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 I74 R1 158 13.7 815430 95.7% 780366 86.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,634,151 Δ1 bp coding (164/534 nt) rrrQ ← lysozyme

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,634,1500G.100.0% 36.6 / NA 10coding (165/534 nt)rrrQlysozyme
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (7/3);  total (7/3)

AATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAAC  >  NZ_CP009273/1634075‑1634228
                                                                           |                                                                              
aaTGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATg                                                                 <  2:94225/90‑1 (MQ=255)
         gACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATg                                                        >  1:70489/1‑90 (MQ=255)
              ggTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGa                                                   >  1:72635/1‑90 (MQ=255)
                             tCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGc                                    >  1:143064/1‑90 (MQ=255)
                                     tttatatTGGGAAAAACGGTTTTTCCACCCCCCACTGT‑GCGCCCCGACAGATGGTCCATATGCCAGAACCCTCGCGGTATGCCATtgtgt                            <  2:239572/87‑1 (MQ=255)
                                             gggAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACct                    >  1:129832/1‑90 (MQ=255)
                                             gggAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACct                    >  2:91601/1‑90 (MQ=255)
                                                     cGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTc            <  2:364663/90‑1 (MQ=255)
                                                       gTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGt          >  2:194312/1‑90 (MQ=255)
                                                               atccaCCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAAc  >  2:102062/1‑90 (MQ=255)
                                                                           |                                                                              
AATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAAC  >  NZ_CP009273/1634075‑1634228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ 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
CAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCT  >  NZ_CP009273/1634074‑1634210
                                                                             |                                                           
CAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATG                                      >  SRR3722212.71349/1‑100 (MQ=60)
     GCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGA                                 >  SRR3722212.73522/1‑100 (MQ=60)
                    CATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGC                  >  SRR3722212.144719/1‑100 (MQ=60)
                                    GTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCT  >  SRR3722212.131335/1‑100 (MQ=60)
                                                                             |                                                           
CAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCT  >  NZ_CP009273/1634074‑1634210

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: ‑