BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525252.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 = 1,329,426 number of mapped reads = 1,213,945 (91.31%) number of supplementary alignments = 5,142 (0.39%) number of secondary alignments = 0 number of mapped bases = 69,907,618 bp number of sequenced bases = 69,884,888 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,621 duplication rate = 2.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6869 >>>>>>> ACTG content number of A's = 17,852,579 bp (25.55%) number of C's = 13,177,425 bp (18.86%) number of T's = 22,439,913 bp (32.11%) number of G's = 16,413,548 bp (23.49%) number of N's = 1,423 bp (0%) GC percentage = 42.34% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 352,710 number of insertions = 4,505 mapped reads with insertion percentage = 0.37% number of deletions = 14,264 mapped reads with deletion percentage = 1.17% homopolymer indels = 44.75% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.2353X There is a 2.07% of reference with a coverageData >= 1X There is a 0.13% 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 7297680 0.029278482720410153 0.41120516267084123 chr2 243199373 5534469 0.0227569213346615 0.30331932809075357 chr3 198022430 7663364 0.038699474599922845 0.21146521000924276 chr4 191154276 2975672 0.015566860769570229 0.13880041012399164 chr5 180915260 3001400 0.01659008753600995 0.1378717880312437 chr6 171115067 4258568 0.024887159702891622 0.18359232870699768 chr7 159138663 4885992 0.03070273375364477 0.3973054119440945 chr8 146364022 3796177 0.02593654470632134 0.23771628834683908 chr9 141213431 2201118 0.015587171732977722 0.1616217256012109 chr10 135534747 3516262 0.02594362019947549 0.23782980709032928 chr11 135006516 3019078 0.0223624613792715 0.19119477895157844 chr12 133851895 2966447 0.022162159153592858 0.16116418164329233 chr13 115169878 2098238 0.018218635258083715 0.14567295850675313 chr14 107349540 2453483 0.02285508629100786 0.16297378882242253 chr15 102531392 1799622 0.01755191229628483 0.14375580875019256 chr16 90354753 1802323 0.019947185290850166 0.16202670748121106 chr17 81195210 1294880 0.015947738789024623 0.13758245982598014 chr18 78077248 1426371 0.01826871510635211 0.2951016624470284 chr19 59128983 1283072 0.021699544536390895 0.2766107960251707 chr20 63025520 1189770 0.018877591172591673 0.14894957642465184 chr21 48129895 860464 0.01787795298535349 0.1479660398008882 chr22 51304566 548100 0.010683259653731405 0.10978604942526242 chrMT 16571 75144 4.5346690000603465 3.0735489515628185 chrX 155270560 3758490 0.02420606971469672 0.17776480541872702 chrY 59373566 201434 0.0033926545695436247 0.1039176885899826