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 F3 I95 R1 196 14.2 808436 96.0% 776098 85.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 3,836,838 (C)5→4 coding (312/1335 nt) adeQ ← adenine permease AdeQ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,836,8340C.100.0% 33.1 / NA 9coding (316/1335 nt)adeQadenine permease AdeQ
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (5/4);  total (5/4)

GGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATC  >  NZ_CP009273/3836750‑3836916
                                                                                    |                                                                                  
ggATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGccccac                                                                               >  2:365105/1‑88 (MQ=255)
            gCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGc                                                                  >  1:321156/1‑90 (MQ=255)
            gCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGc                                                                  >  2:199573/1‑90 (MQ=255)
                  gCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAaagaa                                                            <  2:268731/90‑1 (MQ=255)
                               aaCTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGcccc                                               <  1:75799/90‑1 (MQ=255)
                                                  gcgcCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCa                            <  2:198166/90‑1 (MQ=255)
                                                    gcCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACg                          >  2:119112/1‑90 (MQ=255)
                                                              gTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAg                <  2:63073/90‑1 (MQ=255)
                                                                            gCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATc  >  1:310731/1‑90 (MQ=255)
                                                                            gCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATc  >  2:116293/1‑90 (MQ=255)
                                                                                    |                                                                                  
GGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATC  >  NZ_CP009273/3836750‑3836916

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ 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
CAGTACCGGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATACTGCCGATACCG  >  NZ_CP009273/3836743‑3836934
                                                                                               |                                                                                                
CAGTACCGGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGAC                                                                                             <  SRR3722235.327009/100‑1 (MQ=60)
CAGTACCGGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTCCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGAC                                                                                             <  SRR3722235.211368/100‑1 (MQ=60)
CAGTACCGGATACGAAACACCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGAC                                                                                             <  SRR3722235.290333/100‑1 (MQ=60)
         ATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGC                                                                                    >  SRR3722235.325706/1‑100 (MQ=60)
                                      AACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAG                                                       <  SRR3722235.76661/100‑1 (MQ=60)
                                                                         GCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATC                    >  SRR3722235.315108/1‑100 (MQ=60)
                                                                                   GCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATACTGC          >  SRR3722235.213399/1‑100 (MQ=60)
                                                                                    CCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATACTGCC         >  SRR3722235.339502/1‑100 (MQ=60)
                                                                                            CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATACTGCCGATctgt  >  SRR3722235.183302/1‑96 (MQ=60)
                                                                                            CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATACTGCCGATACCT  >  SRR3722235.238331/1‑100 (MQ=60)
                                                                                            CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATACTGCCGATACCG  >  SRR3722235.46841/1‑100 (MQ=60)
                                                                                               |                                                                                                
CAGTACCGGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATACTGCCGATACCG  >  NZ_CP009273/3836743‑3836934

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑