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
CCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACAC  >  NZ_CP009273/385951‑386128
                                                                                              |                                                                                   
CCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAT                                                                                >  SRR3722077.710270/1‑100 (MQ=60)
           cagaagacggcatacgagatggccgtgggtctcgtgggctcggagatgtgtataagagacagCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGC                                                                     <  SRR3722077.762111/38‑1 (MQ=60)
           ACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGC                                                                     <  SRR3722077.869090/100‑1 (MQ=60)
              ATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGC                                                                  >  SRR3722077.273814/1‑100 (MQ=60)
              ATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGC                                                                  >  SRR3722077.1032883/1‑100 (MQ=60)
                    ACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCG                                                            >  SRR3722077.796566/1‑100 (MQ=60)
                     CCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGG                                                           <  SRR3722077.707330/100‑1 (MQ=60)
                             TTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATG                                                   <  SRR3722077.119775/100‑1 (MQ=60)
                             TTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATG                                                   <  SRR3722077.602904/100‑1 (MQ=60)
                               GAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGAT                                                 <  SRR3722077.480580/100‑1 (MQ=60)
                                AACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATC                                                >  SRR3722077.345696/1‑100 (MQ=60)
                                          gagacagCAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGC                                      <  SRR3722077.498701/93‑1 (MQ=60)
                                                 CAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGT                               >  SRR3722077.829369/1‑100 (MQ=60)
                                                   cggagatgtgtataagagacagCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAA                             <  SRR3722077.1031265/78‑1 (MQ=60)
                                                   GTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAA                             >  SRR3722077.478268/1‑100 (MQ=60)
                                                    TACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAAT                            <  SRR3722077.1151765/100‑1 (MQ=60)
                                                      CTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAA                          >  SRR3722077.163146/1‑100 (MQ=60)
                                                      CTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAA                          <  SRR3722077.695326/100‑1 (MQ=60)
                                                      CTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAA                          <  SRR3722077.440964/100‑1 (MQ=60)
                                                      CTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAA                          <  SRR3722077.849605/100‑1 (MQ=60)
                                                        GCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATC                        <  SRR3722077.556825/100‑1 (MQ=60)
                                                        GCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATC                        <  SRR3722077.66512/100‑1 (MQ=60)
                                                                GCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGctgtctcttatacacat                >  SRR3722077.649664/1‑83 (MQ=60)
                                                                    GATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGGAATAATCTGGGTGGATATG            >  SRR3722077.716044/1‑100 (MQ=60)
                                                                     ATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGctgtctctt           >  SRR3722077.50098/1‑91 (MQ=60)
                                                                       ATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATT         <  SRR3722077.532384/100‑1 (MQ=60)
                                                                         CAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTT       >  SRR3722077.274390/1‑100 (MQ=60)
                                                                          AGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGActgtctcttatacacatctccgagcccacgagacc      >  SRR3722077.598925/1‑65 (MQ=60)
                                                                              ATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACAC  >  SRR3722077.414256/1‑100 (MQ=60)
                                                                                              |                                                                                   
CCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACAC  >  NZ_CP009273/385951‑386128

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑