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
GCGTTCAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGAAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGT  >  NZ_CP009273/3273631‑3273820
                                                                                          |                                                                                                   
GCGTTCAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACT                                                                                            >  SRR3722077.923491/1‑100 (MQ=60)
GCGTTCAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGAAATGGTACT                                                                                            >  SRR3722077.71492/1‑100 (MQ=60)
    TCAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCA                                                                                        <  SRR3722077.726243/100‑1 (MQ=60)
        TGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAG                                                                                    <  SRR3722077.329306/100‑1 (MQ=60)
        TGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAG                                                                                    <  SRR3722077.866546/100‑1 (MQ=60)
          GGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGAAATGGTACTGGCAGAAGGG                                                                                  <  SRR3722077.54184/100‑1 (MQ=60)
               GATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGC                                                                             <  SRR3722077.364875/100‑1 (MQ=60)
                   TGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTA                                                                         >  SRR3722077.773081/1‑100 (MQ=60)
                             AATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGAAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGA                                                               >  SRR3722077.681861/1‑100 (MQ=60)
                              ATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGAC                                                              <  SRR3722077.88241/100‑1 (MQ=60)
                              ATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGAAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGAC                                                              >  SRR3722077.849352/1‑100 (MQ=60)
                                                 gagatgtgtataagagacagCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGAC                                           <  SRR3722077.606939/80‑1 (MQ=60)
                                                 CGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGAC                                           <  SRR3722077.932635/100‑1 (MQ=60)
                                                        GTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTC                                    <  SRR3722077.610756/100‑1 (MQ=60)
                                                               AAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATggctcttatacacatctccgagcccacgagacccacggccatctcgtatgc                             >  SRR3722077.78140/1‑49 (MQ=60)
                                                                           AACAAAACCTGATGGAAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACA                 >  SRR3722077.605759/1‑100 (MQ=60)
                                                                                  CCTGATGGAAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACctgtctcttatacacatctccgagcccacgagacccacggccatctcgtatg          >  SRR3722077.932375/1‑48 (MQ=60)
                                                                                          GAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGT  >  SRR3722077.200696/1‑100 (MQ=60)
                                                                                          AAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGT  >  SRR3722077.1049105/1‑100 (MQ=60)
                                                                                          |                                                                                                   
GCGTTCAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGAAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGT  >  NZ_CP009273/3273631‑3273820

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑