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 835,354 T→G 29.6% V24V (GTT→GTG)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,3540TG29.6% 74.8 / 70.4 82V24V (GTT→GTG) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base T (26/31);  new base G (14/10);  total (41/41)
Fisher's exact test for biased strand distribution p-value = 3.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAG  >  minE/835287‑835423
                                                                   |                                                                     
aaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTAc                                                                     <  1:1770798/70‑1 (MQ=255)
aaaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGAcc                                                                    >  1:2993079/1‑71 (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)
       ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaaaa                                                             <  1:1602300/71‑1 (MQ=255)
        tCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTaaaaa                                                            >  1:1401145/1‑71 (MQ=255)
         cacaAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGtt                                                                       >  1:293543/1‑59 (MQ=255)
          acaAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAAc                                                           <  1:877137/70‑1 (MQ=255)
          acaAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACg                                                          >  1:3793689/1‑71 (MQ=255)
          acaAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACg                                                          >  1:214548/1‑71 (MQ=255)
           caAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                                                         <  1:1160162/71‑1 (MQ=255)
             aGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCt                                                       >  1:3677306/1‑71 (MQ=255)
             aGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCt                                                       >  1:3672907/1‑71 (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                                      <  1:70033/71‑1 (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)
                                      aaGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                              >  1:2958253/1‑71 (MQ=255)
                                      aaGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                              >  1:2162018/1‑71 (MQ=255)
                                       aGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                              <  1:931629/70‑1 (MQ=255)
                                       aGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                              <  1:2416959/70‑1 (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                 >  1:2892066/1‑70 (MQ=255)
                                                    ccATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaac                 >  1:1854520/1‑70 (MQ=255)
                                                    ccACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaa                  <  1:3337043/69‑1 (MQ=255)
                                                       tacCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACg             <  1:2538245/70‑1 (MQ=255)
                                                       cacCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATg                            >  1:3634736/1‑56 (MQ=255)
                                                       cacCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACg             <  1:2316976/71‑1 (MQ=255)
                                                       cacCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACg             <  1:2439287/71‑1 (MQ=255)
                                                        acCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGt            >  1:2166895/1‑71 (MQ=255)
                                                          cTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATg                                   >  1:1677135/1‑46 (MQ=255)
                                                          cTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAat                               >  1:3027312/1‑50 (MQ=255)
                                                          cTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaaca                >  1:1893268/1‑65 (MQ=255)
                                                          cTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTgg          <  1:1327911/71‑1 (MQ=255)
                                                          cTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTg           >  1:3401816/1‑70 (MQ=255)
                                                           tGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATg                            >  1:1440941/1‑52 (MQ=255)
                                                             ttgaGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGaa        <  1:2134511/67‑1 (MQ=255)
                                                             ttCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGaaa       >  1:2118523/1‑71 (MQ=255)
                                                             ttCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGaa        <  1:243508/70‑1 (MQ=255)
                                                             ttCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGa         <  1:2919966/69‑1 (MQ=255)
                                                             ttCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTca                   <  1:3307356/59‑1 (MQ=255)
                                                             ttCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGa         <  1:3215110/69‑1 (MQ=255)
                                                              tCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaac                 >  1:1884875/1‑60 (MQ=255)
                                                              tCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaac                 >  1:699739/1‑60 (MQ=255)
                                                               cAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGaa                                >  1:1486749/1‑44 (MQ=255)
                                                               cAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAAc      <  1:3762977/70‑1 (MQ=255)
                                                                aGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCa    <  1:1729499/71‑1 (MQ=255)
                                                                 gTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAAcc     >  1:2873644/1‑69 (MQ=255)
                                                                 gTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCaa   <  1:3256987/71‑1 (MQ=255)
                                                                  ttACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTca                   <  1:1815241/54‑1 (MQ=255)
                                                                  ttACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAAcc     <  1:2143466/68‑1 (MQ=255)
                                                                  ttACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAg  <  1:942218/71‑1 (MQ=255)
                                                                   |                                                                     
AAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAG  >  minE/835287‑835423

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