Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 8,734,154
Mapped reads 8,734,154 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 8,734,154 / 100%
Mapped reads, first in pair 4,367,077 / 50%
Mapped reads, second in pair 4,367,077 / 50%
Mapped reads, both in pair 8,734,154 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 86.17
Duplicated reads (estimated) 2,915,751 / 33.38%
Duplication rate 32.11%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 287,199,805 / 38.27%
Number/percentage of C's 88,890,522 / 11.85%
Number/percentage of T's 286,296,166 / 38.15%
Number/percentage of G's 87,989,592 / 11.73%
Number/percentage of N's 64,551 / 0.01%
GC Percentage 23.57%

Coverage

Mean 0.7981
Standard Deviation 5.8196

Mapping Quality

Mean Mapping Quality 23.77

Insert size

Mean 143.56
Standard Deviation 93.48
P25/Median/P75 76 / 118 / 182

Mismatches and indels

General error rate 18.64%
Mismatches 136,905,429
Insertions 995,928
Mapped reads with at least one insertion 10%
Deletions 905,090
Mapped reads with at least one deletion 9.37%
Homopolymer indels 48.1%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 75651478 0.8439 3.0297
PGA_scaffold2__36_contigs__length_69596280 69596280 60244764 0.8656 4.2721
PGA_scaffold3__111_contigs__length_57743597 57743597 48178627 0.8344 3.0282
PGA_scaffold4__129_contigs__length_65288255 65288255 51195912 0.7842 4.2995
PGA_scaffold5__109_contigs__length_67248332 67248332 46635649 0.6935 3.2095
PGA_scaffold6__104_contigs__length_61759565 61759565 46052049 0.7457 5.0468
PGA_scaffold7__69_contigs__length_43120122 43120122 33695810 0.7814 2.7697
PGA_scaffold8__63_contigs__length_61151155 61151155 49036164 0.8019 3.055
PGA_scaffold9__45_contigs__length_38581958 38581958 34317943 0.8895 8.0447
PGA_scaffold10__49_contigs__length_53961475 53961475 40614623 0.7527 2.6174
PGA_scaffold11__79_contigs__length_51449921 51449921 35599159 0.6919 3.3914
PGA_scaffold12__71_contigs__length_50438331 50438331 42777756 0.8481 4.1451
PGA_scaffold13__52_contigs__length_44396874 44396874 35326923 0.7957 3.392
PGA_scaffold14__91_contigs__length_45393038 45393038 46422132 1.0227 17.7783
PGA_scaffold15__101_contigs__length_47938513 47938513 31261282 0.6521 2.7941
PGA_scaffold16__33_contigs__length_31980953 31980953 27435488 0.8579 11.5888
PGA_scaffold17__51_contigs__length_34923512 34923512 28021956 0.8024 3.3519
PGA_scaffold18__69_contigs__length_27737463 27737463 19631530 0.7078 4.9052

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 12:58:54
    Generated by QualiMap v.2.2.1