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
A2 F73 I2 R1 76 833.2 37290668 99.4% 37066923 136.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
MC JC AE015451_phaM1 3,760,510 Δ22,673 bp PP_3325 CDS (putative Outer membrane ferric siderophore receptor)–[nikD CDS (nickel ABC transporter ATP‑binding subunit)] 22 genes

Missing coverage evidence...
   seq id start end size ←reads reads→ gene description
* * ÷ AE015451_phaM1 3760510 3783182 22673 921 [0] [0] 909 PP_3325 CDS (putative Outer membrane ferric siderophore receptor)–[nikD CDS (nickel ABC transporter ATP‑binding subunit)] PP_3325 CDS (putative Outer membrane ferric siderophore receptor),PP_3326 CDS (conserved exported protein of unknown function),PP_3328 CDS (putative Ring‑cleaving dioxygenase),PP_5599 CDS (putative transcriptional regulator_ LysR family),PP_3329 CDS (conserved membrane protein of unknown function),PP_5600 CDS (conserved protein of unknown function),PP_3330 CDS (putative Outer membrane ferric siderophore receptor),PP_3331 CDS (conserved membrane protein of unknown function),PP_3332 CDS (putative cytochrome c‑type protein),PP_3333 CDS (conserved protein of unknown function),PP_5743 CDS (putative TonB‑dependent receptor protein),PP_3335 CDS (conserved protein of unknown function),PP_3336 CDS (conserved protein of unknown function),PP_3337 CDS (conserved membrane protein of unknown function),PP_3338 CDS (putative cytochrome bd‑type quinol oxidase),PP_3339 CDS (conserved exported protein of unknown function),PP_3340 CDS (putative TonB‑dependent receptor),nikR CDS (nickel‑responsive regulator),nikA CDS (nickel ABC transporter periplasmic binding protein),nikB CDS (nickel ABC transporter permease subunit),nikC CDS (nickel ABC transporter permease subunit),[nikD CDS (nickel ABC transporter ATP‑binding subunit)]

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? AE015451_phaM1 = 37605090 (0.000)909 (1.090) 141/270 0.0 100% intergenic (+167/‑144) folEB CDS (GTP cyclohydrolase I)/PP_3325 CDS (putative Outer membrane ferric siderophore receptor) –/–
?AE015451_phaM1 3783183 = 0 (0.000)coding (274/771 nt) nikD CDS (nickel ABC transporter ATP‑binding subunit)

GATK/CNVnator alignment

N/A