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 I75 R1 71 32.8 2150506 93.3% 2006422 83.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CTCCAGCGCCTGCTCAAACAACGGTACGTTGCGGTTAACGTGGGTCGGCAGCAGCTTGCTGATCGGCACATCGCAGTTTTCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGGAACACGGTGACGCCAGGTTTACCGCCGAGCAAACCGCCAACGCGGGAT  >  NZ_CP009273/4548615‑4548792
                                                                               |                                                                                                  
CTCCAGCGCCTGCTCAAACAACGGTACGTTGCGGTTAACGTGGGTCGGCAGCAGCTTGCTGATCGGCACATCGCAGTTTTCCAGCAGGTCATAAATAGGC                                                                                <  SRR3722213.236571/100‑1 (MQ=60)
                         ACGTTGCGGTTAACGTGGGTCGGCAGCAGCTTGCTGATCGGCACATCGCAGTTTCCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCA                                                       >  SRR3722213.267763/1‑100 (MQ=60)
                              GCGGTTAACGTGGGTCGGCAGCAGCTTGCTGATCGGCACATCGCAGTTTCCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGG                                                  <  SRR3722213.225313/100‑1 (MQ=60)
                                 ggtctcgtgggctcggagatgtgtataagagacagCATCGCAGTTTTCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGGAAC                                               <  SRR3722213.694551/65‑1 (MQ=60)
                                   TAACGTGGGTCGGCAGCAGCTTGCTGATCGGCACATCGCAGTTTCCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGGAACAC                                             <  SRR3722213.760028/100‑1 (MQ=60)
                                   TAACGTGGGTCGGCAGCAGCTTGCTGATCGGCACATCGCAGTTTCCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGGAACAC                                             <  SRR3722213.869073/100‑1 (MQ=60)
                                     tcggagatgtgtataagagacagGATCGGCACATCGCAGTTTTCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGGAACACGG                                           <  SRR3722213.1065328/77‑1 (MQ=60)
                                     ACGTGGGTCGGCAGCAGCTTGCTGATCGGCACATCGCAGTTTCCCAGCAGGTCATAAATAGTCTGTAACGCCTTTTTACTGTCGCCCATGTGGAACACGG                                           <  SRR3722213.357812/100‑1 (MQ=60)
                                          GGTCGGCAGCAGCTTGCTGATCGGCACATCGCAGTTTCCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACctgtctcttatacacatctccgagcc                                      >  SRR3722213.3011/1‑74 (MQ=60)
                                                      CTTGCTGATCGGCACATCGCAGTTTCCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGGAACACGGTGACGCCAGGTTTACCG                          <  SRR3722213.919280/100‑1 (MQ=60)
                                                            GATCGGCACATCGCAGTTTCCCAGCAGGTCATAAActgtctcttatacacatctccgagcccacgagacccgttattatctcgtatgccgtcttctgctt                    >  SRR3722213.668643/1‑35 (MQ=59)
                                                                 GCACATCGCAGTTTCCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCActgtctcttatacacatctccgagcccacgagacccgtta               >  SRR3722213.444927/1‑60 (MQ=60)
                                                                 GCACATCGCAGTTTCCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGGAACACGGTGACGCCAGGTTTACCGCCGAGCAAACC               >  SRR3722213.320513/1‑100 (MQ=60)
                                                                           GTTTCCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGGAACACGGTGACGCCAGGTTTACCGCCGAGCAAACCGCCAACGCGG     >  SRR3722213.861199/1‑100 (MQ=60)
                                                                              TCCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGGAACACGGTGACGCCAGGTTTACCGCCGAGCAAACCGCCAACGCGGGAT  <  SRR3722213.5387/100‑1 (MQ=60)
                                                                              TCCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGGAACACGGTGACGCCAGGTTTACCGCCGAGCAAACCGCCAACGCGGGAT  <  SRR3722213.621473/100‑1 (MQ=60)
                                                                               |                                                                                                  
CTCCAGCGCCTGCTCAAACAACGGTACGTTGCGGTTAACGTGGGTCGGCAGCAGCTTGCTGATCGGCACATCGCAGTTTTCCAGCAGGTCATAAATAGGCTGTAACGCCTTTTTACTGTCGCCCATGTGGAACACGGTGACGCCAGGTTTACCGCCGAGCAAACCGCCAACGCGGGAT  >  NZ_CP009273/4548615‑4548792

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑