BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174045.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 = 6,537,830 number of mapped reads = 6,382,617 (97.63%) number of supplementary alignments = 615,607 (9.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,198,722 number of mapped paired reads (second in pair) = 3,183,895 number of mapped paired reads (both in pair) = 6,280,298 number of mapped paired reads (singletons) = 102,319 number of mapped bases = 757,567,402 bp number of sequenced bases = 757,103,573 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,656,586 duplication rate = 62.53% >>>>>>> Insert size mean insert size = 1,090,152.6571 std insert size = 9,430,184.5079 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 52.9216 >>>>>>> ACTG content number of A's = 227,244,151 bp (30.01%) number of C's = 148,968,231 bp (19.68%) number of T's = 226,749,483 bp (29.95%) number of G's = 154,133,030 bp (20.36%) number of N's = 8,678 bp (0%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 7,864,742 number of insertions = 81,511 mapped reads with insertion percentage = 1.24% number of deletions = 195,916 mapped reads with deletion percentage = 3% homopolymer indels = 42.59% >>>>>>> Coverage mean coverageData = 0.2447X std coverageData = 3.3283X There is a 5.89% of reference with a coverageData >= 1X There is a 4.51% of reference with a coverageData >= 2X There is a 3.31% of reference with a coverageData >= 3X There is a 2.6% of reference with a coverageData >= 4X There is a 1.86% of reference with a coverageData >= 5X There is a 1.45% of reference with a coverageData >= 6X There is a 1.02% of reference with a coverageData >= 7X There is a 0.8% of reference with a coverageData >= 8X There is a 0.56% of reference with a coverageData >= 9X There is a 0.46% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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% 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 64356422 0.2581996455687868 1.989913006216623 chr2 243199373 63170655 0.2597484287099704 10.007460870915436 chr3 198022430 47454660 0.239642852579882 1.3023430776609586 chr4 191154276 45830800 0.23975817313131934 1.8208837163177454 chr5 180915260 41706414 0.2305301056417242 1.267066115247273 chr6 171115067 40143287 0.234598201688458 1.4050380784220327 chr7 159138663 55776202 0.3504880646131858 2.981418057775034 chr8 146364022 60045714 0.41024913895847986 2.3391488049503355 chr9 141213431 27182298 0.19249088282544455 1.8833169852630531 chr10 135534747 34913312 0.2575967622531512 3.6696918529197924 chr11 135006516 33961890 0.2515574137177201 1.4085730534383225 chr12 133851895 31963728 0.2387992190921167 1.2988316505573503 chr13 115169878 22377995 0.19430423465413413 1.1724843651660615 chr14 107349540 25181753 0.23457718589199358 1.282714247407681 chr15 102531392 19460988 0.18980516718235912 1.143612834897778 chr16 90354753 19371181 0.21439028226882542 1.7524344476010727 chr17 81195210 21106205 0.2599439671379629 1.5303178459649587 chr18 78077248 17019843 0.21798722977531176 2.565368890046916 chr19 59128983 12362900 0.2090835893456852 1.6009132367126704 chr20 63025520 26098901 0.4141005262630122 1.7115046742220177 chr21 48129895 9856394 0.20478735721322475 1.3960189456858811 chr22 51304566 8986136 0.17515275346057893 1.122224800152365 chrMT 16571 1050307 63.382234023293705 50.084330582774 chrX 155270560 25172469 0.16212003743658812 1.0750489988263656 chrY 59373566 3016948 0.05081298300324424 1.1071939313414552