BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174001.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 = 6,245,412 number of mapped reads = 6,087,428 (97.47%) number of supplementary alignments = 632,763 (10.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,045,399 number of mapped paired reads (second in pair) = 3,042,029 number of mapped paired reads (both in pair) = 5,981,290 number of mapped paired reads (singletons) = 106,138 number of mapped bases = 719,813,964 bp number of sequenced bases = 719,401,715 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,704,481 duplication rate = 64.32% >>>>>>> Insert size mean insert size = 931,094.7081 std insert size = 8,367,740.4499 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.7448 >>>>>>> ACTG content number of A's = 217,418,717 bp (30.22%) number of C's = 140,093,158 bp (19.47%) number of T's = 216,761,814 bp (30.13%) number of G's = 145,118,724 bp (20.17%) number of N's = 9,302 bp (0%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 7,230,317 number of insertions = 78,025 mapped reads with insertion percentage = 1.24% number of deletions = 163,922 mapped reads with deletion percentage = 2.62% homopolymer indels = 42.9% >>>>>>> Coverage mean coverageData = 0.2325X std coverageData = 3.2986X There is a 4.94% of reference with a coverageData >= 1X There is a 3.86% of reference with a coverageData >= 2X There is a 2.95% of reference with a coverageData >= 3X There is a 2.41% of reference with a coverageData >= 4X There is a 1.82% of reference with a coverageData >= 5X There is a 1.47% of reference with a coverageData >= 6X There is a 1.09% of reference with a coverageData >= 7X There is a 0.89% of reference with a coverageData >= 8X There is a 0.65% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.01% 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% 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 55686934 0.22341743333108888 2.1228234119171865 chr2 243199373 67256916 0.27655053206078783 10.02328954920192 chr3 198022430 62732775 0.31679630938778 1.6451823592745343 chr4 191154276 42155483 0.220531205904073 1.7660378444309737 chr5 180915260 49542117 0.27384155985514985 1.504369676128156 chr6 171115067 34571651 0.2020374453641771 1.5098207822163157 chr7 159138663 41376094 0.2600002615329249 2.1064408678421254 chr8 146364022 35739142 0.24417982993115617 2.128738255091415 chr9 141213431 27383371 0.19391477712909616 1.7243175040211707 chr10 135534747 37505853 0.27672500100656844 2.955287482129579 chr11 135006516 29930222 0.22169464768648647 1.3882368423691875 chr12 133851895 34054967 0.2544227483667676 1.4560699603835816 chr13 115169878 14910080 0.12946162884708448 1.0377943996427268 chr14 107349540 23216543 0.21627054014390745 1.3452632121765251 chr15 102531392 18465161 0.1800927563726044 1.2124909494673402 chr16 90354753 23438467 0.2594049147586071 2.0611198285128007 chr17 81195210 26591037 0.32749514411010205 1.8198182483508811 chr18 78077248 15362947 0.19676599001030365 2.2179154212247134 chr19 59128983 9791552 0.16559648928851017 1.6965435013365708 chr20 63025520 26535697 0.4210309887169515 2.02669597391706 chr21 48129895 9222476 0.19161637481236973 1.4307687283864379 chr22 51304566 5604785 0.1092453447515763 0.9255694774279278 chrMT 16571 1838332 110.93669663870617 85.75038999617145 chrX 155270560 24562641 0.15819251891665748 1.1434175031083915 chrY 59373566 2338721 0.039389936592321234 1.0224338872176955