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 744 338.8 17650688 97.8% 17262372 93.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GAATAGACCTATCACTGCAT‑AAA‑TAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT  >  NC_000913/4474804‑4474914
                                                        |                                                                   
GAATAGACCTATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                              <  SRR4302541.6376892/94‑1 (MQ=30)
 AATAGACCTATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGC                             >  SRR4302541.1654877/1‑94 (MQ=28)
  ATAGACCTATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCG                            >  SRR4302541.1064698/1‑94 (MQ=26)
  ATAGACCTATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCG                            <  SRR4302541.3516925/94‑1 (MQ=26)
  ATAGACCTATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCG                            <  SRR4302541.2239115/94‑1 (MQ=26)
   TAGACCTATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGA                           >  SRR4302541.170613/1‑94 (MQ=25)
    AGACCTATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATACCA‑ATTATTTACTGAGCGTCGCGAC                          >  SRR4302541.952878/1‑94 (MQ=23)
      ACCTATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCA                        <  SRR4302541.5353577/94‑1 (MQ=23)
      ACCTATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCA                        >  SRR4302541.3941967/1‑94 (MQ=23)
       CCTATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCAT                       <  SRR4302541.8391051/94‑1 (MQ=23)
       CCTATCACTGCAT‑AAAGTAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCAT                       >  SRR4302541.8679884/1‑94 (MQ=23)
        CTATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATC                      >  SRR4302541.4481835/1‑94 (MQ=23)
         TATCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCA                     >  SRR4302541.1969558/1‑94 (MQ=23)
           TCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACC                   <  SRR4302541.3096390/94‑1 (MQ=23)
           TCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACC                   <  SRR4302541.8333602/94‑1 (MQ=23)
           TCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACC                   <  SRR4302541.4433272/94‑1 (MQ=23)
           TCACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACC                   <  SRR4302541.4433271/94‑1 (MQ=23)
            CACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCG                  >  SRR4302541.8058638/1‑94 (MQ=23)
            CACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCG                  >  SRR4302541.5289788/1‑94 (MQ=23)
            CACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCG                  <  SRR4302541.7058721/94‑1 (MQ=23)
             ACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGC                 >  SRR4302541.6583967/1‑94 (MQ=23)
             ACTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGC                 >  SRR4302541.7279158/1‑94 (MQ=23)
              CTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCT                >  SRR4302541.8719114/1‑94 (MQ=25)
              CTGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCT                >  SRR4302541.2557570/1‑94 (MQ=25)
               TGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTT               <  SRR4302541.3798018/94‑1 (MQ=26)
               TGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTT               >  SRR4302541.681467/1‑94 (MQ=26)
               TGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTT               >  SRR4302541.4720154/1‑94 (MQ=26)
               TGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTT               >  SRR4302541.1834900/1‑94 (MQ=26)
               TGCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTT               >  SRR4302541.932997/1‑94 (MQ=26)
                GCATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTT              <  SRR4302541.5070730/94‑1 (MQ=28)
                 CATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTG             >  SRR4302541.259572/1‑94 (MQ=30)
                 CATAAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTG             <  SRR4302541.3712178/94‑1 (MQ=30)
                  ataAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGA            >  SRR4302541.5491823/4‑94 (MQ=33)
                  ataAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGA            <  SRR4302541.8313156/91‑1 (MQ=33)
                  ataAAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGA            >  SRR4302541.7580347/4‑94 (MQ=33)
                   A‑AAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATA          <  SRR4302541.5126128/94‑1 (MQ=36)
                     AAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG         >  SRR4302541.5096756/1‑94 (MQ=38)
                     AAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG         <  SRR4302541.8890563/94‑1 (MQ=38)
                     AAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG         <  SRR4302541.3605955/94‑1 (MQ=38)
                     AAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG         >  SRR4302541.7180695/1‑94 (MQ=38)
                     AAA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG         <  SRR4302541.3216418/94‑1 (MQ=38)
                      AA‑TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGT        >  SRR4302541.3563530/1‑94 (MQ=38)
                         TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT      <  SRR4302541.8550385/94‑1 (MQ=38)
                         TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT      <  SRR4302541.6289598/94‑1 (MQ=38)
                         TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT      <  SRR4302541.6735616/94‑1 (MQ=38)
                         TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT      <  SRR4302541.6635867/94‑1 (MQ=38)
                          AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATG     <  SRR4302541.6655345/94‑1 (MQ=40)
                          AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATG     >  SRR4302541.8892444/1‑94 (MQ=40)
                          AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATG     >  SRR4302541.2947050/1‑94 (MQ=40)
                          AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATG     <  SRR4302541.1025425/94‑1 (MQ=40)
                           ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGC    >  SRR4302541.5372608/1‑94 (MQ=42)
                            TGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCA   >  SRR4302541.449594/1‑94 (MQ=44)
                             GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT  >  SRR4302541.7060258/1‑94 (MQ=46)
                             GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT  <  SRR4302541.8541188/94‑1 (MQ=46)
                             GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT  <  SRR4302541.5011888/94‑1 (MQ=46)
                                                        |                                                                   
GAATAGACCTATCACTGCAT‑AAA‑TAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT  >  NC_000913/4474804‑4474914

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑