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
AGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTT  >  NZ_CP009273/951724‑951893
                                                                                     |                                                                                    
AGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGA                                                                        >  SRR3722077.172757/1‑100 (MQ=60)
  CAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAG                                                                      <  SRR3722077.608955/100‑1 (MQ=60)
    tataagagacagCATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTC                                                                    <  SRR3722077.133720/88‑1 (MQ=60)
       CTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGC                                                                 >  SRR3722077.1038639/1‑100 (MQ=60)
                    GTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTG                                                    <  SRR3722077.250189/100‑1 (MQ=60)
                        TTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTG                                                <  SRR3722077.1063016/100‑1 (MQ=60)
                        TTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTG                                                <  SRR3722077.189358/100‑1 (MQ=60)
                          TTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAG                                              <  SRR3722077.553855/100‑1 (MQ=60)
                             gacagGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGA                                           <  SRR3722077.801199/95‑1 (MQ=60)
                             cggcatacgagatggccgtgggtctcgtgggctcggagatgtgtataagagacaGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGA                                           <  SRR3722077.619872/46‑1 (MQ=60)
                             GGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGA                                           <  SRR3722077.863282/100‑1 (MQ=60)
                             GGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGA                                           <  SRR3722077.1145818/100‑1 (MQ=60)
                                           ATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTC                             <  SRR3722077.14772/100‑1 (MQ=60)
                                             cgtgggtctcgtgggctcggagatgtgtataagagacaGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCAC                           <  SRR3722077.115592/62‑1 (MQ=60)
                                               TTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCG                         <  SRR3722077.216393/100‑1 (MQ=60)
                                               TTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCG                         <  SRR3722077.306524/100‑1 (MQ=60)
                                                     GGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCA                   >  SRR3722077.946821/1‑100 (MQ=60)
                                                     GGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCA                   >  SRR3722077.955043/1‑100 (MQ=60)
                                                     GGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCctgtctcttatacacatctccgagcccacgagacccacggccatctcgtatgccgtcttc                   >  SRR3722077.451040/1‑40 (MQ=60)
                                                         gagatgtgtataagagacagGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAG               <  SRR3722077.312399/80‑1 (MQ=60)
                                                            TGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCA            >  SRR3722077.871205/1‑100 (MQ=60)
                                                                CGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGC        <  SRR3722077.1106060/100‑1 (MQ=60)
                                                                      GACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTCT  >  SRR3722077.794924/1‑100 (MQ=60)
                                                                                     |                                                                                    
AGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTT  >  NZ_CP009273/951724‑951893

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑