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 I1 R1 354 41.7 3110465 93.1% 2895842 61.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 4,434,329 +A intergenic (+92/‑217) fklB → / → cycA FKBP‑type peptidyl‑prolyl cis‑trans isomerase/D‑alanine/D‑serine/glycine transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,434,3261.A85.7% 35.3 / 1.7 14intergenic (+89/‑220)fklB/cycAFKBP‑type peptidyl‑prolyl cis‑trans isomerase/D‑alanine/D‑serine/glycine transporter
Reads supporting (aligned to +/- strand):  ref base . (0/2);  new base A (0/12);  total (0/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

TTGTGTTGC‑AAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGATATGACA  >  W3110S.gb/4434318‑4434385
         |                                                           
ttGTGTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGat        <  1:1116357/63‑1 (MQ=255)
ttGTGTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGat        <  1:1170158/63‑1 (MQ=255)
ttGTGTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGat        <  1:1259028/63‑1 (MQ=255)
ttGTGTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGat        <  1:1494598/63‑1 (MQ=255)
ttGTGTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGat        <  1:1848779/63‑1 (MQ=255)
ttGTGTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGat        <  1:2018931/63‑1 (MQ=255)
ttGTGTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGat        <  1:2462523/63‑1 (MQ=255)
ttGTGTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGat        <  1:600233/63‑1 (MQ=255)
ttGTGTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGat        <  1:611157/63‑1 (MQ=255)
ttGTGTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGAGTTATCACCGTGat        <  1:1185788/63‑1 (MQ=255)
 tgtgTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGat        <  1:2191630/62‑1 (MQ=255)
 tgtgTTGCAAAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGat        <  1:429671/62‑1 (MQ=255)
    gtTGC‑AAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGATATGaca  <  1:1748062/64‑1 (MQ=255)
    gtTGC‑AAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGATATGaca  <  1:454050/64‑1 (MQ=255)
         |                                                           
TTGTGTTGC‑AAAGACCCCGTAAGCGTGTATTTTTGTGAGCTGTTTCGCGTTATCACCGTGATATGACA  >  W3110S.gb/4434318‑4434385

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A