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 I210 R1 226 19.6 1130256 95.4% 1078264 84.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,934,547 T→C intergenic (‑97/+23) lpxM ← / ← mepM lauroyl‑Kdo(2)‑lipid IV(A) myristoyltransferase/murein DD‑endopeptidase MepM

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,934,5470TC100.0% 16.5 / NA 7intergenic (‑97/+23)lpxM/mepMlauroyl‑Kdo(2)‑lipid IV(A) myristoyltransferase/murein DD‑endopeptidase MepM
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (4/3);  total (4/3)

TAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGG  >  NZ_CP009273/1934496‑1934631
                                                   |                                                                                    
tAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGc                                                >  2:422973/1‑90 (MQ=255)
     gcgcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCgg                                           >  1:33291/1‑90 (MQ=255)
       gcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGca                                         >  1:444644/1‑90 (MQ=255)
           cTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAAt                                     <  1:460926/90‑1 (MQ=255)
           cTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAAt                                     <  2:444644/90‑1 (MQ=255)
                      ccAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCt                          <  2:196104/90‑1 (MQ=255)
                                              ctgCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCgg  >  1:302071/1‑90 (MQ=255)
                                                   |                                                                                    
TAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGG  >  NZ_CP009273/1934496‑1934631

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
GCTTTTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGG  >  NZ_CP009273/1934451‑1934631
                                                                                                |                                                                                    
cagatgtgtataagagacagGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACC                                                                                   <  SRR3722092.112903/80‑1 (MQ=60)
                                        TAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGG                                           >  SRR3722092.33863/1‑100 (MQ=60)
                                          GTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCA                                         >  SRR3722092.453379/1‑100 (MQ=60)
                                                        CTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTCTGGCC                           <  SRR3722092.470031/100‑1 (MQ=60)
                                                                                 CCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGG  >  SRR3722092.307383/1‑100 (MQ=60)
                                                                                                |                                                                                    
GCTTTTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGG  >  NZ_CP009273/1934451‑1934631

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑