BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714094.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 721,888 number of mapped reads = 213,713 (29.6%) number of supplementary alignments = 10,525 (1.46%) number of secondary alignments = 0 number of mapped bases = 25,754,633 bp number of sequenced bases = 25,367,198 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 178,796 duplication rate = 42.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.197 >>>>>>> ACTG content number of A's = 5,860,696 bp (23.1%) number of C's = 4,177,965 bp (16.47%) number of T's = 5,505,937 bp (21.7%) number of G's = 9,822,275 bp (38.72%) number of N's = 325 bp (0%) GC percentage = 55.19% >>>>>>> Mismatches and indels general error rate = 0.0384 number of mismatches = 862,835 number of insertions = 27,964 mapped reads with insertion percentage = 11.59% number of deletions = 66,298 mapped reads with deletion percentage = 29.79% homopolymer indels = 33.26% >>>>>>> Coverage mean coverageData = 0.0083X std coverageData = 6.9182X There is a 0.05% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 1520130 0.0060988012543407065 1.2143022222519853 chr2 243199373 6925131 0.028475118642678408 24.278385586173165 chr3 198022430 1069820 0.005402519300465104 1.0948386376422456 chr4 191154276 1164718 0.0060930784514598045 0.916603490725236 chr5 180915260 780587 0.004314655380646165 0.45429328997165913 chr6 171115067 1326840 0.007754080474982369 1.873211493880474 chr7 159138663 1383862 0.008695950901636015 2.3234217527496304 chr8 146364022 1053038 0.0071946506088770915 1.0494170202344442 chr9 141213431 796719 0.005641949171251282 1.029803989311371 chr10 135534747 800094 0.005903238967937868 0.7399639405490812 chr11 135006516 913602 0.006767095597074737 0.7305236799497383 chr12 133851895 861334 0.006434978003113068 0.9692401784290579 chr13 115169878 416181 0.00361362716733971 0.647877789424409 chr14 107349540 500223 0.004659759138231985 0.5776499787483619 chr15 102531392 506988 0.004944710006472944 0.8701356036770628 chr16 90354753 758859 0.008398661661993587 1.9686312376515562 chr17 81195210 697135 0.008585912888211016 1.6294988195747284 chr18 78077248 579939 0.007427759236596044 1.4125769353935982 chr19 59128983 348691 0.005897124934484329 0.7850268018263503 chr20 63025520 324053 0.005141615650295309 0.5882672697443728 chr21 48129895 296362 0.0061575451182679704 1.833950213310251 chr22 51304566 141919 0.0027662060332018013 0.3309461385839018 chrMT 16571 253075 15.272162211091667 127.3772062292291 chrX 155270560 2208859 0.014225871279140103 1.9312652389995921 chrY 59373566 126474 0.0021301398672938054 0.2974708110651604