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 1,933,738 G→A 10.8% Y235Y (TAC→TAT)  lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,933,7380GA10.8% 234.8 / 14.8 83Y235Y (TAC→TAT) lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base G (34/40);  new base A (6/3);  total (40/43)
Fisher's exact test for biased strand distribution p-value = 3.02e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

ATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGATCACCT  >  minE/1933670‑1933808
                                                                    |                                                                      
aTTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTa                                                                      <  1:2983683/71‑1 (MQ=255)
aTTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTa                                                                      >  1:3416192/1‑71 (MQ=255)
 tttCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATa                                                                      >  1:911576/1‑70 (MQ=255)
  ttCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACa                                                                    >  1:1286058/1‑71 (MQ=255)
  ttCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACa                                                                    >  1:1290634/1‑71 (MQ=255)
  ttCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACa                                                                    >  1:3801662/1‑71 (MQ=255)
    cGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACAt                                                                   <  1:3335801/70‑1 (MQ=255)
    cGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACAt                                                                   <  1:638973/70‑1 (MQ=255)
    cGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATg                                                                  >  1:1181427/1‑71 (MQ=255)
     gAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGt                                                                 >  1:587896/1‑71 (MQ=255)
      aaTACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGt                                                                 <  1:1217053/70‑1 (MQ=255)
        tACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATcta                                                              <  1:2333770/71‑3 (MQ=255)
        tACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATct                                                               >  1:1983765/1‑69 (MQ=255)
        tACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTc                                                                >  1:1214196/1‑69 (MQ=255)
        tACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCga                                                              <  1:86483/71‑1 (MQ=255)
         acacGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTa                                                                      <  1:2422356/62‑1 (MQ=255)
          cacGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCgaga                                                            <  1:3669173/71‑1 (MQ=255)
             gCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATcc                                                         <  1:1093881/71‑1 (MQ=255)
             gCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATc                                                          >  1:893998/1‑70 (MQ=255)
               tCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAg                                                       >  1:571229/1‑71 (MQ=255)
                cGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCgaga                                                            >  1:126340/1‑65 (MQ=255)
                   aGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGcgcg                                                   >  1:2184303/1‑71 (MQ=255)
                    gCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                                                  <  1:2949407/71‑1 (MQ=255)
                     ccaccaACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                                                  >  1:3802675/1‑70 (MQ=255)
                        ccaaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGAt                                                           <  1:2319111/58‑1 (MQ=255)
                         caaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtgg                                             >  1:1888811/1‑71 (MQ=255)
                         caaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtgg                                             <  1:2314149/71‑1 (MQ=255)
                          aaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCgaga                                                            >  1:3477225/1‑55 (MQ=255)
                          aaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAAGTACATGTCGAGATCCAGCGCGTTAtggt                                            >  1:2978053/1‑71 (MQ=255)
                           accaccAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtg                                              >  1:135577/1‑68 (MQ=255)
                            ccaccaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtggtgg                                          <  1:2061418/71‑1 (MQ=255)
                            ccaccaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtggtgg                                          <  1:1134267/71‑1 (MQ=255)
                            ccaccaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtggtgg                                          <  1:2897533/71‑1 (MQ=255)
                            caaccaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTAtgatgg                                          >  1:1558106/3‑71 (MQ=255)
                               ccaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCg                                                               >  1:1844443/1‑47 (MQ=255)
                               ccaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCg                                                               >  1:3657825/1‑47 (MQ=255)
                               ccaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATggtgggt                                        >  1:3239038/1‑70 (MQ=255)
                               ccaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATggtgggt                                        >  1:3460855/1‑70 (MQ=255)
                                caGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTa                                                                      <  1:1366743/39‑1 (MQ=255)
                                caGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGa                                      >  1:446239/1‑71 (MQ=255)
                                 aGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCAAGCGCGTTATGGTGGGTGa                                      >  1:3154480/1‑70 (MQ=255)
                                  gACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAAt                                     >  1:649542/1‑70 (MQ=255)
                                  gACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAAt                                     >  1:97730/1‑70 (MQ=255)
                                  gACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCga                                                              <  1:2850073/45‑1 (MQ=255)
                                   aCGTTTCAGATACAGCTCCGGCGCGATACGCAGATACAt                                                                   <  1:770260/39‑1 (MQ=16)
                                   aCGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATa                                    >  1:2535162/1‑70 (MQ=255)
                                     gCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAt                                               <  1:3645636/57‑1 (MQ=255)
                                     gCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAt                                               <  1:654660/57‑1 (MQ=255)
                                     gCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAt                                               <  1:3047046/57‑1 (MQ=255)
                                     gCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAt                                               <  1:3002532/57‑1 (MQ=255)
                                         gAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATaaa                                  >  1:2801156/1‑66 (MQ=255)
                                         gAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg                               <  1:1638514/69‑1 (MQ=255)
                                         gAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg                               <  1:1513571/69‑1 (MQ=255)
                                           ggTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGAcg                            >  1:782838/1‑70 (MQ=255)
                                           gatACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAATAAACGGGcga                           <  1:3758614/69‑2 (MQ=255)
                                            gTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                                                  <  1:1438502/47‑1 (MQ=255)
                                            gTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                                                  <  1:3457676/47‑1 (MQ=255)
                                              aCAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGAcgcg                          >  1:1354442/1‑69 (MQ=255)
                                              aCAGCTCCGGCGCGATACGCAGATACATATCTAAATCCa                                                        >  1:2534954/1‑39 (MQ=16)
                                               cAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAg                       >  1:1155071/1‑71 (MQ=255)
                                               cAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAg                       >  1:2361368/1‑71 (MQ=255)
                                                aGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGc                      <  1:1819896/71‑1 (MQ=255)
                                                 gTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCg                     <  1:3654387/71‑1 (MQ=255)
                                                 gTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCg                     >  1:1475851/1‑71 (MQ=255)
                                                  ttCCGGCGCGATACGCAGGTACATGTCGAGATCCAgcg                                                     <  1:596014/38‑1 (MQ=255)
                                                  ttCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg                               <  1:1904697/60‑1 (MQ=255)
                                                   tCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCgg                    >  1:3460421/1‑70 (MQ=255)
                                                    ccGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATggtggg                                         <  1:2377535/48‑1 (MQ=255)
                                                      ggCGCGATACGCATGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATaa                                   <  1:2995049/52‑1 (MQ=255)
                                                      ggCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATaa                                   <  1:3497882/52‑1 (MQ=255)
                                                      ggCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg                               <  1:1727812/56‑1 (MQ=255)
                                                       gcgcGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtggt                                            <  1:610453/42‑1 (MQ=255)
                                                        cgcgATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATa                                    <  1:982465/49‑1 (MQ=255)
                                                         gcgATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGcc             <  1:2264892/71‑1 (MQ=255)
                                                         gcgATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGcc             <  1:2126745/71‑1 (MQ=255)
                                                         gcgATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGc              >  1:3251873/1‑70 (MQ=255)
                                                           gATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAg           <  1:3706680/71‑1 (MQ=255)
                                                           gATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAg           <  1:1788250/71‑1 (MQ=255)
                                                             tACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAgg          >  1:1957852/1‑70 (MQ=255)
                                                              aCGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGa        >  1:453053/1‑71 (MQ=255)
                                                               cGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGa        <  1:880894/70‑1 (MQ=255)
                                                                gCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGa        <  1:3910733/69‑1 (MQ=255)
                                                                  aGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGATCAc    >  1:516773/1‑71 (MQ=255)
                                                                    gTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAgg          <  1:2381602/63‑1 (MQ=255)
                                                                    gTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGATCACCt  >  1:1026421/1‑71 (MQ=255)
                                                                    gTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGATCACCt  >  1:2798574/1‑71 (MQ=255)
                                                                    |                                                                      
ATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGATCACCT  >  minE/1933670‑1933808

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