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 I227 R1 223 21.3 1167702 97.0% 1132670 86.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 510,152 Δ1 bp coding (164/459 nt) ybbJ ← NfeD family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273510,1510C.100.0% 32.2 / NA 9coding (165/459 nt)ybbJNfeD family protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (6/3);  total (6/3)

TGTGCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTC  >  NZ_CP009273/510063‑510233
                                                                                        |                                                                                  
tgtgTTTTTCTCCGCGCCCCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGca                                                                                   <  1:303402/90‑2 (MQ=255)
        tGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTAAGGATGGCAAACATTACCCCTTG‑CACTCCCAAc                                                                          >  1:7561/1‑90 (MQ=255)
                   ccgccgCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCAcc                                                               >  2:560517/1‑90 (MQ=255)
                         cgACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCAccagccag                                                         <  1:195290/90‑1 (MQ=255)
                         cgACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCAccagccag                                                         <  1:331373/90‑1 (MQ=255)
                                   ttCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGc                                               <  2:417511/90‑1 (MQ=255)
                                             gCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCAc                                     >  2:493843/1‑90 (MQ=255)
                                               cAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCg                                   >  1:178900/1‑90 (MQ=255)
                                                                      ggCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACaaa            >  2:536838/1‑90 (MQ=255)
                                                                                aCCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTc  >  1:263109/1‑90 (MQ=255)
                                                                                        |                                                                                  
TGTGCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTC  >  NZ_CP009273/510063‑510233

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ 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
GCTGTGCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCTCGGC  >  NZ_CP009273/510061‑510249
                                                                                           |                                                                                                 
GCTGTGCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTAAGGATGGCAAACATTACCCCTTG‑CACTCCCAAC                                                                                          >  SRR3722111.7657/1‑100 (MQ=60)
  TGTGTTTTTCTCCGCGCCCCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCC                                                                                        <  SRR3722111.307334/100‑1 (MQ=60)
                           CGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGC                                                               <  SRR3722111.197724/100‑1 (MQ=60)
                           CGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGC                                                               <  SRR3722111.335811/100‑1 (MQ=60)
                                       CCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCG                                                   >  SRR3722111.181148/1‑100 (MQ=60)
                                                                        GGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTC                  >  SRR3722111.266229/1‑100 (MQ=60)
                                                                             ACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCC             >  SRR3722111.572898/1‑100 (MQ=60)
                                                                                       TTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCTCGG   >  SRR3722111.264082/1‑100 (MQ=60)
                                                                                        TGCC‑CTCCCACCCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCTCGGC  <  SRR3722111.447158/100‑1 (MQ=60)
                                                                                           |                                                                                                 
GCTGTGCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCTCGGC  >  NZ_CP009273/510061‑510249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑