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 775,535 G→C 41.5% A386A (GCG→GCC)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported775,5350GC41.5% 91.6 / 143.5 123A386A (GCG→GCC) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base G (23/49);  new base C (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 = 9.71e-01

Only 100 of 126 total aligned reads displayed.

CTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGT  >  Exported/775467‑775604
                                                                    |                                                                     
ctgcGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaa                                                                     <  1:1203667/71‑1 (MQ=255)
ctgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGaa                                                                     <  1:4835775/71‑1 (MQ=255)
ctgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGa                                                                      <  1:312725/70‑1 (MQ=255)
   cgcCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaag                                                                    <  1:239143/69‑2 (MQ=255)
    gcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAAcc                                                                 <  1:5537158/71‑1 (MQ=255)
     ccACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCg                                                                <  1:5590726/71‑1 (MQ=255)
          tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGAcc                                                                 >  1:5220178/1‑65 (MQ=255)
          tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGAcc                                                                 >  1:4222670/1‑65 (MQ=255)
           gggTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAAct                                                           >  1:2477880/1‑69 (MQ=255)
            ggTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAActt                                                          <  1:4593568/70‑3 (MQ=255)
            ggTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCt                                                          <  1:1793318/70‑1 (MQ=255)
             gTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTAt                                                        <  1:1446041/71‑1 (MQ=255)
             gTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                                                        <  1:2038393/71‑1 (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)
                    tgAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTc                                                  >  1:5559034/2‑70 (MQ=255)
                      aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                               >  1:5344229/1‑71 (MQ=255)
                      aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                               >  1:5476851/1‑71 (MQ=255)
                      aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCg                                                 <  1:4433530/69‑1 (MQ=255)
                      aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCg                                                 <  1:2036179/69‑1 (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)
                           gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCt                                                          <  1:295209/55‑1 (MQ=255)
                           gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                          <  1:3995916/71‑1 (MQ=255)
                           gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                          <  1:5212003/71‑1 (MQ=255)
                           gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                          <  1:3725303/71‑1 (MQ=255)
                           gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                          <  1:3635917/71‑1 (MQ=255)
                           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)
                                 ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                                                        <  1:1634366/51‑1 (MQ=255)
                                  tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                                 <  1:3817347/57‑1 (MQ=255)
                                  tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                                 <  1:4156186/57‑1 (MQ=255)
                                   gaTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgatggaag                                  >  1:2912439/2‑69 (MQ=255)
                                   aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                   <  1:5175587/70‑1 (MQ=255)
                                   aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                   <  1:4781315/70‑1 (MQ=255)
                                    aTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgatggaa                                   <  1:4079068/69‑2 (MQ=255)
                                    aTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                                                        <  1:1165710/48‑1 (MQ=255)
                                    aTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggatg                                  <  1:311700/70‑1 (MQ=255)
                                     ttGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                 <  1:4256673/70‑1 (MQ=255)
                                       gTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAAc                                                            >  1:2432984/1‑41 (MQ=25)
                                       gTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAAc                                                            >  1:5672166/1‑41 (MQ=25)
                                       gTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGgcgc                              >  1:349504/1‑71 (MQ=255)
                                        ttAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCt                             <  1:2876027/71‑1 (MQ=255)
                                          aaaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTa                            <  1:3914945/70‑1 (MQ=255)
                                          aaaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTa                            <  1:536297/70‑1 (MQ=255)
                                            aGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTaa                           <  1:1162122/69‑1 (MQ=255)
                                             ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGGCTGATGGATGGCGCTAAAct                        <  1:3408985/71‑1 (MQ=255)
                                              ttATGCAAGGCGCAATCAACGCGAAAACCGAAACCTATGACTTCGa                                                >  1:670494/2‑46 (MQ=38)
                                              gTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTc                                           <  1:3137538/51‑1 (MQ=255)
                                              gTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActg                       >  1:210280/1‑71 (MQ=255)
                                               tATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                                <  1:868828/45‑1 (MQ=255)
                                               tATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                                <  1:2077164/45‑1 (MQ=255)
                                               tATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                                <  1:2508219/45‑1 (MQ=255)
                                                aTGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAgctgct                     >  1:1860602/1‑71 (MQ=255)
                                                 tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                                <  1:2561306/43‑1 (MQ=255)
                                                 tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                      <  1:1580396/53‑1 (MQ=255)
                                                   gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                      >  1:3726986/1‑35 (MQ=12)
                                                   gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                      >  1:1970754/1‑35 (MQ=12)
                                                   gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                      >  1:4330831/1‑35 (MQ=12)
                                                   gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                      >  1:1542456/1‑35 (MQ=12)
                                                   gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc                                           >  1:791745/1‑46 (MQ=21)
                                                   gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc                                           >  1:1877086/1‑46 (MQ=21)
                                                   gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc                                           >  1:4726941/1‑46 (MQ=21)
                                                   gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTga                                        >  1:2877551/1‑49 (MQ=21)
                                                   gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTga                                        >  1:1332533/1‑49 (MQ=21)
                                                   gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTga                                        >  1:1332639/1‑49 (MQ=21)
                                                   gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaa                  <  1:3614765/71‑1 (MQ=255)
                                                   gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                                 <  1:2690109/40‑1 (MQ=255)
                                                   gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                                 <  1:1430011/40‑1 (MQ=255)
                                                   gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                    >  1:1494705/1‑53 (MQ=255)
                                                   gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                  <  1:2123342/71‑1 (MQ=255)
                                                   gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                   >  1:3780148/1‑70 (MQ=255)
                                                   gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGCATGGCGCTAAACTGCTGaa                  <  1:1418655/71‑1 (MQ=255)
                                                    aaGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                 >  1:4507738/1‑71 (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)
                                                          cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTATGATGGATGGCGCTAAACTTCTGAAATGTTCa           <  1:1612606/71‑1 (MQ=255)
                                                            aTCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                 >  1:1237810/1‑47 (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)
                                                                aCGGGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                          <  1:112212/50‑1 (MQ=255)
                                                                aCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                          <  1:1823507/50‑1 (MQ=255)
                                                                aCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGttt     <  1:2189580/71‑1 (MQ=255)
                                                                   cgAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                 >  1:577322/1‑40 (MQ=255)
                                                                   cgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt  <  1:2182948/71‑1 (MQ=255)
                                                                    |                                                                     
CTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGT  >  Exported/775467‑775604

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