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 835,885 T→C 23.4% I201I (ATT→ATC)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,8850TC23.4% 132.4 / 40.4 77I201I (ATT→ATC) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base T (23/36);  new base C (11/7);  total (34/43)
Fisher's exact test for biased strand distribution p-value = 1.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

TTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATC  >  minE/835819‑835954
                                                                   |                                                                     
cctGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTAc                                                                    >  1:965612/3‑70 (MQ=255)
cctGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTAc                                                                    >  1:2959457/3‑70 (MQ=255)
  tGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACATGCCCGAGCGGTGCGATTTACAAg                                                                 >  1:4295982/1‑71 (MQ=255)
   gCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACaaac                                                                >  1:5474769/1‑69 (MQ=255)
   gCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACaaac                                                                >  1:1914269/1‑69 (MQ=255)
    ccGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCg                                                               >  1:4131440/1‑71 (MQ=255)
    ccGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGT‑GCGACCTGCCCGAGCGGTGCGATTTACAAGCGt                                                              >  1:4347390/1‑71 (MQ=255)
      gcgcCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACaa                                                                  >  1:3909760/1‑66 (MQ=255)
      gcgcCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACaa                                                                  >  1:4792923/1‑66 (MQ=255)
      gcgcCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACaa                                                                  >  1:2057523/1‑66 (MQ=255)
        gcCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTga                                                            <  1:1424948/70‑1 (MQ=255)
        gcCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACGCgaa                                                           <  1:4008683/71‑1 (MQ=255)
           tgtgCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACGCgaag                                                          <  1:5114094/69‑1 (MQ=255)
            gtgCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaa                                                           >  1:3075944/1‑67 (MQ=255)
             tgCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTAc                                                                    <  1:2743499/57‑1 (MQ=255)
             tgCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaagaa                                                        <  1:5674081/69‑1 (MQ=255)
             tgCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACGCgaagaa                                                        <  1:5420271/69‑1 (MQ=255)
             tgCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACGCgaagaa                                                        <  1:1690358/69‑1 (MQ=255)
              gCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACaaa                                                                 >  1:298998/1‑58 (MQ=255)
              gCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACaaa                                                                 >  1:4783294/1‑58 (MQ=255)
               cGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCg                                                               <  1:4920128/60‑1 (MQ=255)
               cGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTg                                                             >  1:1109417/1‑62 (MQ=255)
                gAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAagaaga                                                      >  1:5406577/1‑68 (MQ=255)
                 aaCACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATgg                                                   >  1:2365420/1‑70 (MQ=255)
                 aaCACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACGCGAagaagacg                                                    <  1:809713/69‑3 (MQ=255)
                     cTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaagaa                                                        <  1:4544790/61‑1 (MQ=255)
                     cTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCg                                              <  1:3433784/71‑1 (MQ=255)
                          tGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATTGCATCGTCCt                                          >  1:854048/1‑70 (MQ=255)
                          tGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATc                                               >  1:1163641/1‑65 (MQ=255)
                          tGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCt                                          >  1:5067144/1‑70 (MQ=255)
                            aa‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaag                                                          >  1:3137770/1‑52 (MQ=255)
                            aa‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGGGAAGAAGATGGCATCGTCCTGAt                                       <  1:4859008/71‑1 (MQ=255)
                               cccGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCg                                     <  1:4446315/71‑1 (MQ=255)
                                ccGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaagaa                                                        <  1:998695/51‑1 (MQ=255)
                                 cGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGaagaag                                                       <  1:3814880/51‑1 (MQ=255)
                                 cGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAc                                   <  1:2858466/71‑1 (MQ=255)
                                  ggCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGaagaag                                                       <  1:2387615/50‑1 (MQ=255)
                                  ggCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAcc                                  <  1:4683953/71‑1 (MQ=255)
                                    cATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGaagaag                                                       <  1:4593058/48‑1 (MQ=255)
                                      tgtgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaagaa                                                        <  1:2313650/45‑1 (MQ=255)
                                      tgcgtgGCGACCTGCCCAAGCGGCGCTATCTACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGa                              >  1:2592635/4‑71 (MQ=255)
                                       gtgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaagaa                                                        <  1:543383/44‑1 (MQ=255)
                                       gtgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaagaa                                                        <  1:1287185/44‑1 (MQ=255)
                                       gtgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaagaa                                                        <  1:5629327/44‑1 (MQ=255)
                                       gtgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaagaa                                                        <  1:1390108/44‑1 (MQ=255)
                                       gtgtgGCGACCTGCCCGAGCGGGGCGATTTACAAGCGTgaagaa                                                        <  1:1740031/44‑1 (MQ=255)
                                       gcgtgGCGACCTGCCCAAGCGGCGCTATCTACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGa                              >  1:4385442/3‑70 (MQ=255)
                                        tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                             >  1:1775170/1‑70 (MQ=255)
                                        tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                             >  1:534635/1‑70 (MQ=255)
                                        tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                             >  1:456002/1‑70 (MQ=255)
                                        tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                             >  1:2016248/1‑70 (MQ=255)
                                        tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                             >  1:4396349/1‑70 (MQ=255)
                                            gCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATaaa                          >  1:5052181/1‑69 (MQ=255)
                                                 cTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTcc                                           >  1:2232410/1‑47 (MQ=255)
                                                 cTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGtg                   <  1:4317549/71‑1 (MQ=255)
                                                   gCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTg                                         >  1:3817871/1‑47 (MQ=255)
                                                    cccGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGtggc                 <  1:512664/70‑1 (MQ=255)
                                                    cccAAGCGGCGCTATCTACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGATAAATGCCGtggc                 <  1:2476477/70‑1 (MQ=255)
                                                      cGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGtggctgg              >  1:5396429/1‑71 (MQ=255)
                                                        aGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCg            <  1:4305586/71‑1 (MQ=255)
                                                          cGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATg                        <  1:4212846/57‑1 (MQ=255)
                                                          cGGCGCTATCTACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGtt          <  1:3102966/71‑2 (MQ=255)
                                                           ggTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAt         <  1:2869767/71‑1 (MQ=255)
                                                            gTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAcc                                  <  1:3894254/45‑1 (MQ=255)
                                                            gTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAcc                                  <  1:3645624/45‑1 (MQ=255)
                                                            gTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAcc                                  <  1:4924439/45‑1 (MQ=255)
                                                             tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATa                            <  1:4264622/50‑1 (MQ=255)
                                                             tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGtggc                 <  1:2644161/61‑1 (MQ=255)
                                                             tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTa          <  1:1157081/68‑1 (MQ=255)
                                                             tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtgt       <  1:3130205/71‑1 (MQ=255)
                                                             tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATAGACCAGGATa                            <  1:4733414/50‑1 (MQ=255)
                                                              gCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtgtg      >  1:3141955/1‑71 (MQ=255)
                                                              gCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtgtg      >  1:3749414/1‑71 (MQ=255)
                                                               cGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtgtg      >  1:5115664/1‑70 (MQ=255)
                                                                 aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt   <  1:3329174/71‑1 (MQ=255)
                                                                 aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt   <  1:4883487/71‑1 (MQ=255)
                                                                 aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt   <  1:2886675/71‑1 (MQ=255)
                                                                  tttACAAGCGTGAAGAAGATGGCATCGTCCTGATc                                      <  1:2013520/35‑1 (MQ=255)
                                                                  tttACAAGCGTGAAGAAGATGGCATCGTCCTGATc                                      <  1:1611923/35‑1 (MQ=255)
                                                                  tttACAAGCGTGAAGAAGATGGCATCGTCCTGATc                                      <  1:821844/35‑1 (MQ=255)
                                                                  tttACAAGCGTGAAGAAGATGGCATCGTCCTGATc                                      <  1:936548/35‑1 (MQ=255)
                                                                  tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATa                            <  1:262897/45‑1 (MQ=255)
                                                                  tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATa                            <  1:3165576/45‑1 (MQ=255)
                                                                  tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc  <  1:564971/71‑1 (MQ=255)
                                                                  tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc  <  1:2778101/71‑1 (MQ=255)
                                                                  tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc  <  1:870498/71‑1 (MQ=255)
                                                                  tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc  <  1:371163/71‑1 (MQ=255)
                                                                   |                                                                     
TTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATC  >  minE/835819‑835954

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A