Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 13,399,110
Mapped reads 13,399,110 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 13,399,110 / 100%
Mapped reads, first in pair 6,699,555 / 50%
Mapped reads, second in pair 6,699,555 / 50%
Mapped reads, both in pair 13,399,110 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 88.7
Duplicated reads (estimated) 4,791,669 / 35.76%
Duplication rate 31.8%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 455,135,605 / 38.4%
Number/percentage of C's 138,909,338 / 11.72%
Number/percentage of T's 453,669,198 / 38.28%
Number/percentage of G's 137,484,177 / 11.6%
Number/percentage of N's 64,695 / 0.01%
GC Percentage 23.32%

Coverage

Mean 1.2605
Standard Deviation 8.0758

Mapping Quality

Mean Mapping Quality 23.56

Insert size

Mean 142.06
Standard Deviation 85.06
P25/Median/P75 84 / 119 / 175

Mismatches and indels

General error rate 18.65%
Mismatches 216,404,456
Insertions 1,478,476
Mapped reads with at least one insertion 9.61%
Deletions 1,395,172
Mapped reads with at least one deletion 9.4%
Homopolymer indels 48.09%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 119795284 1.3363 7.6115
PGA_scaffold2__36_contigs__length_69596280 69596280 95313973 1.3695 6.4202
PGA_scaffold3__111_contigs__length_57743597 57743597 75429174 1.3063 4.8474
PGA_scaffold4__129_contigs__length_65288255 65288255 81268988 1.2448 6.3102
PGA_scaffold5__109_contigs__length_67248332 67248332 73980167 1.1001 4.8867
PGA_scaffold6__104_contigs__length_61759565 61759565 74050689 1.199 10.399
PGA_scaffold7__69_contigs__length_43120122 43120122 53112287 1.2317 4.5036
PGA_scaffold8__63_contigs__length_61151155 61151155 77122632 1.2612 4.8839
PGA_scaffold9__45_contigs__length_38581958 38581958 54013526 1.4 11.6104
PGA_scaffold10__49_contigs__length_53961475 53961475 62720144 1.1623 4.0901
PGA_scaffold11__79_contigs__length_51449921 51449921 56667892 1.1014 5.07
PGA_scaffold12__71_contigs__length_50438331 50438331 67209918 1.3325 5.8817
PGA_scaffold13__52_contigs__length_44396874 44396874 55638044 1.2532 5.9972
PGA_scaffold14__91_contigs__length_45393038 45393038 72385798 1.5946 20.1678
PGA_scaffold15__101_contigs__length_47938513 47938513 50004918 1.0431 4.7031
PGA_scaffold16__33_contigs__length_31980953 31980953 42782769 1.3378 13.5828
PGA_scaffold17__51_contigs__length_34923512 34923512 44674532 1.2792 5.943
PGA_scaffold18__69_contigs__length_27737463 27737463 31686513 1.1424 7.0598

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 13:22:25
    Generated by QualiMap v.2.2.1