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
A3 F2 I1 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 Exported 775,500 T→C 45.5% L375L (TTA→CTA) ‡ icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported775,5000TC45.5% 28.1 / 137.1 110L375L (TTA→CTA) ‡icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base T (22/38);  new base C (26/24);  total (48/62)
Fisher's exact test for biased strand distribution p-value = 1.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 113 total aligned reads displayed.

ATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATG  >  Exported/775432‑775568
                                                                    |                                                                    
aTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCTCCACATGGGTTGGACCGAAGCGGCTGACtt                                                                     >  1:2604795/1‑70 (MQ=255)
      gCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTg                                                                <  1:2855008/69‑1 (MQ=255)
        tctATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTa                                                             >  1:5074671/1‑70 (MQ=255)
         ctATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGtt                                                              <  1:4630290/68‑1 (MQ=255)
          tattatTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAg                                                          >  1:4560182/1‑71 (MQ=255)
           attattCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTaa                                                                   >  1:4121525/1‑61 (MQ=255)
            ttattCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAAt                                                                  <  1:4349474/61‑1 (MQ=255)
            ttattCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAgg                                                         <  1:4172312/70‑1 (MQ=255)
             tattCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGt                                                        <  1:1409386/70‑1 (MQ=255)
              attCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTAt                                                      >  1:3348039/1‑71 (MQ=255)
               ttCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTAt                                                      <  1:1629049/70‑1 (MQ=255)
                    tcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTAt                                                      >  1:2455663/1‑65 (MQ=255)
                    tcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTAt                                                      >  1:4111056/1‑65 (MQ=255)
                     ccGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGtt                                                              >  1:2983368/1‑56 (MQ=255)
                      cGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAgcc                                               <  1:5646367/70‑3 (MQ=255)
                      cGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGgcg                                              >  1:2200157/1‑71 (MQ=255)
                      cGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGgcg                                              >  1:1289415/1‑71 (MQ=255)
                          gagaTGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAg                                                 >  1:1381896/1‑64 (MQ=255)
                           agaTGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATc                                         <  1:1025373/71‑1 (MQ=255)
                            gatgatGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATgg                                                    <  1:3141336/59‑1 (MQ=255)
                            gatgatGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATgg                                                    <  1:5351897/59‑1 (MQ=255)
                            gatgatGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCa                                        <  1:2100080/71‑1 (MQ=255)
                            gatgatGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCa                                        <  1:327385/71‑1 (MQ=255)
                             ctaatgCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaa                                       <  1:4250170/68‑1 (MQ=255)
                               gatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAAcg                                     >  1:1165095/1‑71 (MQ=255)
                               gatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAAcg                                     >  1:94836/1‑71 (MQ=255)
                               aatgCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatg                                     >  1:454705/2‑69 (MQ=255)
                               aatgCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatg                                     >  1:3045760/2‑69 (MQ=255)
                               aatgCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatg                                     >  1:2445968/2‑69 (MQ=255)
                                atgCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgc                                    >  1:1574736/1‑71 (MQ=255)
                                 tgctgcGCCATATGGGTTTGACTTAAGCGGCTGACCTGATTGTTAAAgg                                                         <  1:4330108/49‑1 (MQ=255)
                                 tgctgcGCCATATGGGTTGGTCTGAAGCGGCTGACCTGATTGTTAAAgg                                                         <  1:1080114/49‑1 (MQ=255)
                                 tgctgcGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAgg                                                         <  1:3782503/49‑1 (MQ=255)
                                  gctgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTa                                                       <  1:5342534/50‑1 (MQ=255)
                                   ctgcGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgcca                                  <  1:989573/70‑3 (MQ=255)
                                   ctgcGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaa                                 <  1:1203667/71‑1 (MQ=255)
                                   ctgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGa                                  <  1:312725/70‑1 (MQ=255)
                                      cgcCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaag                                <  1:239143/69‑2 (MQ=255)
                                       gcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAAcc                             <  1:5537158/71‑1 (MQ=255)
                                        ccACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAgg                                                         <  1:2080807/42‑1 (MQ=255)
                                        ccACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCg                            <  1:5590726/71‑1 (MQ=255)
                                          ataTGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgcc                                   <  1:1050245/60‑2 (MQ=255)
                                          ataTGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgcc                                   <  1:3276543/60‑2 (MQ=255)
                                          acaTGGGTTGGACCGAAGCGGCTGACTTAATTGTTTAAGGTa                                                       <  1:2474800/42‑1 (MQ=255)
                                           taTGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgcc                                   <  1:3320052/60‑2 (MQ=255)
                                           caTGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAgg                                                         <  1:1570199/39‑1 (MQ=255)
                                           caTGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATgg                                                    <  1:4666332/44‑1 (MQ=255)
                                           caTGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTaa                         >  1:487027/1‑71 (MQ=255)
                                            aTGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGaa                                                  >  1:53155/1‑45 (MQ=38)
                                            aTGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCaa                                           <  1:3990670/52‑1 (MQ=255)
                                             tGGGTTGGACTGAAGCGGCTGACCTGATTGTTaaa                                                           >  1:1548558/1‑35 (MQ=25)
                                             tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTa                                                       >  1:5357055/1‑39 (MQ=37)
                                             tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTa                                                       >  1:2179354/1‑39 (MQ=37)
                                             tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTa                                                       >  1:96939/1‑39 (MQ=37)
                                             tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGgcgc                                             >  1:1761179/1‑49 (MQ=38)
                                             tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCa                                        >  1:1300947/1‑54 (MQ=38)
                                             tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGAcc                             >  1:4222670/1‑65 (MQ=255)
                                             tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGAcc                             >  1:5220178/1‑65 (MQ=255)
                                              gggTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAAct                       >  1:2477880/1‑69 (MQ=255)
                                              gggTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAcc                       >  1:3917995/1‑70 (MQ=255)
                                               ggTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAActt                      <  1:4593568/70‑3 (MQ=255)
                                               ggTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCt                      <  1:1793318/70‑1 (MQ=255)
                                                gTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTAt                    <  1:1446041/71‑1 (MQ=255)
                                                 ttGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATg                   <  1:344596/71‑1 (MQ=255)
                                                   ggACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaaga                               >  1:1993168/1‑55 (MQ=255)
                                                   ggACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGAc                 >  1:4050037/1‑71 (MQ=255)
                                                    gACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACt                <  1:3039478/71‑1 (MQ=255)
                                                    gACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACt                <  1:561481/71‑1 (MQ=255)
                                                     aCCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGgcgc                                             <  1:3058461/41‑1 (MQ=255)
                                                     aCCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATc                                         <  1:791951/45‑1 (MQ=255)
                                                     aCCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATc                                         <  1:2646944/45‑1 (MQ=255)
                                                      ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAg                                                 >  1:2111704/1‑36 (MQ=255)
                                                      ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc              <  1:1391276/71‑1 (MQ=255)
                                                       tgAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTc              >  1:5559034/2‑70 (MQ=255)
                                                         aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg           >  1:5476851/1‑71 (MQ=255)
                                                         aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg           >  1:3040542/1‑71 (MQ=255)
                                                         aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaa                                       >  1:2112274/1‑43 (MQ=38)
                                                         aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCg             <  1:2036179/69‑1 (MQ=255)
                                                         aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCg             <  1:4433530/69‑1 (MQ=255)
                                                         aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCg             <  1:334058/69‑1 (MQ=255)
                                                          aGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGc          <  1:1003337/71‑1 (MQ=255)
                                                          aGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGaac          >  1:3739297/1‑69 (MQ=255)
                                                           gCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACg         >  1:76223/1‑71 (MQ=255)
                                                             ggCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                    <  1:1292216/58‑1 (MQ=255)
                                                             ggCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGt                           <  1:4635065/51‑1 (MQ=25)
                                                             ggCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc       >  1:1230933/1‑71 (MQ=255)
                                                              gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCt                      <  1:295209/55‑1 (MQ=255)
                                                              gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCt                      <  1:909384/55‑1 (MQ=255)
                                                              gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt      <  1:3995916/71‑1 (MQ=255)
                                                              gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt      <  1:5212003/71‑1 (MQ=255)
                                                              gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt      <  1:3725303/71‑1 (MQ=255)
                                                              gCTGACCTGATTGTTAAAGGTATGGAAGGCGCAAt                                          <  1:2608550/35‑1 (MQ=37)
                                                              gCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCt      >  1:1036956/1‑71 (MQ=255)
                                                              gCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCt      <  1:5690598/71‑1 (MQ=255)
                                                               cTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt      <  1:3984064/70‑1 (MQ=255)
                                                               cTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGt                           <  1:5204902/49‑1 (MQ=25)
                                                                  aCTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg  >  1:3232674/1‑71 (MQ=255)
                                                                  aCTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg  >  1:4622093/1‑71 (MQ=255)
                                                                    ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                    <  1:1634366/51‑1 (MQ=255)
                                                                    ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                    <  1:5277416/51‑1 (MQ=255)
                                                                    |                                                                    
ATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATG  >  Exported/775432‑775568

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