BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524414.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 = 5,597,732 number of mapped reads = 5,157,407 (92.13%) number of supplementary alignments = 18,116 (0.32%) number of secondary alignments = 0 number of mapped bases = 301,927,898 bp number of sequenced bases = 301,841,693 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 407,379 duplication rate = 5.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.832 >>>>>>> ACTG content number of A's = 75,769,259 bp (25.1%) number of C's = 58,627,914 bp (19.42%) number of T's = 94,221,861 bp (31.22%) number of G's = 73,185,254 bp (24.25%) number of N's = 37,405 bp (0.01%) GC percentage = 43.67% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,476,067 number of insertions = 24,661 mapped reads with insertion percentage = 0.48% number of deletions = 54,235 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.84% >>>>>>> Coverage mean coverageData = 0.0975X std coverageData = 0.8754X There is a 7.59% of reference with a coverageData >= 1X There is a 1.45% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 24148512 0.09688446072116305 2.0134868372403365 chr2 243199373 25515651 0.1049165986131058 0.9560509305073264 chr3 198022430 20029585 0.10114806186349698 0.39426452953740093 chr4 191154276 19656917 0.10283273495801894 0.512092428134739 chr5 180915260 18318420 0.10125414517271789 0.39920881892775756 chr6 171115067 17263688 0.10088935067301817 0.5132949569011205 chr7 159138663 16728358 0.10511812581961934 1.264618290651251 chr8 146364022 15325203 0.10470608002286245 0.7347436582140957 chr9 141213431 12644289 0.08954027184567168 0.6734169119915866 chr10 135534747 14317256 0.10563531726664897 0.7433750406870784 chr11 135006516 13933634 0.10320712223993692 0.7341804689128777 chr12 133851895 13539379 0.10115194110625031 0.425361220010074 chr13 115169878 9499116 0.08247917046504122 0.3562066277822555 chr14 107349540 9141268 0.0851542354070637 0.4028873228805126 chr15 102531392 8824431 0.08606565099594084 0.3681475104896699 chr16 90354753 8692067 0.09619933331011375 0.4513730346256871 chr17 81195210 8051104 0.09915737640188381 0.4708758527846975 chr18 78077248 8204637 0.10508358337629933 1.3917861935352516 chr19 59128983 6058003 0.10245403679613431 1.2948788986202824 chr20 63025520 6436724 0.10212885193172544 0.4193594032434567 chr21 48129895 4016214 0.0834453098225126 0.47014172643282337 chr22 51304566 3574331 0.06966886728951181 0.3275667593510693 chrMT 16571 13128 0.7922273851909963 1.1067789918018072 chrX 155270560 17072609 0.10995393460292795 0.5422499163057626 chrY 59373566 923374 0.015551937709114524 0.39335081178407627