BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174052.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 = 8,318,974 number of mapped reads = 8,089,736 (97.24%) number of supplementary alignments = 852,318 (10.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,052,206 number of mapped paired reads (second in pair) = 4,037,530 number of mapped paired reads (both in pair) = 7,943,168 number of mapped paired reads (singletons) = 146,568 number of mapped bases = 957,639,711 bp number of sequenced bases = 957,114,791 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,331,886 duplication rate = 64.45% >>>>>>> Insert size mean insert size = 917,835.6237 std insert size = 8,772,941.4676 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.6245 >>>>>>> ACTG content number of A's = 289,522,754 bp (30.25%) number of C's = 186,128,178 bp (19.45%) number of T's = 288,834,576 bp (30.18%) number of G's = 192,617,567 bp (20.12%) number of N's = 11,716 bp (0%) GC percentage = 39.57% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 9,971,323 number of insertions = 98,700 mapped reads with insertion percentage = 1.18% number of deletions = 211,856 mapped reads with deletion percentage = 2.55% homopolymer indels = 43.27% >>>>>>> Coverage mean coverageData = 0.3093X std coverageData = 4.3372X There is a 6.27% of reference with a coverageData >= 1X There is a 4.93% of reference with a coverageData >= 2X There is a 3.82% of reference with a coverageData >= 3X There is a 3.16% of reference with a coverageData >= 4X There is a 2.43% of reference with a coverageData >= 5X There is a 1.99% of reference with a coverageData >= 6X There is a 1.5% of reference with a coverageData >= 7X There is a 1.23% of reference with a coverageData >= 8X There is a 0.92% of reference with a coverageData >= 9X There is a 0.77% of reference with a coverageData >= 10X There is a 0.58% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% 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 75575352 0.3032102856826985 3.328218848637088 chr2 243199373 85863243 0.35305700808694107 13.167364213427934 chr3 198022430 74581561 0.3766318845799438 1.8580416871535115 chr4 191154276 48184526 0.2520714001710325 1.6503174265052345 chr5 180915260 63950695 0.3534842500295442 1.734530315468538 chr6 171115067 44546612 0.26033132430120837 2.0738146638308814 chr7 159138663 49538348 0.3112904624566313 2.615603423962156 chr8 146364022 58370400 0.39880292439627 2.892705099964642 chr9 141213431 37415047 0.2649538838837504 2.310541064297066 chr10 135534747 53729245 0.39642413616635147 4.363555577959373 chr11 135006516 32744299 0.24253865643047925 1.5142863952718137 chr12 133851895 46887688 0.3502952871903681 1.7458866050861601 chr13 115169878 22871286 0.19858739452689184 1.3077220732142052 chr14 107349540 31039075 0.2891402701865327 1.592045533966618 chr15 102531392 35019455 0.3415486156668974 1.708608139149055 chr16 90354753 31398377 0.34750111042857923 2.616978404865622 chr17 81195210 36532165 0.44993005129243463 2.2959952926364897 chr18 78077248 18206518 0.23318595962808525 3.485032395840253 chr19 59128983 13532868 0.2288702986824583 2.3657060525059306 chr20 63025520 41560672 0.6594260864487909 2.738857177047433 chr21 48129895 11592458 0.24085774548230368 1.5204728638614424 chr22 51304566 7512798 0.1464352704981463 1.077186686964735 chrMT 16571 1979602 119.46183090942007 89.66975845149645 chrX 155270560 33557114 0.21612026130388143 1.3621042995780357 chrY 59373566 1450307 0.02442681310399985 0.7875102395182578