BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173842.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 = 4,343,812 number of mapped reads = 4,234,716 (97.49%) number of supplementary alignments = 428,694 (9.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,117,479 number of mapped paired reads (second in pair) = 2,117,237 number of mapped paired reads (both in pair) = 4,162,046 number of mapped paired reads (singletons) = 72,670 number of mapped bases = 500,508,726 bp number of sequenced bases = 500,221,261 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,276,628 duplication rate = 64.73% >>>>>>> Insert size mean insert size = 860,150.6955 std insert size = 8,380,562.3242 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.6895 >>>>>>> ACTG content number of A's = 150,506,558 bp (30.09%) number of C's = 98,240,725 bp (19.64%) number of T's = 149,981,179 bp (29.98%) number of G's = 101,486,839 bp (20.29%) number of N's = 5,960 bp (0%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 5,101,973 number of insertions = 50,938 mapped reads with insertion percentage = 1.17% number of deletions = 114,512 mapped reads with deletion percentage = 2.64% homopolymer indels = 43.72% >>>>>>> Coverage mean coverageData = 0.1617X std coverageData = 2.3977X There is a 3.41% of reference with a coverageData >= 1X There is a 2.69% of reference with a coverageData >= 2X There is a 2.07% of reference with a coverageData >= 3X There is a 1.7% of reference with a coverageData >= 4X There is a 1.29% of reference with a coverageData >= 5X There is a 1.04% of reference with a coverageData >= 6X There is a 0.77% of reference with a coverageData >= 7X There is a 0.62% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% 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 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% 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 41345578 0.165879538570939 1.8203865638660657 chr2 243199373 40110719 0.16492936846510703 6.991299305731388 chr3 198022430 38953527 0.19671270067739297 1.3006841925530115 chr4 191154276 26215869 0.1371450827498099 1.2226386609574766 chr5 180915260 30850870 0.17052663219233138 1.1812435153165828 chr6 171115067 27079576 0.15825360369931654 1.3564362246895827 chr7 159138663 32462507 0.20398881320248366 1.8430437945177927 chr8 146364022 27109222 0.18521779894788626 1.5761042592317789 chr9 141213431 20512494 0.1452588033216189 1.278448565656405 chr10 135534747 26967869 0.19897383952766 2.2819970575938116 chr11 135006516 19337410 0.1432331606868516 1.1074972645294594 chr12 133851895 22544304 0.16842723070898621 1.18243591416432 chr13 115169878 11907910 0.10339430940440868 0.9237054310045778 chr14 107349540 11647192 0.10849782868189281 0.9451535920043311 chr15 102531392 12365934 0.12060632123281814 0.9858205676733632 chr16 90354753 17440198 0.1930191541777553 1.552340246626224 chr17 81195210 21332278 0.2627282816313918 1.5737442559207435 chr18 78077248 10014585 0.12826508690470237 1.7111529009811428 chr19 59128983 8353840 0.14128164524662973 1.5067301506317592 chr20 63025520 23057420 0.36584259836332966 1.873138165497596 chr21 48129895 6341753 0.13176328350602054 1.0823940225580329 chr22 51304566 3926318 0.07652960167327018 0.7507570015356884 chrMT 16571 1210891 73.07289843702854 59.63599176629361 chrX 155270560 18604001 0.11981666711319905 0.9848179949787997 chrY 59373566 816461 0.013751254219765072 0.5188580694523771