Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 8,418,704
Mapped reads 8,418,704 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 8,418,704 / 100%
Mapped reads, first in pair 4,209,352 / 50%
Mapped reads, second in pair 4,209,352 / 50%
Mapped reads, both in pair 8,418,704 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 86.54
Duplicated reads (estimated) 2,718,532 / 32.29%
Duplication rate 31.43%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 278,921,142 / 38.39%
Number/percentage of C's 85,246,184 / 11.73%
Number/percentage of T's 278,070,134 / 38.27%
Number/percentage of G's 84,300,891 / 11.6%
Number/percentage of N's 42,240 / 0.01%
GC Percentage 23.34%

Coverage

Mean 0.7727
Standard Deviation 5.4738

Mapping Quality

Mean Mapping Quality 24.21

Insert size

Mean 144.7
Standard Deviation 93.64
P25/Median/P75 77 / 119 / 184

Mismatches and indels

General error rate 18.73%
Mismatches 133,370,064
Insertions 914,141
Mapped reads with at least one insertion 9.49%
Deletions 863,100
Mapped reads with at least one deletion 9.27%
Homopolymer indels 49.48%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 73336531 0.8181 2.6515
PGA_scaffold2__36_contigs__length_69596280 69596280 58064582 0.8343 3.8965
PGA_scaffold3__111_contigs__length_57743597 57743597 46277468 0.8014 2.8779
PGA_scaffold4__129_contigs__length_65288255 65288255 49546463 0.7589 4.3466
PGA_scaffold5__109_contigs__length_67248332 67248332 45002917 0.6692 2.9736
PGA_scaffold6__104_contigs__length_61759565 61759565 44992123 0.7285 4.2313
PGA_scaffold7__69_contigs__length_43120122 43120122 32256930 0.7481 2.583
PGA_scaffold8__63_contigs__length_61151155 61151155 47481491 0.7765 2.9964
PGA_scaffold9__45_contigs__length_38581958 38581958 33264590 0.8622 8.1876
PGA_scaffold10__49_contigs__length_53961475 53961475 39185704 0.7262 2.4642
PGA_scaffold11__79_contigs__length_51449921 51449921 35009654 0.6805 3.3564
PGA_scaffold12__71_contigs__length_50438331 50438331 41397767 0.8208 3.8484
PGA_scaffold13__52_contigs__length_44396874 44396874 33914498 0.7639 3.1163
PGA_scaffold14__91_contigs__length_45393038 45393038 45799938 1.009 17.2974
PGA_scaffold15__101_contigs__length_47938513 47938513 29981520 0.6254 2.671
PGA_scaffold16__33_contigs__length_31980953 31980953 26557154 0.8304 9.3966
PGA_scaffold17__51_contigs__length_34923512 34923512 27052361 0.7746 2.9658
PGA_scaffold18__69_contigs__length_27737463 27737463 19045793 0.6866 4.521

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 13:13:39
    Generated by QualiMap v.2.2.1