Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 9,840,976
Mapped reads 9,840,976 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 9,840,976 / 100%
Mapped reads, first in pair 4,920,488 / 50%
Mapped reads, second in pair 4,920,488 / 50%
Mapped reads, both in pair 9,840,976 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 90.88
Duplicated reads (estimated) 2,849,523 / 28.96%
Duplication rate 24.46%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 336,326,256 / 38.03%
Number/percentage of C's 107,213,002 / 12.12%
Number/percentage of T's 335,010,833 / 37.89%
Number/percentage of G's 105,728,761 / 11.96%
Number/percentage of N's 56,749 / 0.01%
GC Percentage 24.08%

Coverage

Mean 0.9435
Standard Deviation 7.6315

Mapping Quality

Mean Mapping Quality 19.67

Insert size

Mean 165.66
Standard Deviation 96.79
P25/Median/P75 97 / 133 / 206

Mismatches and indels

General error rate 21.38%
Mismatches 177,460,807
Insertions 3,726,566
Mapped reads with at least one insertion 22.01%
Deletions 2,293,855
Mapped reads with at least one deletion 17.64%
Homopolymer indels 39.62%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 86033098 0.9597 3.5455
PGA_scaffold2__36_contigs__length_69596280 69596280 68817947 0.9888 4.8319
PGA_scaffold3__111_contigs__length_57743597 57743597 55537882 0.9618 3.8969
PGA_scaffold4__129_contigs__length_65288255 65288255 60838646 0.9318 9.1474
PGA_scaffold5__109_contigs__length_67248332 67248332 56414939 0.8389 4.7682
PGA_scaffold6__104_contigs__length_61759565 61759565 55268557 0.8949 5.4133
PGA_scaffold7__69_contigs__length_43120122 43120122 39251520 0.9103 3.5109
PGA_scaffold8__63_contigs__length_61151155 61151155 56950326 0.9313 3.756
PGA_scaffold9__45_contigs__length_38581958 38581958 42058465 1.0901 12.6924
PGA_scaffold10__49_contigs__length_53961475 53961475 47407646 0.8785 4.352
PGA_scaffold11__79_contigs__length_51449921 51449921 42771854 0.8313 4.2309
PGA_scaffold12__71_contigs__length_50438331 50438331 49853959 0.9884 5.4954
PGA_scaffold13__52_contigs__length_44396874 44396874 41310330 0.9305 4.5082
PGA_scaffold14__91_contigs__length_45393038 45393038 56147495 1.2369 21.4745
PGA_scaffold15__101_contigs__length_47938513 47938513 37634218 0.7851 3.5301
PGA_scaffold16__33_contigs__length_31980953 31980953 33872063 1.0591 14.2368
PGA_scaffold17__51_contigs__length_34923512 34923512 34013608 0.9739 5.1432
PGA_scaffold18__69_contigs__length_27737463 27737463 24899607 0.8977 7.425

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
    • 2019/08/12 17:02:47
    Generated by QualiMap v.2.2.1