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 775,538 A→G 39.7% K387K (AAA→AAG)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported775,5380AG39.7% 94.3 / 128.7 121K387K (AAA→AAG) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base A (25/48);  new base G (31/17);  total (56/65)
Fisher's exact test for biased strand distribution p-value = 1.47e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01

Only 100 of 123 total aligned reads displayed.

GCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAC  >  Exported/775471‑775607
                                                                   |                                                                     
gcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAAcc                                                                    <  1:5537158/71‑1 (MQ=255)
 ccACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCg                                                                   <  1:5590726/71‑1 (MQ=255)
    caTGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTaa                                                                >  1:487027/1‑71 (MQ=255)
      tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGAcc                                                                    >  1:5220178/1‑65 (MQ=255)
      tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGAcc                                                                    >  1:4222670/1‑65 (MQ=255)
       gggTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAcc                                                              >  1:3917995/1‑70 (MQ=255)
        ggTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAActt                                                             <  1:4593568/70‑3 (MQ=255)
        ggTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCt                                                             <  1:1793318/70‑1 (MQ=255)
         gTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                                                           <  1:2038393/71‑1 (MQ=255)
            ggACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGAc                                                        >  1:4050037/1‑71 (MQ=255)
             gACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACt                                                       <  1:3039478/71‑1 (MQ=255)
               ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                     <  1:1391276/71‑1 (MQ=255)
                tgAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTc                                                     >  1:5559034/2‑70 (MQ=255)
                  aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                                  >  1:3040542/1‑71 (MQ=255)
                  aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                                  >  1:5476851/1‑71 (MQ=255)
                  aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                                  >  1:5344229/1‑71 (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)
                      ggCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGt                                                                  <  1:4635065/51‑1 (MQ=25)
                      ggCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc                                              >  1:1230933/1‑71 (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                                         >  1:4622093/1‑71 (MQ=255)
                           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)
                               gaTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgatggaag                                     >  1:2912439/2‑69 (MQ=255)
                               aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                      <  1:5175587/70‑1 (MQ=255)
                                aTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATg                                                          >  1:188082/1‑49 (MQ=25)
                                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)
                                  tGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                       >  1:3630303/1‑66 (MQ=255)
                                   gTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAAc                                                               >  1:2432984/1‑41 (MQ=25)
                                   gTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAAc                                                               >  1:5672166/1‑41 (MQ=25)
                                   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)
                                         ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGGCTGATGGATGGCGCTAAAct                           <  1:3408985/71‑1 (MQ=255)
                                          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)
                                             tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                                   <  1:2561306/43‑1 (MQ=255)
                                             tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                         <  1:1580396/53‑1 (MQ=255)
                                               gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                         >  1:1542456/1‑35 (MQ=12)
                                               gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                         >  1:4330831/1‑35 (MQ=12)
                                               gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                         >  1:1970754/1‑35 (MQ=12)
                                               gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                         >  1:3726986/1‑35 (MQ=12)
                                               gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                         >  1:5521586/1‑35 (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                                           >  1:1332639/1‑49 (MQ=21)
                                               gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTga                                           >  1:1332533/1‑49 (MQ=21)
                                               gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaa                     <  1:3614765/71‑1 (MQ=255)
                                               gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa                      >  1:1651041/1‑70 (MQ=255)
                                               gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                                    <  1:2690109/40‑1 (MQ=255)
                                               gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                                    <  1:1430011/40‑1 (MQ=255)
                                               gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                       >  1:1150515/1‑53 (MQ=255)
                                               gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                       >  1:1494705/1‑53 (MQ=255)
                                               gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                      >  1:1523257/1‑70 (MQ=255)
                                               gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                      >  1:2422665/1‑70 (MQ=255)
                                               gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                      >  1:2611725/1‑70 (MQ=255)
                                               gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                      >  1:3780148/1‑70 (MQ=255)
                                               gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGCATGGCGCTAAACTGCTGaa                     <  1:1418655/71‑1 (MQ=255)
                                                aaGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaaa                    >  1:3417508/1‑71 (MQ=255)
                                                aaGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                    >  1:4507738/1‑71 (MQ=255)
                                                  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)
                                                      cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGtt                >  1:2122522/1‑69 (MQ=255)
                                                        aTCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                    >  1:1237810/1‑47 (MQ=255)
                                                         tCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGgcg                                  <  1:3514670/48‑1 (MQ=16)
                                                         tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGtt                <  1:2951441/66‑1 (MQ=255)
                                                         tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag           >  1:437349/1‑71 (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)
                                                                gAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt     >  1:758211/1‑70 (MQ=255)
                                                                  aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAc  >  1:4910777/1‑71 (MQ=255)
                                                                   aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                    >  1:3692746/1‑52 (MQ=255)
                                                                   |                                                                     
GCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAC  >  Exported/775471‑775607

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