Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 16,341,846
Mapped reads 16,341,846 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 16,341,846 / 100%
Mapped reads, first in pair 8,170,923 / 50%
Mapped reads, second in pair 8,170,923 / 50%
Mapped reads, both in pair 16,341,846 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 84.13
Duplicated reads (estimated) 6,207,512 / 37.99%
Duplication rate 36.56%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 528,156,358 / 38.52%
Number/percentage of C's 159,067,969 / 11.6%
Number/percentage of T's 526,416,265 / 38.39%
Number/percentage of G's 157,432,626 / 11.48%
Number/percentage of N's 115,830 / 0.01%
GC Percentage 23.08%

Coverage

Mean 1.4582
Standard Deviation 8.7388

Mapping Quality

Mean Mapping Quality 24.43

Insert size

Mean 133.99
Standard Deviation 88.79
P25/Median/P75 70 / 110 / 169

Mismatches and indels

General error rate 18.58%
Mismatches 249,840,773
Insertions 1,669,407
Mapped reads with at least one insertion 8.94%
Deletions 1,585,823
Mapped reads with at least one deletion 8.8%
Homopolymer indels 49.52%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 139918490 1.5608 4.5817
PGA_scaffold2__36_contigs__length_69596280 69596280 111118803 1.5966 7.0946
PGA_scaffold3__111_contigs__length_57743597 57743597 87581042 1.5167 4.719
PGA_scaffold4__129_contigs__length_65288255 65288255 93319455 1.4293 6.7865
PGA_scaffold5__109_contigs__length_67248332 67248332 84976575 1.2636 4.8768
PGA_scaffold6__104_contigs__length_61759565 61759565 84232708 1.3639 6.9731
PGA_scaffold7__69_contigs__length_43120122 43120122 61728119 1.4315 4.5276
PGA_scaffold8__63_contigs__length_61151155 61151155 88873584 1.4533 4.69
PGA_scaffold9__45_contigs__length_38581958 38581958 62664420 1.6242 12.9958
PGA_scaffold10__49_contigs__length_53961475 53961475 74249813 1.376 4.1593
PGA_scaffold11__79_contigs__length_51449921 51449921 65281467 1.2688 5.4436
PGA_scaffold12__71_contigs__length_50438331 50438331 78177826 1.55 6.107
PGA_scaffold13__52_contigs__length_44396874 44396874 64172449 1.4454 5.2644
PGA_scaffold14__91_contigs__length_45393038 45393038 84183489 1.8545 26.7636
PGA_scaffold15__101_contigs__length_47938513 47938513 57309313 1.1955 4.4502
PGA_scaffold16__33_contigs__length_31980953 31980953 49556176 1.5496 14.9345
PGA_scaffold17__51_contigs__length_34923512 34923512 51057930 1.462 5.1334
PGA_scaffold18__69_contigs__length_27737463 27737463 35693016 1.2868 8.1262

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 12:55:49
    Generated by QualiMap v.2.2.1