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 I200 R1 216 30.8 1683622 97.2% 1636480 87.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTT  >  NZ_CP009273/3770964‑3771125
                                                                                |                                                                                 
TGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACAT                                                                <  SRR3722079.259509/100‑1 (MQ=60)
  GTTTATGGTTTCTTCTACGGGTTGTGCCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATACGATCTCGGTGGAAACCGGGCCGTTTGACATCA                                                              >  SRR3722079.387840/1‑100 (MQ=60)
               TCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTAT                                                 <  SRR3722079.785357/100‑1 (MQ=60)
                      GTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCG                                          >  SRR3722079.380707/1‑100 (MQ=60)
                            gagatgtgtataagagacagTTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACC                                    <  SRR3722079.527676/80‑1 (MQ=60)
                                 TCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGA                               >  SRR3722079.280571/1‑100 (MQ=60)
                                  CGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGAC                              >  SRR3722079.574594/1‑100 (MQ=60)
                                   GCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACC                             <  SRR3722079.254217/100‑1 (MQ=60)
                                   GCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACC                             <  SRR3722079.507200/100‑1 (MQ=60)
                                        GATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTCTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGT                        >  SRR3722079.759904/1‑100 (MQ=60)
                                        GATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCtgtctcttatacacatctccgagcccacgagaccagaga                        >  SRR3722079.578982/1‑61 (MQ=60)
                                        GATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCctgtctcttatacacatctccga                        >  SRR3722079.507429/1‑77 (MQ=60)
                                           CATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTG                     >  SRR3722079.152323/1‑100 (MQ=60)
                                           CATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTG                     >  SRR3722079.534337/1‑100 (MQ=60)
                                                TTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAAT                >  SRR3722079.31883/1‑100 (MQ=60)
                                                  GCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGC              <  SRR3722079.49790/100‑1 (MQ=60)
                                                       GGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCctgtc         >  SRR3722079.379631/1‑95 (MQ=60)
                                                        GTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCG        >  SRR3722079.813716/1‑100 (MQ=60)
                                                              GTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTT  >  SRR3722079.777547/1‑100 (MQ=60)
                                                              GTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTT  >  SRR3722079.435339/1‑100 (MQ=60)
                                                              GTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGAAAATGCTGATCGTCGGTT  >  SRR3722079.624788/1‑100 (MQ=60)
                                                                                |                                                                                 
TGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTT  >  NZ_CP009273/3770964‑3771125

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑