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
CGCGTGTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC  >  NZ_CP009273/3896525‑3896720
                                                                                                |                                                                                                   
CGCGTGTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCG                                                                                                  <  SRR3722077.657931/100‑1 (MQ=60)
    TGTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGA                                                                                              >  SRR3722077.1133558/1‑100 (MQ=60)
     GTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGAC                                                                                             <  SRR3722077.996136/100‑1 (MQ=60)
     GTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGAC                                                                                             <  SRR3722077.169801/100‑1 (MQ=60)
     GTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGAC                                                                                             <  SRR3722077.879472/100‑1 (MQ=60)
       AACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCG                                                                                           >  SRR3722077.159795/1‑100 (MQ=60)
         cggcatacgagatggccgtgggtctcgtgggctcggagatgtgtataagagacagGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCT                                                                                         <  SRR3722077.560626/45‑1 (MQ=60)
         CGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCT                                                                                         <  SRR3722077.545022/100‑1 (MQ=60)
                       CATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACC                                                                           >  SRR3722077.122429/1‑100 (MQ=60)
                              CGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAG                                                                    >  SRR3722077.291976/1‑100 (MQ=60)
                                              ACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCAT                                                    >  SRR3722077.197661/1‑100 (MQ=60)
                                                 tgtaaaagagacagaaaAAAGACGGTGGGGGCGTAATGCTCGAAGTGGTCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATG                                                 <  SRR3722077.18842/83‑1 (MQ=60)
                                                  tttgttggtagcaagaaaagccgggggGGGCGTAATGCTGGAAGTGGTCGATGACCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGG                                                <  SRR3722077.1015515/73‑1 (MQ=60)
                                                  TTTGTTGGTAGCGAGAAAAGCCCGGGGGGGCGTAATGCTCGAAGGGGTGGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGG                                                <  SRR3722077.213134/100‑1 (MQ=59)
                                                   ATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGC                                               >  SRR3722077.941106/1‑100 (MQ=60)
                                                    TGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCA                                              >  SRR3722077.539552/1‑100 (MQ=60)
                                                            gacagaaaagccggtggGGGCGTAATCCTCGAGGTGGTCGATCCCCGCTCGTTTACCCCACCCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAA                                      <  SRR3722077.414491/83‑1 (MQ=44)
                                                            gacagaaaagccgggggGGGCGTAATGCTCGAGGTGGTCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAA                                      <  SRR3722077.21262/83‑1 (MQ=60)
                                                              GAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATG                                    >  SRR3722077.625038/1‑100 (MQ=60)
                                                              GAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATG                                    >  SRR3722077.1084727/1‑100 (MQ=60)
                                                              GAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATG                                    >  SRR3722077.21477/1‑100 (MQ=60)
                                                               agaaaagccgggggGGGCGTAATGCCCGAAGGGGTCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG                                   <  SRR3722077.819248/86‑1 (MQ=60)
                                                               AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG                                   >  SRR3722077.628564/1‑100 (MQ=60)
                                                               AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG                                   >  SRR3722077.937435/1‑100 (MQ=60)
                                                               AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG                                   >  SRR3722077.1079500/1‑100 (MQ=60)
                                                                                CGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGG                  >  SRR3722077.210567/1‑100 (MQ=60)
                                                                                           AAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCG       >  SRR3722077.77759/1‑100 (MQ=60)
                                                                                               GGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTctgtctcttatacacatctccgagcccacgagaccca   >  SRR3722077.1030028/1‑63 (MQ=60)
                                                                                                GTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC  >  SRR3722077.14160/1‑100 (MQ=60)
                                                                                                ATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC  >  SRR3722077.737068/1‑100 (MQ=60)
                                                                                                |                                                                                                   
CGCGTGTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC  >  NZ_CP009273/3896525‑3896720

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑