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 I3 R1 375 42.1 2927644 71.4% 2090337 57.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 3,744,316 G→A N313N (AAC→AAT)  yidZ ← predicted DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,744,3160GA87.5% 54.9 / 1.3 24N313N (AAC→AAT) yidZpredicted DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/3);  new base A (21/0);  total (21/3)
Fisher's exact test for biased strand distribution p-value = 4.94e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01

TCGCGTTTCATACGATTCGGTTATGCCATCGACGCGTAAAGGTTTTTAATGGTTTCCCGTAACCAGACGA  >  W3110S.gb/3744275‑3744344
                                         |                            
tCGCGTTTCATACGATTCGGTTATGCCATCGACGCGTAAAGGTTTTTAATGGTTTCCCGTaa          <  1:1659852/62‑1 (MQ=255)
tCGCGTTTCATACGATTCGGTTATGCCATCGACGCGTAAAGGTTTTTAATGGTTTCCCGTaa          <  1:1838378/62‑1 (MQ=255)
tCGCGTTTCATACGATTCGGTTATGCCATCGACGCGTAAAGGTTTTTAATGGTTTCCCGTaa          <  1:453758/62‑1 (MQ=255)
        cATACGATTCGGTTTTGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:2055675/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGttt                 >  1:1444354/1‑47 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGtt                  >  1:2125821/1‑46 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACg   >  1:2794628/1‑61 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:950846/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:1222555/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:853890/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:848116/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:718730/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:51770/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:2502082/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:2299834/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:2248993/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:211986/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:2043253/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:2006165/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:1927428/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:1923581/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:1806471/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGATTTTTAATGGTTTCCCGTAACCAGACGa  >  1:1374205/1‑62 (MQ=255)
        cATACGATTCGGTTATGCCATCGACGCGTAAAGAATTTTAATGGTTTCCCGTAACCAGAcca  >  1:539505/1‑60 (MQ=255)
                                         |                            
TCGCGTTTCATACGATTCGGTTATGCCATCGACGCGTAAAGGTTTTTAATGGTTTCCCGTAACCAGACGA  >  W3110S.gb/3744275‑3744344

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