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 775,547 C→T 38.6% T390T (ACC→ACT)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported775,5470CT38.6% 125.4 / 139.3 140T390T (ACC→ACT) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base C (34/52);  new base T (34/20);  total (68/72)
Fisher's exact test for biased strand distribution p-value = 9.11e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 143 total aligned reads displayed.

GGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATC  >  Exported/775478‑775616
                                                                     |                                                                     
gggTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAcc                                                                       >  1:3917995/1‑70 (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)
     ggACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGAc                                                                 >  1:4050037/1‑71 (MQ=255)
      gACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACt                                                                <  1:3039478/71‑1 (MQ=255)
      gACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACt                                                                <  1:561481/71‑1 (MQ=255)
        ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                              <  1:1391276/71‑1 (MQ=255)
           aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                                           >  1:5476851/1‑71 (MQ=255)
           aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                                           >  1:5344229/1‑71 (MQ=255)
           aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                                           >  1:3040542/1‑71 (MQ=255)
           aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCg                                                             <  1:334058/69‑1 (MQ=255)
            aGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGc                                                          <  1:1003337/71‑1 (MQ=255)
             gCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACg                                                         >  1:76223/1‑71 (MQ=255)
               ggCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                                                                    <  1:1292216/58‑1 (MQ=255)
               ggCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc                                                       >  1:1230933/1‑71 (MQ=255)
                gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCt                                                                      <  1:909384/55‑1 (MQ=255)
                gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                      <  1:3725303/71‑1 (MQ=255)
                gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                      <  1:3995916/71‑1 (MQ=255)
                gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                      <  1:5212003/71‑1 (MQ=255)
                gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                      <  1:3635917/71‑1 (MQ=255)
                gCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCt                                                      >  1:1036956/1‑71 (MQ=255)
                      ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                                                                    <  1:1634366/51‑1 (MQ=255)
                      ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                                                                    <  1:5277416/51‑1 (MQ=255)
                      ctgaTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgatgg                                                 >  1:2006119/4‑70 (MQ=255)
                       tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                                             <  1:4156186/57‑1 (MQ=255)
                       tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                                             <  1:3817347/57‑1 (MQ=255)
                        aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                               <  1:5175587/70‑1 (MQ=255)
                        aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                               <  1:4781315/70‑1 (MQ=255)
                         aTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATg                                                                   >  1:3750268/1‑49 (MQ=25)
                         aTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATg                                                                   >  1:188082/1‑49 (MQ=25)
                         aTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                                                                    <  1:1165710/48‑1 (MQ=255)
                          ttGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                             <  1:4256673/70‑1 (MQ=255)
                           tGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                                >  1:3630303/1‑66 (MQ=255)
                            gTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGgcgc                                          >  1:349504/1‑71 (MQ=255)
                               aaaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTa                                        <  1:536297/70‑1 (MQ=255)
                               aaaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTa                                        <  1:3914945/70‑1 (MQ=255)
                                aaGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTaag                                      >  1:5649732/1‑70 (MQ=255)
                                aaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                      <  1:2884133/71‑1 (MQ=255)
                                 aGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTaa                                       <  1:1162122/69‑1 (MQ=255)
                                   gTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTc                                                       <  1:3137538/51‑1 (MQ=255)
                                    tATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                                            <  1:868828/45‑1 (MQ=255)
                                    tATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                                            <  1:2508219/45‑1 (MQ=255)
                                    tATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                                            <  1:2077164/45‑1 (MQ=255)
                                      tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                                            <  1:2561306/43‑1 (MQ=255)
                                        gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                                  >  1:3726986/1‑35 (MQ=12)
                                        gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                                  >  1:1542456/1‑35 (MQ=12)
                                        gAAGGCGCAATCAATGCCAAGACCGTAACTTATGa                                                                  >  1:5521586/1‑35 (MQ=12)
                                        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)
                                        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                                             <  1:1430011/40‑1 (MQ=255)
                                        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                              <  1:3147756/71‑1 (MQ=255)
                                        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                              <  1:2123342/71‑1 (MQ=255)
                                        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                               >  1:2422665/1‑70 (MQ=255)
                                        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                               >  1:2611725/1‑70 (MQ=255)
                                        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                               >  1:1523257/1‑70 (MQ=255)
                                        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                               >  1:3780148/1‑70 (MQ=255)
                                         aaGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaaa                             >  1:3417508/1‑71 (MQ=255)
                                         aaGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                             >  1:4507738/1‑71 (MQ=255)
                                           ggCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaaa                             >  1:4129865/1‑69 (MQ=255)
                                               cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                      >  1:2774159/1‑56 (MQ=255)
                                               cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGtt                         >  1:2122522/1‑69 (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)
                                                  tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                    >  1:437349/1‑71 (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)
                                                        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             >  1:1538154/4‑70 (MQ=255)
                                                          aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGa            <  1:3293415/68‑1 (MQ=255)
                                                          aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGa            <  1:668343/68‑1 (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)
                                                              ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgc         >  1:4789614/1‑70 (MQ=255)
                                                               cGTAACCTATGACTTCGAGCGTCTGATGGATGgcgc                                          <  1:3263534/36‑1 (MQ=255)
                                                               cGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa            >  1:4844237/1‑66 (MQ=255)
                                                                gTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGat      <  1:2866702/71‑1 (MQ=255)
                                                                gTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGat      <  1:1918057/71‑1 (MQ=255)
                                                                gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTg             >  1:1147991/1‑64 (MQ=255)
                                                                gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat      <  1:808205/71‑1 (MQ=255)
                                                                 tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa            >  1:4331059/1‑64 (MQ=255)
                                                                 tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat      >  1:4107747/1‑70 (MQ=255)
                                                                  aaCTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGatca    >  1:4187107/1‑71 (MQ=255)
                                                                  aaCCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTc                        >  1:269890/1‑51 (MQ=255)
                                                                     cTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatcatc  >  1:3039223/1‑70 (MQ=255)
                                                                     |                                                                     
GGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATC  >  Exported/775478‑775616

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