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
TCTACATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGTAGGTTTAACCTGTTGCAT  >  NZ_CP009273/886100‑886288
                                                                                         |                                                                                                   
TCTACATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAA                                                                                           >  SRR3722077.776190/1‑100 (MQ=60)
   gggctcggagatgtgtataagagacagTCATTGCTCAATTTCTCAGCCAGTTCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGG                                                                                        <  SRR3722077.673252/73‑1 (MQ=60)
              CTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATT                                                                             >  SRR3722077.601557/1‑100 (MQ=60)
                GAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTC                                                                           <  SRR3722077.910377/100‑1 (MQ=60)
                    ATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTC                                                                       <  SRR3722077.707587/100‑1 (MQ=60)
                              TCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATT                                                             >  SRR3722077.57185/1‑100 (MQ=60)
                              TCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATT                                                             <  SRR3722077.1120952/100‑1 (MQ=60)
                                   GCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGC                                                        >  SRR3722077.487398/1‑100 (MQ=60)
                                   GCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGC                                                        <  SRR3722077.838770/100‑1 (MQ=60)
                                    CTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCC                                                       <  SRR3722077.369802/100‑1 (MQ=60)
                                    CTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCC                                                       <  SRR3722077.797747/100‑1 (MQ=60)
                                    CTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCC                                                       <  SRR3722077.1030376/100‑1 (MQ=60)
                                           ggctcggagatgtgtataagagacagCAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATG                                                <  SRR3722077.199600/74‑1 (MQ=60)
                                              CAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATC                                             <  SRR3722077.868160/100‑1 (MQ=60)
                                                        TTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAAT                                   <  SRR3722077.334110/100‑1 (MQ=60)
                                                              gagacagCAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTC                             <  SRR3722077.962021/93‑1 (MQ=60)
                                                                                         ACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGActgtctcttatacacatctccgagcccacgagacccacggccatctcgtatgccgtcttct  >  SRR3722077.357279/1‑39 (MQ=60)
                                                                                         |                                                                                                   
TCTACATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGTAGGTTTAACCTGTTGCAT  >  NZ_CP009273/886100‑886288

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑