BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716938.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 = 502,432 number of mapped reads = 344,643 (68.59%) number of supplementary alignments = 359 (0.07%) number of secondary alignments = 0 number of mapped bases = 17,960,360 bp number of sequenced bases = 17,955,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,914 duplication rate = 4.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1336 >>>>>>> ACTG content number of A's = 3,682,982 bp (20.51%) number of C's = 3,280,232 bp (18.27%) number of T's = 6,237,238 bp (34.74%) number of G's = 4,754,760 bp (26.48%) number of N's = 261 bp (0%) GC percentage = 44.75% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 132,669 number of insertions = 1,089 mapped reads with insertion percentage = 0.31% number of deletions = 2,882 mapped reads with deletion percentage = 0.83% homopolymer indels = 39.41% >>>>>>> Coverage mean coverageData = 0.0058X std coverageData = 0.0887X There is a 0.53% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 1773855 0.00711675257972577 0.09936159742507517 chr2 243199373 1575386 0.006477755187304698 0.12555827520831456 chr3 198022430 1218093 0.006151288013181133 0.08424785451515904 chr4 191154276 1116855 0.0058426890748706035 0.08382405766940472 chr5 180915260 1106015 0.0061134422823149355 0.08361762280763024 chr6 171115067 756135 0.004418868620143193 0.07869084565975758 chr7 159138663 1044331 0.006562396468041207 0.09270283747029961 chr8 146364022 1097317 0.007497177140977992 0.09442176171331809 chr9 141213431 799394 0.005660892128596465 0.08532837840571847 chr10 135534747 918162 0.006774366133579015 0.09425011303851355 chr11 135006516 756551 0.005603811004203678 0.08299025745777727 chr12 133851895 830459 0.006204312609843887 0.08468010954653597 chr13 115169878 312219 0.002710943220761248 0.05674588061267802 chr14 107349540 568509 0.005295868058680084 0.07898995506179748 chr15 102531392 347996 0.003394043455491173 0.0626740823376423 chr16 90354753 483847 0.005354970092165489 0.08344561580304355 chr17 81195210 707909 0.008718605444828581 0.1022938365205483 chr18 78077248 496017 0.006352900655514908 0.09022626637149178 chr19 59128983 485386 0.008208935371000715 0.11038038956874946 chr20 63025520 493232 0.00782590925072891 0.09737314061901269 chr21 48129895 250772 0.0052103167895961545 0.08084002600758651 chr22 51304566 206572 0.004026386267452296 0.07010205692204595 chrMT 16571 1550 0.0935369018164263 0.3246940322871564 chrX 155270560 559716 0.0036047786521797823 0.0655236744159448 chrY 59373566 54082 9.10876735953505E-4 0.036315961283788195