BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173843.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,515,036 number of mapped reads = 4,389,781 (97.23%) number of supplementary alignments = 433,252 (9.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,198,420 number of mapped paired reads (second in pair) = 2,191,361 number of mapped paired reads (both in pair) = 4,307,690 number of mapped paired reads (singletons) = 82,091 number of mapped bases = 517,405,523 bp number of sequenced bases = 517,121,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,405,070 duplication rate = 64.82% >>>>>>> Insert size mean insert size = 770,706.145 std insert size = 7,939,024.9693 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.7622 >>>>>>> ACTG content number of A's = 155,700,012 bp (30.11%) number of C's = 101,411,042 bp (19.61%) number of T's = 155,178,262 bp (30.01%) number of G's = 104,826,164 bp (20.27%) number of N's = 5,628 bp (0%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 5,377,306 number of insertions = 52,768 mapped reads with insertion percentage = 1.16% number of deletions = 115,462 mapped reads with deletion percentage = 2.56% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.1671X std coverageData = 2.5126X There is a 3.48% of reference with a coverageData >= 1X There is a 2.75% of reference with a coverageData >= 2X There is a 2.13% of reference with a coverageData >= 3X There is a 1.75% of reference with a coverageData >= 4X There is a 1.34% of reference with a coverageData >= 5X There is a 1.08% of reference with a coverageData >= 6X There is a 0.81% of reference with a coverageData >= 7X There is a 0.65% of reference with a coverageData >= 8X There is a 0.48% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 36004086 0.14444933318741862 2.1549605272399055 chr2 243199373 41861722 0.17212923488910475 7.326923534957787 chr3 198022430 51114569 0.25812514774210177 1.4874212454209867 chr4 191154276 27883047 0.14586671867073484 1.2610010610149411 chr5 180915260 31898092 0.17631509912430826 1.2154378963568737 chr6 171115067 29977285 0.1751878751857661 1.380235113654862 chr7 159138663 30123792 0.18929273020221365 1.7662271744563895 chr8 146364022 27427766 0.18739418079123296 1.7871290175182935 chr9 141213431 17200141 0.12180244384827672 1.2218438542575087 chr10 135534747 22254347 0.16419661741796737 2.1453244214709146 chr11 135006516 19561897 0.1448959470963609 1.1474445871046368 chr12 133851895 24794063 0.18523505401249643 1.2461371223982118 chr13 115169878 17032846 0.14789323645892896 1.1171032775022216 chr14 107349540 17017055 0.15852005513950038 1.1468835974583966 chr15 102531392 14135303 0.1378631726759352 1.063377384820424 chr16 90354753 18067783 0.19996494263007947 1.6331271736992816 chr17 81195210 20637173 0.2541673702180215 1.553544708331175 chr18 78077248 10433615 0.13363195126959393 2.0372984226897426 chr19 59128983 8553995 0.1446667026219612 1.5483027701243797 chr20 63025520 20052875 0.31817071878185216 1.7457534822569538 chr21 48129895 6475996 0.13455246474150837 1.0743769270982635 chr22 51304566 4536186 0.08841680874953703 0.8219834031484325 chrMT 16571 647669 39.08448494357613 31.774664090634726 chrX 155270560 18825986 0.12124633285279579 1.004729458859331 chrY 59373566 888234 0.01496009183615483 0.5754843138487828