BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716480.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 = 2,335,654
number of mapped reads = 2,107,148 (90.22%)
number of supplementary alignments = 11,765 (0.5%)
number of secondary alignments = 0
number of mapped bases = 122,011,299 bp
number of sequenced bases = 121,977,077 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 110,833
duplication rate = 4.09%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.6436
>>>>>>> ACTG content
number of A's = 32,065,047 bp (26.29%)
number of C's = 23,297,027 bp (19.1%)
number of T's = 36,782,253 bp (30.16%)
number of G's = 29,831,821 bp (24.46%)
number of N's = 929 bp (0%)
GC percentage = 43.56%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 602,207
number of insertions = 9,903
mapped reads with insertion percentage = 0.47%
number of deletions = 21,726
mapped reads with deletion percentage = 1.02%
homopolymer indels = 42.23%
>>>>>>> Coverage
mean coverageData = 0.0394X
std coverageData = 0.3365X
There is a 3.38% of reference with a coverageData >= 1X
There is a 0.42% of reference with a coverageData >= 2X
There is a 0.07% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% 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 14439978 0.05793356879941334 0.5362065821820138
chr2 243199373 12634387 0.05195073837628685 0.4847016802036069
chr3 198022430 7837140 0.039577031753423086 0.226730436570269
chr4 191154276 5262118 0.02752812079390785 0.2181470205800497
chr5 180915260 8768657 0.04846831052283815 0.25085955364591966
chr6 171115067 4610401 0.026943279050932436 0.21477485451768683
chr7 159138663 8122787 0.05104219708066795 0.5620497089465764
chr8 146364022 5451765 0.03724798571058672 0.2959936337706874
chr9 141213431 3379829 0.023934189376079957 0.2504484859323218
chr10 135534747 5306866 0.03915502199594618 0.28845683727931537
chr11 135006516 5335131 0.03951758150695482 0.32433736951800307
chr12 133851895 4932969 0.03685393471642669 0.2209209455483974
chr13 115169878 3539310 0.030731212548475564 0.19987691638011748
chr14 107349540 2610752 0.02432010421283594 0.1883226246534695
chr15 102531392 5259739 0.05129881587875058 0.25943355252918093
chr16 90354753 3690772 0.040847568915384005 0.2447670469622283
chr17 81195210 4608373 0.05675671015568529 0.2974505952398542
chr18 78077248 3921616 0.05022738506357191 0.5662643466552243
chr19 59128983 1932156 0.032676969938752375 0.4050291557945341
chr20 63025520 2489416 0.03949853963918108 0.23169106967808573
chr21 48129895 1566232 0.032541770556532484 0.21912437129729476
chr22 51304566 1451249 0.028286936488265 0.1905312232623439
chrMT 16571 15038 0.9074889867841409 1.084337937722135
chrX 155270560 4562712 0.029385557700055954 0.2224854195216655
chrY 59373566 281906 0.004748005198138175 0.11482807073462516