BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524603.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 = 913,009 number of mapped reads = 848,344 (92.92%) number of supplementary alignments = 1,804 (0.2%) number of secondary alignments = 0 number of mapped bases = 49,425,973 bp number of sequenced bases = 49,409,539 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,040 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3072 >>>>>>> ACTG content number of A's = 12,685,676 bp (25.67%) number of C's = 9,506,921 bp (19.24%) number of T's = 15,563,603 bp (31.5%) number of G's = 11,653,028 bp (23.58%) number of N's = 311 bp (0%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 236,801 number of insertions = 3,844 mapped reads with insertion percentage = 0.45% number of deletions = 9,589 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 0.016X std coverageData = 0.1708X There is a 1.47% of reference with a coverageData >= 1X There is a 0.09% 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 4924810 0.019758466318926443 0.28953683412116915 chr2 243199373 4406916 0.018120589480302648 0.19054837472516123 chr3 198022430 3519684 0.017774168310125273 0.1416033930102695 chr4 191154276 2223738 0.011633210862622817 0.1255317438363827 chr5 180915260 3013918 0.01665928015138137 0.13709572859024388 chr6 171115067 3219523 0.01881495917597952 0.15284114890398906 chr7 159138663 2975277 0.018696129173838793 0.21024054997186747 chr8 146364022 4423175 0.03022037068645189 0.22955788869160595 chr9 141213431 1736101 0.012294163435487946 0.14541664639232843 chr10 135534747 2110793 0.015573814440366351 0.16357672504758092 chr11 135006516 2509061 0.018584740013585715 0.165955771118925 chr12 133851895 1636707 0.01222774619664518 0.11922747987376593 chr13 115169878 1100625 0.009556535260026932 0.10518104735534836 chr14 107349540 906150 0.008441116748148153 0.10083443104636057 chr15 102531392 1251289 0.012203959934534 0.12093358244309911 chr16 90354753 1433716 0.015867632331417032 0.13708247244020708 chr17 81195210 1252373 0.015424222685057406 0.13390806860737867 chr18 78077248 1298156 0.0166265593787322 0.2245176054662886 chr19 59128983 930935 0.01574414022984295 0.2030051792114475 chr20 63025520 910255 0.014442641647383472 0.13020482206142944 chr21 48129895 422068 0.008769352187450232 0.10609698845536511 chr22 51304566 851755 0.01660193363686187 0.1370190427854627 chrMT 16571 2234 0.13481383139219116 0.3963220185626237 chrX 155270560 2253531 0.01451357552906359 0.13840654811300052 chrY 59373566 113183 0.001906286039817787 0.06448273755172954