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 F2 I200 R1 216 30.8 1683622 97.2% 1636480 87.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
AATCGGCGTCACAGATGGAATAAACAAAACAATTGACTGATAATGTTTATTACAAGTTGTCTACATGTTAATTATAATATTATACAGCGTTTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAAC  >  NZ_CP009273/579847‑580041
                                                                                                |                                                                                                  
AATCGGCGTCACAGATGGAATAAACAAAACAATTGACTGATAATGTTTATTACAAGTTGTCTACATGTTAATTATAATATTATACAGCG‑TTTTTTTGATG                                                                                                <  SRR3722079.177736/100‑1 (MQ=60)
                                                     gatgtgtataagagacagTTATAATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATAC                                           <  SRR3722079.380349/82‑1 (MQ=60)
                                                     AAGTTGTCTACATGTTAATTATAATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATAC                                           <  SRR3722079.530877/100‑1 (MQ=60)
                                                                       TTATAATATTATACAGCGTTTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGT                          >  SRR3722079.843586/1‑100 (MQ=60)
                                                                            ATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACctgtctcttatacacatctccga                    >  SRR3722079.552521/1‑77 (MQ=60)
                                                                            ATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTA                    >  SRR3722079.82387/1‑100 (MQ=60)
                                                                                               TTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAAC  <  SRR3722079.185149/100‑1 (MQ=60)
                                                                                                |                                                                                                  
AATCGGCGTCACAGATGGAATAAACAAAACAATTGACTGATAATGTTTATTACAAGTTGTCTACATGTTAATTATAATATTATACAGCGTTTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAAC  >  NZ_CP009273/579847‑580041

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑