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 F1 I2 R1 1873 183.1 9376148 98.2% 9207377 93.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGCGTT‑‑GTGACGGGATGAACGACGCCGAAATGCTGTCG  >  NC_000913/4008309‑4008461
                                                                                           |                                                                        
GCGAGCGCGTCAACGTCAGTTCCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑AA                                                                    <  SRR4302535.3445904/94‑1 (MQ=60)
                                                               caAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAT         >  SRR4302535.2044988/3‑94 (MQ=18)
                                                               caAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAT         <  SRR4302535.2250476/92‑1 (MQ=18)
                                                               caAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAT         >  SRR4302535.2493380/3‑94 (MQ=18)
                                                               caAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAT         >  SRR4302535.4497158/3‑94 (MQ=18)
                                                               A‑AAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATG        >  SRR4302535.1057512/1‑94 (MQ=19)
                                                               A‑AAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATG        >  SRR4302535.4621718/1‑94 (MQ=19)
                                                                 AAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGC       >  SRR4302535.3891097/1‑94 (MQ=21)
                                                                  AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCT      <  SRR4302535.2927986/94‑1 (MQ=21)
                                                                  AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCT      <  SRR4302535.4480591/94‑1 (MQ=21)
                                                                  AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCT      >  SRR4302535.4686452/1‑94 (MQ=21)
                                                                   AGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTG     <  SRR4302535.3137592/94‑1 (MQ=23)
                                                                   AGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTG     <  SRR4302535.4663384/94‑1 (MQ=23)
                                                                    GGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGT    >  SRR4302535.4137075/1‑94 (MQ=25)
                                                                      CCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCG  <  SRR4302535.3291791/94‑1 (MQ=28)
                                                                                           |                                                                        
GCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGCGTT‑‑GTGACGGGATGAACGACGCCGAAATGCTGTCG  >  NC_000913/4008309‑4008461

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑