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 1624 250.6 12620048 98.0% 12367647 93.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGA  >  NC_000913/4474810‑4474961
                                                                      |                                                                                             
ACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCA                                                                       >  SRR4302533.1633318/1‑94 (MQ=19)
ACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCA                                                                       <  SRR4302533.3813881/94‑1 (MQ=19)
 CCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCAT                                                                      >  SRR4302533.3187978/1‑94 (MQ=18)
 CCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCAT                                                                      >  SRR4302533.5632033/1‑94 (MQ=18)
  CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                                                                     <  SRR4302533.1094256/94‑1 (MQ=16)
        CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCT                                                               >  SRR4302533.1197422/1‑94 (MQ=16)
        CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCT                                                               >  SRR4302533.2088223/1‑94 (MQ=16)
           CATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTG                                                            >  SRR4302533.5706532/1‑94 (MQ=21)
               AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG                                                        >  SRR4302533.211499/1‑94 (MQ=28)
               AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG                                                        >  SRR4302533.6296712/1‑94 (MQ=28)
               AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG                                                        <  SRR4302533.6133200/94‑1 (MQ=28)
               AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG                                                        <  SRR4302533.6081766/94‑1 (MQ=28)
                AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT                                                       >  SRR4302533.318713/1‑94 (MQ=28)
                 ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTA                                                      >  SRR4302533.1167317/1‑94 (MQ=28)
                  TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT                                                     >  SRR4302533.4370559/1‑94 (MQ=28)
                    ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC                                                   >  SRR4302533.6047079/1‑94 (MQ=32)
                    ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC                                                   <  SRR4302533.2694274/94‑1 (MQ=32)
                     TGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCA                                                  <  SRR4302533.6234426/94‑1 (MQ=34)
                      GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT                                                 <  SRR4302533.4917826/94‑1 (MQ=36)
                      GTGATGCCGGGATGGTTTGTATTTCACGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT                                                 <  SRR4302533.6125012/94‑1 (MQ=36)
                                                                      AATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGA  >  SRR4302533.3907826/1‑94 (MQ=60)
                                                                      AATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGA  <  SRR4302533.614135/94‑1 (MQ=60)
                                                                      |                                                                                             
ACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGA  >  NC_000913/4474810‑4474961

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑