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 I198 R1 96 36.2 2313912 84.6% 1957569 85.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GCACGACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGACGCCACAGC  >  NZ_CP009273/2849717‑2849914
                                                                                                   |                                                                                                  
GCACGACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATC                                                                                                    <  SRR3722077.790507/100‑1 (MQ=60)
    GACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATG                                                                                                <  SRR3722077.983472/100‑1 (MQ=60)
    GACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATG                                                                                                <  SRR3722077.360080/100‑1 (MQ=60)
    GACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATG                                                                                                <  SRR3722077.402817/100‑1 (MQ=60)
                            atacgagatggccgtgggtctcgtgggctcggagatgtgtataagagacagCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTC                                                                        <  SRR3722077.1027803/49‑1 (MQ=60)
                            GCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTC                                                                        <  SRR3722077.590401/100‑1 (MQ=60)
                                            TCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACC                                                        >  SRR3722077.973757/1‑100 (MQ=60)
                                                          ACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATC                                          <  SRR3722077.140720/100‑1 (MQ=60)
                                                              CAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATG                                      <  SRR3722077.1065331/100‑1 (MQ=60)
                                                                    GCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGA                                >  SRR3722077.211255/1‑100 (MQ=60)
                                                                    GCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGA                                <  SRR3722077.636220/100‑1 (MQ=60)
                                                                          CAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACG                          >  SRR3722077.494770/1‑100 (MQ=60)
                                                                             gagatgtgtataagagacagATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTT                       <  SRR3722077.1058073/80‑1 (MQ=60)
                                                                             ATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTT                       >  SRR3722077.400103/1‑100 (MQ=60)
                                                                              TCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTA                      <  SRR3722077.131543/100‑1 (MQ=60)
                                                                                TGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAG                    <  SRR3722077.211285/100‑1 (MQ=60)
                                                                                  CCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGAT                  <  SRR3722077.922731/100‑1 (MQ=60)
                                                                                          GCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGAC          >  SRR3722077.363314/1‑100 (MQ=60)
                                                                                            ATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGACGC        >  SRR3722077.399253/1‑100 (MQ=60)
                                                                                                 ATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACtgtctcttatacacatctccgagcccacgagacccacggccatctcgtatgccg   >  SRR3722077.803947/1‑46 (MQ=60)
                                                                                                 ATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGACGCCACAG   >  SRR3722077.876849/1‑100 (MQ=60)
                                                                                                  TCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGACGCCACAGC  <  SRR3722077.772356/100‑1 (MQ=60)
                                                                                                   |                                                                                                  
GCACGACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGACGCCACAGC  >  NZ_CP009273/2849717‑2849914

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: ‑