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 2,422,871 T→C 100% L199L (TTA→TTG)  rffA ← TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,422,8710TC79.0% 151.4 / 35.2 76L199L (TTA→TTG) rffATDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase
Reads supporting (aligned to +/- strand):  ref base T (14/2);  new base C (60/0);  total (74/2)
Fisher's exact test for biased strand distribution p-value = 4.21e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAGAACTGGCTGCGGTTAGTGCCCTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTAATCAGCGTC  >  minE/2422818‑2422895
                                                     |                        
aagatCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:297779/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTAt                >  1:91896/1‑64 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATc               >  1:2055253/1‑65 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATc               >  1:748338/1‑65 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATc               >  1:1245912/1‑65 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATc               >  1:1675284/1‑65 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATc               >  1:52677/1‑65 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATc               >  1:1456121/1‑65 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:2199430/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1997540/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:271705/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:243626/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:2306944/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:2265080/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:2257210/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1108590/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:2153716/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:2135223/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:2108653/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:2013772/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:2003092/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:327596/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:364405/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:446049/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:455076/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:554367/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:564419/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:572170/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:62691/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:723274/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:815267/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:838106/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:849627/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:861794/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:909305/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1934238/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1274231/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1371608/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1240876/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1238175/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1462169/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1466801/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1231709/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1495422/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1498157/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1520185/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1551367/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1612115/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1183144/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1674780/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1702616/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1712350/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1754996/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1773118/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1776373/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1787728/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:109427/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATCg              >  1:1877593/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGCCTTTTTCACGGATGATCTCGCCTCGTTCGATCAACGCTTTATCg              >  1:763721/1‑66 (MQ=255)
aagaaCTGGCTGCGGTTTGTGACTTTTTCACGGATGATCTCGGCTCGTTCGATCAACGCTTTATc               >  1:1121590/1‑65 (MQ=255)
           gCGGTTAGTGCCCTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTAATCAGCGTc  <  1:1891844/67‑1 (MQ=255)
           gCGGTTAGTGCCCTTTTCACGGATGATCTCGGCGCGGTCGATTAACGCTTTATCGTTAATCAGCGTc  <  1:1587656/67‑1 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:841968/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:111101/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:966229/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:674478/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:1419063/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:568160/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:513679/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:1628811/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:237485/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:1716898/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:2084759/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:1814145/1‑46 (MQ=255)
                       cTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTa           >  1:1959411/1‑46 (MQ=255)
                       cTTTTAACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGtt            >  1:1430741/1‑45 (MQ=255)
                                                     |                        
AAGAACTGGCTGCGGTTAGTGCCCTTTTCACGGATGATCTCGGCTCGTTCGATTAACGCTTTATCGTTAATCAGCGTC  >  minE/2422818‑2422895

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