BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716859.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 = 1,363,754 number of mapped reads = 1,285,026 (94.23%) number of supplementary alignments = 31,824 (2.33%) number of secondary alignments = 0 number of mapped bases = 98,902,796 bp number of sequenced bases = 98,863,323 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,956 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0804 >>>>>>> ACTG content number of A's = 24,422,927 bp (24.7%) number of C's = 20,869,124 bp (21.11%) number of T's = 28,964,226 bp (29.3%) number of G's = 24,603,317 bp (24.89%) number of N's = 3,729 bp (0%) GC percentage = 46% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 638,459 number of insertions = 7,661 mapped reads with insertion percentage = 0.59% number of deletions = 18,981 mapped reads with deletion percentage = 1.45% homopolymer indels = 39.17% >>>>>>> Coverage mean coverageData = 0.0319X std coverageData = 0.282X There is a 2.75% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11211911 0.0449824797026283 0.5131737706138623 chr2 243199373 9434522 0.03879336481677525 0.29600126749486366 chr3 198022430 6035352 0.03047812310958915 0.2017905508630199 chr4 191154276 4931994 0.02580111783635957 0.2552085284441637 chr5 180915260 4632862 0.025607911681966463 0.18071578714731615 chr6 171115067 6605949 0.038605302945064444 0.23005447090084638 chr7 159138663 6198634 0.0389511504190531 0.34377626621353835 chr8 146364022 6467226 0.044185899728828165 0.3119086920311675 chr9 141213431 3011769 0.021327780074970347 0.19638477410534308 chr10 135534747 4030443 0.02973734108198837 0.3848410624956931 chr11 135006516 4267485 0.03160947431603968 0.2441865894709902 chr12 133851895 3535449 0.026413141181153992 0.18236708086133263 chr13 115169878 1922649 0.016694026540516087 0.14315826717565833 chr14 107349540 2002789 0.018656707797723212 0.16260740495052367 chr15 102531392 1918959 0.01871581924880138 0.15259726364247575 chr16 90354753 3743444 0.04143051555904314 0.24790377926391327 chr17 81195210 1947098 0.02398045401939351 0.19058327854233872 chr18 78077248 2963883 0.03796090507698222 0.30058891021588113 chr19 59128983 2582686 0.04367885035330305 0.4104924781020566 chr20 63025520 2366595 0.037549789355169144 0.23995757481093313 chr21 48129895 1540970 0.032016899268116 0.2430735570342129 chr22 51304566 1510208 0.02943613244871811 0.19924147963574293 chrMT 16571 28566 1.723854927282602 1.867960631531685 chrX 155270560 5658202 0.0364409196437496 0.22489907069308637 chrY 59373566 353151 0.005947949968172705 0.21705717657007223