BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525198.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 = 1,308,609 number of mapped reads = 1,169,116 (89.34%) number of supplementary alignments = 4,180 (0.32%) number of secondary alignments = 0 number of mapped bases = 71,678,452 bp number of sequenced bases = 71,654,747 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,930 duplication rate = 1.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8367 >>>>>>> ACTG content number of A's = 18,245,705 bp (25.46%) number of C's = 14,644,983 bp (20.44%) number of T's = 22,610,304 bp (31.55%) number of G's = 16,152,058 bp (22.54%) number of N's = 1,697 bp (0%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 345,641 number of insertions = 5,293 mapped reads with insertion percentage = 0.45% number of deletions = 14,687 mapped reads with deletion percentage = 1.25% homopolymer indels = 43.5% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.242X There is a 2.14% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% 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 7375453 0.02959051002725486 0.46434147441482293 chr2 243199373 5634043 0.02316635495602203 0.24740742338458854 chr3 198022430 5730914 0.028940731613080396 0.18044711190791532 chr4 191154276 3847207 0.02012618854521465 0.1559465852565015 chr5 180915260 3349341 0.018513313912823053 0.1430486126569501 chr6 171115067 4326210 0.025282460953599137 0.179610107895944 chr7 159138663 5145569 0.03233387099651579 0.4231228868381646 chr8 146364022 3926295 0.026825547332936777 0.2150726794371625 chr9 141213431 2220801 0.015726556491641366 0.16908268417778788 chr10 135534747 4628989 0.03415352226982797 0.2742798822771893 chr11 135006516 3132086 0.02319951727366996 0.18826975960617598 chr12 133851895 2865023 0.021404426138307567 0.15547322461919358 chr13 115169878 1484001 0.012885322323602705 0.12056428557830948 chr14 107349540 2574783 0.023985039898633938 0.16464882535857417 chr15 102531392 2084878 0.020334045596494 0.14950842740476453 chr16 90354753 2056807 0.022763683499859712 0.17105139598895788 chr17 81195210 1390628 0.01712697091367828 0.14358259248352898 chr18 78077248 1470238 0.018830556117961535 0.3158206835680402 chr19 59128983 1220616 0.02064327742623275 0.31914226510980015 chr20 63025520 1302306 0.020663153592386067 0.1533531784742177 chr21 48129895 883801 0.018362828341927612 0.15167288226364883 chr22 51304566 619587 0.012076644406269805 0.1152490323281763 chrMT 16571 77844 4.697604248385734 3.342140037785823 chrX 155270560 4124653 0.026564295253395105 0.18173270857164875 chrY 59373566 206379 0.003475940791563707 0.11099794333490061