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 835,342 C→T 39.2% H20H (CAC→CAT)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,3420CT39.2% 56.0 / 76.6 74H20H (CAC→CAT) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base C (20/25);  new base T (16/13);  total (36/38)
Fisher's exact test for biased strand distribution p-value = 4.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACG  >  minE/835277‑835412
                                                                 |                                                                      
gaaaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTg                                                                   <  1:1483715/68‑1 (MQ=255)
cGTAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTg                                                                   <  1:1840511/71‑1 (MQ=255)
 aaaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGt                                                                  <  1:3036642/69‑1 (MQ=255)
  aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                                                 <  1:2435410/70‑1 (MQ=255)
  aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGt                                                                  <  1:3089650/69‑1 (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)
              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                                           <  1:3680397/71‑1 (MQ=255)
                        gTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTg                                           <  1:1312074/71‑1 (MQ=255)
                        gTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTg                                           <  1:1227733/71‑1 (MQ=255)
                        gTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTg                                           <  1:973566/71‑1 (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                           <  1:2687975/71‑1 (MQ=255)
                                        aTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGc                           <  1:70033/71‑1 (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)
                                                aaGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                   >  1:2162018/1‑71 (MQ=255)
                                                aaGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                   >  1:2958253/1‑71 (MQ=255)
                                                 aGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                   <  1:2416959/70‑1 (MQ=255)
                                                 aGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                   <  1:931629/70‑1 (MQ=255)
                                                 aGTGCATCGGCTG‑CACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATg                 >  1:2513863/1‑71 (MQ=255)
                                                  gTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAatat                  >  1:1832505/1‑70 (MQ=255)
                                                   tGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGc                <  1:2472128/71‑1 (MQ=255)
                                                   tGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGc                <  1:2742999/71‑1 (MQ=255)
                                                     cATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGt              >  1:3270565/1‑71 (MQ=255)
                                                     cATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGt              >  1:2047527/1‑71 (MQ=255)
                                                      aTCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTg             <  1:69819/71‑1 (MQ=255)
                                                         ggCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGtt          >  1:430549/1‑71 (MQ=255)
                                                         ggCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGt           <  1:2436538/70‑1 (MQ=255)
                                                          gCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGttt         <  1:109/71‑2 (MQ=255)
                                                          gCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGtt          >  1:2297446/1‑70 (MQ=255)
                                                          gCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTc         <  1:2074764/71‑1 (MQ=255)
                                                           cTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGttt         <  1:3108489/70‑2 (MQ=255)
                                                            tGCCATACCTGTTCGGTGACCTGTAAAAACGTCTgg                                          <  1:1868602/36‑1 (MQ=25)
                                                            tGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaa       >  1:2051205/1‑71 (MQ=255)
                                                            tGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaa       >  1:2398714/1‑71 (MQ=255)
                                                            tGCCACACCTGCTCGATCACCTGCAAGAACGTCTGGACCAGCCGCGAAGGCATGGAGTACGCCTGGTTcaa       >  1:709105/1‑71 (MQ=255)
                                                              ccATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaac      >  1:1854520/1‑70 (MQ=255)
                                                              ccATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaac      >  1:2892066/1‑70 (MQ=255)
                                                              ccACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaa       <  1:3337043/69‑1 (MQ=255)
                                                                 cacCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATg                 >  1:3634736/1‑56 (MQ=255)
                                                                 cacCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACg  <  1:2316976/71‑1 (MQ=255)
                                                                 cacCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACg  <  1:2439287/71‑1 (MQ=255)
                                                                 |                                                                      
CGTAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACG  >  minE/835277‑835412

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