Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 20,533,044
Mapped reads 20,533,044 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 20,533,044 / 100%
Mapped reads, first in pair 10,266,522 / 50%
Mapped reads, second in pair 10,266,522 / 50%
Mapped reads, both in pair 20,533,044 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 90.93
Duplicated reads (estimated) 7,057,472 / 34.37%
Duplication rate 29.81%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 721,855,131 / 38.77%
Number/percentage of C's 210,617,088 / 11.31%
Number/percentage of T's 720,101,097 / 38.67%
Number/percentage of G's 209,532,944 / 11.25%
Number/percentage of N's 166,894 / 0.01%
GC Percentage 22.56%

Coverage

Mean 1.9805
Standard Deviation 9.9461

Mapping Quality

Mean Mapping Quality 24.51

Insert size

Mean 152.24
Standard Deviation 87.13
P25/Median/P75 93 / 130 / 188

Mismatches and indels

General error rate 18.71%
Mismatches 341,867,643
Insertions 2,215,908
Mapped reads with at least one insertion 9.41%
Deletions 2,167,633
Mapped reads with at least one deletion 9.54%
Homopolymer indels 50.43%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 189546243 2.1144 5.6458
PGA_scaffold2__36_contigs__length_69596280 69596280 150475428 2.1621 7.5608
PGA_scaffold3__111_contigs__length_57743597 57743597 118522432 2.0526 6.0709
PGA_scaffold4__129_contigs__length_65288255 65288255 129643935 1.9857 9.2621
PGA_scaffold5__109_contigs__length_67248332 67248332 116742679 1.736 6.3138
PGA_scaffold6__104_contigs__length_61759565 61759565 114927620 1.8609 8.3348
PGA_scaffold7__69_contigs__length_43120122 43120122 83918716 1.9462 6.0252
PGA_scaffold8__63_contigs__length_61151155 61151155 121756328 1.9911 6.6267
PGA_scaffold9__45_contigs__length_38581958 38581958 84308533 2.1852 16.6239
PGA_scaffold10__49_contigs__length_53961475 53961475 99944181 1.8521 5.0926
PGA_scaffold11__79_contigs__length_51449921 51449921 89908714 1.7475 6.5516
PGA_scaffold12__71_contigs__length_50438331 50438331 105897682 2.0995 8.0871
PGA_scaffold13__52_contigs__length_44396874 44396874 86892569 1.9572 7.0606
PGA_scaffold14__91_contigs__length_45393038 45393038 112964109 2.4886 28.4904
PGA_scaffold15__101_contigs__length_47938513 47938513 78067968 1.6285 5.7574
PGA_scaffold16__33_contigs__length_31980953 31980953 65919513 2.0612 13.8076
PGA_scaffold17__51_contigs__length_34923512 34923512 68818395 1.9705 5.7829
PGA_scaffold18__69_contigs__length_27737463 27737463 48050100 1.7323 8.316

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 12:49:21
    Generated by QualiMap v.2.2.1