Input data and parameters 

QualiMap command line

qualimap bamqc -bam LG1-016252-18horse/LC061273_1/sorted.bam -nw 400 -hm 3

Alignment

Command line: "/data/shares/horsecov/.snakemake/conda/872b36850c9d6157ac4050b6010d8f56/bin/bowtie2-align-s --wrapper basic-0 -x LC061273_1/LC061273_1 -S LG1-016252-18horse/LC061273_1/mapped.sam -p 32 -1 LG1-016252-18horse/reads_1.fastq -2 LG1-016252-18horse/reads_2.fastq"
Draw chromosome limits: no
Analyze overlapping paired-end reads: no
Program: bowtie2 (2.4.4)
Analysis date: Thu Nov 18 14:15:47 EST 2021
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: LG1-016252-18horse/LC061273_1/sorted.bam

Summary 

Globals

Reference size 30,916
Number of reads 298,093,978
Mapped reads 2,756,177 / 0.92%
Unmapped reads 295,337,801 / 99.08%
Mapped paired reads 2,756,177 / 0.92%
Mapped reads, first in pair 1,379,252 / 0.46%
Mapped reads, second in pair 1,376,925 / 0.46%
Mapped reads, both in pair 2,745,146 / 0.92%
Mapped reads, singletons 11,031 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 150 / 141.89
Duplicated reads (estimated) 2,726,724 / 0.91%
Duplication rate 97.73%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 123,839,592 / 30.94%
Number/percentage of C's 76,010,695 / 18.99%
Number/percentage of T's 124,060,972 / 31%
Number/percentage of G's 76,310,072 / 19.07%
Number/percentage of N's 11,086 / 0%
GC Percentage 38.06%

Coverage

Mean 12,954.0089
Standard Deviation 11,397.5949

Mapping Quality

Mean Mapping Quality 41.12

Insert size

Mean 260.12
Standard Deviation 877.71
P25/Median/P75 162 / 211 / 278

Mismatches and indels

General error rate 0.97%
Mismatches 3,719,949
Insertions 51,874
Mapped reads with at least one insertion 1.67%
Deletions 112,411
Mapped reads with at least one deletion 3.94%
Homopolymer indels 30.32%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
LC061273.1 30916 400486140 12,954.0089 11,397.5949

Coverage across reference 

Coverage Histogram 

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