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 I197 R1 189 12.7 697584 97.1% 677354 86.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,300,524 Δ1 bp coding (504/1005 nt) oppF → murein tripeptide/oligopeptide ABC transporter ATP‑binding protein OppF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,300,5220G.100.0% 15.0 / NA 5coding (502/1005 nt)oppFmurein tripeptide/oligopeptide ABC transporter ATP‑binding protein OppF
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (3/2);  total (3/2)

GATTAACCGCTATCCGCATGAGTTCTCTGGTGGGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATCTGTGATGAGCCGGTGTCGGCG  >  NZ_CP009273/1300491‑1300602
                               |                                                                                
gATTAACCGCTATCCGCATGAGTTCTCTGGT‑GGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATc                       >  1:206408/1‑90 (MQ=255)
gATTAACCGCTATCCGCATGAGTTCTCTGGT‑GGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATc                       >  2:251592/1‑90 (MQ=255)
                 aTGAGTTCTCTGGT‑GGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATCTGTGATGAGCCGGTGTc      <  1:217881/90‑1 (MQ=255)
                 aTGAGTTCTCTGGT‑GGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATCTGTGATGAGCCGGTGTc      <  1:71750/90‑1 (MQ=255)
                     gTTCTCTGGT‑GGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATCTGTGATGAGCCGGTGTCGgcg  >  2:250901/1‑90 (MQ=255)
                               |                                                                                
GATTAACCGCTATCCGCATGAGTTCTCTGGTGGGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATCTGTGATGAGCCGGTGTCGGCG  >  NZ_CP009273/1300491‑1300602

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGCCTAACCTGATTAACCGCTATCCGCATGAGTTCTCTGGTGGGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATCTGTGATGAGCCGGTGTCGGCGCTGGAC  >  NZ_CP009273/1300481‑1300608
                                           |                                                                                    
TGCCTAACCTGATTAACCGCTATCCGCATGAGTTCTCTGGT‑GGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATC                             >  SRR3722076.209073/1‑100 (MQ=60)
                           ATGAGTTCTCTGGT‑GGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATCTGTGATGAGCCGGTGTCGGCGCTGGAC  <  SRR3722076.220821/100‑1 (MQ=60)
                           ATGAGTTCTCTGGT‑GGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATCTGTGATGAGCCGGTGTCGGCGCTGGAC  <  SRR3722076.72646/100‑1 (MQ=60)
                                           |                                                                                    
TGCCTAACCTGATTAACCGCTATCCGCATGAGTTCTCTGGTGGGCAGTGCCAGCGTATCGGGATTGCGCGTGCTCTTATTCTTGAACCGAAGCTGATTATCTGTGATGAGCCGGTGTCGGCGCTGGAC  >  NZ_CP009273/1300481‑1300608

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑