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 884 257.2 12958910 96.9% 12557183 93.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GAATAGACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGG  >  NC_000913/4474804‑4474949
                                                               |                                                                                              
GAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                                                                 >  SRR4302534.958612/1‑94 (MQ=30)
GAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                                                                 <  SRR4302534.6268895/94‑1 (MQ=30)
GAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                                                                 <  SRR4302534.4778871/94‑1 (MQ=30)
GAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                                                                 >  SRR4302534.365223/1‑94 (MQ=30)
 AATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGC                                                                >  SRR4302534.488566/1‑94 (MQ=28)
 AATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGC                                                                >  SRR4302534.2292060/1‑94 (MQ=28)
  ATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCG                                                               <  SRR4302534.5754023/94‑1 (MQ=26)
   TAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGA                                                              >  SRR4302534.2076163/1‑94 (MQ=25)
   TAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGA                                                              >  SRR4302534.2106766/1‑94 (MQ=25)
   TAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGA                                                              >  SRR4302534.2727712/1‑94 (MQ=25)
    AGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGAC                                                             >  SRR4302534.3972114/1‑94 (MQ=23)
    AGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGAC                                                             >  SRR4302534.6434607/1‑94 (MQ=23)
    AGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGAC                                                             >  SRR4302534.3566492/1‑94 (MQ=23)
    AGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGAC                                                             >  SRR4302534.515199/1‑94 (MQ=23)
        CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATC                                                         >  SRR4302534.1997468/1‑94 (MQ=23)
        CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATC                                                         >  SRR4302534.712796/1‑94 (MQ=23)
            CACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCG                                                     >  SRR4302534.3195034/1‑94 (MQ=23)
            CACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCG                                                     >  SRR4302534.6512785/1‑94 (MQ=23)
            CACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCG                                                     >  SRR4302534.5090705/1‑94 (MQ=23)
              CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCT                                                   <  SRR4302534.2747548/94‑1 (MQ=25)
              CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCT                                                   <  SRR4302534.1749441/94‑1 (MQ=25)
                   A‑AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATA                                             <  SRR4302534.626776/94‑1 (MQ=36)
                     AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG                                            <  SRR4302534.5367205/94‑1 (MQ=38)
                     AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG                                            >  SRR4302534.1630916/1‑94 (MQ=38)
                     AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG                                            >  SRR4302534.3958905/1‑94 (MQ=38)
                      AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGT                                           <  SRR4302534.3399522/94‑1 (MQ=38)
                      AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGT                                           >  SRR4302534.6516617/1‑94 (MQ=38)
                       ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTA                                          <  SRR4302534.727920/94‑1 (MQ=38)
                       ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTA                                          >  SRR4302534.2201514/1‑94 (MQ=38)
                        TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT                                         <  SRR4302534.4944404/94‑1 (MQ=38)
                        TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT                                         <  SRR4302534.3735664/94‑1 (MQ=38)
                        TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT                                         <  SRR4302534.5667432/94‑1 (MQ=38)
                        TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT                                         >  SRR4302534.2503119/1‑94 (MQ=38)
                        TAATGTGATGCCGGGATGGCTTGTATTTCCCCGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT                                         >  SRR4302534.633443/1‑94 (MQ=38)
                         AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATG                                        >  SRR4302534.3865867/1‑94 (MQ=40)
                         AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATG                                        <  SRR4302534.1121608/94‑1 (MQ=40)
                          ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGC                                       <  SRR4302534.267429/94‑1 (MQ=42)
                           TGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCA                                      <  SRR4302534.2201741/94‑1 (MQ=44)
                            GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGCCCATCACCGCTTTGATAGTATGCAT                                     <  SRR4302534.6395245/94‑1 (MQ=36)
                            GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT                                     <  SRR4302534.465477/94‑1 (MQ=46)
                            GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT                                     <  SRR4302534.151707/94‑1 (MQ=46)
                                                              TTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCG   <  SRR4302534.3205101/94‑1 (MQ=60)
                                                               TATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGG  >  SRR4302534.1405015/1‑94 (MQ=60)
                                                               |                                                                                              
GAATAGACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGG  >  NC_000913/4474804‑4474949

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: ‑