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 1,933,949 G→A 17.4% A165V (GCG→GTG) ‡ lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,933,9490GA17.4% 143.9 / 21.8 63A165V (GCG→GTG) ‡lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base G (26/26);  new base A (9/2);  total (35/28)
Fisher's exact test for biased strand distribution p-value = 9.29e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.20e-01

GCGCACTTTAAAGGTGTTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGTCAGCAGACGCAA  >  minE/1933882‑1934016
                                                                   |                                                                   
gcgcACTTTAAAGGTGTTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCtt                                                                  >  1:2034617/1‑71 (MQ=255)
gcgcACTTTAAAGGTGTTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCtt                                                                  >  1:2889091/1‑71 (MQ=255)
    aCTTTAAAGGTGTTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCt                                                               >  1:1833314/1‑70 (MQ=255)
    aCTTTAAAGGTGTTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCt                                                               >  1:1618405/1‑70 (MQ=255)
    aCTTTAAAGGTGTTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCt                                                               >  1:1491716/1‑70 (MQ=255)
    aCTTTAAAGGTGTTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTg                                                              <  1:2649665/71‑1 (MQ=255)
        tAAAGGTGTTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATc                                                           <  1:2915678/70‑1 (MQ=255)
        tAAAGGTGTTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATc                                                           <  1:1473676/70‑1 (MQ=255)
        tAAAGGTGTTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATc                                                           <  1:2278985/70‑1 (MQ=255)
             gtgtTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGc                                                       >  1:624358/1‑69 (MQ=255)
                  gCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCtt                                                                  >  1:3413519/1‑53 (MQ=255)
                  gCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGt                                                >  1:3877097/1‑71 (MQ=255)
                  gCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATACTGCAAGCCg                                                 <  1:1179262/70‑1 (MQ=255)
                   cGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGt                                                <  1:3171502/70‑1 (MQ=255)
                    gggATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATc                                                           >  1:3075143/1‑58 (MQ=255)
                    gggATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATc                                                           >  1:3622749/1‑58 (MQ=255)
                    gggATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATc                                                           >  1:2168081/1‑58 (MQ=255)
                     ggATTCTTCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGt                                                <  1:805195/68‑1 (MQ=255)
                     ggATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGt                                                <  1:2804304/68‑1 (MQ=255)
                     ggATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTgg                                              >  1:3499569/1‑70 (MQ=255)
                        ttCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGcc                                                  <  1:1034422/63‑1 (MQ=255)
                        ttCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAAtt                                          >  1:3209376/1‑71 (MQ=255)
                         ttaTCGTTAGCGATGAGGTCCAGATAACGTTGACGATAACGGACTTCCTGATCCTGCAGACCATGGAAtt                                          >  1:606104/3‑70 (MQ=255)
                           aTCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTAt                                       >  1:3705092/1‑71 (MQ=255)
                              gTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATcc                                     <  1:1311780/70‑1 (MQ=255)
                              gTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATcc                                     <  1:2830040/70‑1 (MQ=255)
                               ttGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCgg                                   <  1:3227969/71‑1 (MQ=255)
                                   cgatgaggtCCAGATAACGTTGACGATAACGGACTTCCTGATCCTGCAGACCATGGAATTTATCTggta                                 >  1:2147575/2‑67 (MQ=255)
                                    gatgagatCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCg                              >  1:1843248/1‑71 (MQ=255)
                                     atgagatCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGa                                             <  1:1865289/55‑1 (MQ=255)
                                     atgagatCGAGATAACGCTGACAATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTAt                                       >  1:1278203/1‑61 (MQ=255)
                                       gagatCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCt                                                         <  1:1945349/41‑1 (MQ=255)
                                       gagatCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCaa                                                     <  1:1774235/45‑1 (MQ=255)
                                        agatCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATc                                      >  1:210819/1‑59 (MQ=255)
                                        agatCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCg                              >  1:1281842/1‑67 (MQ=255)
                                        agatCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACg                          >  1:2977955/1‑71 (MQ=255)
                                          atCGAGATAACGCTGACGATAGCGCGCTTCCTGATcc                                                          <  1:1401615/37‑1 (MQ=255)
                                          atCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAAtt                                          <  1:1400419/53‑1 (MQ=255)
                                          atCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAg                                <  1:486779/63‑1 (MQ=255)
                                             gagaTAACGCTGACGATAGCGCGCTTCCTGATCATGCa                                                      >  1:1880361/1‑38 (MQ=255)
                                              agaTAACGTTGACGATAACGGACTTCCTGATCCTGCAGACCATGGAATTTATCTGGTAAAGGACGTAGt                      >  1:1346340/1‑69 (MQ=255)
                                              agaTAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAAttt                                         <  1:366453/50‑1 (MQ=255)
                                               gaTAACGTTGACGATAACGGACTTCCTGATCCTGCAGACCATGGAATTTATCTGGTAAAGGACgt                         >  1:2572066/1‑64 (MQ=255)
                                                aTAACGCTGACGATAGCGCGCTTCCTGAGCCTGCAAGCCGTGGAATTTATCCGGc                                  <  1:2164308/55‑1 (MQ=255)
                                                 tAACGTTGACGATAACGGACTTCCTGATCCTGCAGACCATGGAATTTATCTGGTAAAGGACGTAGTGCtt                  >  1:1584586/1‑70 (MQ=255)
                                                  aaCGTTGACGATAACGGACTTCCTGATCCTGCAGACCATGGAATTTa                                        >  1:2402927/1‑47 (MQ=255)
                                                  aaCGTTGACGATAACGGACTTCCTGATCCTGCAGACCATGGAATTTa                                        >  1:2165279/1‑47 (MQ=255)
                                                   aCGTTGACGATAACGGACTTCCTGATCCTGCAGACCATGGAATTTATCTGGTAAAGGACGTAGTGCttta                <  1:3901868/70‑2 (MQ=255)
                                                   aCGTTGACGATAACGGACTTCCTGATCCTGCAGACCATGGAATTTATCTGGTAAAGGACGTAGTGCttta                <  1:3022798/70‑2 (MQ=255)
                                                   aCGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCCGCGGACGCAGTGCTTTgg               <  1:1927494/71‑1 (MQ=255)
                                                   aCGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTg                <  1:3189770/70‑1 (MQ=255)
                                                    cGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTgg                                              <  1:2426346/39‑1 (MQ=255)
                                                    cGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGt              >  1:3601980/1‑71 (MQ=255)
                                                     gCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGt              <  1:3547776/70‑1 (MQ=255)
                                                       tGACGATAACGGACTTCCTGATCCTGCAGACCATGGAATTTATCTGGTAAAGGACGTAGTGCTTTAGTcag           >  1:119124/1‑71 (MQ=255)
                                                        gACGATAACGGACTTCCTGATCCTGCAGACCATGGAATTTATCTGGTAAAGGACgta                        >  1:3114064/1‑55 (MQ=255)
                                                          cGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGTcagcag        <  1:2671373/71‑1 (MQ=255)
                                                          cGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGTcag           >  1:2228930/1‑68 (MQ=255)
                                                           gATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTAt                                       >  1:1529379/1‑39 (MQ=255)
                                                           gATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTAt                                       >  1:3690804/1‑39 (MQ=255)
                                                           gATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTAt                                       >  1:1524875/1‑39 (MQ=255)
                                                           gATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGTCAGCAGa       <  1:1193225/71‑1 (MQ=255)
                                                             tAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGTc             >  1:2968468/1‑63 (MQ=255)
                                                               gcgcgcTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGTCAGCAGACGc    <  1:1660476/70‑1 (MQ=255)
                                                                cgcgcTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGt              <  1:1574511/59‑1 (MQ=255)
                                                                cgcgcTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGTCAGCAGACGCaa  <  1:3551784/71‑1 (MQ=255)
                                                                cgcgcTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGTCAGCAGACGCaa  <  1:3120687/71‑1 (MQ=255)
                                                                   |                                                                   
GCGCACTTTAAAGGTGTTGCGGGATTCATCGTTGGAGATGAGATCGAGATAACGCTGACGATAGCGCGCTTCCTGATCCTGCAAGCCGTGGAATTTATCCGGCAGCGGACGCAGTGCTTTGGTCAGCAGACGCAA  >  minE/1933882‑1934016

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A