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 I200 R1 216 30.8 1683622 97.2% 1636480 87.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
AACATTATCGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAATATC  >  NZ_CP009273/2797279‑2797470
                                                                                                  |                                                                                             
AACATTATCGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTCC                                                                                              <  SRR3722079.202886/100‑1 (MQ=60)
            GTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAG                                                                                 >  SRR3722079.322887/1‑100 (MQ=60)
                   TCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACC                                                                           <  SRR3722079.147845/100‑1 (MQ=60)
                       CTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATAC                                                                      <  SRR3722079.379799/100‑1 (MQ=60)
                               GAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACC                                                              <  SRR3722079.747723/100‑1 (MQ=60)
                                    TCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATC                                                         <  SRR3722079.334001/100‑1 (MQ=60)
                                       CCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGT                                                      >  SRR3722079.579682/1‑100 (MQ=60)
                                                                    TATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGG                         <  SRR3722079.539438/100‑1 (MQ=60)
                                                                     ATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGG                         <  SRR3722079.829795/100‑1 (MQ=60)
                                                                          GGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACT                    >  SRR3722079.325087/1‑100 (MQ=60)
                                                                          GGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACT                    >  SRR3722079.772280/1‑100 (MQ=60)
                                                                            TTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACA                 <  SRR3722079.270909/100‑1 (MQ=60)
                                                                             TTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACAT                <  SRR3722079.323676/100‑1 (MQ=60)
                                                                                  GCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGC            <  SRR3722079.819400/100‑1 (MQ=60)
                                                                                       CGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATGAA      <  SRR3722079.680686/100‑1 (MQ=60)
                                                                                       CGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAA      <  SRR3722079.748418/100‑1 (MQ=60)
                                                                                        GATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAA      <  SRR3722079.153740/100‑1 (MQ=60)
                                                                                        GATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAA      <  SRR3722079.385996/100‑1 (MQ=60)
                                                                                          TGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAATA    <  SRR3722079.104272/100‑1 (MQ=60)
                                                                                           GTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAATATC  <  SRR3722079.322295/100‑1 (MQ=60)
                                                                                                  |                                                                                             
AACATTATCGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAATATC  >  NZ_CP009273/2797279‑2797470

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑