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
CCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGA  >  NC_000913/4474811‑4474961
                                                                     |                                                                                             
CCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCAT                                                                      >  SRR4302535.4673479/1‑94 (MQ=18)
 CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                                                                     >  SRR4302535.608446/1‑94 (MQ=16)
 CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                                                                     >  SRR4302535.256948/1‑94 (MQ=16)
       CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCT                                                               >  SRR4302535.3109987/1‑94 (MQ=16)
       CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCT                                                               <  SRR4302535.1583109/94‑1 (MQ=16)
          CATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTG                                                            <  SRR4302535.3310029/94‑1 (MQ=21)
            taAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGAT                                                          <  SRR4302535.2479488/92‑1 (MQ=25)
            A‑AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATA                                                         >  SRR4302535.1351298/1‑94 (MQ=26)
              AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG                                                        >  SRR4302535.1228544/1‑94 (MQ=28)
               AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT                                                       >  SRR4302535.51271/1‑94 (MQ=28)
                ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTA                                                      <  SRR4302535.358320/94‑1 (MQ=28)
                 TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT                                                     >  SRR4302535.2127482/1‑94 (MQ=28)
                  AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATG                                                    >  SRR4302535.3517061/1‑94 (MQ=30)
                   ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC                                                   <  SRR4302535.2319897/94‑1 (MQ=32)
                   ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC                                                   >  SRR4302535.2379915/1‑94 (MQ=32)
                   ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTCGATAGTATGC                                                   >  SRR4302535.4602569/1‑94 (MQ=23)
                     GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT                                                 <  SRR4302535.4394344/94‑1 (MQ=36)
                                                        TATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGG              >  SRR4302535.1191314/1‑94 (MQ=60)
                                                                     AATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGA  >  SRR4302535.471415/1‑94 (MQ=60)
                                                                     |                                                                                             
CCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGA  >  NC_000913/4474811‑4474961

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑