Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 8,062,088
Mapped reads 8,062,088 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 8,062,088 / 100%
Mapped reads, first in pair 4,031,044 / 50%
Mapped reads, second in pair 4,031,044 / 50%
Mapped reads, both in pair 8,062,088 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 85.02
Duplicated reads (estimated) 2,718,797 / 33.72%
Duplication rate 33%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 261,750,813 / 38.29%
Number/percentage of C's 80,650,483 / 11.8%
Number/percentage of T's 261,140,511 / 38.2%
Number/percentage of G's 80,047,205 / 11.71%
Number/percentage of N's 48,304 / 0.01%
GC Percentage 23.51%

Coverage

Mean 0.727
Standard Deviation 3.7995

Mapping Quality

Mean Mapping Quality 24.28

Insert size

Mean 141.44
Standard Deviation 92.49
P25/Median/P75 74 / 118 / 183

Mismatches and indels

General error rate 18.42%
Mismatches 123,499,396
Insertions 825,463
Mapped reads with at least one insertion 8.96%
Deletions 782,943
Mapped reads with at least one deletion 8.78%
Homopolymer indels 49.07%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 69345656 0.7736 2.5969
PGA_scaffold2__36_contigs__length_69596280 69596280 55103330 0.7918 3.1697
PGA_scaffold3__111_contigs__length_57743597 57743597 44090258 0.7636 2.6795
PGA_scaffold4__129_contigs__length_65288255 65288255 47178386 0.7226 3.1771
PGA_scaffold5__109_contigs__length_67248332 67248332 42466736 0.6315 2.5659
PGA_scaffold6__104_contigs__length_61759565 61759565 41362647 0.6697 3.4354
PGA_scaffold7__69_contigs__length_43120122 43120122 31332018 0.7266 2.5296
PGA_scaffold8__63_contigs__length_61151155 61151155 44765297 0.732 2.7511
PGA_scaffold9__45_contigs__length_38581958 38581958 30556903 0.792 5.5817
PGA_scaffold10__49_contigs__length_53961475 53961475 36713497 0.6804 2.2749
PGA_scaffold11__79_contigs__length_51449921 51449921 33036133 0.6421 2.9719
PGA_scaffold12__71_contigs__length_50438331 50438331 39225305 0.7777 3.6206
PGA_scaffold13__52_contigs__length_44396874 44396874 32212772 0.7256 2.872
PGA_scaffold14__91_contigs__length_45393038 45393038 41488325 0.914 10.0238
PGA_scaffold15__101_contigs__length_47938513 47938513 28558109 0.5957 2.5061
PGA_scaffold16__33_contigs__length_31980953 31980953 24125595 0.7544 5.2207
PGA_scaffold17__51_contigs__length_34923512 34923512 25757418 0.7375 2.7528
PGA_scaffold18__69_contigs__length_27737463 27737463 17769448 0.6406 3.5519

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 14:09:45
    Generated by QualiMap v.2.2.1