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 F3 I0 R1 328 90.1 2317887 85.2% 1974839 62.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,984,500 T→C 100% T11T (ACT→ACC)  creD → inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,984,5000TC89.5% 262.2 / 16.6 95T11T (ACT→ACC) creDinner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (10/0);  new base C (85/0);  total (95/0)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.28e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGA  >  minE/2984444‑2984546
                                                        |                                              
gctgcCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTg                                      >  1:287392/1‑67 (MQ=255)
gctgcCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTg                                      >  1:408954/1‑67 (MQ=255)
gctgcCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTg                                      >  1:654186/1‑67 (MQ=255)
gctgcCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTg                                      >  1:1198352/1‑67 (MQ=255)
gctgcCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTg                                      >  1:855236/1‑67 (MQ=255)
                        aTGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGAtt               >  1:1077131/1‑66 (MQ=255)
                        aTGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGAtt               >  1:604321/1‑66 (MQ=255)
                        aTGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGAtt               >  1:1046985/1‑66 (MQ=255)
                        aTGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGAtt               >  1:63742/1‑66 (MQ=255)
                        aTGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGAtt               >  1:1027882/1‑66 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTAt                             >  1:1122589/1‑40 (MQ=37)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGa           >  1:1189216/1‑58 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:452676/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:496583/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:499225/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:418495/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:412020/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:411607/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:2246424/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:388144/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:380704/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:380472/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:360575/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:333248/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:330720/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:324375/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:301208/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:251884/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:2262987/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:97621/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:720119/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1026069/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:944546/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:920905/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:826598/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:814306/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:794958/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:789821/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:789612/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:748992/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:521424/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:699557/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:679782/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:662636/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:647129/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:626253/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:617635/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:560393/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:543345/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:527021/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1307707/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:2225833/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1561600/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1516374/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1487608/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1484995/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1439923/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1404880/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1362284/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1325830/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1308178/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1567041/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1255410/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1250423/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1242243/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1241305/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1220595/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1195419/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1178370/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1104341/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1066364/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1044880/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1867864/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:2215155/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:2212030/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:2097916/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:2091140/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:2015975/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:197555/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1948983/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1935602/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1577508/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1857510/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1780710/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1772974/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1753414/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1654738/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1607376/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:160547/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATCGCTGTTGTTGATTCCGATAATGCTGa  >  1:48574/1‑67 (MQ=255)
                                    ccccTGTTCTGGAAAATGACCACCTTGTTTGGTGAAGTATTGCTGTTGTTGATTCCGATAATGCTg   >  1:1524250/1‑66 (MQ=255)
                                    ccccTGTTATGGAAAATGACCACCTTGTTTGGTGCAGTAtt                            >  1:2006716/1‑41 (MQ=255)
                                    ccccTGTTATGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAAt       >  1:1048511/1‑62 (MQ=255)
                                    ccccTGTACTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:1658256/1‑67 (MQ=255)
                                    ccccAGTTCTGGAAAATGACCACCTTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGa  >  1:297654/1‑67 (MQ=255)
                                                        |                                              
GCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGA  >  minE/2984444‑2984546

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A