BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525138.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 = 1,148,378 number of mapped reads = 1,029,841 (89.68%) number of supplementary alignments = 31,810 (2.77%) number of secondary alignments = 0 number of mapped bases = 78,231,428 bp number of sequenced bases = 78,199,338 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,486 duplication rate = 1.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2108 >>>>>>> ACTG content number of A's = 20,495,850 bp (26.21%) number of C's = 16,036,181 bp (20.51%) number of T's = 23,190,359 bp (29.66%) number of G's = 18,473,873 bp (23.62%) number of N's = 3,075 bp (0%) GC percentage = 44.13% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 581,501 number of insertions = 6,819 mapped reads with insertion percentage = 0.65% number of deletions = 18,112 mapped reads with deletion percentage = 1.73% homopolymer indels = 41.99% >>>>>>> Coverage mean coverageData = 0.0253X std coverageData = 0.2581X There is a 2.31% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6398746 0.025671936039027964 0.3642875204903794 chr2 243199373 6616099 0.027204424577196587 0.38834757360961997 chr3 198022430 4981990 0.025158715606105834 0.1688773154538634 chr4 191154276 4977765 0.02604056317317223 0.1881097757198881 chr5 180915260 4665855 0.025790278829989244 0.17241713794029626 chr6 171115067 4348788 0.02541440725380425 0.18454549460364247 chr7 159138663 4323621 0.027168891069544805 0.3460578194417501 chr8 146364022 4023831 0.027491940608191268 0.35514752202838906 chr9 141213431 3159981 0.02237734029704299 0.2462652955001645 chr10 135534747 3714949 0.027409569001519588 0.25762781688019837 chr11 135006516 3541899 0.02623502261179749 0.24686968125986777 chr12 133851895 3581584 0.02675781317851346 0.17582429641459446 chr13 115169878 2416860 0.020985174613105 0.1539157059332003 chr14 107349540 2393356 0.022294981422370325 0.17685270921280186 chr15 102531392 2261075 0.022052514414317128 0.15822479902376663 chr16 90354753 2422018 0.026805651275478556 0.18779444246835955 chr17 81195210 2254061 0.02776100954723807 0.20029853080409088 chr18 78077248 2077303 0.026605740509706488 0.40708664838980496 chr19 59128983 1816130 0.030714717349358097 0.2974245981224454 chr20 63025520 1679805 0.026652774939421364 0.17854018386903678 chr21 48129895 1033597 0.02147515592959428 0.16726868325966135 chr22 51304566 977367 0.019050292716636566 0.14762884753602723 chrMT 16571 2392 0.1443485607386398 0.38815966878621094 chrX 155270560 4362376 0.02809531955059607 0.2129598457601562 chrY 59373566 199980 0.0033681655570426744 0.09275390253476117