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 1,486,279 T→C 73.4% T345A (ACA→GCA)  nuoN ← NADH:ubiquinone oxidoreductase, membrane subunit N

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,486,2790TC73.4% 143.6 / 54.4 90T345A (ACA→GCA) nuoNNADH:ubiquinone oxidoreductase, membrane subunit N
Reads supporting (aligned to +/- strand):  ref base T (11/13);  new base C (41/25);  total (52/38)
Fisher's exact test for biased strand distribution p-value = 2.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

AGGTAGTAGTAGAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGCCA  >  minE/1486215‑1486344
                                                                |                                                                 
aGGTAGTAGTAGAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGac                                                             <  1:465882/71‑1 (MQ=255)
   tagtagtagAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACacc                                                          <  1:571675/71‑1 (MQ=255)
           gagGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGc                                                    >  1:2203860/1‑69 (MQ=255)
                  aTTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTa                                           <  1:1196300/71‑1 (MQ=255)
                   ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGacac                                                           <  1:4936390/54‑1 (MQ=255)
                   ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGacac                                                           <  1:2261615/54‑1 (MQ=255)
                   ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACg                                             >  1:2562355/1‑68 (MQ=255)
                   ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACg                                             >  1:888655/1‑68 (MQ=255)
                   ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAg                                          <  1:3641067/71‑1 (MQ=255)
                   ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAg                                          <  1:113793/71‑1 (MQ=255)
                   ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAg                                          <  1:4741051/71‑1 (MQ=255)
                   ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAg                                          <  1:833214/71‑1 (MQ=255)
                    tGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAg                                          >  1:4470077/1‑70 (MQ=255)
                     gCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGt                                            <  1:5677166/67‑1 (MQ=255)
                     gCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAg                                          >  1:3939694/1‑69 (MQ=255)
                     gCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGaa                                        >  1:4215687/1‑71 (MQ=255)
                     gCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGaa                                        >  1:3141997/1‑71 (MQ=255)
                     gCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGaa                                        >  1:877617/1‑71 (MQ=255)
                     gCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGaa                                        >  1:807442/1‑71 (MQ=255)
                      ccGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCt                                                                 >  1:4324676/1‑45 (MQ=255)
                        gAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCt                                                                 >  1:2579300/1‑43 (MQ=255)
                        gAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCt                                                                 >  1:2784383/1‑43 (MQ=255)
                           ccGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTAcc                                  <  1:5695087/71‑1 (MQ=255)
                             gACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGa                                <  1:893858/71‑1 (MQ=255)
                             gACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGa                                <  1:4372873/71‑1 (MQ=255)
                             gACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGa                                <  1:2649885/71‑1 (MQ=255)
                              aCAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGa                                >  1:875106/1‑70 (MQ=255)
                              aCAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGa                                >  1:5173577/1‑70 (MQ=255)
                               cAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGaa                                        >  1:1291728/1‑61 (MQ=255)
                               cAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGaa                                        >  1:899619/1‑61 (MQ=255)
                               cAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGCCCGCCAGCACGTAGAACTTACCGAt                               >  1:596858/1‑70 (MQ=255)
                                  ccACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAg                           <  1:3684528/71‑1 (MQ=255)
                                  ccACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAg                           >  1:1910787/1‑71 (MQ=255)
                                  ccACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAg                           >  1:5580125/1‑71 (MQ=255)
                                  ccACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAGCTTACCGATAAAg                           >  1:2786717/1‑71 (MQ=255)
                                  ccACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAg                           >  1:159628/1‑71 (MQ=255)
                                  ccACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAg                           >  1:4277515/1‑71 (MQ=255)
                                   cACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGa                                         <  1:2156217/56‑1 (MQ=255)
                                   cACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGc                          >  1:1141653/1‑71 (MQ=255)
                                    aCGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGa                                         <  1:4393999/55‑1 (MQ=255)
                                     cGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGcc                         >  1:2871616/1‑70 (MQ=255)
                                     cGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGcc                         >  1:1025791/1‑70 (MQ=255)
                                     cGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCAAGTAGAACTTACCGATAAAGcc                         >  1:1513051/1‑70 (MQ=255)
                                      ggCACCCACCAGCCACCACAAGTGTGCCTGGacac                                                           <  1:2296334/35‑1 (MQ=255)
                                        cacccaccAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTAc                                   <  1:1180411/57‑1 (MQ=255)
                                         acccaccAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCg                    <  1:1928214/71‑1 (MQ=255)
                                           ccaccaGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGt                   >  1:2866063/1‑70 (MQ=255)
                                           ccaccaGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGt                   >  1:595304/1‑70 (MQ=255)
                                             accaGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTAc                                   >  1:37128/1‑52 (MQ=255)
                                               caGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGa                                <  1:2133470/53‑1 (MQ=255)
                                                aGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAg                                          >  1:3483574/1‑42 (MQ=255)
                                                aGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAg                                          >  1:710870/1‑42 (MQ=255)
                                                aGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAg                                          >  1:1019941/1‑42 (MQ=255)
                                                aGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAg                                          >  1:218230/1‑42 (MQ=255)
                                                aGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTAc                                   >  1:4119223/1‑49 (MQ=255)
                                                aGCCACCACAAGTGTGCCTGGACACCGACCGACAGCACGTAGAACTTAc                                   >  1:1343124/1‑49 (MQ=255)
                                                 gCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACtt                                     <  1:3090602/46‑1 (MQ=255)
                                                 gCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACtt                                     <  1:2748463/46‑1 (MQ=255)
                                                 gCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCAt                <  1:1970177/67‑1 (MQ=255)
                                                  ccaccaCAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACtt                                     <  1:2279460/45‑1 (MQ=255)
                                                   caccacAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGa           >  1:281523/1‑70 (MQ=255)
                                                    accacAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGcc                         <  1:2224333/55‑1 (MQ=255)
                                                    accacAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATa         <  1:4936013/71‑1 (MQ=255)
                                                     ccacAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACt                                      <  1:3538077/41‑1 (MQ=255)
                                                     ccacAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACt                                      <  1:5426285/41‑1 (MQ=255)
                                                     ccacAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTc                  <  1:1430494/61‑1 (MQ=255)
                                                     ccacAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTc                  <  1:5235359/61‑1 (MQ=255)
                                                      cacaAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGAt          <  1:5426407/68‑1 (MQ=255)
                                                      cacaAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGAt          <  1:2391455/68‑1 (MQ=255)
                                                      cacaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCgg             <  1:1168344/65‑1 (MQ=255)
                                                      cacaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCg              >  1:987492/1‑64 (MQ=255)
                                                       acaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATaaa                            >  1:2100085/1‑49 (MQ=255)
                                                       acaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATaaa                            >  1:1313091/1‑49 (MQ=255)
                                                       acaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATaaa                            >  1:3301340/1‑49 (MQ=255)
                                                       acaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATaaa                            >  1:1593048/1‑49 (MQ=255)
                                                       acaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATaaa                            >  1:4703866/1‑49 (MQ=255)
                                                       acaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCg                    <  1:5552047/57‑1 (MQ=255)
                                                       acaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGt                   >  1:1165558/1‑58 (MQ=255)
                                                       acaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATa         >  1:232052/1‑68 (MQ=255)
                                                       acaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATa         >  1:2811155/1‑68 (MQ=255)
                                                        caAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATAc        >  1:1707496/1‑68 (MQ=255)
                                                        caAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAg                      >  1:4836509/1‑54 (MQ=255)
                                                        caAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAg                      >  1:1504087/1‑54 (MQ=255)
                                                        caAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAg                      >  1:983892/1‑54 (MQ=255)
                                                        caAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCgg     <  1:4804318/71‑1 (MQ=255)
                                                         aaGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCggg            >  1:2255620/1‑63 (MQ=255)
                                                         aaGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGa           >  1:5433109/1‑64 (MQ=255)
                                                         aaGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGc    <  1:3787586/71‑1 (MQ=255)
                                                         aaGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGc    <  1:5083173/71‑1 (MQ=255)
                                                          aGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGc    >  1:5489269/1‑70 (MQ=255)
                                                             gtgcCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGCCa  >  1:4014396/1‑69 (MQ=255)
                                                                |                                                                 
AGGTAGTAGTAGAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGCCA  >  minE/1486215‑1486344

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