BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173920.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 = 5,922,194 number of mapped reads = 5,773,274 (97.49%) number of supplementary alignments = 602,057 (10.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,890,313 number of mapped paired reads (second in pair) = 2,882,961 number of mapped paired reads (both in pair) = 5,672,254 number of mapped paired reads (singletons) = 101,020 number of mapped bases = 685,205,593 bp number of sequenced bases = 684,765,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,579,372 duplication rate = 65.99% >>>>>>> Insert size mean insert size = 893,027.4555 std insert size = 8,587,754.2396 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.7566 >>>>>>> ACTG content number of A's = 206,148,403 bp (30.1%) number of C's = 133,495,565 bp (19.5%) number of T's = 206,174,213 bp (30.11%) number of G's = 138,939,246 bp (20.29%) number of N's = 8,075 bp (0%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 6,943,103 number of insertions = 70,015 mapped reads with insertion percentage = 1.17% number of deletions = 186,177 mapped reads with deletion percentage = 3.15% homopolymer indels = 42.18% >>>>>>> Coverage mean coverageData = 0.2213X std coverageData = 3.1503X There is a 4.4% of reference with a coverageData >= 1X There is a 3.52% of reference with a coverageData >= 2X There is a 2.75% of reference with a coverageData >= 3X There is a 2.29% of reference with a coverageData >= 4X There is a 1.77% of reference with a coverageData >= 5X There is a 1.45% of reference with a coverageData >= 6X There is a 1.1% of reference with a coverageData >= 7X There is a 0.9% of reference with a coverageData >= 8X There is a 0.67% of reference with a coverageData >= 9X There is a 0.56% of reference with a coverageData >= 10X There is a 0.42% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% 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 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% 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 0.02% 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 62704759 0.25157313048379526 1.8154971826711614 chr2 243199373 50856681 0.2091151813948139 9.414296805416722 chr3 198022430 42942911 0.2168588225081371 1.3899195791153194 chr4 191154276 42518519 0.22243038392716885 1.6139488983673917 chr5 180915260 32771059 0.18114038030843832 1.255343213733538 chr6 171115067 33826781 0.19768440963763875 1.4071216961758894 chr7 159138663 54269546 0.3410204973256562 2.9517050386957213 chr8 146364022 68674247 0.4692016935692024 2.413007115579275 chr9 141213431 24468643 0.17327419089477403 1.4804384228002017 chr10 135534747 32101962 0.23685411092404224 3.623947609522427 chr11 135006516 28203197 0.2089024873436479 1.3669957794341456 chr12 133851895 27486249 0.205348224617963 1.331129056076552 chr13 115169878 18221543 0.1582144855619279 1.181562364379258 chr14 107349540 24117583 0.2246640553839355 1.4106864203956995 chr15 102531392 17072247 0.16650751215783746 1.1844257836755654 chr16 90354753 16670341 0.18449877230033487 1.734419554990919 chr17 81195210 17763088 0.21877014666259254 1.520628225597023 chr18 78077248 12110321 0.1551069141166451 1.8749693148703057 chr19 59128983 9371208 0.1584875559249852 1.3942757434903557 chr20 63025520 24099957 0.3823841040898988 1.8369342631273726 chr21 48129895 8779797 0.18241878566325564 1.3286466642725134 chr22 51304566 7815466 0.1523347064274942 1.0981006841379664 chrMT 16571 245377 14.807615714199505 15.253013410440298 chrX 155270560 26837552 0.17284378957607932 1.2259583254093411 chrY 59373566 1276559 0.021500460322696466 0.8128784176184658