Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 9,439,830
Mapped reads 9,439,830 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 9,439,830 / 100%
Mapped reads, first in pair 4,719,915 / 50%
Mapped reads, second in pair 4,719,915 / 50%
Mapped reads, both in pair 9,439,830 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 81.47
Duplicated reads (estimated) 3,505,430 / 37.13%
Duplication rate 38.11%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 292,937,046 / 38.19%
Number/percentage of C's 91,288,872 / 11.9%
Number/percentage of T's 292,128,083 / 38.09%
Number/percentage of G's 90,641,888 / 11.82%
Number/percentage of N's 43,495 / 0.01%
GC Percentage 23.72%

Coverage

Mean 0.8157
Standard Deviation 5.6512

Mapping Quality

Mean Mapping Quality 24.43

Insert size

Mean 126.88
Standard Deviation 87.97
P25/Median/P75 64 / 103 / 161

Mismatches and indels

General error rate 18.44%
Mismatches 138,630,667
Insertions 939,994
Mapped reads with at least one insertion 8.74%
Deletions 875,977
Mapped reads with at least one deletion 8.42%
Homopolymer indels 49.05%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 77551570 0.8651 3.5456
PGA_scaffold2__36_contigs__length_69596280 69596280 61857256 0.8888 4.4315
PGA_scaffold3__111_contigs__length_57743597 57743597 48783198 0.8448 3.0826
PGA_scaffold4__129_contigs__length_65288255 65288255 52415017 0.8028 4.3572
PGA_scaffold5__109_contigs__length_67248332 67248332 47696591 0.7093 3.1049
PGA_scaffold6__104_contigs__length_61759565 61759565 47339203 0.7665 6.4752
PGA_scaffold7__69_contigs__length_43120122 43120122 34366447 0.797 2.7915
PGA_scaffold8__63_contigs__length_61151155 61151155 49885608 0.8158 3.0548
PGA_scaffold9__45_contigs__length_38581958 38581958 34845944 0.9032 7.8696
PGA_scaffold10__49_contigs__length_53961475 53961475 41342929 0.7662 2.6524
PGA_scaffold11__79_contigs__length_51449921 51449921 36574690 0.7109 3.4717
PGA_scaffold12__71_contigs__length_50438331 50438331 43616489 0.8647 3.919
PGA_scaffold13__52_contigs__length_44396874 44396874 35833002 0.8071 3.495
PGA_scaffold14__91_contigs__length_45393038 45393038 47185670 1.0395 14.9784
PGA_scaffold15__101_contigs__length_47938513 47938513 31865837 0.6647 2.8656
PGA_scaffold16__33_contigs__length_31980953 31980953 28546182 0.8926 12.6819
PGA_scaffold17__51_contigs__length_34923512 34923512 28635401 0.8199 3.8121
PGA_scaffold18__69_contigs__length_27737463 27737463 20298417 0.7318 5.1192

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 13:01:34
    Generated by QualiMap v.2.2.1