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 1,933,720 T→C 11.3% E241E (GAA→GAG)  lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,933,7200TC11.3% 230.9 / 18.2 88E241E (GAA→GAG) lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base T (40/38);  new base C (6/4);  total (46/42)
Fisher's exact test for biased strand distribution p-value = 7.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.65e-01

CGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCG  >  minE/1933650‑1933789
                                                                      |                                                                     
cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGt                                                                       >  1:2433687/1‑71 (MQ=255)
  ttACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTc                                                                     <  1:1908235/71‑1 (MQ=255)
    aCGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTcc                                                                    <  1:495593/70‑1 (MQ=255)
      ggAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgc                                                                 >  1:623995/1‑71 (MQ=255)
       gAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgcg                                                                <  1:792838/71‑1 (MQ=255)
        aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCTGACGCTTGAGGTACAGTTCCGgcgc                                                               <  1:2946860/71‑1 (MQ=255)
        aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgcgc                                                               >  1:3912495/1‑71 (MQ=255)
        aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgcgc                                                               >  1:2645146/1‑71 (MQ=255)
         aGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgcgc                                                               >  1:1843283/1‑70 (MQ=255)
          gTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACAAGACGCTTGAGGTACAGTTCCGGCGCGa                                                             >  1:1364136/1‑71 (MQ=255)
             aCGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATAc                                                          >  1:3718751/1‑71 (MQ=255)
              cGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATAc                                                          <  1:1133437/70‑1 (MQ=255)
              cGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACg                                                         <  1:616068/71‑1 (MQ=255)
               ggTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACg                                                         >  1:1168678/1‑70 (MQ=255)
                gTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCa                                                       <  1:1078146/71‑1 (MQ=255)
                 ttGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                                                        <  1:3474315/69‑1 (MQ=255)
                 ttGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAg                                                      >  1:3080684/1‑71 (MQ=255)
                 ttGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAg                                                      >  1:3582482/1‑71 (MQ=255)
                    aTTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTa                                                   <  1:2983683/71‑1 (MQ=255)
                    aTTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTa                                                   >  1:3416192/1‑71 (MQ=255)
                     tttCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATa                                                   >  1:911576/1‑70 (MQ=255)
                      ttCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTcc                                                                    >  1:1181936/1‑52 (MQ=255)
                      ttCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACa                                                 >  1:1286058/1‑71 (MQ=255)
                      ttCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACa                                                 >  1:3801662/1‑71 (MQ=255)
                      ttCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACa                                                 >  1:1290634/1‑71 (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)
                         gAATACACGCTCGAAGCCACCAACCACCAGACGCTT‑AGGTACAGTTCCGgcgc                                                               <  1:339026/53‑1 (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)
                                   tCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCg                                                                   <  1:2364790/40‑1 (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)
                                         ccaccaACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATa                                                           >  1:3723678/1‑42 (MQ=255)
                                         ccaccaACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                               >  1:3802675/1‑70 (MQ=255)
                                          caccaACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAg                                                      <  1:3878224/46‑1 (MQ=255)
                                          caccaACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAg                                                      <  1:1007358/46‑1 (MQ=255)
                                           accaaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATAc                                                          <  1:489179/41‑1 (MQ=255)
                                            ccaaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGAt                                        <  1:2319111/58‑1 (MQ=255)
                                             caaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtgg                          <  1:2314149/71‑1 (MQ=255)
                                             caaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtgg                          >  1:1888811/1‑71 (MQ=255)
                                              aaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCgaga                                         >  1:3477225/1‑55 (MQ=255)
                                              aaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAAGTACATGTCGAGATCCAGCGCGTTAtggt                         >  1:2978053/1‑71 (MQ=255)
                                               accaccAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtg                           >  1:135577/1‑68 (MQ=255)
                                                ccaccaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtggtgg                       <  1:1134267/71‑1 (MQ=255)
                                                ccaccaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtggtgg                       <  1:2061418/71‑1 (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                     >  1:3460855/1‑70 (MQ=255)
                                                   ccaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATggtgggt                     >  1:3239038/1‑70 (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                            <  1:3047046/57‑1 (MQ=255)
                                                         gCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAt                            <  1:3002532/57‑1 (MQ=255)
                                                         gCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAt                            <  1:654660/57‑1 (MQ=255)
                                                             gAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATaaa               >  1:2801156/1‑66 (MQ=255)
                                                             gAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg            <  1:1513571/69‑1 (MQ=255)
                                                             gAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg            <  1:1638514/69‑1 (MQ=255)
                                                               ggTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGAcg         >  1:782838/1‑70 (MQ=255)
                                                               gatACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAATAAACGGGcga        <  1:3758614/69‑2 (MQ=255)
                                                                gTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                               <  1:3457676/47‑1 (MQ=255)
                                                                gTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                               <  1:1438502/47‑1 (MQ=255)
                                                                  aCAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGAcgcg       >  1:1354442/1‑69 (MQ=255)
                                                                  aCAGCTCCGGCGCGATACGCAGATACATATCTAAATCCa                                     >  1:2534954/1‑39 (MQ=16)
                                                                   cAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAg    >  1:2361368/1‑71 (MQ=255)
                                                                   cAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAg    >  1:1155071/1‑71 (MQ=255)
                                                                    aGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGc   <  1:1819896/71‑1 (MQ=255)
                                                                     gTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCg  >  1:1475851/1‑71 (MQ=255)
                                                                     gTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCg  <  1:3654387/71‑1 (MQ=255)
                                                                      ttCCGGCGCGATACGCAGGTACATGTCGAGATCCAgcg                                  <  1:596014/38‑1 (MQ=255)
                                                                      ttCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg            <  1:1904697/60‑1 (MQ=255)
                                                                      |                                                                     
CGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCG  >  minE/1933650‑1933789

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