BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716492.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 = 849,151 number of mapped reads = 730,232 (86%) number of supplementary alignments = 3,816 (0.45%) number of secondary alignments = 0 number of mapped bases = 41,785,926 bp number of sequenced bases = 41,773,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,747 duplication rate = 1.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4428 >>>>>>> ACTG content number of A's = 10,438,377 bp (24.99%) number of C's = 8,663,838 bp (20.74%) number of T's = 13,146,971 bp (31.47%) number of G's = 9,524,168 bp (22.8%) number of N's = 569 bp (0%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 215,990 number of insertions = 2,703 mapped reads with insertion percentage = 0.37% number of deletions = 7,831 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.01% >>>>>>> Coverage mean coverageData = 0.0135X std coverageData = 0.152X There is a 1.26% of reference with a coverageData >= 1X There is a 0.07% 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 3400994 0.013644876736335193 0.24793270733646447 chr2 243199373 3462320 0.014236549861499848 0.1913787904092572 chr3 198022430 2788932 0.014083919685259898 0.12546848390259235 chr4 191154276 2694268 0.014094730478328404 0.12979093554340743 chr5 180915260 2493530 0.013782861655782934 0.12362799008354007 chr6 171115067 2358078 0.013780656731998941 0.13183246997892584 chr7 159138663 2341161 0.014711453243766413 0.17069573176964303 chr8 146364022 2086599 0.014256228897563365 0.14565731359239836 chr9 141213431 1786356 0.012650043181799046 0.1316594675502551 chr10 135534747 2005320 0.014795615474163241 0.1479477733762469 chr11 135006516 1908084 0.014133273389559952 0.14161275071966986 chr12 133851895 1895212 0.014159022552501031 0.1259177850471498 chr13 115169878 1299263 0.011281274431844063 0.11197007955883781 chr14 107349540 1241173 0.011561977815647837 0.11806125592941281 chr15 102531392 1213388 0.011834307291956008 0.11707214684436193 chr16 90354753 1219104 0.013492416940147023 0.12563901898770588 chr17 81195210 1173302 0.014450384450018665 0.12970732672448232 chr18 78077248 1093480 0.014005104278265545 0.18718989313050674 chr19 59128983 890440 0.01505928150328579 0.1797516034701877 chr20 63025520 886954 0.014072934265357906 0.12528771415239093 chr21 48129895 548286 0.01139179713564719 0.11659433537265576 chr22 51304566 523750 0.01020864302799092 0.10724233545016484 chrMT 16571 1089 0.06571721682457304 0.26716925923808854 chrX 155270560 2344861 0.015101774605565924 0.1361596931706144 chrY 59373566 129982 0.0021892233995175563 0.06946540088390375