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
AACCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAGGTTGAAGCACTGG  >  NZ_CP009273/2189225‑2189408
                                                                                       |                                                                                                
ANCCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTA                                                                                      >  SRR3722077.703148/1‑100 (MQ=60)
AACCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTA                                                                                      >  SRR3722077.1049274/1‑100 (MQ=60)
 ACCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTAT                                                                                     <  SRR3722077.1068683/100‑1 (MQ=60)
      TTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGC                                                                                <  SRR3722077.1171050/100‑1 (MQ=60)
                   TGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGG                                                                   >  SRR3722077.1162456/1‑100 (MQ=60)
                    GACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGC                                                                  <  SRR3722077.1080954/100‑1 (MQ=60)
                    GACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGC                                                                  <  SRR3722077.152350/100‑1 (MQ=60)
                                 CCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATC                                                     <  SRR3722077.713175/100‑1 (MQ=60)
                                   ataagagacagAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCG                                                   <  SRR3722077.767918/89‑1 (MQ=60)
                                         GCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATctgtctcttatacacatctccgagcccacgagacccacggccatc                                             >  SRR3722077.371843/1‑55 (MQ=60)
                                                  GACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGGATCCAGCctgtctcttatacacatctccgagcccacgaacgtccgattatc                                    >  SRR3722077.11658/1‑56 (MQ=60)
                                                               GAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATA                       <  SRR3722077.985143/100‑1 (MQ=60)
                                                                  GCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGA                    <  SRR3722077.629596/100‑1 (MQ=60)
                                                                     gagacagATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGC                 <  SRR3722077.629693/93‑1 (MQ=60)
                                                                          CAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAGGTT            >  SRR3722077.876948/1‑100 (MQ=60)
                                                                               CGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAGGTTGAAGC       <  SRR3722077.546829/100‑1 (MQ=60)
                                                                                    CTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAGGTTGAAGCACTGG  <  SRR3722077.337709/100‑1 (MQ=60)
                                                                                       |                                                                                                
AACCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAGGTTGAAGCACTGG  >  NZ_CP009273/2189225‑2189408

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑