BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716230.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 = 1,699,355 number of mapped reads = 1,526,254 (89.81%) number of supplementary alignments = 7,552 (0.44%) number of secondary alignments = 0 number of mapped bases = 87,342,095 bp number of sequenced bases = 87,318,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,145 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6208 >>>>>>> ACTG content number of A's = 22,069,867 bp (25.28%) number of C's = 15,480,300 bp (17.73%) number of T's = 28,567,442 bp (32.72%) number of G's = 21,199,589 bp (24.28%) number of N's = 1,388 bp (0%) GC percentage = 42.01% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 468,464 number of insertions = 6,695 mapped reads with insertion percentage = 0.44% number of deletions = 13,936 mapped reads with deletion percentage = 0.91% homopolymer indels = 41.59% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.258X There is a 2.54% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6899520 0.027681054403471277 0.4206462777585814 chr2 243199373 7270125 0.0298936831551782 0.30543256793440643 chr3 198022430 5701846 0.02879394016122315 0.18418919521328536 chr4 191154276 5752066 0.030091223279776383 0.2082217107119202 chr5 180915260 5265078 0.029102453822856072 0.18712118851553472 chr6 171115067 4985526 0.02913551732998474 0.20258632565003085 chr7 159138663 4803588 0.03018492118411225 0.28370978690061194 chr8 146364022 4380233 0.029926978912891585 0.287447593913871 chr9 141213431 3582477 0.025369237009757236 0.2594649860216431 chr10 135534747 4106370 0.03029754428950976 0.25891825605248286 chr11 135006516 3898847 0.02887895425728933 0.2546841500374781 chr12 133851895 3961744 0.02959796721592922 0.19270833835519408 chr13 115169878 2750298 0.023880358716712367 0.16699038899598073 chr14 107349540 2596655 0.024188785531824356 0.18154318803154298 chr15 102531392 2486150 0.024247695769116253 0.16886681719165628 chr16 90354753 2432947 0.02692660783434381 0.19677171724491643 chr17 81195210 2272551 0.027988732340245195 0.19212319891832375 chr18 78077248 3404983 0.043610438216265 0.4655039110823273 chr19 59128983 1675280 0.02833263680520262 0.3315502565023718 chr20 63025520 1813439 0.028773090646455595 0.1887545626171499 chr21 48129895 1164675 0.024198577620001042 0.1871871754523377 chr22 51304566 941844 0.018357898203446455 0.14689731168540854 chrMT 16571 11484 0.6930179228773158 0.9593569879280907 chrX 155270560 4917463 0.03167028572576797 0.23123635603863496 chrY 59373566 266906 0.00449536751759192 0.11078978281144604