BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174019.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 = 3,432,338 number of mapped reads = 3,368,720 (98.15%) number of supplementary alignments = 303,549 (8.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,682,541 number of mapped paired reads (second in pair) = 1,686,179 number of mapped paired reads (both in pair) = 3,328,176 number of mapped paired reads (singletons) = 40,544 number of mapped bases = 402,409,665 bp number of sequenced bases = 402,220,580 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,556,921 duplication rate = 64.36% >>>>>>> Insert size mean insert size = 695,468.4817 std insert size = 7,673,839.1221 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 52.9727 >>>>>>> ACTG content number of A's = 123,239,454 bp (30.64%) number of C's = 77,206,463 bp (19.2%) number of T's = 122,678,965 bp (30.5%) number of G's = 79,090,723 bp (19.66%) number of N's = 4,975 bp (0%) GC percentage = 38.86% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 3,658,534 number of insertions = 41,331 mapped reads with insertion percentage = 1.18% number of deletions = 72,110 mapped reads with deletion percentage = 2.08% homopolymer indels = 44.24% >>>>>>> Coverage mean coverageData = 0.13X std coverageData = 1.9215X There is a 2.85% of reference with a coverageData >= 1X There is a 2.19% of reference with a coverageData >= 2X There is a 1.63% of reference with a coverageData >= 3X There is a 1.34% of reference with a coverageData >= 4X There is a 1% of reference with a coverageData >= 5X There is a 0.82% of reference with a coverageData >= 6X There is a 0.6% of reference with a coverageData >= 7X There is a 0.5% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.04% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% 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% 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 35287202 0.1415731758598106 1.1653160199286825 chr2 243199373 31564313 0.12978780582629215 5.381663949480505 chr3 198022430 26391505 0.13327533148643816 1.0592178300944244 chr4 191154276 26510769 0.13868781569918948 1.1796654198345173 chr5 180915260 21231558 0.11735636894311735 0.9780912067920263 chr6 171115067 20302612 0.11864888554787523 1.012147915915205 chr7 159138663 31326275 0.19684892664958484 1.967183660288931 chr8 146364022 40977111 0.2799671014779848 1.7930843033186412 chr9 141213431 13903195 0.09845518872776343 0.9867094599629646 chr10 135534747 17825317 0.13151842899739946 2.2644873039381004 chr11 135006516 17531969 0.12986016911954087 1.030270907908601 chr12 133851895 14816315 0.11069185834089237 0.9537042866266121 chr13 115169878 11021123 0.0956944922699319 0.8993094415467057 chr14 107349540 13871761 0.12922049782421052 1.0309454046566573 chr15 102531392 9527914 0.0929267984579786 0.866654059972628 chr16 90354753 8670165 0.09595693322298164 1.1140061642667807 chr17 81195210 9079638 0.11182479853183458 1.0024606514668335 chr18 78077248 7260083 0.0929858977611506 1.0757993887452333 chr19 59128983 4539487 0.07677262096660786 0.8918484477942697 chr20 63025520 14944990 0.23712600863904018 1.3914817667658979 chr21 48129895 4853948 0.10085099915551447 0.9420448865299056 chr22 51304566 3679299 0.07171484502958275 0.7289519636130662 chrMT 16571 792376 47.817029750769414 45.71110349438011 chrX 155270560 15870582 0.10221243486208847 0.9121646809412237 chrY 59373566 630158 0.010613443699844472 0.429997767257523