BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173933.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,356,954 number of mapped reads = 5,240,156 (97.82%) number of supplementary alignments = 712,143 (13.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,619,184 number of mapped paired reads (second in pair) = 2,620,972 number of mapped paired reads (both in pair) = 5,168,240 number of mapped paired reads (singletons) = 71,916 number of mapped bases = 595,232,556 bp number of sequenced bases = 594,799,526 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,154,758 duplication rate = 64.04% >>>>>>> Insert size mean insert size = 1,084,160.7877 std insert size = 9,596,798.7248 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 52.5282 >>>>>>> ACTG content number of A's = 177,689,523 bp (29.87%) number of C's = 118,066,489 bp (19.85%) number of T's = 176,165,921 bp (29.62%) number of G's = 122,872,637 bp (20.66%) number of N's = 4,956 bp (0%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 5,164,058 number of insertions = 66,696 mapped reads with insertion percentage = 1.22% number of deletions = 181,731 mapped reads with deletion percentage = 3.38% homopolymer indels = 40.73% >>>>>>> Coverage mean coverageData = 0.1923X std coverageData = 3.5773X There is a 4.28% of reference with a coverageData >= 1X There is a 3.17% of reference with a coverageData >= 2X There is a 2.33% of reference with a coverageData >= 3X There is a 1.86% of reference with a coverageData >= 4X There is a 1.38% of reference with a coverageData >= 5X There is a 1.14% of reference with a coverageData >= 6X There is a 0.84% of reference with a coverageData >= 7X There is a 0.73% of reference with a coverageData >= 8X There is a 0.54% of reference with a coverageData >= 9X There is a 0.49% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 44394943 0.1781136705773744 1.7674754418575627 chr2 243199373 53199830 0.2187498649513377 11.559248824094112 chr3 198022430 40773544 0.20590366454951592 1.3447366597482544 chr4 191154276 38252889 0.20011526710498487 1.8516886319263677 chr5 180915260 38380208 0.2121446692777602 1.3653403870437808 chr6 171115067 35854457 0.2095341902300164 1.5138851890283003 chr7 159138663 30911949 0.19424537329435776 1.5797259112329867 chr8 146364022 29113197 0.19890951753156932 2.0055925290786547 chr9 141213431 27312430 0.1934124099003019 1.650044275746694 chr10 135534747 30782284 0.22711728675746892 2.14359575917587 chr11 135006516 29359183 0.21746493332218128 1.4209337070497499 chr12 133851895 26620364 0.19887924634910847 1.3504428717953985 chr13 115169878 21266993 0.1846575977097067 1.2874238591347944 chr14 107349540 17236200 0.16056147050094485 1.1862577114883377 chr15 102531392 16669757 0.16258198269657745 1.2044804297804517 chr16 90354753 18259665 0.2020885940554782 1.6044593117506702 chr17 81195210 17233438 0.2122469786087135 1.4368097392050323 chr18 78077248 15826192 0.2026991525111131 2.300683403555318 chr19 59128983 11145802 0.18849980896847152 1.4838264765825506 chr20 63025520 13228491 0.20989102509586594 1.4272809056905857 chr21 48129895 8707985 0.18092674002301481 1.6073360141634068 chr22 51304566 7935549 0.15467529732148985 1.4318751899117035 chrMT 16571 607491 36.65988775571782 37.438391540567046 chrX 155270560 17656832 0.1137165474253458 1.0021065926244739 chrY 59373566 4502883 0.07583986112607756 1.2572330929128965