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 I79 R1 9 10.0 590080 95.6% 564116 85.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 3,754,231 G→T R127S (CGC→AGC)  selA ← L‑seryl‑tRNA(Sec) selenium transferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,754,2310GT100.0% 34.5 / NA 11R127S (CGC→AGC) selAL‑seryl‑tRNA(Sec) selenium transferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (3/8);  total (3/8)

CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAAC  >  NZ_CP009273/3754150‑3754272
                                                                                 |                                         
cATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt                                   <  1:179822/90‑1 (MQ=255)
           aCGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCa                        <  2:192719/90‑1 (MQ=255)
                        cTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt                                   <  1:136333/66‑1 (MQ=255)
                        cTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt                                   >  2:136333/1‑66 (MQ=255)
                               ccccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGa    <  1:135413/90‑1 (MQ=255)
                               ccccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGa    <  1:202144/90‑1 (MQ=255)
                               ccccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGa    <  2:82543/90‑1 (MQ=255)
                               ccccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTACAGATCATACTCGAGGGTCACTGGCGa    <  2:270023/90‑1 (MQ=255)
                                 ccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAAc  >  2:55437/1‑90 (MQ=255)
                                          ggCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCAc          <  1:231640/73‑1 (MQ=255)
                                          ggCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCAc          >  2:231640/1‑73 (MQ=255)
                                                                                 |                                         
CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAAC  >  NZ_CP009273/3754150‑3754272

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ 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
CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCTTCCGCCTGTAAAGCTCGCCCAAGGT  >  NZ_CP009273/3754150‑3754329
                                                                                 |                                                                                                  
tgtataagagacaGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATC                                                                                  <  SRR3722217.138104/87‑1 (MQ=60)
CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATC                                                                                  <  SRR3722217.182323/100‑1 (MQ=60)
                         gagacagCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGC                                                         <  SRR3722217.235092/93‑1 (MQ=60)
                               CCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCC                                                   <  SRR3722217.137169/100‑1 (MQ=60)
                               CCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCC                                                   <  SRR3722217.205123/100‑1 (MQ=60)
                                                                                CTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCTTCCGCCTGTAAAGCTCGCCCAAGGT  >  SRR3722217.185695/1‑100 (MQ=60)
                                                                                 |                                                                                                  
CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCTTCCGCCTGTAAAGCTCGCCCAAGGT  >  NZ_CP009273/3754150‑3754329

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: ‑