BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716241.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 2,212,583
number of mapped reads = 2,022,807 (91.42%)
number of supplementary alignments = 35,437 (1.6%)
number of secondary alignments = 0
number of mapped bases = 157,639,402 bp
number of sequenced bases = 157,569,166 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 101,139
duplication rate = 3.05%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.6217
>>>>>>> ACTG content
number of A's = 40,011,412 bp (25.39%)
number of C's = 31,546,108 bp (20.02%)
number of T's = 48,097,681 bp (30.52%)
number of G's = 37,905,243 bp (24.06%)
number of N's = 8,722 bp (0.01%)
GC percentage = 44.08%
>>>>>>> Mismatches and indels
general error rate = 0.0085
number of mismatches = 1,306,255
number of insertions = 15,469
mapped reads with insertion percentage = 0.75%
number of deletions = 40,182
mapped reads with deletion percentage = 1.96%
homopolymer indels = 43.81%
>>>>>>> Coverage
mean coverageData = 0.0509X
std coverageData = 0.5835X
There is a 4.3% of reference with a coverageData >= 1X
There is a 0.52% of reference with a coverageData >= 2X
There is a 0.09% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 12848127 0.05154702102026057 0.9377240925494127
chr2 243199373 13809273 0.05678169655478511 0.8935237298442098
chr3 198022430 10556696 0.05331060728827537 0.2735254403066218
chr4 191154276 9927081 0.05193229891441194 0.29813249488748456
chr5 180915260 9500873 0.05251559763394199 0.27393788203263253
chr6 171115067 9213618 0.05384457465688863 0.36078280381614286
chr7 159138663 8923753 0.05607532972675534 0.7641658626829796
chr8 146364022 8198417 0.05601388160814548 0.7430111582522727
chr9 141213431 6912619 0.04895156891981472 0.6567131941572868
chr10 135534747 7592710 0.05602039453395667 0.5935961795973574
chr11 135006516 7179002 0.05317522600168424 0.5625449701448945
chr12 133851895 7300398 0.05454086399000926 0.2817971041848943
chr13 115169878 4822122 0.04186964581138134 0.2322982805083346
chr14 107349540 4731955 0.044079881478765535 0.3559178265530147
chr15 102531392 4515442 0.04403960496313168 0.2496456420374397
chr16 90354753 4661901 0.05159552591549888 0.3320495634519064
chr17 81195210 2483381 0.030585314084414585 0.23017791613254499
chr18 78077248 4473542 0.05729635860116381 1.2556793199632046
chr19 59128983 3409497 0.057662026759364354 0.7336674353526337
chr20 63025520 3131725 0.04968979232539454 0.29246490349348725
chr21 48129895 2082298 0.04326412929012208 0.2673626896242024
chr22 51304566 1754062 0.034189198676780545 0.21383432455104467
chrMT 16571 21233 1.2813348621085028 1.529848173199169
chrX 155270560 9145762 0.05890209966396721 0.42499270465237327
chrY 59373566 443915 0.007476643730646059 0.19611391296627184