BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867870.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 = 2,202,037 number of mapped reads = 2,029,548 (92.17%) number of supplementary alignments = 9,058 (0.41%) number of secondary alignments = 0 number of mapped bases = 119,748,459 bp number of sequenced bases = 119,712,993 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,030 duplication rate = 3.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6826 >>>>>>> ACTG content number of A's = 30,781,313 bp (25.71%) number of C's = 23,534,110 bp (19.66%) number of T's = 37,232,614 bp (31.1%) number of G's = 28,148,629 bp (23.51%) number of N's = 16,327 bp (0.01%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 601,189 number of insertions = 7,241 mapped reads with insertion percentage = 0.35% number of deletions = 22,223 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.35% >>>>>>> Coverage mean coverageData = 0.0387X std coverageData = 0.352X There is a 3.37% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9707949 0.038948544886473924 0.6165461898495888 chr2 243199373 10095755 0.041512257517209966 0.5140165168988852 chr3 198022430 7872902 0.03975762745664721 0.22322335855053999 chr4 191154276 7644291 0.03999016480280043 0.26563535457980736 chr5 180915260 7213365 0.03987151222069382 0.2251370270989012 chr6 171115067 6836818 0.039954506168647326 0.2626478595796661 chr7 159138663 6552578 0.041175273666839846 0.4127261669691901 chr8 146364022 5972810 0.040807911113565874 0.38235259778009445 chr9 141213431 5051957 0.03577532933110307 0.287902077253646 chr10 135534747 5836993 0.043066395365020306 0.36364620100660605 chr11 135006516 5429682 0.040217925481463426 0.30699911021474874 chr12 133851895 5476068 0.04091139688384688 0.2303051388720358 chr13 115169878 3764191 0.032683815120477945 0.20307248270201264 chr14 107349540 3641227 0.03391935354357364 0.21542427051547341 chr15 102531392 3427885 0.03343254132353923 0.20497807590439882 chr16 90354753 3577226 0.0395909001046132 0.2428105261214891 chr17 81195210 3355846 0.04133059080701928 0.2463474602670935 chr18 78077248 3192238 0.04088563674785259 0.5426385686205808 chr19 59128983 2561388 0.043318654745000434 0.47350185125406724 chr20 63025520 2612487 0.04145125657035436 0.2359338387051236 chr21 48129895 1595237 0.033144410558136474 0.23896788359335405 chr22 51304566 1458047 0.028419439314621625 0.18941501789061407 chrMT 16571 25315 1.5276688190211816 1.410764967258613 chrX 155270560 6442800 0.04149402179009337 0.2562325973693013 chrY 59373566 403404 0.0067943367255387695 0.23631219421077673