BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR8751212.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,613,075
number of mapped reads = 3,772,429 (81.78%)
number of supplementary alignments = 211,482 (4.58%)
number of secondary alignments = 0
number of mapped bases = 371,808,012 bp
number of sequenced bases = 371,682,125 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 99,921
duplication rate = 1.42%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 51.1253
>>>>>>> ACTG content
number of A's = 109,592,773 bp (29.49%)
number of C's = 76,143,933 bp (20.49%)
number of T's = 110,261,665 bp (29.67%)
number of G's = 75,681,032 bp (20.36%)
number of N's = 2,722 bp (0%)
GC percentage = 40.85%
>>>>>>> Mismatches and indels
general error rate = 0.0044
number of mismatches = 1,334,993
number of insertions = 227,389
mapped reads with insertion percentage = 5.8%
number of deletions = 56,498
mapped reads with deletion percentage = 1.46%
homopolymer indels = 52.6%
>>>>>>> Coverage
mean coverageData = 0.1201X
std coverageData = 1.0415X
There is a 9.92% of reference with a coverageData >= 1X
There is a 1.5% of reference with a coverageData >= 2X
There is a 0.26% of reference with a coverageData >= 3X
There is a 0.06% of reference with a coverageData >= 4X
There is a 0.02% 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 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% 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 36679817 0.14716038360442038 2.845119664533482
chr2 243199373 30097199 0.12375524915518595 0.5181547431463912
chr3 198022430 24666184 0.12456257606777171 0.4702030110674624
chr4 191154276 20058184 0.10493191373861813 0.40204832703200766
chr5 180915260 28282316 0.15632907915009492 0.46104529916875414
chr6 171115067 19426276 0.11352755979109659 0.6082361214328937
chr7 159138663 21567741 0.13552797663004118 0.6750620216595816
chr8 146364022 24389811 0.16663802119348703 0.668079289561658
chr9 141213431 16567654 0.11732350019878775 0.621076911515588
chr10 135534747 15989369 0.11797247092658829 1.4772594280584959
chr11 135006516 16916221 0.1252992929615338 0.5116867469813597
chr12 133851895 16836029 0.1257810283522695 0.4041467391419323
chr13 115169878 10537010 0.09149102337331641 0.33787091468336733
chr14 107349540 9761318 0.09093022662230318 0.3554926358896673
chr15 102531392 12538194 0.12228639205444514 0.3953548983662593
chr16 90354753 9983849 0.11049611302683766 0.6641124080178071
chr17 81195210 11910717 0.14669236030056454 0.5736590549696876
chr18 78077248 6280659 0.08044160316716081 1.343959761827548
chr19 59128983 7282150 0.12315703112972533 1.909590044789323
chr20 63025520 7294340 0.11573629221940572 0.3919568051501174
chr21 48129895 4019276 0.08350892932552627 0.3590640118273826
chr22 51304566 3729356 0.07269052816858444 0.30645444353415235
chrMT 16571 157254 9.489710940800194 7.927193416340244
chrX 155270560 15805303 0.1017920138885311 0.39773636129468803
chrY 59373566 1031785 0.01737785128149453 0.7976102094854272