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 1,015,214 C→A 27.1% L285L (CTG→CTT)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,2140CA27.1% 184.0 / 51.7 92L285L (CTG→CTT) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base C (28/39);  new base A (11/14);  total (39/53)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

CGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCT  >  minE/1015147‑1015284
                                                                   |                                                                      
cgcCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAg                                                                      <  1:3368764/70‑1 (MQ=255)
  ccGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGAcc                                                                   <  1:2376671/71‑1 (MQ=255)
    gTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGAc                                                                    >  1:4623788/1‑68 (MQ=255)
     tGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGAc                                                                    <  1:502631/67‑1 (MQ=255)
     tGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAg                                                                >  1:4065708/1‑71 (MQ=255)
     tGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAg                                                                >  1:2578522/1‑71 (MQ=255)
       aCGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAt                                                              >  1:2604271/1‑71 (MQ=255)
       aCGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAgtt                                                              <  1:4418975/71‑3 (MQ=255)
       aCGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAgtt                                                              <  1:5281815/71‑3 (MQ=255)
       aCGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAgt                                                               <  1:2940748/70‑2 (MQ=255)
         gTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAttt                                                            <  1:1041444/71‑1 (MQ=255)
         gTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAttt                                                            <  1:2163767/71‑1 (MQ=255)
          tGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtttt                                                           <  1:3543896/71‑1 (MQ=255)
          tGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtttt                                                           <  1:2860717/71‑1 (MQ=255)
          tGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGtttct                                                           <  1:2047092/71‑3 (MQ=255)
             cAGGCGAATCACGGGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTgcg                                                        >  1:1171393/1‑71 (MQ=255)
                gCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtttt                                                           <  1:5482134/65‑1 (MQ=255)
                gCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtt                                                             <  1:2447383/63‑1 (MQ=255)
                gCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtt                                                             <  1:2112087/63‑1 (MQ=255)
                 cGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtttt                                                           <  1:2560277/64‑1 (MQ=255)
                  gAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCg                                                   <  1:1013409/71‑1 (MQ=255)
                  gAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCg                                                   <  1:2654855/71‑1 (MQ=255)
                   aaTCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAg                                                                      >  1:5381085/1‑51 (MQ=255)
                    aTCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                 >  1:1184460/1‑71 (MQ=255)
                     tCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                 <  1:4131335/70‑1 (MQ=255)
                     tCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATc                                                <  1:3377907/71‑1 (MQ=255)
                     tCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATc                                                <  1:2457002/71‑1 (MQ=255)
                     tCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATc                                                <  1:2829265/71‑1 (MQ=255)
                       aCGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAg                                              >  1:187400/1‑71 (MQ=255)
                       aCGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAg                                              >  1:3904013/1‑71 (MQ=255)
                        cgcgGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGc                                             <  1:3186520/71‑1 (MQ=255)
                        cgcgAATTTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGtttca                                                           >  1:4392976/1‑55 (MQ=255)
                        cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGttt                                                             <  1:5358661/55‑1 (MQ=255)
                        cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGttt                                                             <  1:828371/55‑1 (MQ=255)
                        cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGttt                                                             <  1:2828699/55‑1 (MQ=255)
                        cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGttt                                                             <  1:1347161/55‑1 (MQ=255)
                        cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTgggc                                                       >  1:813981/1‑61 (MQ=255)
                        cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTggg                                                        >  1:3676836/1‑58 (MQ=255)
                         gcgGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGc                                             >  1:2286505/1‑70 (MQ=255)
                           ggATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAAt                                          >  1:2359578/1‑71 (MQ=255)
                             aTGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTc                                        <  1:2320369/71‑1 (MQ=255)
                             aTGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAt                                                              <  1:1610945/49‑1 (MQ=255)
                              tGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGa                                                                     <  1:472575/41‑1 (MQ=255)
                              tGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCt                                       <  1:2910283/71‑1 (MQ=255)
                                tCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGtttct                                                           >  1:199845/1‑47 (MQ=19)
                                tCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTcctg                                     >  1:5068033/1‑68 (MQ=255)
                                tCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTcctg                                     >  1:2990150/1‑68 (MQ=255)
                                tCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                 <  1:3395182/59‑1 (MQ=255)
                                tCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                 <  1:287885/59‑1 (MQ=255)
                                     aGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTcc                                 <  1:89427/70‑1 (MQ=255)
                                      gCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAg                               <  1:5613530/71‑1 (MQ=255)
                                       cGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAgc                              >  1:2203378/1‑70 (MQ=255)
                                          aGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAgctg                            <  1:4441711/70‑4 (MQ=255)
                                          aGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCtttt                                    >  1:2533073/1‑62 (MQ=255)
                                          aGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCtttt                                    >  1:4026848/1‑62 (MQ=255)
                                           gTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                          >  1:5691118/1‑71 (MQ=255)
                                            tATTTATCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGc                                             <  1:1991901/51‑1 (MQ=255)
                                            tATTTACCGCCAAACTGCGCGCCAAGACCGAGtttc                                                            <  1:2963042/36‑2 (MQ=12)
                                            tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGc                                             <  1:5644418/51‑1 (MQ=255)
                                            tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGc                                             <  1:3916370/51‑1 (MQ=255)
                                            tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTc                            <  1:5335744/68‑1 (MQ=255)
                                            tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTc                            <  1:2062810/68‑1 (MQ=255)
                                            tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTc                            <  1:170607/68‑1 (MQ=255)
                                            tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCcac                         <  1:4015888/71‑1 (MQ=255)
                                             aTTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                 >  1:4286222/1‑46 (MQ=255)
                                             aTTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCcac                         >  1:2587251/1‑70 (MQ=255)
                                              tttACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                 <  1:3136481/45‑1 (MQ=255)
                                              tttACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                 <  1:548298/45‑1 (MQ=255)
                                                tACCACCAAACTGCGCCCCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATcg                     >  1:4337732/1‑71 (MQ=255)
                                                tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                 <  1:2772074/43‑1 (MQ=255)
                                                tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                 <  1:791727/43‑1 (MQ=255)
                                                tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCttt                                     >  1:2086504/1‑55 (MQ=255)
                                                tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAg                               >  1:4687202/1‑61 (MQ=255)
                                                tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATcg                     >  1:5206192/1‑71 (MQ=255)
                                                tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATcg                     >  1:4518929/1‑71 (MQ=255)
                                                 accaccAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCa                                            >  1:1342216/1‑47 (MQ=255)
                                                 accaccAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCa                                            >  1:3226614/1‑47 (MQ=255)
                                                   caccaAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                 <  1:3732206/40‑1 (MQ=255)
                                                   caccaAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCgg                  <  1:4782366/71‑1 (MQ=255)
                                                     ccaAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGaa                >  1:4364390/1‑71 (MQ=255)
                                                      caAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAAc               >  1:2584735/1‑71 (MQ=255)
                                                       aaaCTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACg              >  1:3177950/1‑71 (MQ=255)
                                                        aaCTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACGc             >  1:5115266/1‑71 (MQ=255)
                                                        aaCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCtttt                                    <  1:3385621/48‑1 (MQ=255)
                                                        aaCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGtt                             >  1:2185789/1‑55 (MQ=255)
                                                        aaCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGc             >  1:3749115/1‑71 (MQ=255)
                                                         aCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTc                                  <  1:2063972/49‑1 (MQ=255)
                                                         aCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                          <  1:1751104/57‑1 (MQ=255)
                                                         aCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGcc            >  1:310655/1‑71 (MQ=255)
                                                          cTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTc                                  >  1:4284153/1‑48 (MQ=255)
                                                             cgcACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTg          <  1:1220813/69‑1 (MQ=255)
                                                               cACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGaa                >  1:1358784/1‑61 (MQ=255)
                                                                 cccAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                          <  1:2871839/49‑1 (MQ=255)
                                                                 cccAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                          <  1:4259719/49‑1 (MQ=255)
                                                                  ccAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                          <  1:4973735/48‑1 (MQ=255)
                                                                  ccAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGc   >  1:4095523/1‑71 (MQ=255)
                                                                  ccAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGc   >  1:5649973/1‑71 (MQ=255)
                                                                   cAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCt  <  1:5475389/71‑1 (MQ=255)
                                                                   cAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCt  >  1:4954005/1‑71 (MQ=255)
                                                                   |                                                                      
CGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCT  >  minE/1015147‑1015284

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