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 775,580 A→G 30.0% 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
*minE775,5800AG30.0% 115.9 / 59.1 123K401K (AAA→AAG) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base A (57/29);  new base G (17/20);  total (74/49)
Fisher's exact test for biased strand distribution p-value = 4.49e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 130 total aligned reads displayed.

GGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGT  >  minE/775512‑775634
                                                                    |                                                      
ggTATGGAAGGCGCAATCAACGCGAAAACTGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                        >  1:2001127/1‑69 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                        >  1:103650/1‑69 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                        >  1:293677/1‑69 (MQ=255)
      gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                        >  1:2552578/1‑63 (MQ=255)
      gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                                                   >  1:432009/1‑68 (MQ=255)
      gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                                                   >  1:2774260/1‑68 (MQ=255)
           cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAAt                                              >  1:166868/1‑68 (MQ=255)
           cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg                                             >  1:2528833/1‑69 (MQ=255)
           cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg                                             >  1:1975014/1‑69 (MQ=255)
            gcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg                                             >  1:3230096/1‑68 (MQ=255)
            gcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg                                             >  1:1159998/1‑68 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:617799/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:3222826/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:1428818/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:1431610/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:293957/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:2885405/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:2879782/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:1856523/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:2482237/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:2786476/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:571311/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:2681697/1‑69 (MQ=255)
                 cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga                                       >  1:663349/1‑69 (MQ=255)
                 cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga                                       >  1:2289865/1‑69 (MQ=255)
                 cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga                                       >  1:157687/1‑69 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAATGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:678165/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:2178148/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:2167968/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:649822/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:1134059/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:2662660/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:3386772/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:412918/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:307168/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:328662/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:1222316/66‑1 (MQ=255)
                  aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                      >  1:3304954/1‑69 (MQ=255)
                  aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                      >  1:1683526/1‑69 (MQ=255)
                  aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                      >  1:48945/1‑69 (MQ=255)
                  aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                      >  1:1719292/1‑69 (MQ=255)
                   atgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:2992589/66‑1 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:1165290/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:349641/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:1572673/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:458608/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:3202750/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:2468269/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:2330927/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:681535/1‑69 (MQ=255)
                        aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                <  1:1202619/69‑1 (MQ=255)
                        aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                <  1:1885426/69‑1 (MQ=255)
                        aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                <  1:1934197/69‑1 (MQ=255)
                        aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                <  1:2858904/69‑1 (MQ=255)
                         aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                <  1:496910/68‑1 (MQ=255)
                              gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                          <  1:1309409/69‑1 (MQ=255)
                                          ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa               <  1:761351/68‑1 (MQ=255)
                                          ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa               <  1:1072836/68‑1 (MQ=255)
                                          ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa               <  1:2697408/68‑1 (MQ=255)
                                          ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa               <  1:152698/68‑1 (MQ=255)
                                          ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa               <  1:2104128/68‑1 (MQ=255)
                                            cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa             >  1:1818368/1‑68 (MQ=255)
                                            cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa             >  1:1368037/1‑68 (MQ=255)
                                            cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa             >  1:104701/1‑68 (MQ=255)
                                            cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa             >  1:2135354/1‑68 (MQ=255)
                                            cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATAGAAAACa             >  1:586691/1‑68 (MQ=255)
                                              aGCGTCTGATGGATGGCGCTAAACT‑CTGAAATCTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:2737585/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:3096993/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:965042/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:2049888/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:1456762/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:2888772/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:1666042/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:1755709/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:1903743/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:2064121/68‑1 (MQ=255)
                                                cGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:75843/67‑1 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:855365/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:1303656/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:282178/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:2697353/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:2669303/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:1776108/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:1780087/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:2073004/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:1987695/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtca     >  1:1910976/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtca     >  1:1921171/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGATTggag                               >  1:2853218/1‑40 (MQ=25)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:2205448/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:98499/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:1265009/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:804584/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:3322973/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:2424204/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:1032596/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:506864/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:2836682/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:2938651/1‑69 (MQ=255)
                                                             gcgcTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          >  1:1316402/1‑54 (MQ=255)
                                                                    |                                                      
GGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGT  >  minE/775512‑775634

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