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
A6 F1 I0 R2 251 90.0 5200563 86.9% 4519289 59.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 775,580 A→G 8.8% K401K (AAA→AAG)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE775,5800AG 8.8% 226.3 / 10.5 79K401K (AAA→AAG) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base A (41/31);  new base G (4/3);  total (45/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

Only 100 of 102 total aligned reads displayed.

AAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATT  >  minE/775510‑775647
                                                                      |                                                                   
aaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                     <  1:681110/71‑1 (MQ=255)
aaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                     >  1:2830966/1‑71 (MQ=255)
aaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                     >  1:4691561/1‑71 (MQ=255)
aaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                     >  1:3765108/1‑71 (MQ=255)
      tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc                                                                    <  1:939983/66‑1 (MQ=255)
      tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc                                                                    <  1:933888/66‑1 (MQ=255)
      tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc                                                                    <  1:1772275/66‑1 (MQ=255)
        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                                                              >  1:989281/1‑70 (MQ=255)
        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                                                              >  1:4658591/1‑70 (MQ=255)
          aGGCGCAATCAACTCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                                                            <  1:4160267/70‑1 (MQ=255)
             cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                                                            >  1:2391016/1‑67 (MQ=255)
             cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                                                            >  1:1779641/1‑67 (MQ=255)
             cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                                                            >  1:1774478/1‑67 (MQ=255)
             cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaaa                                                            >  1:488470/1‑67 (MQ=255)
              gcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGtt                                                        >  1:2005204/1‑70 (MQ=255)
                  tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgctg                                                               >  1:1296442/1‑59 (MQ=255)
                  tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                                                             >  1:1932466/1‑61 (MQ=255)
                  tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                                   >  1:1525222/1‑71 (MQ=255)
                  tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                                   >  1:1519065/1‑71 (MQ=255)
                  tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                                   >  1:1008689/1‑71 (MQ=255)
                  tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                                   >  1:2974269/1‑71 (MQ=255)
                  tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                                   >  1:2968105/1‑71 (MQ=255)
                   cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                     >  1:4067391/1‑52 (MQ=255)
                   cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                     >  1:3421183/1‑52 (MQ=255)
                   cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                     >  1:4112656/1‑52 (MQ=255)
                   cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                     >  1:4116269/1‑52 (MQ=255)
                   cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                     >  1:3518763/1‑52 (MQ=255)
                   cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                     >  1:1581657/1‑52 (MQ=255)
                   cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGt                                                  >  1:3671804/1‑71 (MQ=255)
                    aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt                                                 <  1:4146556/71‑1 (MQ=255)
                    aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt                                                 <  1:2771650/71‑1 (MQ=255)
                        cgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                             <  1:1640628/71‑1 (MQ=255)
                        cgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                             <  1:4369187/71‑1 (MQ=255)
                        cgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                             <  1:1192956/71‑1 (MQ=255)
                         gAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                             <  1:175640/70‑1 (MQ=255)
                            aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                                                              <  1:4495973/50‑1 (MQ=255)
                            aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                                                              <  1:3804028/50‑1 (MQ=255)
                            aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                                                              <  1:1923476/50‑1 (MQ=255)
                            aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                                                              <  1:4542498/50‑1 (MQ=255)
                            aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                                                              <  1:2277545/50‑1 (MQ=255)
                              ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                                       <  1:2662816/71‑1 (MQ=255)
                               cGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGa                                      <  1:1492228/71‑1 (MQ=255)
                                 tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCag                                                     <  1:1264457/54‑1 (MQ=255)
                                 tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCag                                                     <  1:952432/54‑1 (MQ=255)
                                      tATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTg                                            >  1:2575260/1‑58 (MQ=255)
                                          aCTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAAc                           <  1:2220263/71‑1 (MQ=255)
                                           cTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                             <  1:2091709/52‑1 (MQ=255)
                                            ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAAc                           <  1:200760/69‑1 (MQ=255)
                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                            >  1:1036730/1‑66 (MQ=255)
                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                            >  1:4307537/1‑66 (MQ=255)
                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                            >  1:4670839/1‑66 (MQ=255)
                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                            >  1:615486/1‑66 (MQ=255)
                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                            >  1:920139/1‑66 (MQ=255)
                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                            >  1:3838587/1‑66 (MQ=255)
                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                            >  1:2324348/1‑66 (MQ=255)
                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTAAGAGTTTGGTGACGCGATCATCGaaaa                            >  1:702098/1‑66 (MQ=255)
                                               gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                       <  1:2675509/70‑1 (MQ=255)
                                               gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                       <  1:530199/70‑1 (MQ=255)
                                               gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                       <  1:234235/70‑1 (MQ=255)
                                               gAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGAGATCATCGAAAACATGt                       <  1:1174415/70‑1 (MQ=255)
                                                aGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt                       <  1:2489055/69‑1 (MQ=255)
                                                     cTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTgg                                              >  1:3645845/1‑41 (MQ=255)
                                                     cTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                                           >  1:3653056/1‑44 (MQ=255)
                                                     cTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                                           >  1:2289484/1‑44 (MQ=255)
                                                     cTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                                           >  1:1048013/1‑44 (MQ=255)
                                                     cTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                                           >  1:4473567/1‑44 (MQ=255)
                                                     cTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                                           >  1:4747777/1‑44 (MQ=255)
                                                     cTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                                           >  1:107080/1‑44 (MQ=255)
                                                     cTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGa                                           >  1:4438996/1‑44 (MQ=255)
                                                        atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat                                     >  1:2257935/1‑47 (MQ=255)
                                                        atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat                                     >  1:1189648/1‑47 (MQ=255)
                                                        atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat                                     >  1:3074056/1‑47 (MQ=255)
                                                          ggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGtt           >  1:4302522/1‑71 (MQ=255)
                                                          ggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGtt           >  1:4380685/1‑71 (MQ=255)
                                                          ggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGtt           >  1:2294506/1‑71 (MQ=255)
                                                          ggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGtt           >  1:1093829/1‑71 (MQ=255)
                                                          ggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGtt           >  1:3367555/1‑71 (MQ=255)
                                                          ggaaggCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaaaa                            <  1:3802820/54‑1 (MQ=255)
                                                          ggaaggCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaaaa                            <  1:3796755/54‑1 (MQ=255)
                                                           gatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGcc                 <  1:5063702/64‑1 (MQ=255)
                                                           gatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGcc                 <  1:4664684/64‑1 (MQ=255)
                                                            atggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGcc                 <  1:4066564/63‑1 (MQ=255)
                                                            aaggCGCTAAGCTTCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACa                          >  1:3348691/3‑54 (MQ=255)
                                                            aaggCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACa                          >  1:812079/3‑54 (MQ=255)
                                                            aaggCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACa                          >  1:4743693/3‑54 (MQ=255)
                                                            aaggCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACa                          >  1:3927844/3‑54 (MQ=255)
                                                               gcgcTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTa      <  1:3009855/71‑1 (MQ=255)
                                                                cgcTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaaaa                            <  1:2074765/48‑1 (MQ=39)
                                                                  cTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAt   >  1:4467167/1‑71 (MQ=255)
                                                                     aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt  >  1:4449925/1‑69 (MQ=255)
                                                                     aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt  <  1:4193328/69‑1 (MQ=255)
                                                                      aCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCCTCGaaa                             <  1:668113/41‑1 (MQ=255)
                                                                      aCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCCTCGaaa                             <  1:3557/41‑1 (MQ=255)
                                                                      aCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaa                             <  1:5092064/41‑1 (MQ=255)
                                                                      aCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaa                             <  1:4806127/41‑1 (MQ=255)
                                                                      aCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaa                             <  1:3043059/41‑1 (MQ=255)
                                                                      aCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaa                             <  1:1259462/41‑1 (MQ=255)
                                                                      aCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaa                             <  1:3154665/41‑1 (MQ=255)
                                                                      aCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaa                             <  1:3963061/41‑1 (MQ=255)
                                                                      aCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaa                             <  1:1595957/41‑1 (MQ=255)
                                                                      |                                                                   
AAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATT  >  minE/775510‑775647

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