Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 6,876,230
Mapped reads 6,876,230 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 6,876,230 / 100%
Mapped reads, first in pair 3,438,115 / 50%
Mapped reads, second in pair 3,438,115 / 50%
Mapped reads, both in pair 6,876,230 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 90.07
Duplicated reads (estimated) 2,043,439 / 29.72%
Duplication rate 27.11%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 236,977,495 / 38.37%
Number/percentage of C's 72,631,669 / 11.76%
Number/percentage of T's 236,203,424 / 38.25%
Number/percentage of G's 71,748,062 / 11.62%
Number/percentage of N's 36,863 / 0.01%
GC Percentage 23.38%

Coverage

Mean 0.6568
Standard Deviation 4.968

Mapping Quality

Mean Mapping Quality 24.05

Insert size

Mean 153.66
Standard Deviation 91.82
P25/Median/P75 90 / 129 / 192

Mismatches and indels

General error rate 18.63%
Mismatches 112,662,997
Insertions 781,154
Mapped reads with at least one insertion 9.9%
Deletions 735,594
Mapped reads with at least one deletion 9.65%
Homopolymer indels 49.26%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 62082870 0.6926 2.5529
PGA_scaffold2__36_contigs__length_69596280 69596280 49815302 0.7158 3.4002
PGA_scaffold3__111_contigs__length_57743597 57743597 39344125 0.6814 2.6151
PGA_scaffold4__129_contigs__length_65288255 65288255 42093850 0.6447 3.8046
PGA_scaffold5__109_contigs__length_67248332 67248332 38423761 0.5714 2.7234
PGA_scaffold6__104_contigs__length_61759565 61759565 37768697 0.6115 4.6725
PGA_scaffold7__69_contigs__length_43120122 43120122 27848674 0.6458 2.504
PGA_scaffold8__63_contigs__length_61151155 61151155 40227091 0.6578 2.9276
PGA_scaffold9__45_contigs__length_38581958 38581958 28544636 0.7398 7.3002
PGA_scaffold10__49_contigs__length_53961475 53961475 33177070 0.6148 2.2429
PGA_scaffold11__79_contigs__length_51449921 51449921 29433201 0.5721 2.9406
PGA_scaffold12__71_contigs__length_50438331 50438331 35590300 0.7056 3.7881
PGA_scaffold13__52_contigs__length_44396874 44396874 29033748 0.654 2.911
PGA_scaffold14__91_contigs__length_45393038 45393038 38397347 0.8459 15.4533
PGA_scaffold15__101_contigs__length_47938513 47938513 25485419 0.5316 2.4539
PGA_scaffold16__33_contigs__length_31980953 31980953 22281687 0.6967 8.3559
PGA_scaffold17__51_contigs__length_34923512 34923512 23310354 0.6675 2.8803
PGA_scaffold18__69_contigs__length_27737463 27737463 16107396 0.5807 3.6018

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 13:12:41
    Generated by QualiMap v.2.2.1