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
GCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTC  >  NZ_CP009273/1671820‑1671986
                                                                               |                                                                                       
GCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACG                                                                     >  SRR3722077.60659/1‑100 (MQ=60)
   ATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAA                                                                  >  SRR3722077.542207/1‑100 (MQ=60)
         GTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACTCAATTTCAT                                                            >  SRR3722077.127856/1‑100 (MQ=60)
           CACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCA                                                          >  SRR3722077.864574/1‑100 (MQ=60)
             CGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATC                                                        >  SRR3722077.301274/1‑100 (MQ=60)
                           AGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGA                                          <  SRR3722077.715981/100‑1 (MQ=60)
                                    ATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAA                                 <  SRR3722077.111883/100‑1 (MQ=60)
                                    ATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAA                                 <  SRR3722077.375295/100‑1 (MQ=60)
                                       AATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGA                              <  SRR3722077.1011281/100‑1 (MQ=60)
                                              GATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGA                       >  SRR3722077.353877/1‑100 (MQ=60)
                                               ATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCACCTAACGGCGCATTGACCTTCAGAATGATCTCTGAC                      <  SRR3722077.55186/100‑1 (MQ=60)
                                                         GGCCAGATAAAACTCACCAGCGGTGTACCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGC            >  SRR3722077.727702/1‑100 (MQ=60)
                                                              GATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACCGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTC       <  SRR3722077.340294/100‑1 (MQ=60)
                                                                   AACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTC  >  SRR3722077.933220/1‑100 (MQ=60)
                                                                               |                                                                                       
GCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTC  >  NZ_CP009273/1671820‑1671986

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑