >  1:1762631/1‑71 (MQ=255)
            ccAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCg                                                           <  1:1543994/70‑1 (MQ=255)
              aaaGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGc                                                        <  1:2125921/71‑1 (MQ=255)
               aaGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCg                                                       >  1:1180998/1‑71 (MQ=255)
                aGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCgg                                                      <  1:2819798/71‑1 (MQ=255)
                aGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCgg                                                      <  1:2011002/71‑1 (MQ=255)
                aGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCgg                                                      <  1:938874/71‑1 (MQ=255)
                aGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCgg                                                      <  1:2842143/71‑1 (MQ=255)
                aGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCgg                                                      <  1:2988767/71‑1 (MQ=255)
                aGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCgg                                                      <  1:268631/71‑1 (MQ=255)
                aGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCgg                                                      >  1:2575661/1‑71 (MQ=255)
                   tCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTg                                                   >  1:2342417/1‑71 (MQ=255)
                     tGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGtt                                                    <  1:2064173/68‑1 (MQ=255)
                       ggTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGtt                                                    <  1:859070/66‑1 (MQ=255)
                         tATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTcagc                                              >  1:1908517/1‑70 (MQ=255)
                           tCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTcagcca                                            <  1:602215/70‑1 (MQ=255)
                           tCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTcagcca                                            <  1:1781224/70‑1 (MQ=255)
                            cGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTcagccagc                                          >  1:2241864/1‑71 (MQ=255)
                             gCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCg                                         >  1:646800/1‑71 (MQ=255)
                              tcGATAACGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACg                                         <  1:193340/69‑1 (MQ=255)
                              ccGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCgt                                        <  1:3605062/71‑1 (MQ=255)
                               cGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctc                                                                     >  1:3751619/1‑41 (MQ=255)
                               cGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCgtg                                       <  1:3817949/71‑1 (MQ=255)
                               cGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCgtg                                       <  1:737673/71‑1 (MQ=255)
                                gATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTcagcca                                            >  1:3554393/1‑65 (MQ=255)
                                gATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTca                                                >  1:2322669/1‑61 (MQ=255)
                                gATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCgtgt                                      >  1:584115/1‑71 (MQ=255)
                                gATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCgtgt                                      >  1:345795/1‑71 (MQ=255)
                                 aTAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGc                                                              <  1:3161867/46‑1 (MQ=255)
                                 aTAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTcagcca                                            <  1:1569443/64‑1 (MQ=255)
                                  tAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTc                                    <  1:1020665/71‑1 (MQ=255)
                                  tAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTc                                    <  1:2633304/71‑1 (MQ=255)
                                    aCGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTcc                                   <  1:1988737/70‑1 (MQ=255)
                                     cGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGc                                                              <  1:1981437/42‑1 (MQ=255)
                                     cGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCgg                                 <  1:422534/71‑1 (MQ=255)
                                      gACTGGATTGAAGTCTTCAACAGCAACGGTGctct                                                                    <  1:3050920/35‑1 (MQ=255)
                                            aTTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCg                                                           <  1:3698452/38‑1 (MQ=255)
                                              tGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGa                        >  1:120265/1‑71 (MQ=255)
                                                aaGTCTTCAACAGCAACGGTGCACTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGc                                <  1:2488119/61‑1 (MQ=255)
                                                 aGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCgg                                 <  1:2297830/59‑1 (MQ=255)
                                                 aGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                     <  1:3099332/71‑1 (MQ=255)
                                                 aGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                     <  1:2098452/71‑1 (MQ=255)
                                                 aGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                     <  1:992511/71‑1 (MQ=255)
                                                 aGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                     <  1:3534834/71‑1 (MQ=255)
                                                  gtattCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCat                    <  1:2917968/68‑1 (MQ=255)
                                                  gTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                    <  1:1371996/71‑1 (MQ=255)
                                                  gTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                    >  1:3940907/1‑71 (MQ=255)
                                                     ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTcc                                   >  1:2716712/1‑53 (MQ=255)
                                                     ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatgat                 >  1:2106827/1‑71 (MQ=255)
                                                     ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                    <  1:1572509/68‑1 (MQ=255)
                                                     ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                    <  1:1945452/68‑1 (MQ=255)
                                                     atCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatga                  <  1:755669/69‑1 (MQ=255)
                                                      tCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatgatg                >  1:2692629/1‑71 (MQ=255)
                                                       cAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatgatg                <  1:1467150/70‑1 (MQ=255)
                                                       cAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatgatg                <  1:2167323/70‑1 (MQ=255)
                                                       cAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatgatg                <  1:2265125/70‑1 (MQ=255)
                                                       cAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatga                  <  1:1150338/68‑1 (MQ=255)
                                                         aCAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAc             <  1:2522119/71‑1 (MQ=255)
                                                          cAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAcc            <  1:465427/71‑1 (MQ=255)
                                                          cAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAc             >  1:1048619/1‑70 (MQ=255)
                                                          cAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAc             >  1:3352417/1‑70 (MQ=255)
                                                             cAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAc          <  1:1064500/70‑1 (MQ=255)
                                                              aaCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgc        >  1:2375329/1‑71 (MQ=255)
                                                              aaCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgc        <  1:2197837/71‑1 (MQ=255)
                                                               aCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgcg       <  1:2606534/71‑1 (MQ=255)
                                                               aCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgcg       <  1:2548474/71‑1 (MQ=255)
                                                                cGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgcg       <  1:999822/70‑1 (MQ=255)
                                                                cGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgcc       >  1:2651998/1‑69 (MQ=255)
                                                                   tGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAgg   <  1:1451599/71‑1 (MQ=255)
                                                                    gCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAgg   >  1:2691125/1‑70 (MQ=255)
                                                                     ctctGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCTCAGGa  <  1:2769790/70‑1 (MQ=255)
                                                                     ctctGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGa  <  1:3419235/70‑1 (MQ=255)
                                                                      |                                                                    
GTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGA  >  minE/834904‑835042

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