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 775,607 C→A 34.9% D410E (GAC→GAA)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported775,6070CA34.9% 151.8 / 82.4 106D410E (GAC→GAA) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base C (25/44);  new base A (13/24);  total (38/68)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

Only 100 of 115 total aligned reads displayed.

AAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGT  >  Exported/775537‑775673
                                                                      |                                                                  
aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAc                                                                    >  1:4910777/1‑71 (MQ=255)
   ccGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagcg                                                                 <  1:917785/71‑1 (MQ=255)
   ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                                                                 <  1:976317/71‑1 (MQ=255)
   ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgc                                                                  >  1:2939731/1‑70 (MQ=255)
   ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgc                                                                  >  1:4789614/1‑70 (MQ=255)
     gTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGat                                                               <  1:1918057/71‑1 (MQ=255)
     gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat                                                               <  1:808205/71‑1 (MQ=255)
     gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat                                                               <  1:5216023/71‑1 (MQ=255)
      tAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGat                                                               >  1:1113823/1‑70 (MQ=255)
      tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatc                                                              <  1:4950922/71‑1 (MQ=255)
      tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat                                                               >  1:4107747/1‑70 (MQ=255)
       aaCTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGatca                                                             >  1:3448444/1‑71 (MQ=255)
       aaCTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGatca                                                             >  1:4187107/1‑71 (MQ=255)
        acttATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGatcat                                                            >  1:4867709/4‑71 (MQ=255)
         ccTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatcatc                                                           <  1:882236/71‑1 (MQ=255)
          ttATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagcg                                                                 <  1:4209301/63‑1 (MQ=255)
          cTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatcatc                                                           >  1:3039223/1‑70 (MQ=255)
           tATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCg                                                          >  1:716730/1‑70 (MQ=255)
            aTGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGa                                                         >  1:4982221/1‑70 (MQ=255)
            aTGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGa                                                         >  1:4506782/1‑70 (MQ=255)
            aTGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCg                                                          <  1:3577782/69‑1 (MQ=255)
            aTGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGa                                                         >  1:4938828/1‑70 (MQ=255)
            aTGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGa                                                         <  1:612903/70‑1 (MQ=255)
             tGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                                                        <  1:4182287/70‑1 (MQ=255)
             tGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaa                                                        <  1:3684003/70‑1 (MQ=255)
             tGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaa                                                        <  1:5304580/70‑1 (MQ=255)
               aCTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                                                      <  1:3354007/70‑1 (MQ=255)
                 ttCGAACGTCTGATGGAAGGCTCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaaaa                                                      <  1:838483/68‑1 (MQ=255)
                 ttCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaaaa                                                      <  1:4308074/68‑1 (MQ=255)
                  tCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                                                                 <  1:2784171/56‑1 (MQ=255)
                   cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaa                                                       >  1:2665221/1‑65 (MQ=255)
                   cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATg                                                  >  1:2732202/1‑70 (MQ=255)
                   cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGa                                                         <  1:5070083/63‑1 (MQ=255)
                   cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACa                                                    >  1:5101980/1‑68 (MQ=255)
                   cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACAt                                                   <  1:4707189/69‑1 (MQ=255)
                    gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGt                                                 <  1:4468762/67‑1 (MQ=255)
                    gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGt                                                 <  1:821401/67‑1 (MQ=255)
                    gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGt                                                 <  1:3918859/67‑1 (MQ=255)
                    gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGt                                                 <  1:5161875/67‑1 (MQ=255)
                    gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGt                                                 <  1:2152004/67‑1 (MQ=255)
                    gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTa                                                <  1:126651/68‑1 (MQ=255)
                    gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTa                                                <  1:3284446/68‑1 (MQ=255)
                    gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                                                 <  1:5572578/70‑1 (MQ=255)
                    gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                                                 <  1:5091881/70‑1 (MQ=255)
                    gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                                                 <  1:2160050/70‑1 (MQ=255)
                    gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTa                                                <  1:5222899/71‑1 (MQ=255)
                    gAGCGTCTGATGGATGGCGCTAAACTCCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                                                 <  1:5111052/70‑1 (MQ=255)
                      acGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTAAt                                              >  1:3286924/2‑71 (MQ=255)
                       cGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTAAt                                              >  1:3118/1‑70 (MQ=255)
                         tCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                                                                 <  1:3225806/49‑1 (MQ=255)
                         tCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                                                      <  1:2275925/60‑1 (MQ=255)
                         tCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                                                        <  1:2184924/58‑1 (MQ=255)
                         tCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                                                        <  1:84957/58‑1 (MQ=255)
                         tCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATg                                                  <  1:3378872/64‑1 (MQ=255)
                           tGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                                                        <  1:539490/56‑1 (MQ=255)
                           tGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCg                                          >  1:2912800/1‑70 (MQ=255)
                           tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGTTGAAGCGatca                                                             <  1:453510/51‑1 (MQ=255)
                           tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGatca                                                             <  1:841040/51‑1 (MQ=255)
                             atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                                                 <  1:1355639/61‑1 (MQ=255)
                              tggaaggCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagc                                                                  >  1:2191942/1‑43 (MQ=37)
                               ggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTaa                                               >  1:1638684/1‑61 (MQ=255)
                                gatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatc                                                              >  1:1832269/1‑45 (MQ=255)
                                gatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                                                      >  1:349245/1‑53 (MQ=255)
                                gatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACAt                                                   >  1:3560578/1‑56 (MQ=255)
                                        tAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTa                                                <  1:2679235/51‑1 (MQ=255)
                                        tAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGa                                                         <  1:5595785/42‑1 (MQ=255)
                                        tAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                                                 <  1:3138762/50‑1 (MQ=255)
                                         aaaCTGCTGAAATGTTCAGAGTTTGGTGACGCGatc                                                              <  1:4422220/36‑1 (MQ=255)
                                         aaaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGa                                                         >  1:1235101/1‑41 (MQ=255)
                                         aaaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                                                 <  1:4946092/49‑1 (MQ=255)
                                         aaaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTa                                                >  1:5397496/1‑50 (MQ=255)
                                          agctgctgAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTAAt                                              >  1:3716266/3‑51 (MQ=255)
                                          agctgctgAAATGTTCAGAGTTTGGGGAAGCGATCATCGAAAACATGTAAt                                              >  1:1400745/3‑51 (MQ=255)
                                          aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAg                                       >  1:4241989/1‑58 (MQ=255)
                                          aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGtt                                     >  1:3587362/1‑60 (MQ=255)
                                          aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAttt                           >  1:5093262/1‑70 (MQ=255)
                                          aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAttt                           <  1:539151/70‑1 (MQ=255)
                                          aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt                            <  1:281240/69‑1 (MQ=255)
                                          aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt                            >  1:193289/1‑69 (MQ=255)
                                             tgctgAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATtta                          >  1:2946396/1‑68 (MQ=255)
                                             tgctgAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATtta                          >  1:2701041/1‑68 (MQ=255)
                                              gctgAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGtt                                     >  1:2882838/1‑56 (MQ=255)
                                              gctgAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGtt                                 <  1:3934010/60‑1 (MQ=255)
                                               ctgAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATttatta                       <  1:3214149/69‑1 (MQ=255)
                                                tgAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACa                                                    >  1:2473966/1‑39 (MQ=255)
                                                tgAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACa                                                    >  1:3502916/1‑39 (MQ=255)
                                                 gAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAAc                                                     <  1:1807055/37‑1 (MQ=255)
                                                 gAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAAc                                                     <  1:1988551/37‑1 (MQ=255)
                                                 gAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                                                 <  1:1544157/41‑1 (MQ=255)
                                                  aaaTGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTaa                      <  1:5456649/67‑1 (MQ=255)
                                                   aaTGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt                            <  1:3971627/60‑1 (MQ=255)
                                                       ttCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGt             <  1:488630/71‑1 (MQ=255)
                                                        tCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACggg                  <  1:1337311/65‑1 (MQ=255)
                                                        tCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGAGt             <  1:1431016/70‑1 (MQ=255)
                                                         cAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTaa           >  1:3820460/1‑71 (MQ=255)
                                                           gagTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACg         <  1:5521901/71‑1 (MQ=255)
                                                              tttGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTaaa                              <  1:2844737/47‑1 (MQ=255)
                                                              tttGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTaaa                              <  1:4486209/47‑1 (MQ=255)
                                                              tttGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTaaa                              <  1:3972409/47‑1 (MQ=255)
                                                                  gTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCgt  <  1:3745447/71‑1 (MQ=255)
                                                                      |                                                                  
AAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGT  >  Exported/775537‑775673

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A