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
AGCCGGTTCGGTTGCGACTGTGGCACCGACCACAATGGCACTACTGGCAGCCTCTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGACCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAGTCATAAATGTGTTTTTCCAGCAGTGAGAAGCAGAAGAAC  >  NZ_CP009273/4084554‑4084743
                                                                                                   |                                                                                          
AGCCGGTTCGGTTGCGACTGTGGCACCGACCACAATGGCACTACTGGCAGCCTCTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGG                                                                                            >  SRR3722077.780975/1‑100 (MQ=60)
                 CTGTGGCACCGACCACAATGGCACTACTGGCAGCCTCTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGGCCCGCCGCGACGGGCGG                                                                           >  SRR3722077.200068/1‑100 (MQ=60)
                 CTGTGGCACCGACCACAATGGCACTACTGGCAGCCTCTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGACCCGCCGCGACGGGCGG                                                                           >  SRR3722077.181490/1‑100 (MQ=60)
                     GGCACCGACCACAATGGCACTACTGGCAGCCTTTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGCCCCGCCGCGACGGGCGGCATC                                                                       <  SRR3722077.1022344/100‑1 (MQ=60)
                         CCGCCCACAATGGCACTACTGGCAGCCTCTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGGCCCGCCGCGACGGGCGGCATCAGCG                                                                   <  SRR3722077.998439/100‑1 (MQ=60)
                                           CTGGCAGCTTTTTTTTCCTGTGGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGACCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGG                                                 <  SRR3722077.981870/100‑1 (MQ=60)
                                                 GCCTCTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGACCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCtgtctcttatacac                                           >  SRR3722077.1044388/1‑86 (MQ=60)
                                                 GCCTCTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGACCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCtgtctcttatacac                                           >  SRR3722077.726957/1‑86 (MQ=60)
                                                   CTCTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGGCCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAG                                         >  SRR3722077.408957/1‑100 (MQ=60)
                                                    TCTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGGCCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAGT                                        >  SRR3722077.746230/1‑100 (MQ=60)
                                                     CTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGACCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAGTC                                       >  SRR3722077.468961/1‑100 (MQ=60)
                                                          TCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGGCCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAGTCATAAA                                  <  SRR3722077.511216/100‑1 (MQ=60)
                                                          TCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGGCCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAGTCATAAA                                  <  SRR3722077.746988/100‑1 (MQ=60)
                                                          TCCTGGCGGGAAAACGTTTTGGGCGAAATGAACGTCGCAAGACCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAGTCATAAA                                  <  SRR3722077.1089637/100‑1 (MQ=60)
                                                           ctggcggggaaaatatttgGGGCGAAATGAACGTCGAAAGACCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAGTCATAAAT                                 <  SRR3722077.288054/81‑1 (MQ=60)
                                                           CCTGTGGGGAAAACAGTTTGGGCGCAATGAACGTCGCAAGCCCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAGTCATAAAT                                 <  SRR3722077.360569/100‑1 (MQ=60)
                                                                          GTTTGGGCGCAATGAACGTCGCAAGGCCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAGTCATAAATGTGTTTTTCCAGCAG                  >  SRR3722077.690245/1‑100 (MQ=60)
                                                                                          CGTCGCAAGGCCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAGTCATAAATGTGTTTTTCCAGCAGTGAGAAGCAGAAGAAC  <  SRR3722077.46006/100‑1 (MQ=60)
                                                                                                   |                                                                                          
AGCCGGTTCGGTTGCGACTGTGGCACCGACCACAATGGCACTACTGGCAGCCTCTTTTTCCTGTCGGGTAAACAGTTTGGGCGCAATGAACGTCGCAAGACCCGCCGCGACGGGCGGCATCAGCGCGACAACGCCGACGATGGCGTACCAGTCATAAATGTGTTTTTCCAGCAGTGAGAAGCAGAAGAAC  >  NZ_CP009273/4084554‑4084743

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑