Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 15,792,158
Mapped reads 15,792,158 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 15,792,158 / 100%
Mapped reads, first in pair 7,896,079 / 50%
Mapped reads, second in pair 7,896,079 / 50%
Mapped reads, both in pair 15,792,158 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 92.09
Duplicated reads (estimated) 4,898,191 / 31.02%
Duplication rate 26.82%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 563,597,708 / 38.85%
Number/percentage of C's 163,079,204 / 11.24%
Number/percentage of T's 562,092,875 / 38.75%
Number/percentage of G's 161,840,067 / 11.16%
Number/percentage of N's 18,851 / 0%
GC Percentage 22.4%

Coverage

Mean 1.5427
Standard Deviation 6.8618

Mapping Quality

Mean Mapping Quality 24.79

Insert size

Mean 164.41
Standard Deviation 92.1
P25/Median/P75 100 / 141 / 208

Mismatches and indels

General error rate 18.7%
Mismatches 266,529,247
Insertions 1,652,090
Mapped reads with at least one insertion 9.15%
Deletions 1,682,344
Mapped reads with at least one deletion 9.64%
Homopolymer indels 51.71%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 146360651 1.6327 4.0863
PGA_scaffold2__36_contigs__length_69596280 69596280 116447567 1.6732 5.1603
PGA_scaffold3__111_contigs__length_57743597 57743597 93493204 1.6191 4.7259
PGA_scaffold4__129_contigs__length_65288255 65288255 100457098 1.5387 6.1988
PGA_scaffold5__109_contigs__length_67248332 67248332 90254303 1.3421 4.5261
PGA_scaffold6__104_contigs__length_61759565 61759565 89050779 1.4419 5.6967
PGA_scaffold7__69_contigs__length_43120122 43120122 65326708 1.515 4.4024
PGA_scaffold8__63_contigs__length_61151155 61151155 95206149 1.5569 5.0773
PGA_scaffold9__45_contigs__length_38581958 38581958 65724963 1.7035 11.1391
PGA_scaffold10__49_contigs__length_53961475 53961475 77319821 1.4329 3.7948
PGA_scaffold11__79_contigs__length_51449921 51449921 71304075 1.3859 5.0169
PGA_scaffold12__71_contigs__length_50438331 50438331 82626649 1.6382 5.9168
PGA_scaffold13__52_contigs__length_44396874 44396874 67545773 1.5214 5.0823
PGA_scaffold14__91_contigs__length_45393038 45393038 87981398 1.9382 19.4421
PGA_scaffold15__101_contigs__length_47938513 47938513 61894376 1.2911 4.3099
PGA_scaffold16__33_contigs__length_31980953 31980953 51072527 1.597 8.0597
PGA_scaffold17__51_contigs__length_34923512 34923512 54256813 1.5536 4.4129
PGA_scaffold18__69_contigs__length_27737463 27737463 37427589 1.3494 5.4659

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 14:01:45
    Generated by QualiMap v.2.2.1