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 835,324 T→C 40.6% D14D (GAT→GAC)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,3240TC40.6% 37.1 / 77.8 69D14D (GAT→GAC) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base T (13/28);  new base C (17/11);  total (30/39)
Fisher's exact test for biased strand distribution p-value = 2.58e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.30e-01

CAATGACCAGGTACAGGAGAGCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAA  >  minE/835256‑835393
                                                                      |                                                                     
cAATGACCAGGTACAGGAGAGCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGAt                                                                       >  1:2548940/1‑69 (MQ=255)
cAATGACCAGGTACAGGAGAGCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATaa                                                                     <  1:2397116/71‑1 (MQ=255)
   tGACCAGGTACAGGAGAGCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTg                                                                  >  1:2816562/1‑71 (MQ=255)
      tcAGGTACAGGAG‑GCGAA‑AAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTAt                                                               <  1:1038941/70‑1 (MQ=255)
       cAGGTACAGGAG‑GCGAA‑AAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTAt                                                               >  1:322274/1‑70 (MQ=255)
        aGGTACAGGAGAGTG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCAt                                                               <  1:3222746/69‑1 (MQ=255)
        aGGTACAGGAG‑GCGAA‑AAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCg                                                             >  1:580056/1‑71 (MQ=255)
         ggTACAGGAGAGCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCgg                                                            <  1:2976711/71‑1 (MQ=255)
          gTACAGGAG‑GCG‑AAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGc                                                           >  1:3140096/1‑71 (MQ=255)
            aCAGGAGAGCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCa                                                                <  1:3797985/64‑1 (MQ=255)
            aCAGGAGAGCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCa                                                                <  1:1988319/64‑1 (MQ=255)
             cAGGAGAGCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTg                                                         <  1:2270425/70‑1 (MQ=255)
                gagaGCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGcc                                                       >  1:3111585/1‑69 (MQ=255)
                 agagCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGc                                                                 <  1:549269/58‑1 (MQ=255)
                  gagCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATaa                                                                     >  1:681826/1‑53 (MQ=255)
                     cG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTg                                                <  1:1840511/71‑1 (MQ=255)
                       gaaaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTg                                                <  1:1483715/68‑1 (MQ=255)
                        aaaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGt                                               <  1:3036642/69‑1 (MQ=255)
                         aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                              <  1:2435410/70‑1 (MQ=255)
                         aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGt                                               <  1:3089650/69‑1 (MQ=255)
                          aaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTg                                                         >  1:969075/1‑59 (MQ=255)
                          aaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                              >  1:3637829/1‑70 (MQ=255)
                          aaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTc                                             >  1:3290229/1‑71 (MQ=255)
                           aaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTcg                                            <  1:2871943/71‑2 (MQ=255)
                           aaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTcg                                            >  1:2703013/1‑70 (MQ=255)
                            aaTGAAAATCCGTTCCCAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTcg                                            <  1:3485491/70‑2 (MQ=255)
                             aTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGt                                          >  1:1483404/1‑71 (MQ=255)
                              tGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGt                                          >  1:2539524/1‑70 (MQ=255)
                                 aaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTAc                                       <  1:1770798/70‑1 (MQ=255)
                                 aaaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTcg                                            >  1:2777663/1‑64 (MQ=255)
                                 aaaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGAcc                                      >  1:2993079/1‑71 (MQ=255)
                                  aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCacac                                                   <  1:290989/57‑1 (MQ=255)
                                  aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCt                                     <  1:1588623/71‑1 (MQ=255)
                                   aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATa                                                                      <  1:1946984/37‑1 (MQ=255)
                                   aTTCGTTCACAAGTCGGCATGGTGCGGAATCTCGATAAGTGCATCGGCTGc                                                        <  1:997862/51‑1 (MQ=255)
                                     ccGTTCTCAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGt                                   >  1:507840/2‑70 (MQ=255)
                                     ccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTg                                    >  1:1325990/2‑69 (MQ=255)
                                     ccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGt                                   >  1:1927102/2‑70 (MQ=255)
                                        ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCt                                                 <  1:405315/53‑1 (MQ=255)
                                        ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCt                                                 <  1:3455879/53‑1 (MQ=255)
                                        ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaaaa                               <  1:1602300/71‑1 (MQ=255)
                                         tCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTaaaaa                              >  1:1401145/1‑71 (MQ=255)
                                         tCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCcac                                                     <  1:2654955/48‑1 (MQ=255)
                                          cacaAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGtt                                         >  1:293543/1‑59 (MQ=255)
                                           acaAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAAc                             <  1:877137/70‑1 (MQ=255)
                                           acaAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACg                            >  1:214548/1‑71 (MQ=255)
                                           acaAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACg                            >  1:3793689/1‑71 (MQ=255)
                                            caAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                           <  1:1160162/71‑1 (MQ=255)
                                              aGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCt                         >  1:3672907/1‑71 (MQ=255)
                                              aGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCt                         >  1:3677306/1‑71 (MQ=255)
                                              aGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCt                         >  1:3855265/1‑71 (MQ=255)
                                               gTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTg                        <  1:973566/71‑1 (MQ=255)
                                               gTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTg                        <  1:1312074/71‑1 (MQ=255)
                                               gTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTg                        <  1:1227733/71‑1 (MQ=255)
                                               gTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTg                        <  1:3680397/71‑1 (MQ=255)
                                                tCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTgg                       <  1:3619794/71‑1 (MQ=255)
                                                   gCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACATCTGTTCAGTTACCTGTAAAAACGTCTGGAcc                    <  1:1836487/71‑1 (MQ=255)
                                                       ggTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGcc                >  1:52784/1‑71 (MQ=255)
                                                             gAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCt                         >  1:2396373/1‑56 (MQ=255)
                                                              aacctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGaa           <  1:2160995/66‑1 (MQ=255)
                                                              aacctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAg          >  1:1130916/4‑70 (MQ=255)
                                                              aacctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAg          >  1:2376194/4‑70 (MQ=255)
                                                               aTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGc        <  1:70033/71‑1 (MQ=255)
                                                               aTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGc        <  1:2687975/71‑1 (MQ=255)
                                                               aTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGc        <  1:3043866/71‑1 (MQ=255)
                                                                cctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGca       <  1:3542248/70‑2 (MQ=255)
                                                                  tcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt              >  1:3842024/1‑62 (MQ=255)
                                                                   cGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTg     >  1:1826224/1‑70 (MQ=255)
                                                                    gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGa   <  1:1793399/71‑1 (MQ=255)
                                                                     aTAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGaa  <  1:3952560/71‑1 (MQ=255)
                                                                      |                                                                     
CAATGACCAGGTACAGGAGAGCG‑T‑AAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAA  >  minE/835256‑835393

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