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 2,661,110 T→C 100% D207D (GAT→GAC)  glpR → DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,661,1100TC76.5% 214.0 / 65.3 115D207D (GAT→GAC) glpRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base T (26/1);  new base C (88/0);  total (114/1)
Fisher's exact test for biased strand distribution p-value = 2.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

Only 100 of 115 total aligned reads displayed.

GTTCGCACCAAACGCGCCATTATTGAGAACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGTAACGCGATGGTCAATATGGGCAGCATCAGCATGGTAGATG  >  minE/2661054‑2661168
                                                        |                                                          
                          taaCTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:2209828/2‑49 (MQ=255)
                          gaACTCGCGCCATGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:429276/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCTATCACTCGAAATTTGGCCGt                                          >  1:1383719/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGaa                                                    >  1:242387/1‑39 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCg                                           >  1:1528494/1‑48 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1865079/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1048492/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1387610/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1395354/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:155567/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1584603/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1657126/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:492625/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:2247335/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:2131262/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1892240/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:191380/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1944919/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1947643/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1954311/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:2043860/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:2306208/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:89788/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1383250/1‑49 (MQ=255)
                          gaACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGt                                          >  1:1263265/1‑49 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGtagcatc               >  1:169055/1‑54 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCTGCATGGTCGATg  >  1:280877/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGtc      >  1:948121/1‑62 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGAt   >  1:375983/1‑66 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGAt   >  1:1354203/1‑66 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGAt   >  1:1342068/1‑66 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGAt   >  1:943124/1‑66 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGAt   >  1:1641981/1‑66 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:263090/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:904458/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:908774/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:925095/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:336613/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:300699/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:389548/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:931987/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:2312347/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:2295187/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:958313/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1019846/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:982557/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:34601/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:866146/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:865752/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:438303/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:842183/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:498315/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:508465/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:76828/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:517650/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:58251/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:597195/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:726649/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:60934/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:609823/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:711740/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:691464/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1230995/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:2197354/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1437466/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1425749/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1379582/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1357511/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1318392/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1310242/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1281820/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1238369/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1617803/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1219408/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:117470/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1165194/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1132096/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1112899/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1087773/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1084825/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1075223/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1908584/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:2123199/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:2122868/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:2121138/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:2076648/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:201053/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1991529/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1961117/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1958957/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1627960/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1903564/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:186864/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1853294/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1766095/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1722894/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1720448/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1679374/1‑67 (MQ=255)
                                                gTTGTCGACCACTCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1631039/1‑67 (MQ=255)
                                                gTTGTCGACCAATCAAAATTTGGCCGTAACGCAATGGTCAATATGGGTAGCATCAGCATGGTCGATg  >  1:1097320/1‑67 (MQ=255)
                                                        |                                                          
GTTCGCACCAAACGCGCCATTATTGAGAACTCGCGCCACGTTATGCTGGTTGTCGATCACTCGAAATTTGGCCGTAACGCGATGGTCAATATGGGCAGCATCAGCATGGTAGATG  >  minE/2661054‑2661168

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