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
GAATAAGGACGCGCCTTACGCACGTCGAAGTCGATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGGCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGTTTTGCAGCGCCGCTTTCTCGTAAGACGCCAGACGTTTCGGCATCCAGTCGAGG  >  NZ_CP009273/2396003‑2396188
                                                                                                |                                                                                         
GAATAAGGACGCGCCTTACGCACGTCGAAGTCGATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGGCGG                                                                                        >  SRR3722077.1005381/1‑100 (MQ=60)
GAATAAGGACGCGCCTTACGCACGTCGAAGTCGATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGGCGG                                                                                        >  SRR3722077.292016/1‑100 (MQ=60)
GAATAAGGACGCGCCTTACGCACGTCGAAGTCGATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGCCGG                                                                                        >  SRR3722077.272201/1‑100 (MQ=60)
GAATAAGGACGCGCCTTACGCACGTCGAAGTCGATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGCCGG                                                                                        >  SRR3722077.745013/1‑100 (MQ=60)
GAATAAGGACGCGCCTTACGCACGTCGAAGTCGATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGCCGG                                                                                        >  SRR3722077.554325/1‑100 (MQ=60)
        ACGCGCCTTACGCACGTCGAAGTCGATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGGCGGCAACGCCC                                                                                <  SRR3722077.282859/100‑1 (MQ=60)
             CCTTACGCACGTCGAAGTCGATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGGCGGCAACGCCCTGGGA                                                                           >  SRR3722077.934860/1‑100 (MQ=60)
                         CGAAGTCGATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGCCGGCAACGCCCTGGGAACGACCTTTCAG                                                               <  SRR3722077.1170594/100‑1 (MQ=60)
                              TCGATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGGCGGCAACGCCCTGGGAACGACCTTTCAGAATGG                                                          <  SRR3722077.1078431/100‑1 (MQ=60)
                                 ATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGCCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGT                                                       >  SRR3722077.723351/1‑100 (MQ=60)
                                       GTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGCCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGTTTTGCA                                                 >  SRR3722077.1109825/1‑100 (MQ=60)
                                                       CGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGCCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGTTTTGCAGCGCCGCTTTCTCGTA                                 >  SRR3722077.1085796/1‑100 (MQ=60)
                                                          CAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGGCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGTTTTGCAGCtgtctcttatacacatc                              >  SRR3722077.827783/1‑83 (MQ=60)
                                                           AGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGGCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGTTTTGCAGCGCCGCTTTCTCGTAAGAC                             >  SRR3722077.1066817/1‑100 (MQ=60)
                                                                    CCACTCCAGCGCCTCTTTCGCGCCATAGGCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGTTTTGCAGCGCCGCTTTCTCGTAAGACGCCAGACGT                    >  SRR3722077.502385/1‑100 (MQ=60)
                                                                    CCACTCCAGCGCCTCTTTCGCGCCATAGCCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGTTTTGCAGCGCCGCTTTCTCGTAAGACGCCAGACGT                    >  SRR3722077.488160/1‑100 (MQ=60)
                                                                       CTCCAGCGCCTCTTTCGCGCCATAGCCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGTTTTGCAGCGCCGCTTTCTCGTAAGACGCCAGACGTTTC                 >  SRR3722077.624695/1‑100 (MQ=60)
                                                                               CCTCTTTCGCGCCATAGCCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGTTTTGCAGCGCCGCTTTCTCGTAAGACGCCAGACGTTTCGGCATCCA         >  SRR3722077.882224/1‑100 (MQ=60)
                                                                                  CTTTCGCGCCATAGCCGGCAACGCCCTGGGAACGACCTTTCAGAATGGGGTTTTGCAGCGCCGCTTTCTCGTAAGACGCCAGACGTTTCGGCATCCAGTC      >  SRR3722077.350924/1‑100 (MQ=60)
                                                                                      CGCGCCATAGGCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGTTTTGCAGCGCCGCTTTCTCGTAAGACGCCAGACGTTTCGGCATCCAGTCGAGG  <  SRR3722077.534387/100‑1 (MQ=60)
                                                                                                |                                                                                         
GAATAAGGACGCGCCTTACGCACGTCGAAGTCGATCCCGGTAGCACGCAGGCCCGCGCCAGTGGTGCCCCACTCCAGCGCCTCTTTCGCGCCATAGGCGGCAACGCCCTGGGAACGACCTTTCAGAATGGTGTTTTGCAGCGCCGCTTTCTCGTAAGACGCCAGACGTTTCGGCATCCAGTCGAGG  >  NZ_CP009273/2396003‑2396188

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑