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 I209 R1 216 14.4 815930 96.1% 784108 85.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 3,798,416 (T)8→7 coding (61/936 nt) rfaS ← LPS core biosynthesis protein RfaS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,798,4090T.100.0% 19.4 / NA 6coding (68/936 nt)rfaSLPS core biosynthesis protein RfaS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (5/1);  total (5/1)

TCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG  >  NZ_CP009273/3798338‑3798493
                                                                       |                                                                                    
tccCTATTTTTGATATTTTTTTTTTAATCCAGGTATGTTTTTTTAGGGGTGTTATATTTTTTATTTTTTAC‑TTTTTGTCAGTTATTGAAt                                                                   >  1:191285/1‑90 (MQ=255)
tccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAt                                                                   >  2:354123/1‑90 (MQ=255)
     aTTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCAttt                                                              >  1:244360/1‑90 (MQ=255)
                                         tttGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTataaaataaa                          >  2:248248/1‑90 (MQ=255)
                                             gtgtTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGt                      <  2:244360/90‑1 (MQ=255)
                                                                 ttGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAg  >  1:178180/1‑90 (MQ=255)
                                                                       |                                                                                    
TCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG  >  NZ_CP009273/3798338‑3798493

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG  >  NZ_CP009273/3798333‑3798493
                                                                                   |                                                                             
ATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTT                                                              >  SRR3722091.248168/1‑100 (MQ=60)
                                                            ATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG  >  SRR3722091.180732/1‑100 (MQ=60)
                                                                                   |                                                                             
ATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG  >  NZ_CP009273/3798333‑3798493

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: ‑