Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 13,475,352
Mapped reads 13,475,352 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 13,475,352 / 100%
Mapped reads, first in pair 6,737,676 / 50%
Mapped reads, second in pair 6,737,676 / 50%
Mapped reads, both in pair 13,475,352 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 83.45
Duplicated reads (estimated) 5,097,751 / 37.83%
Duplication rate 36.79%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 428,382,900 / 38.2%
Number/percentage of C's 133,916,068 / 11.94%
Number/percentage of T's 426,861,808 / 38.06%
Number/percentage of G's 132,307,973 / 11.8%
Number/percentage of N's 65,146 / 0.01%
GC Percentage 23.74%

Coverage

Mean 1.1926
Standard Deviation 8.3493

Mapping Quality

Mean Mapping Quality 24.28

Insert size

Mean 132.97
Standard Deviation 89.36
P25/Median/P75 69 / 110 / 168

Mismatches and indels

General error rate 18.63%
Mismatches 204,809,762
Insertions 1,369,600
Mapped reads with at least one insertion 8.9%
Deletions 1,283,950
Mapped reads with at least one deletion 8.64%
Homopolymer indels 48.9%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 114531375 1.2776 4.6418
PGA_scaffold2__36_contigs__length_69596280 69596280 90959025 1.307 6.2049
PGA_scaffold3__111_contigs__length_57743597 57743597 71245865 1.2338 4.1694
PGA_scaffold4__129_contigs__length_65288255 65288255 76022416 1.1644 6.0129
PGA_scaffold5__109_contigs__length_67248332 67248332 70193502 1.0438 4.4788
PGA_scaffold6__104_contigs__length_61759565 61759565 68732130 1.1129 8.6483
PGA_scaffold7__69_contigs__length_43120122 43120122 49383638 1.1453 3.9831
PGA_scaffold8__63_contigs__length_61151155 61151155 73072722 1.195 4.4939
PGA_scaffold9__45_contigs__length_38581958 38581958 50898026 1.3192 11.2439
PGA_scaffold10__49_contigs__length_53961475 53961475 61195826 1.1341 3.7231
PGA_scaffold11__79_contigs__length_51449921 51449921 52151115 1.0136 4.8894
PGA_scaffold12__71_contigs__length_50438331 50438331 64567815 1.2801 5.6777
PGA_scaffold13__52_contigs__length_44396874 44396874 52434558 1.181 4.9797
PGA_scaffold14__91_contigs__length_45393038 45393038 70185697 1.5462 23.1264
PGA_scaffold15__101_contigs__length_47938513 47938513 45923566 0.958 4.0465
PGA_scaffold16__33_contigs__length_31980953 31980953 41224710 1.289 19.9506
PGA_scaffold17__51_contigs__length_34923512 34923512 41661560 1.1929 5.2736
PGA_scaffold18__69_contigs__length_27737463 27737463 29507553 1.0638 7.2779

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 13:03:02
    Generated by QualiMap v.2.2.1