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
CTTTCTGACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCAGCAC  >  NZ_CP009273/2859899‑2860094
                                                                                                   |                                                                                                
CTTTCTGACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAAT                                                                                                  <  SRR3722077.796212/100‑1 (MQ=60)
 gtataagagacaGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATC                                                                                                 <  SRR3722077.1065078/88‑1 (MQ=60)
      GACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCG                                                                                            >  SRR3722077.186010/1‑100 (MQ=60)
                    TACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGG                                                                              <  SRR3722077.566350/100‑1 (MQ=60)
                    TACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGG                                                                              >  SRR3722077.570872/1‑100 (MQ=60)
                            GAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCA                                                                      >  SRR3722077.506498/1‑100 (MQ=60)
                                      TCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGAC                                                            >  SRR3722077.354344/1‑100 (MQ=60)
                                      TCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGAC                                                            >  SRR3722077.742692/1‑100 (MQ=60)
                                           ATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACA                                                       >  SRR3722077.376514/1‑100 (MQ=60)
                                           ATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACA                                                       >  SRR3722077.314090/1‑100 (MQ=60)
                                                     TGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTG                                             <  SRR3722077.665366/100‑1 (MQ=60)
                                                                      GCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCC                            <  SRR3722077.1142875/100‑1 (MQ=60)
                                                                       CGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGATGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCA                           >  SRR3722077.294762/1‑100 (MQ=60)
                                                                               GCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCG                   >  SRR3722077.708909/1‑100 (MQ=60)
                                                                                    GGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCG              >  SRR3722077.320459/1‑100 (MQ=60)
                                                                                             CCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCAG     >  SRR3722077.1175140/1‑100 (MQ=60)
                                                                                                GAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCAGCAC  <  SRR3722077.825809/100‑1 (MQ=60)
                                                                                                   |                                                                                                
CTTTCTGACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCAGCAC  >  NZ_CP009273/2859899‑2860094

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: ‑