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
CCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCTGCGCCCCCGACT  >  NZ_CP009273/3898738‑3898925
                                                                                          |                                                                                                 
CCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTC                                                                                          >  SRR3722077.387297/1‑100 (MQ=60)
          GACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTT                                                                               >  SRR3722077.337055/1‑100 (MQ=60)
                  CCACATGGTTACCTATGTCCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCA                                                                       <  SRR3722077.466187/100‑1 (MQ=60)
                     gatggctgtgggtctcgtgggctcggagatgtgtataagagacagCCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCC                                                                    <  SRR3722077.106699/55‑1 (MQ=60)
                     CATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCC                                                                    >  SRR3722077.615475/1‑100 (MQ=60)
                     CATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCC                                                                    >  SRR3722077.189605/1‑100 (MQ=60)
                            ACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATT                                                             >  SRR3722077.995745/1‑100 (MQ=60)
                             CCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATT                                                             <  SRR3722077.575121/100‑1 (MQ=60)
                                  GACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTctgtc                                                       >  SRR3722077.1118196/1‑95 (MQ=60)
                                      ACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCctgtctcttatacacatctccgagcccacg                                                   >  SRR3722077.829409/1‑70 (MQ=60)
                                                     CCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATG                                    >  SRR3722077.645310/1‑100 (MQ=60)
                                                      CGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGC                                   <  SRR3722077.129076/100‑1 (MQ=60)
                                                          TTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCA                               >  SRR3722077.265597/1‑100 (MQ=60)
                                                            aagagacagTAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAG                              <  SRR3722077.875381/91‑1 (MQ=60)
                                                              ACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGAC                            <  SRR3722077.354732/100‑1 (MQ=60)
                                                                     TAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTctgtctcttatacacatctccgagcccacgagacccacgg                     >  SRR3722077.807460/1‑60 (MQ=60)
                                                                     TAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTctgtctcttatacacatctccgagcccacgagacccacgg                     >  SRR3722077.778596/1‑60 (MQ=60)
                                                                     TAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAAT                     >  SRR3722077.574584/1‑100 (MQ=60)
                                                                     TAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG                    >  SRR3722077.771434/1‑100 (MQ=60)
                                                                     TAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG                    >  SRR3722077.603659/1‑100 (MQ=60)
                                                                           TACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCctgtctcttatacacatctcc              >  SRR3722077.470190/1‑79 (MQ=60)
                                                                                  GGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCTGCGCCCC       >  SRR3722077.1090311/1‑100 (MQ=60)
                                                                                        TTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCTGCGCCCCCGACT  >  SRR3722077.852580/1‑100 (MQ=60)
                                                                                          |                                                                                                 
CCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCTGCGCCCCCGACT  >  NZ_CP009273/3898738‑3898925

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: ‑