BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716701.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 = 2,264,925 number of mapped reads = 2,040,371 (90.09%) number of supplementary alignments = 29,890 (1.32%) number of secondary alignments = 0 number of mapped bases = 158,796,818 bp number of sequenced bases = 158,730,307 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,663 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9252 >>>>>>> ACTG content number of A's = 37,156,819 bp (23.41%) number of C's = 32,863,513 bp (20.7%) number of T's = 48,927,443 bp (30.82%) number of G's = 39,773,639 bp (25.06%) number of N's = 8,893 bp (0.01%) GC percentage = 45.76% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,367,040 number of insertions = 14,716 mapped reads with insertion percentage = 0.71% number of deletions = 37,274 mapped reads with deletion percentage = 1.8% homopolymer indels = 44.35% >>>>>>> Coverage mean coverageData = 0.0513X std coverageData = 0.466X There is a 4.19% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15403775 0.06180034753052832 0.5760586722404422 chr2 243199373 13193601 0.05425014397549454 0.9145582532920529 chr3 198022430 11406202 0.05760055565422564 0.29381999795061087 chr4 191154276 5978914 0.03127795059107127 0.23789826995305072 chr5 180915260 8547772 0.04724737979538045 0.2608338800198722 chr6 171115067 11297781 0.06602446644865002 0.3690655796394229 chr7 159138663 7957413 0.05000301529490668 0.5735791557204345 chr8 146364022 10351445 0.0707239720428016 0.6114522257876305 chr9 141213431 6843450 0.04846175007248425 0.43612927988734446 chr10 135534747 7334481 0.054115134032751026 0.4063394436048028 chr11 135006516 6640482 0.0491863814928755 0.32835040138880833 chr12 133851895 6069057 0.04534158444301442 0.2533133519599208 chr13 115169878 4643855 0.04032178448604417 0.23896824424867524 chr14 107349540 4013537 0.03738755657453213 0.2540516938714666 chr15 102531392 3638569 0.035487365664556667 0.2427124760954275 chr16 90354753 4390607 0.04859298326010586 0.2962481401658463 chr17 81195210 6184031 0.07616251007910442 0.3559468199501339 chr18 78077248 4551637 0.05829658596573486 0.8200030679432858 chr19 59128983 5343934 0.0903775733805535 0.5474848508306839 chr20 63025520 3325671 0.05276705372680781 0.29885309808636495 chr21 48129895 2927362 0.06082211482073668 0.30561409825298924 chr22 51304566 3636201 0.07087480283918589 0.3331985259431404 chrMT 16571 286846 17.310120089312655 11.515482120912196 chrX 155270560 4478996 0.028846395607770074 0.25154605005993563 chrY 59373566 351199 0.005915073384677619 0.1631707532235189