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 593 264.2 13311096 97.8% 13018251 93.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GAATAGACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCA  >  NC_000913/4474804‑4474913
                                                       |                                                                  
GAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                             >  SRR4302547.2724918/1‑94 (MQ=30)
GAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                             >  SRR4302547.3602510/1‑94 (MQ=30)
  ATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCG                           <  SRR4302547.1968575/94‑1 (MQ=26)
    AGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGAC                         >  SRR4302547.6010941/1‑94 (MQ=23)
    AGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGAC                         >  SRR4302547.5203257/1‑94 (MQ=23)
    AGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGAC                         >  SRR4302547.1384358/1‑94 (MQ=23)
      ACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCA                       >  SRR4302547.962300/1‑94 (MQ=23)
       CCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCAT                      <  SRR4302547.5545493/94‑1 (MQ=23)
        CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATA                     >  SRR4302547.2121929/1‑94 (MQ=21)
          ATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCAC                   >  SRR4302547.4563808/1‑94 (MQ=23)
          ATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCAC                   >  SRR4302547.2794413/1‑94 (MQ=23)
           TCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACC                  >  SRR4302547.1736114/1‑94 (MQ=23)
            CACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCG                 <  SRR4302547.5292096/94‑1 (MQ=23)
             ACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGC                >  SRR4302547.4615315/1‑94 (MQ=23)
             ACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGC                >  SRR4302547.1431912/1‑94 (MQ=23)
              CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCT               >  SRR4302547.3438102/1‑94 (MQ=25)
              CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCT               <  SRR4302547.5020789/94‑1 (MQ=25)
                 CATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTG            >  SRR4302547.5683741/1‑94 (MQ=30)
                  ataAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGA           >  SRR4302547.1888056/4‑94 (MQ=33)
                   taAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGAT          <  SRR4302547.5468146/92‑1 (MQ=34)
                   A‑AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATA         <  SRR4302547.665297/94‑1 (MQ=36)
                     AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG        >  SRR4302547.4063796/1‑94 (MQ=38)
                     AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG        <  SRR4302547.2280010/94‑1 (MQ=38)
                      AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGT       <  SRR4302547.5844499/94‑1 (MQ=38)
                          ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGC   <  SRR4302547.3369200/94‑1 (MQ=42)
                           TGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCA  <  SRR4302547.546162/94‑1 (MQ=44)
                                                       |                                                                  
GAATAGACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCA  >  NC_000913/4474804‑4474913

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑