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 775,580 A→G 40.5% K401K (AAA→AAG)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported775,5800AG40.5% 84.7 / 163.2 148K401K (AAA→AAG) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base A (42/46);  new base G (22/38);  total (64/84)
Fisher's exact test for biased strand distribution p-value = 2.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

Only 100 of 165 total aligned reads displayed.

AAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTT  >  Exported/775510‑775648
                                                                      |                                                                    
aaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                      <  1:2884133/71‑1 (MQ=255)
   gTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActg                                                                   >  1:210280/1‑71 (MQ=255)
     aTGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAgctgct                                                                 >  1:1860602/1‑71 (MQ=255)
        gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa                                                               >  1:1651041/1‑70 (MQ=255)
        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                                                              <  1:2123342/71‑1 (MQ=255)
        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                                                              <  1:3147756/71‑1 (MQ=255)
        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                                                               >  1:2611725/1‑70 (MQ=255)
        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                                                               >  1:1523257/1‑70 (MQ=255)
        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGCATGGCGCTAAACTGCTGaa                                                              <  1:1418655/71‑1 (MQ=255)
         aaGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaaa                                                             >  1:3417508/1‑71 (MQ=255)
           ggCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaaa                                                             >  1:4129865/1‑69 (MQ=255)
             cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGtt                                                         <  1:379986/71‑1 (MQ=255)
               cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                      >  1:2774159/1‑56 (MQ=255)
               cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTATGATGGATGGCGCTAAACTTCTGAAATGTTCa                                                       <  1:1612606/71‑1 (MQ=255)
                  tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGtt                                                         <  1:2951441/66‑1 (MQ=255)
                  tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                                    >  1:1999120/1‑71 (MQ=255)
                  tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                                    >  1:437349/1‑71 (MQ=255)
                    aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAgtgt                                                   <  1:1036445/70‑1 (MQ=255)
                     aCGGGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                      <  1:112212/50‑1 (MQ=255)
                     aCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                      <  1:1823507/50‑1 (MQ=255)
                     aCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGttt                                                 <  1:2189580/71‑1 (MQ=255)
                         gAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                              >  1:758211/1‑70 (MQ=255)
                          aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCag                                                      >  1:3383367/4‑61 (MQ=255)
                          aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTg                                             >  1:4825945/4‑70 (MQ=255)
                          aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGa                                            <  1:3300178/68‑1 (MQ=255)
                          aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGa                                            <  1:668343/68‑1 (MQ=255)
                           agaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa                                                               >  1:3718769/3‑51 (MQ=255)
                           agaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa                                                               >  1:640260/3‑51 (MQ=255)
                           aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAc                                           >  1:4910777/1‑71 (MQ=255)
                            aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                                                             >  1:3692746/1‑52 (MQ=255)
                              ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                                        <  1:976317/71‑1 (MQ=255)
                              ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgc                                         >  1:2939731/1‑70 (MQ=255)
                              ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgc                                         >  1:4789614/1‑70 (MQ=255)
                               cGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                                            >  1:41491/1‑66 (MQ=255)
                                gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTg                                             >  1:1147991/1‑64 (MQ=255)
                                gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat                                      <  1:5216023/71‑1 (MQ=255)
                                 tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                                            >  1:4331059/1‑64 (MQ=255)
                                 tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatc                                     <  1:4950922/71‑1 (MQ=255)
                                  aaCTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGatca                                    >  1:3448444/1‑71 (MQ=255)
                                  aaCCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTc                                                        >  1:269890/1‑51 (MQ=255)
                                    ccTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatcatc                                  <  1:882236/71‑1 (MQ=255)
                                     ttATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagcg                                        <  1:4209301/63‑1 (MQ=255)
                                       aTGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGa                                >  1:4982221/1‑70 (MQ=255)
                                       aTGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGa                                >  1:4506782/1‑70 (MQ=255)
                                       aTGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCg                                 <  1:3577782/69‑1 (MQ=255)
                                        tGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                               <  1:4182287/70‑1 (MQ=255)
                                        tGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaa                               <  1:3684003/70‑1 (MQ=255)
                                        tGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaa                               <  1:5304580/70‑1 (MQ=255)
                                          aCTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                                            >  1:1053756/1‑55 (MQ=255)
                                          aCTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                             <  1:3354007/70‑1 (MQ=255)
                                           cTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                              <  1:5495997/52‑1 (MQ=255)
                                           cTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                              <  1:4529868/52‑1 (MQ=255)
                                            ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGttt                                                 <  1:3593329/48‑1 (MQ=255)
                                            ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGttt                                                 <  1:3940177/48‑1 (MQ=255)
                                            ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGttt                                                 <  1:2818027/48‑1 (MQ=255)
                                            ttCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaaaa                             <  1:5492544/68‑1 (MQ=255)
                                             tCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                                            >  1:391449/1‑52 (MQ=255)
                                             tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGttt                                                 <  1:2511959/47‑1 (MQ=38)
                                             tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                                                  <  1:4886163/46‑1 (MQ=38)
                                             tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                                                  <  1:1550097/46‑1 (MQ=38)
                                             tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                                                  <  1:176410/46‑1 (MQ=38)
                                             tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                                                  <  1:3824699/46‑1 (MQ=38)
                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATg                         >  1:2732202/1‑70 (MQ=255)
                                              cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGa                                            >  1:5459182/1‑51 (MQ=255)
                                              cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGa                                <  1:5070083/63‑1 (MQ=255)
                                              cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACa                           >  1:5101980/1‑68 (MQ=255)
                                               gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGt                        <  1:2152004/67‑1 (MQ=255)
                                               gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGt                        <  1:5161875/67‑1 (MQ=255)
                                               gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGt                        <  1:821401/67‑1 (MQ=255)
                                               gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTa                       <  1:3284446/68‑1 (MQ=255)
                                               gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTa                       <  1:126651/68‑1 (MQ=255)
                                               gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                        <  1:2160050/70‑1 (MQ=255)
                                               gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                        <  1:826627/70‑1 (MQ=255)
                                                 acGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTAAt                     >  1:3286924/2‑71 (MQ=255)
                                                    tCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt                                                  <  1:4693766/39‑1 (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)
                                                      tGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                               <  1:539490/56‑1 (MQ=255)
                                                      tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGTTGAAGCGatca                                    <  1:453510/51‑1 (MQ=255)
                                                      tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGatca                                    <  1:841040/51‑1 (MQ=255)
                                                      tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaa                               <  1:4853538/56‑1 (MQ=255)
                                                       gatggaagGCGCTAAGCTGCTTAAATGTTCAGAGTTTGGTGaa                                           <  1:2282279/43‑2 (MQ=37)
                                                        atggatggCGCTAAACTGCTGAAATGTTCAGAGtt                                                  >  1:3421879/1‑35 (MQ=255)
                                                         tggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                              >  1:3095976/1‑38 (MQ=255)
                                                          ggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTaa                      >  1:3973974/1‑61 (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)
                                                                   tAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTa               <  1:1538374/59‑1 (MQ=255)
                                                                    aaaCTGCTGAAATGTTCAGAGTTTGGTGACGCGatc                                     <  1:4422220/36‑1 (MQ=255)
                                                                    aaaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                        <  1:4946092/49‑1 (MQ=255)
                                                                    aaaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                        <  1:2501518/49‑1 (MQ=255)
                                                                     aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAg              >  1:4241989/1‑58 (MQ=255)
                                                                     aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAttt  <  1:539151/70‑1 (MQ=255)
                                                                     aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAttt  >  1:5093262/1‑70 (MQ=255)
                                                                     aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt   >  1:193289/1‑69 (MQ=255)
                                                                     aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt   <  1:281240/69‑1 (MQ=255)
                                                                      |                                                                    
AAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTT  >  Exported/775510‑775648

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