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 775,532 C→T 41.5% N385N (AAC→AAT)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported775,5320CT41.5% 85.9 / 134.8 123N385N (AAC→AAT) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base C (23/49);  new base T (32/19);  total (55/68)
Fisher's exact test for biased strand distribution p-value = 9.16e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.32e-01

Only 100 of 131 total aligned reads displayed.

GATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTT  >  Exported/775463‑775601
                                                                     |                                                                     
gatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAAcg                                                                      >  1:94836/1‑71 (MQ=255)
gatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAAcg                                                                      >  1:1165095/1‑71 (MQ=255)
 atgCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgc                                                                     >  1:1574736/1‑71 (MQ=255)
    ctgcGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaa                                                                  <  1:1203667/71‑1 (MQ=255)
       cgcCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaag                                                                 <  1:239143/69‑2 (MQ=255)
        gcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAAcc                                                              <  1:5537158/71‑1 (MQ=255)
         ccACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCg                                                             <  1:5590726/71‑1 (MQ=255)
           ataTGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgcc                                                                    <  1:1050245/60‑2 (MQ=255)
            taTGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgcc                                                                    <  1:285809/60‑2 (MQ=255)
            taTGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgcc                                                                    <  1:3320052/60‑2 (MQ=255)
            caTGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTaa                                                          >  1:487027/1‑71 (MQ=255)
              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                                                 <  1:561481/71‑1 (MQ=255)
                     gACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACt                                                 <  1:3039478/71‑1 (MQ=255)
                          aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                            >  1:5344229/1‑71 (MQ=255)
                          aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                            >  1:3040542/1‑71 (MQ=255)
                          aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                            >  1:5476851/1‑71 (MQ=255)
                          aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCg                                              <  1:4433530/69‑1 (MQ=255)
                          aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCg                                              <  1:334058/69‑1 (MQ=255)
                          aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCg                                              <  1:2036179/69‑1 (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                                                       <  1:909384/55‑1 (MQ=255)
                               gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                       <  1:3635917/71‑1 (MQ=255)
                               gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                       <  1:3725303/71‑1 (MQ=255)
                               gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                       <  1:3995916/71‑1 (MQ=255)
                               gCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCt                                       >  1:1036956/1‑71 (MQ=255)
                               gCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCt                                       <  1:5690598/71‑1 (MQ=255)
                                cTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGt                                                            <  1:5204902/49‑1 (MQ=25)
                                   aCTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                   >  1:3232674/1‑71 (MQ=255)
                                     ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                                                     <  1:5277416/51‑1 (MQ=255)
                                     ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                                                     <  1:1634366/51‑1 (MQ=255)
                                     ctgaTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgatgg                                  >  1:2006119/4‑70 (MQ=255)
                                      tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                              <  1:3817347/57‑1 (MQ=255)
                                      tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                              <  1:4156186/57‑1 (MQ=255)
                                       gaTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgatggaag                               >  1:2912439/2‑69 (MQ=255)
                                       aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                <  1:4781315/70‑1 (MQ=255)
                                       aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                <  1:5175587/70‑1 (MQ=255)
                                        aTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATg                                                    >  1:188082/1‑49 (MQ=25)
                                        aTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATg                                                    >  1:3750268/1‑49 (MQ=25)
                                        aTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgatggaa                                <  1:4079068/69‑2 (MQ=255)
                                        aTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggatg                               <  1:311700/70‑1 (MQ=255)
                                         ttGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                              <  1:4256673/70‑1 (MQ=255)
                                          tGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                 >  1:3630303/1‑66 (MQ=255)
                                           gTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGgcgc                           >  1:349504/1‑71 (MQ=255)
                                              aaaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTa                         <  1:3914945/70‑1 (MQ=255)
                                              aaaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTa                         <  1:536297/70‑1 (MQ=255)
                                               aaGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTaag                       >  1:5649732/1‑70 (MQ=255)
                                               aaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                       <  1:2884133/71‑1 (MQ=255)
                                                aGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTaa                        <  1:1162122/69‑1 (MQ=255)
                                                  ttATGCAAGGCGCAATCAACGCGAAAACCGAAACCTATGACTTCGa                                             >  1:670494/2‑46 (MQ=38)
                                                  gTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTc                                        <  1:3137538/51‑1 (MQ=255)
                                                  gTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActg                    >  1:210280/1‑71 (MQ=255)
                                                   tATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                             <  1:2077164/45‑1 (MQ=255)
                                                   tATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                             <  1:2508219/45‑1 (MQ=255)
                                                   tATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                             <  1:868828/45‑1 (MQ=255)
                                                    aTGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAgctgct                  >  1:1860602/1‑71 (MQ=255)
                                                     tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                             <  1:2561306/43‑1 (MQ=255)
                                                     tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                   <  1:1580396/53‑1 (MQ=255)
                                                       gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                   >  1:5521586/1‑35 (MQ=12)
                                                       gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                   >  1:1542456/1‑35 (MQ=12)
                                                       gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                   >  1:4330831/1‑35 (MQ=12)
                                                       gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc                                        >  1:1877086/1‑46 (MQ=21)
                                                       gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc                                        >  1:4726941/1‑46 (MQ=21)
                                                       gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTga                                     >  1:1332639/1‑49 (MQ=21)
                                                       gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTga                                     >  1:1332533/1‑49 (MQ=21)
                                                       gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTga                                     >  1:2877551/1‑49 (MQ=21)
                                                       gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa                >  1:1651041/1‑70 (MQ=255)
                                                       gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                              <  1:1430011/40‑1 (MQ=255)
                                                       gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                              <  1:2690109/40‑1 (MQ=255)
                                                       gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                 >  1:1494705/1‑53 (MQ=255)
                                                       gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                 >  1:1150515/1‑53 (MQ=255)
                                                       gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa               <  1:3147756/71‑1 (MQ=255)
                                                       gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                >  1:3780148/1‑70 (MQ=255)
                                                       gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                >  1:2422665/1‑70 (MQ=255)
                                                       gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGCATGGCGCTAAACTGCTGaa               <  1:1418655/71‑1 (MQ=255)
                                                        aaGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaaa              >  1:3417508/1‑71 (MQ=255)
                                                        aaGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa              >  1:4507738/1‑71 (MQ=255)
                                                           gcgcAATCAATGCCAAGACCGTAACTTATGACTTCGAACGt                                         <  1:1197820/41‑1 (MQ=12)
                                                              cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                       >  1:2774159/1‑56 (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)
                                                                     |                                                                     
GATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTT  >  Exported/775463‑775601

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