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 775,571 T→A 43.1% D398E (GAT→GAA)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported775,5710TA43.1% 58.7 / 180.9 137D398E (GAT→GAA) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base T (31/47);  new base A (21/38);  total (52/85)
Fisher's exact test for biased strand distribution p-value = 7.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.59e-01

Only 100 of 165 total aligned reads displayed.

AATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCG  >  Exported/775502‑775633
                                                                     |                                                              
aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                                                <  1:4781315/70‑1 (MQ=255)
aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                                                <  1:5175587/70‑1 (MQ=255)
 aTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggatg                                                               <  1:311700/70‑1 (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)
             aTGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAgctgct                                                  >  1:1860602/1‑71 (MQ=255)
                gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa                                                >  1:1651041/1‑70 (MQ=255)
                gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                                               <  1:3147756/71‑1 (MQ=255)
                gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                                                >  1:2422665/1‑70 (MQ=255)
                gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGCATGGCGCTAAACTGCTGaa                                               <  1:1418655/71‑1 (MQ=255)
                     cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGtt                                          <  1:379986/71‑1 (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                                     >  1:437349/1‑71 (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)
                                cgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                               <  1:2182948/71‑1 (MQ=255)
                                  aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTg                              >  1:1538154/4‑70 (MQ=255)
                                  aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGa                             <  1:3293415/68‑1 (MQ=255)
                                  aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGa                             <  1:3300178/68‑1 (MQ=255)
                                   agaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa                                                >  1:3718769/3‑51 (MQ=255)
                                   agaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa                                                >  1:640260/3‑51 (MQ=255)
                                    aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                                              >  1:3692746/1‑52 (MQ=255)
                                      ccGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagcg                         <  1:917785/71‑1 (MQ=255)
                                      ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgc                          >  1:4789614/1‑70 (MQ=255)
                                       cGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                             >  1:4844237/1‑66 (MQ=255)
                                       cGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                             >  1:41491/1‑66 (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)
                                         tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatc                      <  1:4950922/71‑1 (MQ=255)
                                         tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat                       >  1:4107747/1‑70 (MQ=255)
                                          aaCTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGatca                     >  1:4187107/1‑71 (MQ=255)
                                           acttATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGatcat                    >  1:4867709/4‑71 (MQ=255)
                                             ttATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagcg                         <  1:4209301/63‑1 (MQ=255)
                                              tATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCg                  >  1:716730/1‑70 (MQ=255)
                                               aTGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGa                 >  1:4506782/1‑70 (MQ=255)
                                               aTGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGa                 >  1:4982221/1‑70 (MQ=255)
                                               aTGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGa                 <  1:612903/70‑1 (MQ=255)
                                               aTGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGa                 >  1:4938828/1‑70 (MQ=255)
                                                tGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaa                <  1:5304580/70‑1 (MQ=255)
                                                tGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaa                <  1:3684003/70‑1 (MQ=255)
                                                  aCTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                             >  1:1053756/1‑55 (MQ=255)
                                                   cTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                               <  1:4529868/52‑1 (MQ=255)
                                                   cTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                               <  1:5495997/52‑1 (MQ=255)
                                                    ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGttt                                  <  1:3940177/48‑1 (MQ=255)
                                                    ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGttt                                  <  1:3593329/48‑1 (MQ=255)
                                                    ttCGAACGTCTGATGGAAGGCTCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaaaa              <  1:838483/68‑1 (MQ=255)
                                                    ttCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaaaa              <  1:5492544/68‑1 (MQ=255)
                                                    ttCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaaaa              <  1:4308074/68‑1 (MQ=255)
                                                     tCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                             >  1:391449/1‑52 (MQ=255)
                                                     tCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                         <  1:2784171/56‑1 (MQ=255)
                                                     tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGttt                                  <  1:2511959/47‑1 (MQ=38)
                                                     tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGttt                                  <  1:2690855/47‑1 (MQ=38)
                                                     tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                                   <  1:4886163/46‑1 (MQ=38)
                                                     tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                                   <  1:176410/46‑1 (MQ=38)
                                                     tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                                   <  1:1550097/46‑1 (MQ=38)
                                                     tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGtt                                   <  1:3824699/46‑1 (MQ=38)
                                                      cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaa               >  1:2665221/1‑65 (MQ=255)
                                                      cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATg          >  1:2732202/1‑70 (MQ=255)
                                                      cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGa                             >  1:5459182/1‑51 (MQ=255)
                                                      cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGa                 <  1:5070083/63‑1 (MQ=255)
                                                      cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACa            >  1:5101980/1‑68 (MQ=255)
                                                       gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGt         <  1:2152004/67‑1 (MQ=255)
                                                       gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGt         <  1:821401/67‑1 (MQ=255)
                                                       gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGt         <  1:3918859/67‑1 (MQ=255)
                                                       gaacGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTa        <  1:3284446/68‑1 (MQ=255)
                                                       gAGCGTCTGATGGATGGCGCTAAACTCCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt         <  1:5111052/70‑1 (MQ=255)
                                                            tCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt                                   <  1:4693766/39‑1 (MQ=255)
                                                            tCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                         <  1:3225806/49‑1 (MQ=255)
                                                            tCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                <  1:84957/58‑1 (MQ=255)
                                                            tCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATg          <  1:3378872/64‑1 (MQ=255)
                                                              tGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                <  1:539490/56‑1 (MQ=255)
                                                              tGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCg  >  1:2912800/1‑70 (MQ=255)
                                                              tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGTTGAAGCGatca                     <  1:453510/51‑1 (MQ=255)
                                                               gatggatgGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCg  >  1:2096488/1‑69 (MQ=255)
                                                               gatggaagGCGCTAAGCTGCTTAAATGTTCAGAGTTTGGTGaa                            <  1:2282279/43‑2 (MQ=37)
                                                               gatggaagGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGaa                            <  1:3245968/43‑2 (MQ=38)
                                                                atggatggCGCTAAACTGCTGAAATGTTCAGAGtt                                   >  1:3421879/1‑35 (MQ=255)
                                                                atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt         <  1:1355639/61‑1 (MQ=255)
                                                                atggaaggCGCTAAGCTGCTGAAATGTTCAGAGTTTg                                 >  1:2153878/1‑37 (MQ=37)
                                                                 tggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                               >  1:3423067/1‑38 (MQ=255)
                                                                 tggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                               >  1:3095976/1‑38 (MQ=255)
                                                                 tggaaggCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagc                          >  1:2191942/1‑43 (MQ=37)
                                                                   gatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                               <  1:4131663/36‑1 (MQ=255)
                                                                   gatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                               <  1:841309/36‑1 (MQ=255)
                                                                   gatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa              >  1:349245/1‑53 (MQ=255)
                                                                   gatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACAt           >  1:3560578/1‑56 (MQ=255)
                                                                   gatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACAt           >  1:4335646/1‑56 (MQ=255)
                                                                     |                                                              
AATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCG  >  Exported/775502‑775633

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