Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 17,282,682
Mapped reads 17,282,682 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 17,282,682 / 100%
Mapped reads, first in pair 8,641,341 / 50%
Mapped reads, second in pair 8,641,341 / 50%
Mapped reads, both in pair 17,282,682 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 81.37
Duplicated reads (estimated) 6,829,199 / 39.51%
Duplication rate 39.81%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 536,604,770 / 38.26%
Number/percentage of C's 166,228,712 / 11.85%
Number/percentage of T's 534,930,060 / 38.14%
Number/percentage of G's 164,900,688 / 11.76%
Number/percentage of N's 79,303 / 0.01%
GC Percentage 23.61%

Coverage

Mean 1.4916
Standard Deviation 9.1584

Mapping Quality

Mean Mapping Quality 24.39

Insert size

Mean 125.83
Standard Deviation 86.61
P25/Median/P75 64 / 103 / 159

Mismatches and indels

General error rate 18.85%
Mismatches 259,463,988
Insertions 1,641,218
Mapped reads with at least one insertion 8.36%
Deletions 1,585,291
Mapped reads with at least one deletion 8.34%
Homopolymer indels 49.44%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 142546415 1.5901 5.0247
PGA_scaffold2__36_contigs__length_69596280 69596280 112991649 1.6235 7.3874
PGA_scaffold3__111_contigs__length_57743597 57743597 89037978 1.542 5.0802
PGA_scaffold4__129_contigs__length_65288255 65288255 97386344 1.4916 7.5873
PGA_scaffold5__109_contigs__length_67248332 67248332 87675890 1.3038 5.6619
PGA_scaffold6__104_contigs__length_61759565 61759565 85222422 1.3799 7.4933
PGA_scaffold7__69_contigs__length_43120122 43120122 62800335 1.4564 4.8468
PGA_scaffold8__63_contigs__length_61151155 61151155 91131920 1.4903 5.4722
PGA_scaffold9__45_contigs__length_38581958 38581958 63637936 1.6494 13.9191
PGA_scaffold10__49_contigs__length_53961475 53961475 74988020 1.3897 4.2548
PGA_scaffold11__79_contigs__length_51449921 51449921 67983185 1.3213 5.9416
PGA_scaffold12__71_contigs__length_50438331 50438331 79394903 1.5741 6.8018
PGA_scaffold13__52_contigs__length_44396874 44396874 65184293 1.4682 6.0427
PGA_scaffold14__91_contigs__length_45393038 45393038 86710026 1.9102 27.63
PGA_scaffold15__101_contigs__length_47938513 47938513 58145721 1.2129 4.694
PGA_scaffold16__33_contigs__length_31980953 31980953 50756538 1.5871 14.3156
PGA_scaffold17__51_contigs__length_34923512 34923512 52216041 1.4952 5.2163
PGA_scaffold18__69_contigs__length_27737463 27737463 37823083 1.3636 8.0662

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 13:04:49
    Generated by QualiMap v.2.2.1