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 775,559 G→A 40.1% E394E (GAG→GAA)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported775,5590GA40.1% 108.6 / 153.0 147E394E (GAG→GAA) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base G (37/51);  new base A (29/30);  total (66/81)
Fisher's exact test for biased strand distribution p-value = 4.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 150 total aligned reads displayed.

AAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTA  >  Exported/775489‑775627
                                                                      |                                                                    
aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                                                      >  1:3040542/1‑71 (MQ=255)
aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                                                      >  1:5476851/1‑71 (MQ=255)
 aGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGc                                                                     <  1:1003337/71‑1 (MQ=255)
  gCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACg                                                                    >  1:76223/1‑71 (MQ=255)
    ggCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc                                                                  >  1:1230933/1‑71 (MQ=255)
     gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                                 <  1:3995916/71‑1 (MQ=255)
     gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                                 <  1:5212003/71‑1 (MQ=255)
     gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                                 <  1:3725303/71‑1 (MQ=255)
     gCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCt                                                                 <  1:5690598/71‑1 (MQ=255)
         aCTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                                             >  1:3232674/1‑71 (MQ=255)
         aCTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                                             >  1:4622093/1‑71 (MQ=255)
           ctgaTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgatgg                                                            >  1:2006119/4‑70 (MQ=255)
             aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                                          <  1:5175587/70‑1 (MQ=255)
             aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                                          <  1:4781315/70‑1 (MQ=255)
              aTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgatggaa                                                          <  1:4079068/69‑2 (MQ=255)
              aTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggatg                                                         <  1:311700/70‑1 (MQ=255)
                tGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                                           >  1:3630303/1‑66 (MQ=255)
                    aaaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTa                                                   <  1:536297/70‑1 (MQ=255)
                    aaaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTa                                                   <  1:3914945/70‑1 (MQ=255)
                     aaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                 <  1:2884133/71‑1 (MQ=255)
                          aTGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAgctgct                                            >  1:1860602/1‑71 (MQ=255)
                           tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                                             <  1:1580396/53‑1 (MQ=255)
                             gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc                                                                  >  1:1877086/1‑46 (MQ=21)
                             gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc                                                                  >  1:4726941/1‑46 (MQ=21)
                             gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTga                                                               >  1:2877551/1‑49 (MQ=21)
                             gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTga                                                               >  1:1332639/1‑49 (MQ=21)
                             gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTga                                                               >  1:1332533/1‑49 (MQ=21)
                             gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaa                                         <  1:3614765/71‑1 (MQ=255)
                             gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa                                          >  1:1651041/1‑70 (MQ=255)
                             gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                                           >  1:1494705/1‑53 (MQ=255)
                             gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                                           >  1:1150515/1‑53 (MQ=255)
                             gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                                         <  1:3147756/71‑1 (MQ=255)
                             gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                                         <  1:2123342/71‑1 (MQ=255)
                             gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                                          >  1:1523257/1‑70 (MQ=255)
                              aaGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaaa                                        >  1:3417508/1‑71 (MQ=255)
                              aaGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                                        >  1:4507738/1‑71 (MQ=255)
                                ggCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaaa                                        >  1:4129865/1‑69 (MQ=255)
                                 gcgcAATCAATGCCAAGACCGTAACTTATGACTTCGAACGt                                                                   <  1:1197820/41‑1 (MQ=12)
                                  cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGtt                                    <  1:379986/71‑1 (MQ=255)
                                    cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                 >  1:2774159/1‑56 (MQ=255)
                                    cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTa                                                   <  1:5410040/54‑1 (MQ=255)
                                    cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGtt                                    >  1:2122522/1‑69 (MQ=255)
                                       tCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGgcg                                                      <  1:3514670/48‑1 (MQ=16)
                                       tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGtt                                    <  1:2951441/66‑1 (MQ=255)
                                       tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                               >  1:1999120/1‑71 (MQ=255)
                                         aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTa                                                   <  1:3365003/49‑1 (MQ=255)
                                         aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAgtgt                              <  1:1036445/70‑1 (MQ=255)
                                          aCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGttt                            <  1:2189580/71‑1 (MQ=255)
                                             cgAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                                        >  1:577322/1‑40 (MQ=255)
                                             cgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                         <  1:2182948/71‑1 (MQ=255)
                                              gAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                         >  1:758211/1‑70 (MQ=255)
                                               aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCag                                 >  1:3383367/4‑61 (MQ=255)
                                               aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTg                        >  1:4825945/4‑70 (MQ=255)
                                               aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGa                       <  1:668343/68‑1 (MQ=255)
                                               aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGa                       <  1:3300178/68‑1 (MQ=255)
                                               aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGa                       <  1:3293415/68‑1 (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)
                                                  aCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                         <  1:4540412/66‑1 (MQ=255)
                                                   ccGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagcg                   <  1:917785/71‑1 (MQ=255)
                                                   ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgc                    >  1:2939731/1‑70 (MQ=255)
                                                    cGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                       >  1:41491/1‑66 (MQ=255)
                                                    cGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                       >  1:4844237/1‑66 (MQ=255)
                                                     gTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGat                 <  1:2866702/71‑1 (MQ=255)
                                                     gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTg                        >  1:1147991/1‑64 (MQ=255)
                                                     gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat                 <  1:5216023/71‑1 (MQ=255)
                                                     gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat                 <  1:808205/71‑1 (MQ=255)
                                                      tAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGat                 >  1:1113823/1‑70 (MQ=255)
                                                      tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                       >  1:4331059/1‑64 (MQ=255)
                                                      tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                       >  1:2508949/1‑64 (MQ=255)
                                                      tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatc                <  1:4950922/71‑1 (MQ=255)
                                                       aaCTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGatca               >  1:3448444/1‑71 (MQ=255)
                                                       aaCTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGatca               >  1:4187107/1‑71 (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)
                                                             tGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaa          <  1:3684003/70‑1 (MQ=255)
                                                             tGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaa          <  1:5304580/70‑1 (MQ=255)
                                                               aCTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                       >  1:1053756/1‑55 (MQ=255)
                                                                cTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                         <  1:5495997/52‑1 (MQ=255)
                                                                 ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGttt                            <  1:2818027/48‑1 (MQ=255)
                                                                 ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGttt                            <  1:3940177/48‑1 (MQ=255)
                                                                 ttCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaaaa        <  1:4308074/68‑1 (MQ=255)
                                                                  tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGttt                            <  1:2690855/47‑1 (MQ=38)
                                                                  tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGttt                            <  1:2511959/47‑1 (MQ=38)
                                                                  tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                             <  1:5483609/46‑1 (MQ=38)
                                                                  tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                             <  1:176410/46‑1 (MQ=38)
                                                                  tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                             <  1:1550097/46‑1 (MQ=38)
                                                                  tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                             <  1:3824699/46‑1 (MQ=38)
                                                                  tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                             <  1:4886163/46‑1 (MQ=38)
                                                                   cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaa         >  1:2665221/1‑65 (MQ=255)
                                                                   cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATg    >  1:2732202/1‑70 (MQ=255)
                                                                   cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACa      >  1:5101980/1‑68 (MQ=255)
                                                                    gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt   <  1:5091881/70‑1 (MQ=255)
                                                                    gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt   <  1:826627/70‑1 (MQ=255)
                                                                    gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt   <  1:5572578/70‑1 (MQ=255)
                                                                      |                                                                    
AAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTA  >  Exported/775489‑775627

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