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
CCAGGCGTGTCATGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCCATGCCGGGAAACAAAGAAAACTC  >  NZ_CP009273/1818858‑1819053
                                                                                                  |                                                                                                 
CCAGGCGTGTCATGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGT                                                                                                  <  SRR3722077.603205/100‑1 (MQ=60)
     tggccgtgggtctcgtgggctcggagatgtgtataagagacagGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGG                                                                                             <  SRR3722077.357155/57‑1 (MQ=60)
     CGTGTCATGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGG                                                                                             <  SRR3722077.1014066/100‑1 (MQ=60)
     CGTGTCATGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGG                                                                                             <  SRR3722077.829012/100‑1 (MQ=60)
     CGTGTCATGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGG                                                                                             <  SRR3722077.466878/100‑1 (MQ=60)
        GTCATGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGctg                                                                                          >  SRR3722077.967497/1‑97 (MQ=60)
            TGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTT                                                                                      <  SRR3722077.720522/100‑1 (MQ=60)
                GTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAG                                                                                  >  SRR3722077.51799/1‑100 (MQ=60)
                 TTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGC                                                                                 <  SRR3722077.1115791/100‑1 (MQ=60)
                                                         TTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAA                                         >  SRR3722077.519340/1‑100 (MQ=60)
                                                         TTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAA                                         >  SRR3722077.250538/1‑100 (MQ=60)
                                                         TTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAA                                         <  SRR3722077.174925/100‑1 (MQ=60)
                                                         TTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAA                                         <  SRR3722077.829581/100‑1 (MQ=60)
                                                                         TGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCC                         <  SRR3722077.769577/100‑1 (MQ=60)
                                                                               GGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCCATGCCG                   >  SRR3722077.509177/1‑100 (MQ=60)
                                                                                     AGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGCTCTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCCATGCCGGGAAAC             >  SRR3722077.569998/1‑100 (MQ=60)
                                                                                          GGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCCATGCCGGGAAACAAAGA        <  SRR3722077.239095/100‑1 (MQ=60)
                                                                                                GTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCGTCTCGCCGCCTTCCAGCAACGTCACTActgtctcttatacacatctccgagcccacga  >  SRR3722077.675484/1‑69 (MQ=60)
                                                                                                  |                                                                                                 
CCAGGCGTGTCATGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCCATGCCGGGAAACAAAGAAAACTC  >  NZ_CP009273/1818858‑1819053

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: ‑