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
A1 F28 I3 R1 178 99.0 1887089 95.3% 1798395 63.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 2,462,875 (T)6→7 coding (1731/2145 nt) yfcX ← fused enoyl‑CoA hydratase, 3‑hydroxybutyryl‑CoA epimerase, dodecenoyl‑CoA D‑isomerase, and 3‑hydroxyacyl‑CoA dehydrogenase, subunit of anaerobic fatty acid oxidation complex

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,462,8691.T89.4% 285.2 / 27.0 85coding (1737/2145 nt)yfcXfused enoyl‑CoA hydratase, 3‑hydroxybutyryl‑CoA epimerase, dodecenoyl‑CoA D‑isomerase, and 3‑hydroxyacyl‑CoA dehydrogenase, subunit of anaerobic fatty acid oxidation complex
Reads supporting (aligned to +/- strand):  ref base . (9/0);  new base T (76/0);  total (85/0)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

GCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑TTTTTTCTGCCTTTGCGATCGT  >  W3110S.gb/2462827‑2462891
                                           |                      
gCTTTTACGCCCTTTCTGACCATAAAGATAGAACCCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1306458/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:412145/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:580294/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:54460/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:494173/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:484132/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:455894/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:454625/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:452082/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:450413/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:435107/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:671736/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:402819/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:345772/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:340076/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:32913/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:29573/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:274071/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:248560/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:247548/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:230040/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:861234/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:995858/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:950568/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:948990/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:935324/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:901342/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:901296/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:882358/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:876774/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:867729/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:664783/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:822958/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:763810/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:761123/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:736096/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:719033/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:709751/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:694520/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:692367/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:215413/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1090391/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1560425/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1035982/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1527864/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1506497/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1081365/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1420385/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1377294/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1338868/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1571517/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1295394/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1123383/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1268891/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1246637/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1163915/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1224485/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1209910/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1194406/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1706597/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1020095/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1855687/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1855228/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1787653/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1767746/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:173070/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1730372/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1696862/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1688683/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1674905/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1666070/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1034442/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1605931/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1583888/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCATTTTTTTCTGCCTTTGCGAtc    >  1:1100474/1‑64 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑ttttttt                 >  1:1676451/1‑49 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑TTTTTTCTGCCTTTGCGAtcgt  >  1:1498339/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑TTTTTTCTGCCTTTGCGAtcgt  >  1:96905/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑TTTTTTCTGCCTTTGCGAtcgt  >  1:798025/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑TTTTTTCTGCCTTTGCGAtcgt  >  1:1278879/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑TTTTTTCTGCCTTTGCGAtcgt  >  1:1870513/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑TTTTTTCTGCCTTTGCGAtcgt  >  1:518848/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑TTTTTTCTGCCTTTGCGAtcgt  >  1:163839/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑TTTTTTCTGCCTTTGCGAtcgt  >  1:1007777/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑TTTTTTCTGCCTTTGCGAtcgt  >  1:1882744/1‑65 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGCCCA‑t                       >  1:719963/1‑44 (MQ=255)
gCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCAGGCCATTTTTTTCTGCCTTTGCGAtcg   >  1:1323734/1‑65 (MQ=255)
                                           |                      
GCTTTTACGCCCTTTCTGACCATAAAGATAGAAACCCCGGCCA‑TTTTTTCTGCCTTTGCGATCGT  >  W3110S.gb/2462827‑2462891

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