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
GGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAAC  >  NZ_CP009273/2778843‑2779017
                                                                                           |                                                                                   
GGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTAC                                                                             >  SRR3722077.1040470/1‑100 (MQ=60)
GGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTAC                                                                             >  SRR3722077.9424/1‑100 (MQ=60)
GGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACT                                                                            >  SRR3722077.1086647/1‑100 (MQ=60)
 GGTATAGTAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTT                                                                           >  SRR3722077.403624/1‑100 (MQ=60)
      AATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAA                                                                      >  SRR3722077.363898/1‑100 (MQ=60)
            TGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGT                                                                 >  SRR3722077.1013693/1‑100 (MQ=60)
            TGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGT                                                                 >  SRR3722077.336624/1‑100 (MQ=60)
            TGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTA                                                                >  SRR3722077.208188/1‑100 (MQ=60)
            TGATAATACTCTGGCTTTATCGTTAACTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGT                                                                 >  SRR3722077.457920/1‑100 (MQ=60)
                 ATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGA                                                            <  SRR3722077.844538/100‑1 (MQ=60)
                  TACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGAT                                                           >  SRR3722077.221384/1‑100 (MQ=60)
                   ACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGctgtctctta                                                          >  SRR3722077.237273/1‑90 (MQ=60)
                   ACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATG                                                          <  SRR3722077.576077/100‑1 (MQ=60)
                           TTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAC                                                 <  SRR3722077.570898/100‑1 (MQ=60)
                           TTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAC                                                 <  SRR3722077.302453/100‑1 (MQ=60)
                           TTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAC                                                 <  SRR3722077.181550/100‑1 (MQ=60)
                            TTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAC                                                 <  SRR3722077.330922/100‑1 (MQ=60)
                            TTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAC                                                 <  SRR3722077.5996/100‑1 (MQ=60)
                                 GTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGC                                            <  SRR3722077.337084/100‑1 (MQ=60)
                                    AATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGT                                         >  SRR3722077.498722/1‑100 (MQ=60)
                                        ACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGctgtc                                     >  SRR3722077.358501/1‑95 (MQ=60)
                                        ACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGT                                    >  SRR3722077.839818/1‑100 (MQ=60)
                                           attcaaaagtacctggaaaaatgcctGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCC                                 >  SRR3722077.281696/27‑100 (MQ=60)
                                             ATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCAC                               <  SRR3722077.854512/100‑1 (MQ=60)
                                              TTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACG                              >  SRR3722077.813512/1‑100 (MQ=60)
                                                  ACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACC                          <  SRR3722077.1105958/100‑1 (MQ=60)
                                                     TGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAA                       <  SRR3722077.371294/100‑1 (MQ=60)
                                                       TAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGGGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAAC                     <  SRR3722077.864137/100‑1 (MQ=60)
                                                         AGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACAC                   <  SRR3722077.744282/100‑1 (MQ=60)
                                                                          GCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAA   <  SRR3722077.294150/100‑1 (MQ=60)
                                                                          GCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAAC  >  SRR3722077.233607/1‑100 (MQ=60)
                                                                          GCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAAC  >  SRR3722077.1171883/1‑100 (MQ=60)
                                                                          GCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAAC  >  SRR3722077.994144/1‑100 (MQ=60)
                                                                                           |                                                                                   
GGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAAC  >  NZ_CP009273/2778843‑2779017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑