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
A5 F28 I2 R1 721 0.0 1472758 54.8% 807071 56.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 4,113,538 T→A T138S (ACC→TCC)  yrfF ← predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,113,5380TA77.0% 143.6 / 36.8 74T138S (ACC→TCC) yrfFpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (0/17);  new base A (57/0);  total (57/17)
Fisher's exact test for biased strand distribution p-value = 4.36e-17
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATCGTTGA  >  W3110S.gb/4113505‑4113570
                                 |                                
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:60722/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:261610/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:317775/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:214183/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:189481/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:160979/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:69698/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:638152/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:638119/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:863784/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:421826/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:907776/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:915163/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:523542/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:1148223/61‑1 (MQ=255)
cGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTAATCTCATc       <  1:214921/61‑1 (MQ=255)
    gAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATc       <  1:373931/57‑1 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCACCGGTATTCTCATCGTTGa  >  1:720277/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGtt    >  1:339762/1‑59 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:99556/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:596614/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:64459/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:562771/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:568765/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:584947/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:559313/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:606449/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:661864/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:662586/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:682121/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:714488/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:723927/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:789439/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:837178/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:840904/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:887015/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:898420/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:906709/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:936719/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:969401/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:976469/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:98212/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1002330/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1388899/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1042521/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1054826/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1165197/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1183543/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1186536/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1210725/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1219218/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1227886/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1243078/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1251956/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1312008/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1330246/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:527059/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:32193/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:51531/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:4903/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:432259/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:412683/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:391938/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:385882/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:339282/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1436113/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:271556/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:267948/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:256516/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:219287/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:15082/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATAGTTGa  >  1:1272758/1‑61 (MQ=255)
     aGTGAAATAACCAGCGGCAGCGAATCGGAATGAATCAGTTCAACGGAATTCTCATCGTTGa  >  1:109956/1‑61 (MQ=255)
     aGTGAAATAACCAGCGCCAGCGAATCGGAATGAATCAGTTCAACGGTATTCTCATCGTTGa  >  1:1254577/1‑61 (MQ=255)
                                 |                                
CGTTGAGTGAAATAACCAGCGGCAGCGAATCGGTATGAATCAGTTCAACGGTATTCTCATCGTTGA  >  W3110S.gb/4113505‑4113570

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A