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 1,015,454 C→G 20.5% P205P (CCG→CCC)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,4540CG20.5% 164.9 / 38.4 83P205P (CCG→CCC) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base C (33/33);  new base G (7/10);  total (40/43)
Fisher's exact test for biased strand distribution p-value = 5.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.64e-01

TATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGA  >  minE/1015384‑1015521
                                                                      |                                                                   
tatGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTcccc                                                                     <  1:4375839/71‑1 (MQ=255)
tatGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTcccc                                                                     >  1:5045484/1‑71 (MQ=255)
     tACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGt                                                                <  1:142070/71‑1 (MQ=255)
     tACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGt                                                                <  1:4563966/71‑1 (MQ=255)
     tACGGAGGACAGGCCGCCGTACCCAGCGTGAGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGt                                                                <  1:2622271/71‑1 (MQ=255)
       cGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGt                                                                >  1:4328100/1‑69 (MQ=255)
       cGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGt                                                                >  1:1383487/1‑69 (MQ=255)
         gaggaCAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAg                                                             >  1:2282417/1‑70 (MQ=255)
           ggaCAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTaa                                                          >  1:666597/1‑71 (MQ=255)
            ggcAGGCTGCAGTACCGAGGGTACGCATTTTCTCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAg                                                             <  1:4801432/65‑1 (MQ=255)
              cAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGc                                                       >  1:4211564/1‑71 (MQ=255)
                 gccgccGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTc                                                               <  1:867798/60‑1 (MQ=255)
                     ccgTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGtt                                                >  1:5261989/1‑71 (MQ=255)
                     ccgTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGtt                                                <  1:3999617/71‑1 (MQ=255)
                       gTACCGAGGGTACACATTTTCTCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGATTTGGTTTc                                              >  1:5678796/1‑71 (MQ=255)
                       gTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTc                                              >  1:3458471/1‑71 (MQ=255)
                       gTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTc                                              >  1:3451956/1‑71 (MQ=255)
                         aCCGAGGGTACGCATTTTCTCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAgca                                                           >  1:4605434/1‑54 (MQ=255)
                            cAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa                                          >  1:2520491/1‑70 (MQ=255)
                            cAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGAt                                         <  1:2061669/71‑1 (MQ=255)
                            cAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGAt                                         <  1:2068252/71‑1 (MQ=255)
                             aGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa                                          >  1:1410421/1‑69 (MQ=255)
                                gTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATagag                                     <  1:3478245/71‑1 (MQ=255)
                                gTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATa                                        >  1:1316827/1‑68 (MQ=255)
                                 tGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTgg                                                  <  1:2885404/57‑1 (MQ=255)
                                 tGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAgaga                                    <  1:1084939/71‑1 (MQ=255)
                                 tGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAgaga                                    <  1:3181154/71‑1 (MQ=255)
                                   cgcATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGAt                                   <  1:4789657/70‑1 (MQ=255)
                                   cgcATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATa                                  >  1:5430970/1‑71 (MQ=255)
                                     cATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAg                                                             <  1:1173456/42‑1 (MQ=255)
                                     cATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATAc                                 <  1:2189701/70‑1 (MQ=255)
                                      aTCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGt                               >  1:377443/1‑71 (MQ=255)
                                      aTCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGt                               >  1:5617337/1‑71 (MQ=255)
                                       ttttctCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTg                                                   <  1:3261203/48‑1 (MQ=255)
                                       ttttctCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTGGt                                                 <  1:4397292/50‑1 (MQ=255)
                                         ttctCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGtttt                            >  1:399374/1‑71 (MQ=255)
                                         ttctCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTAGTAGAGATACGttt                             >  1:3581867/1‑68 (MQ=255)
                                         ttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa                                          >  1:5276588/1‑57 (MQ=255)
                                         ttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa                                          >  1:466936/1‑57 (MQ=255)
                                         ttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa                                          >  1:5182584/1‑57 (MQ=255)
                                         ttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCt                             >  1:3010719/1‑70 (MQ=255)
                                          tctcGACGAGGAAGTTTTTCAGTTTGCCGGGCGTCAGCATGGCTTTGGTTTCCTGGTAGAGAt                                   <  1:4334658/63‑1 (MQ=255)
                                          tctcGACGAGGAAGTTTTTCAGTTTGCCGGGCGTCAGCAGGGCTTTGGTTTCCTGGTAGAGAt                                   <  1:460578/63‑1 (MQ=255)
                                          tctcGACGAGGAAGTTTTTCAGTTTGCCGGGCGTCAGCAGGGCTTTGGTTTCCTGGTAGAGAt                                   <  1:2530501/63‑1 (MQ=255)
                                          tctcGACGAGGAAGTTTTTCAGTTTGCCGGGCGTCAGCAGGGCTTTGGTTTCCTGGTAGAGAt                                   <  1:2717369/63‑1 (MQ=255)
                                          tctcGACGAGGAAGTTTTTCAGTTTGCCGGGCGTCAGCAGGGCTTTGGTTTCCTGGTAGAGAt                                   <  1:5227161/63‑1 (MQ=255)
                                          tctcAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTaa                                                          >  1:3294336/1‑40 (MQ=255)
                                          tctcAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATAc                                 <  1:4694561/65‑1 (MQ=255)
                                          tctcAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATAc                                 <  1:5426159/65‑1 (MQ=255)
                                           ctcAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCt                             <  1:4258569/68‑1 (MQ=255)
                                            tcAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATagag                                     >  1:4370668/1‑59 (MQ=255)
                                             cAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCttt                                                    >  1:105406/1‑43 (MQ=255)
                                              aaCCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTaa                                                          >  1:2427887/1‑36 (MQ=255)
                                              aaCCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGt                          <  1:3086951/68‑1 (MQ=255)
                                              aaCCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGt                          <  1:3157312/68‑1 (MQ=255)
                                              aaCCAGGCAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGt                          <  1:5590001/68‑1 (MQ=255)
                                                   ggTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa                                          <  1:1424968/47‑1 (MQ=255)
                                                    gTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAac                 <  1:1417246/71‑1 (MQ=255)
                                                    gTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAac                 <  1:4787093/71‑1 (MQ=255)
                                                      aaTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCt                                            >  1:2897564/1‑42 (MQ=255)
                                                      aaTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCt                                            >  1:2734046/1‑42 (MQ=255)
                                                      aaTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGcc                     >  1:625148/1‑65 (MQ=255)
                                                      aaTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAacca               >  1:3940664/1‑71 (MQ=255)
                                                       aTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTg                           <  1:4766448/58‑1 (MQ=255)
                                                       aTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAaccac              <  1:4047212/71‑1 (MQ=255)
                                                       aTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAaccac              <  1:3980521/71‑1 (MQ=255)
                                                        tttttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATa                                  >  1:1575859/1‑50 (MQ=255)
                                                        tttttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATa                                  >  1:5466074/1‑50 (MQ=255)
                                                        tttttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATa                                  >  1:3440364/1‑50 (MQ=255)
                                                         ttttCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATAAGTTTTGttgg                       >  1:2718277/1‑58 (MQ=255)
                                                         ttttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAaccacc             <  1:3273283/70‑1 (MQ=255)
                                                          tttCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAgccgccgc           >  1:5472185/1‑69 (MQ=255)
                                                          tttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTc                              <  1:4008520/52‑1 (MQ=255)
                                                            tCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGca                     >  1:2195172/1‑58 (MQ=255)
                                                            tCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGc                      <  1:4831137/58‑1 (MQ=255)
                                                             cAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCt         <  1:3567305/70‑1 (MQ=255)
                                                              aGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCtt        <  1:1191864/70‑1 (MQ=255)
                                                              aGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACg                                <  1:3921417/46‑1 (MQ=255)
                                                              aGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCg                    >  1:3458132/1‑58 (MQ=255)
                                                              aGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCg                    >  1:4799489/1‑58 (MQ=255)
                                                               gTTTCCCCAGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTg      >  1:1338241/1‑71 (MQ=255)
                                                                  tCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGa                   <  1:5494009/55‑1 (MQ=255)
                                                                  tCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGc    >  1:1573830/1‑70 (MQ=255)
                                                                  tCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGc    <  1:3885495/70‑1 (MQ=255)
                                                                  tCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGc    <  1:3608082/70‑1 (MQ=255)
                                                                    cccGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGa  <  1:1886545/70‑1 (MQ=255)
                                                                    cccGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGa  <  1:862705/70‑1 (MQ=255)
                                                                      |                                                                   
TATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGA  >  minE/1015384‑1015521

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