Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 15,270,176
Mapped reads 15,270,176 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 15,270,176 / 100%
Mapped reads, first in pair 7,635,088 / 50%
Mapped reads, second in pair 7,635,088 / 50%
Mapped reads, both in pair 15,270,176 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 91.89
Duplicated reads (estimated) 4,741,242 / 31.05%
Duplication rate 26.98%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 541,967,603 / 38.73%
Number/percentage of C's 159,326,782 / 11.39%
Number/percentage of T's 540,246,665 / 38.61%
Number/percentage of G's 157,828,012 / 11.28%
Number/percentage of N's 76,329 / 0.01%
GC Percentage 22.66%

Coverage

Mean 1.4883
Standard Deviation 9.2124

Mapping Quality

Mean Mapping Quality 24.04

Insert size

Mean 155.53
Standard Deviation 88.3
P25/Median/P75 94 / 131 / 192

Mismatches and indels

General error rate 18.77%
Mismatches 257,363,345
Insertions 1,728,108
Mapped reads with at least one insertion 9.85%
Deletions 1,665,113
Mapped reads with at least one deletion 9.84%
Homopolymer indels 49.56%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 143751942 1.6036 4.6408
PGA_scaffold2__36_contigs__length_69596280 69596280 115093240 1.6537 7.769
PGA_scaffold3__111_contigs__length_57743597 57743597 88734160 1.5367 4.9789
PGA_scaffold4__129_contigs__length_65288255 65288255 95953435 1.4697 7.416
PGA_scaffold5__109_contigs__length_67248332 67248332 87080269 1.2949 5.3665
PGA_scaffold6__104_contigs__length_61759565 61759565 85585018 1.3858 6.9267
PGA_scaffold7__69_contigs__length_43120122 43120122 62465860 1.4486 4.6407
PGA_scaffold8__63_contigs__length_61151155 61151155 90847622 1.4856 5.4861
PGA_scaffold9__45_contigs__length_38581958 38581958 63725148 1.6517 13.7927
PGA_scaffold10__49_contigs__length_53961475 53961475 76523670 1.4181 4.1509
PGA_scaffold11__79_contigs__length_51449921 51449921 65455376 1.2722 5.903
PGA_scaffold12__71_contigs__length_50438331 50438331 80807159 1.6021 6.8019
PGA_scaffold13__52_contigs__length_44396874 44396874 65348932 1.4719 5.6561
PGA_scaffold14__91_contigs__length_45393038 45393038 84692735 1.8658 27.984
PGA_scaffold15__101_contigs__length_47938513 47938513 57912727 1.2081 4.6956
PGA_scaffold16__33_contigs__length_31980953 31980953 50780893 1.5878 15.733
PGA_scaffold17__51_contigs__length_34923512 34923512 51623463 1.4782 4.9674
PGA_scaffold18__69_contigs__length_27737463 27737463 36157999 1.3036 8.3455

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped Reads Nucleotide Content 

Mapped Reads GC-content Distribution 

Homopolymer Indels 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram 

Contents

  • Summary
  • Coverage across reference
  • Coverage Histogram
  • Coverage Histogram (0-50X)
  • Genome Fraction Coverage
  • Duplication Rate Histogram
  • Mapped Reads Nucleotide Content
  • Mapped Reads GC-content Distribution
  • Homopolymer Indels
  • Mapping Quality Across Reference
  • Mapping Quality Histogram
  • Insert Size Across Reference
  • Insert Size Histogram
    • 2019/09/12 13:32:07
    Generated by QualiMap v.2.2.1