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 I1 R1 1061 294.1 15065038 98.6% 14854127 93.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GAATAGACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCG  >  NC_000913/4474804‑4474948
                                                               |                                                                                             
GAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                                                                <  SRR4302542.132341/94‑1 (MQ=30)
 AATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGC                                                               <  SRR4302542.1498834/94‑1 (MQ=28)
 AATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGC                                                               >  SRR4302542.6644119/1‑94 (MQ=28)
 AATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGC                                                               >  SRR4302542.1126975/1‑94 (MQ=28)
 AATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGC                                                               >  SRR4302542.3649613/1‑94 (MQ=28)
  ATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCG                                                              >  SRR4302542.2899476/1‑94 (MQ=26)
  ATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCG                                                              <  SRR4302542.7370775/94‑1 (MQ=26)
   TAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGA                                                             <  SRR4302542.4452650/94‑1 (MQ=25)
    AGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGAC                                                            >  SRR4302542.5502012/1‑94 (MQ=23)
    AGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGAC                                                            >  SRR4302542.5653157/1‑94 (MQ=23)
    AGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGAC                                                            >  SRR4302542.381652/1‑94 (MQ=23)
      ACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCA                                                          >  SRR4302542.7431552/1‑94 (MQ=23)
      ACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCA                                                          <  SRR4302542.5337903/94‑1 (MQ=23)
      ACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCA                                                          <  SRR4302542.7056609/94‑1 (MQ=23)
      ACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCA                                                          >  SRR4302542.1396898/1‑94 (MQ=23)
       CCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCAT                                                         >  SRR4302542.4638770/1‑94 (MQ=23)
          ATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCAC                                                      <  SRR4302542.3136584/94‑1 (MQ=23)
           TCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACC                                                     <  SRR4302542.7427422/94‑1 (MQ=23)
            CACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCG                                                    <  SRR4302542.351942/94‑1 (MQ=23)
            CACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCG                                                    <  SRR4302542.7267259/94‑1 (MQ=23)
             ACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGC                                                   >  SRR4302542.4447186/1‑94 (MQ=23)
             ACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGC                                                   >  SRR4302542.2305718/1‑94 (MQ=23)
               TGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTT                                                 <  SRR4302542.5429925/94‑1 (MQ=26)
                GCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTT                                                <  SRR4302542.7072041/94‑1 (MQ=28)
                 CATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTG                                               <  SRR4302542.2441076/94‑1 (MQ=30)
                 CATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTG                                               >  SRR4302542.7012773/1‑94 (MQ=30)
                 CATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTG                                               <  SRR4302542.5702333/94‑1 (MQ=30)
                  ataAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGA                                              >  SRR4302542.4884433/4‑94 (MQ=33)
                   A‑AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATA                                            >  SRR4302542.4930069/1‑94 (MQ=36)
                     AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG                                           <  SRR4302542.5421732/94‑1 (MQ=38)
                     AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG                                           >  SRR4302542.4549804/1‑94 (MQ=38)
                     AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG                                           >  SRR4302542.2921034/1‑94 (MQ=38)
                      AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGT                                          >  SRR4302542.3012641/1‑94 (MQ=38)
                       ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTA                                         >  SRR4302542.522869/1‑94 (MQ=38)
                        TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT                                        <  SRR4302542.698711/94‑1 (MQ=38)
                         AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATG                                       <  SRR4302542.6564044/94‑1 (MQ=40)
                          ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGC                                      >  SRR4302542.5199202/1‑94 (MQ=42)
                          ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGC                                      >  SRR4302542.1976152/1‑94 (MQ=42)
                          ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGC                                      <  SRR4302542.1296638/94‑1 (MQ=42)
                           TGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCA                                     >  SRR4302542.4842162/1‑94 (MQ=44)
                                                              TTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCG  >  SRR4302542.5389361/1‑94 (MQ=60)
                                                               |                                                                                             
GAATAGACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCG  >  NC_000913/4474804‑4474948

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑