BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717052.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 = 1,004,164 number of mapped reads = 797,245 (79.39%) number of supplementary alignments = 3,001 (0.3%) number of secondary alignments = 0 number of mapped bases = 44,741,751 bp number of sequenced bases = 44,729,168 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,868 duplication rate = 1.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.7545 >>>>>>> ACTG content number of A's = 10,835,552 bp (24.22%) number of C's = 9,610,714 bp (21.49%) number of T's = 13,051,490 bp (29.18%) number of G's = 11,230,193 bp (25.11%) number of N's = 1,219 bp (0%) GC percentage = 46.59% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 236,011 number of insertions = 3,593 mapped reads with insertion percentage = 0.45% number of deletions = 7,315 mapped reads with deletion percentage = 0.91% homopolymer indels = 33.44% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 0.1474X There is a 1.33% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4384815 0.017591992278326158 0.17590239734367258 chr2 243199373 3863078 0.015884407728304465 0.17695666466968707 chr3 198022430 3007406 0.01518719874309188 0.13666586620984505 chr4 191154276 2889932 0.015118322542782146 0.14689228247751066 chr5 180915260 2713442 0.014998414174680456 0.13199782628287773 chr6 171115067 1945463 0.011369326115507993 0.1170409078064672 chr7 159138663 2572875 0.016167504184699602 0.16377820345326108 chr8 146364022 2756562 0.018833603793697334 0.15291158232321203 chr9 141213431 1951197 0.013817361324504607 0.13323808527885764 chr10 135534747 2330511 0.017194933783290272 0.21881810270266802 chr11 135006516 1860759 0.013782734753335905 0.14567990601373312 chr12 133851895 2189061 0.01635435194996679 0.13876885206418937 chr13 115169878 776310 0.006740564577137088 0.08890437621945727 chr14 107349540 1429972 0.013320709152549699 0.12530418563672108 chr15 102531392 893330 0.008712746238732427 0.10056290323665054 chr16 90354753 1223565 0.013541788996977281 0.13435286371269495 chr17 81195210 1773899 0.02184733557558383 0.1655721850366416 chr18 78077248 1200175 0.015371635537154179 0.16297667941726895 chr19 59128983 1169068 0.01977148837482965 0.17057341558191222 chr20 63025520 1159688 0.01840029245296191 0.1511477665783758 chr21 48129895 603879 0.01254685887014713 0.13003806930179618 chr22 51304566 494326 0.009635126822825087 0.1078044034924296 chrMT 16571 5157 0.31120632430149053 0.626015992050243 chrX 155270560 1403988 0.009042203493051097 0.10885377443114078 chrY 59373566 143293 0.002413414077234303 0.08449834930449085