BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524544.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 = 2,344,288 number of mapped reads = 2,146,260 (91.55%) number of supplementary alignments = 11,984 (0.51%) number of secondary alignments = 0 number of mapped bases = 124,057,425 bp number of sequenced bases = 124,024,166 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,360 duplication rate = 2.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2094 >>>>>>> ACTG content number of A's = 32,573,089 bp (26.26%) number of C's = 23,604,037 bp (19.03%) number of T's = 39,286,159 bp (31.68%) number of G's = 28,557,097 bp (23.03%) number of N's = 3,784 bp (0%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 589,707 number of insertions = 9,605 mapped reads with insertion percentage = 0.45% number of deletions = 19,813 mapped reads with deletion percentage = 0.92% homopolymer indels = 39.74% >>>>>>> Coverage mean coverageData = 0.0401X std coverageData = 0.3307X There is a 3.51% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.06% 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 0.01% 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 8824864 0.035405584806948186 0.5342031082916907 chr2 243199373 10384165 0.0426981569561859 0.3857816210697486 chr3 198022430 7490898 0.03782853285862617 0.21326604405537725 chr4 191154276 7733721 0.04045800680911789 0.2621650379850552 chr5 180915260 6846289 0.03784251809383023 0.21694958195249814 chr6 171115067 6446067 0.03767094922155511 0.23731270497005627 chr7 159138663 7818884 0.04913252287409251 0.4364858005109152 chr8 146364022 5464182 0.03733282213302392 0.3164975088208226 chr9 141213431 5660216 0.04008270289814005 0.3405198549005556 chr10 135534747 4690949 0.03461067441251799 0.34031779679119795 chr11 135006516 4723899 0.03499015558626815 0.2786812160273751 chr12 133851895 9290758 0.06941073191380667 0.3378803678115419 chr13 115169878 4649345 0.04036945320025433 0.22063165281950198 chr14 107349540 4421499 0.04118787094942372 0.24958106761284657 chr15 102531392 3131078 0.030537749843482082 0.19517546654406204 chr16 90354753 3507447 0.03881862197110981 0.23427048997732267 chr17 81195210 3704098 0.04561966155392664 0.24809036913921112 chr18 78077248 3880403 0.04969953602872888 0.6270454357425465 chr19 59128983 2067775 0.034970582869656326 0.40582655814611857 chr20 63025520 3846438 0.061029849495886745 0.28246097045071744 chr21 48129895 1521082 0.03160368415513892 0.23057631830040431 chr22 51304566 1231422 0.024002191150004074 0.16847300314931252 chrMT 16571 20092 1.2124796330939593 1.3621534069412924 chrX 155270560 6343809 0.04085648303194115 0.26291640555000284 chrY 59373566 358045 0.00603037722207893 0.15236995152411087