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 3,909,227 A→C A20A (GCT→GCG)  xylF ← D‑xylose transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,909,2270AC88.8% 438.6 / 32.6 169A20A (GCT→GCG) xylFD‑xylose transporter subunit
Reads supporting (aligned to +/- strand):  ref base A (19/0);  new base C (0/150);  total (19/150)
Fisher's exact test for biased strand distribution p-value = 1.63e-25
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01

Only 100 of 169 total aligned reads displayed.

GCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGTG  >  W3110S.gb/3909195‑3909254
                                |                           
gCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGt   >  1:10566/1‑59 (MQ=255)
gCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGTg  >  1:1348791/1‑60 (MQ=255)
gCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGTg  >  1:791136/1‑60 (MQ=255)
gCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGTg  >  1:518523/1‑60 (MQ=255)
gCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGTg  >  1:798979/1‑60 (MQ=255)
gCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGTg  >  1:167032/1‑60 (MQ=255)
gCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGTg  >  1:1307770/1‑60 (MQ=255)
gCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGTg  >  1:866190/1‑60 (MQ=255)
gCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGTg  >  1:299783/1‑60 (MQ=255)
gCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACCTTGGTAAGCAGGAGTGAGGTg  >  1:817482/1‑60 (MQ=255)
gCCATACCTATTTTGACTTCTTTGGAGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGTg  >  1:942150/1‑60 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTTGTAAGCa             <  1:286851/39‑1 (MQ=38)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGcg             <  1:172952/39‑2 (MQ=39)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:540438/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:539761/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:589365/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:525753/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:577428/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:583142/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:678542/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:522267/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:487543/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:478716/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:467696/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:454574/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:452989/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:43393/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:413055/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:359598/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:344852/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:341897/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:846231/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1000739/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:971902/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:954070/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:932193/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:918298/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:892563/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:875123/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:870286/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:868838/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:8485/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:638163/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:808102/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:797194/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:778837/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:757341/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:727814/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:688341/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:982386/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:661967/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:652917/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:650962/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1143535/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:135556/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:132353/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1304065/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1262471/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1260105/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1259819/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1224252/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1204761/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1195383/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1190476/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:114874/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1386748/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:114194/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1120749/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1084948/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1084348/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:106839/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1060733/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1051340/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1036771/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1034751/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1021693/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1017661/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:176672/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:31117/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:25345/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:253232/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:242058/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:227042/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:226579/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:214186/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:199956/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:192793/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:186951/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:185067/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:333742/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:154944/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:152069/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1472640/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1452897/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1450054/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:144281/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1420354/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1415748/39‑1 (MQ=255)
          ttttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:1398821/39‑1 (MQ=255)
            ttGACTTCTTTGGCGTGTGCCGCAACGTTGGTAAGCa             <  1:553129/37‑1 (MQ=255)
                                |                           
GCCATACCTATTTTGACTTCTTTGGCGTGTGCAGCAACGTTGGTAAGCAGGAGTGAGGTG  >  W3110S.gb/3909195‑3909254

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