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
AAAATGATATTGGCGAGATATTTATGAACTCTCTGGCAGGTATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGATCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGATCAATACCTGATAAATCAATCGCAAACAGCAAGAACCAGTG  >  NZ_CP009273/4073064‑4073258
                                                                                                   |                                                                                               
AAAATGATATTGGCGAGATATTTATGAACTCTCTGGCAGGTATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGT                                                                                                 >  SRR3722077.668578/1‑100 (MQ=60)
     GATATTGGCGAGATATTTATGAACTCTCTGGCAGGTATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCG                                                                                            >  SRR3722077.216481/1‑100 (MQ=60)
      ATATTGGCGAGATATTTATGAACTCTCTGGCAGGTATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGA                                                                                           >  SRR3722077.501608/1‑100 (MQ=60)
                    TTTATGAACTCTCTGGCAGGTATAGATATGGGCAGAATTTTACTCTATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATC                                                                             >  SRR3722077.1028924/1‑100 (MQ=60)
                    TTTATGAACTCTCTGGCAGGTATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGATCTCGAGGTGCAGCGTAATC                                                                             >  SRR3722077.1177238/1‑100 (MQ=60)
                          gtataagagaCAGGTATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTC                                                                       <  SRR3722077.164400/90‑1 (MQ=60)
                              CTCTGGCAGGTATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGC                                                                   >  SRR3722077.549755/1‑100 (MQ=60)
                                       GTATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATT                                                          >  SRR3722077.1000716/1‑100 (MQ=60)
                                       GTATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGATCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATT                                                          >  SRR3722077.629020/1‑100 (MQ=60)
                                         ATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAA                                                        >  SRR3722077.1010917/1‑100 (MQ=60)
                                         ATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAA                                                        >  SRR3722077.424347/1‑100 (MQ=60)
                                          gacggcatacgagatggccgtgggtctcgtgggctcggagatgtgtataagagacaGATCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAG                                                       <  SRR3722077.69501/44‑1 (MQ=60)
                                            GATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGG                                                     <  SRR3722077.843408/100‑1 (MQ=60)
                                             ATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGA                                                    <  SRR3722077.890651/100‑1 (MQ=60)
                                                 GGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGATCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCG                                                >  SRR3722077.1130596/1‑100 (MQ=60)
                                                      GAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGA                                           >  SRR3722077.645288/1‑100 (MQ=60)
                                                       AATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGAT                                          <  SRR3722077.1164758/100‑1 (MQ=60)
                                                       AATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGAT                                          <  SRR3722077.1119602/100‑1 (MQ=60)
                                                        ATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGATC                                         >  SRR3722077.1110251/1‑100 (MQ=60)
                                                        ATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGATCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGATC                                         >  SRR3722077.497609/1‑100 (MQ=60)
                                                             ACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGATCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGATCAATAC                                    <  SRR3722077.1171274/100‑1 (MQ=60)
                                                                     TATCGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGATCAATACCTGATAAA                            <  SRR3722077.1035190/100‑1 (MQ=60)
                                                                        CGAATGAGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGATCctgtctcttatacaca                         >  SRR3722077.471182/1‑84 (MQ=60)
                                                                            tgtataagagacagAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGATCAATACCTGATAAATCAATCG                     <  SRR3722077.848144/86‑1 (MQ=60)
                                                                              AGGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGATCAATACCTGATAAATCAATCGCA                   >  SRR3722077.35570/1‑100 (MQ=60)
                                                                               GGTGATTAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGATCAATACCTGATAAATCAATCGCAA                  >  SRR3722077.917353/1‑100 (MQ=60)
                                                                                  GATTAAGCAACTTGATGATCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGctgtctcttatacacatctccgagcccacgagacccac               >  SRR3722077.1103852/1‑62 (MQ=60)
                                                                                     TAAGCAACTTGATGTTCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTTGATCAATACCTGATAAATCAATCGCAAACAGCA            <  SRR3722077.1063711/100‑1 (MQ=60)
                                                                                               GATGATCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGATCAATACCTGATAAATCAATCGCAAACAGCAAGAACCAGTG  <  SRR3722077.184638/100‑1 (MQ=60)
                                                                                                   |                                                                                               
AAAATGATATTGGCGAGATATTTATGAACTCTCTGGCAGGTATAGATATGGGCAGAATTTTACTCGATTTATCGAATGAGGTGATTAAGCAACTTGATGATCTCGAGGTGCAGCGTAATCTTCCTCGTGCGGACCTATTAAGGGAAGCGGTAGATCAATACCTGATAAATCAATCGCAAACAGCAAGAACCAGTG  >  NZ_CP009273/4073064‑4073258

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑