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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 775,559 G→A 56.9% E394E (GAG→GAA)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE775,5590GA56.9% 31.8 / 91.0 116E394E (GAG→GAA) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base G (28/22);  new base A (46/20);  total (74/42)
Fisher's exact test for biased strand distribution p-value = 1.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 129 total aligned reads displayed.

GCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGT  >  minE/775494‑775626
                                                                 |                                                                   
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAGTCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:1396900/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACg                                                                   >  1:1390632/1‑68 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACg                                                                   >  1:3039768/1‑68 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:905341/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:2132907/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:2186227/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:1397277/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:2329954/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:132555/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:2398648/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:2425631/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:2963093/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:3228760/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:3321646/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:1111701/1‑69 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                                                  >  1:360874/1‑69 (MQ=255)
                  ggTATGGAAGGCGCAATCAACGCGAAAACTGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                >  1:2001127/1‑69 (MQ=255)
                  ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                >  1:2992324/1‑69 (MQ=255)
                  ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                >  1:342781/1‑69 (MQ=255)
                  ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                >  1:103650/1‑69 (MQ=255)
                  ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                >  1:2089885/1‑69 (MQ=255)
                  ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                                                 <  1:1600196/68‑1 (MQ=255)
                  ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                                                 <  1:1002253/68‑1 (MQ=255)
                  ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                                                 <  1:413514/68‑1 (MQ=255)
                        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                >  1:2552578/1‑63 (MQ=255)
                        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                                                 <  1:251616/62‑1 (MQ=255)
                        gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                                           >  1:432009/1‑68 (MQ=255)
                             cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg                                     >  1:2528833/1‑69 (MQ=255)
                              gcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg                                     >  1:1159998/1‑68 (MQ=255)
                              gcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg                                     >  1:2859510/1‑68 (MQ=255)
                              gcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg                                     >  1:3230096/1‑68 (MQ=255)
                                  tCAACGCGAAGACCGTAACCTATGACTTCGAACTTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                >  1:817912/1‑69 (MQ=255)
                                  tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                >  1:1749670/1‑69 (MQ=255)
                                  tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                >  1:2885405/1‑69 (MQ=255)
                                  tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                >  1:1856523/1‑69 (MQ=255)
                                  tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                >  1:2786476/1‑69 (MQ=255)
                                  tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                >  1:2681697/1‑69 (MQ=255)
                                  tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                >  1:293957/1‑69 (MQ=255)
                                  tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                >  1:617799/1‑69 (MQ=255)
                                  tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                >  1:571311/1‑69 (MQ=255)
                                  tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                >  1:3222826/1‑69 (MQ=255)
                                  tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                >  1:1431610/1‑69 (MQ=255)
                                  tCAACCCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTa                                                  >  1:418862/1‑51 (MQ=255)
                                   cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga                               >  1:2289865/1‑69 (MQ=255)
                                   cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga                               >  1:663349/1‑69 (MQ=255)
                                   cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga                               >  1:157687/1‑69 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAATGCGCTAAGCTGCTGAAATGTTCagag                              <  1:678165/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:2167968/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:307168/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:1222316/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:649822/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:3299891/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:1945265/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:2662660/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:2021907/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:2178148/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:2333005/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:3386772/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:1134059/66‑1 (MQ=255)
                                    aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:61971/66‑1 (MQ=255)
                                    aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                              >  1:3304954/1‑69 (MQ=255)
                                    aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                              >  1:48945/1‑69 (MQ=255)
                                    aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                              >  1:1719292/1‑69 (MQ=255)
                                    aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                              >  1:1683526/1‑69 (MQ=255)
                                     atgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:2895741/66‑1 (MQ=255)
                                      cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTaa                                                 >  1:715857/1‑48 (MQ=38)
                                      cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                            >  1:349641/1‑69 (MQ=255)
                                      cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                            >  1:458608/1‑69 (MQ=255)
                                      cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                            >  1:681535/1‑69 (MQ=255)
                                      cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                            >  1:2806041/1‑69 (MQ=255)
                                      cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                            >  1:3202750/1‑69 (MQ=255)
                                      cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                            >  1:2468269/1‑69 (MQ=255)
                                      cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                            >  1:2330927/1‑69 (MQ=255)
                                          aagaCCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                              <  1:16376/60‑1 (MQ=255)
                                          aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                        <  1:1885426/69‑1 (MQ=255)
                                          aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                        <  1:1202619/69‑1 (MQ=255)
                                          aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                        <  1:2858904/69‑1 (MQ=255)
                                          aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                        <  1:1934197/69‑1 (MQ=255)
                                          aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                        <  1:1287802/69‑1 (MQ=255)
                                           aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                        <  1:496910/68‑1 (MQ=255)
                                                gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                  <  1:1309409/69‑1 (MQ=255)
                                                            ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa       <  1:2697408/68‑1 (MQ=255)
                                                            ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa       <  1:1072836/68‑1 (MQ=255)
                                                            ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa       <  1:152698/68‑1 (MQ=255)
                                                            ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa       <  1:2104128/68‑1 (MQ=255)
                                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa     >  1:104701/1‑68 (MQ=255)
                                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa     >  1:1818368/1‑68 (MQ=255)
                                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa     >  1:2135354/1‑68 (MQ=255)
                                                              cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa     >  1:1368037/1‑68 (MQ=255)
                                                                aGCGTCTGATGGATGGCGCTAAACT‑CTGAAATCTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt  <  1:2737585/68‑1 (MQ=255)
                                                                 gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt  <  1:1666042/68‑1 (MQ=255)
                                                                 gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt  <  1:1809346/68‑1 (MQ=255)
                                                                 gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt  <  1:1404555/68‑1 (MQ=255)
                                                                 gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt  <  1:965042/68‑1 (MQ=255)
                                                                 gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt  <  1:1903743/68‑1 (MQ=255)
                                                                 gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt  <  1:2049888/68‑1 (MQ=255)
                                                                 gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt  <  1:1456762/68‑1 (MQ=255)
                                                                 gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt  <  1:3096993/68‑1 (MQ=255)
                                                                 gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt  <  1:2888772/68‑1 (MQ=255)
                                                                 gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt  <  1:1196288/68‑1 (MQ=255)
                                                                 |                                                                   
GCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGT  >  minE/775494‑775626

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