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 I85 R1 6 9.1 514804 96.7% 497815 86.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 4,047,675 C→G A322P (GCG→CCG)  glnG ← nitrogen regulation protein NR(I)

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,047,6750CG100.0% 11.0 / NA 5A322P (GCG→CCG) glnGnitrogen regulation protein NR(I)
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (4/1);  total (4/1)

GACGCGTCAGAGCAGCTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGCCAGACGGGGAATATCTTCCCGACGTTCGCGCAGCGGC  >  NZ_CP009273/4047588‑4047712
                                                                                       |                                     
gACGCGTCAGAGCAGCTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGGCa                                     >  1:165135/1‑90 (MQ=255)
     gTCAGAGCAGCTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGGCAGACgg                                >  1:121608/1‑90 (MQ=255)
     gTCAGAGCAGCTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGGCAGACgg                                >  1:143334/1‑90 (MQ=255)
              gcTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGGCAGACGGGGAATATCt                       >  1:134829/1‑90 (MQ=255)
                                   aaCTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGGCAGACGGGGAATATCTTCCCGACGTTCGCGCAgcggc  <  2:57557/90‑1 (MQ=255)
                                                                                       |                                     
GACGCGTCAGAGCAGCTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGCCAGACGGGGAATATCTTCCCGACGTTCGCGCAGCGGC  >  NZ_CP009273/4047588‑4047712

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ 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
GGCCACGCCAGACGCGTCAGAGCAGCTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGCCAGACGGGGAATATCT  >  NZ_CP009273/4047578‑4047691
                                                                                                 |                
GGCCACGCCAGACGCGTCAGAGCAGCTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGGCA                >  SRR3722224.167517/1‑100 (MQ=60)
     CGCCAGACGCGTCAGAGCAGCTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGGCAGACGG           >  SRR3722224.123151/1‑100 (MQ=60)
     CGCCAGACGCGTCAGAGCAGCTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGGCAGACGG           >  SRR3722224.145294/1‑100 (MQ=60)
              CGTCAGAGCAGCTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGGCAGACGGGGAATATCT  >  SRR3722224.136652/1‑100 (MQ=60)
                                                                                                 |                
GGCCACGCCAGACGCGTCAGAGCAGCTTCGGTTTCCGGATGCAGTAACTTCGCTTCTACGCCCAGTTCGCGCGCGGCAACCTGTAAAAAATGGCGCGCCAGACGGGGAATATCT  >  NZ_CP009273/4047578‑4047691

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑