BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354882.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 16,407,702 number of mapped reads = 16,283,025 (99.24%) number of supplementary alignments = 437,310 (2.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,148,311 number of mapped paired reads (second in pair) = 8,134,714 number of mapped paired reads (both in pair) = 16,252,252 number of mapped paired reads (singletons) = 30,773 number of mapped bases = 2,098,382,305 bp number of sequenced bases = 2,097,141,547 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,678,094 duplication rate = 40.16% >>>>>>> Insert size mean insert size = 239,661.4624 std insert size = 5,608,378.3293 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 53.9084 >>>>>>> ACTG content number of A's = 604,444,800 bp (28.82%) number of C's = 433,489,131 bp (20.67%) number of T's = 610,397,271 bp (29.11%) number of G's = 448,784,999 bp (21.4%) number of N's = 25,346 bp (0%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 15,665,783 number of insertions = 421,063 mapped reads with insertion percentage = 2.42% number of deletions = 440,443 mapped reads with deletion percentage = 2.58% homopolymer indels = 44.38% >>>>>>> Coverage mean coverageData = 0.6778X std coverageData = 19.3353X There is a 27.16% of reference with a coverageData >= 1X There is a 18.71% of reference with a coverageData >= 2X There is a 7.4% of reference with a coverageData >= 3X There is a 5.23% of reference with a coverageData >= 4X There is a 2.08% of reference with a coverageData >= 5X There is a 1.46% of reference with a coverageData >= 6X There is a 0.6% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.02% 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 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 170643050 0.6846243725105905 18.755590353675217 chr2 243199373 191622847 0.7879249219939395 60.462868444114655 chr3 198022430 138841060 0.701138047846398 1.7428541432094955 chr4 191154276 145342373 0.7603406841916526 10.324353273711598 chr5 180915260 125243597 0.6922776829328825 1.4517217474786874 chr6 171115067 119569094 0.6987642648674532 2.768681514859121 chr7 159138663 114638103 0.7203661312650339 11.319117772358652 chr8 146364022 103503303 0.7071635610013505 2.900928061839608 chr9 141213431 89396641 0.6330604700058594 9.646109077234671 chr10 135534747 117357086 0.8658819129237759 25.333297048392723 chr11 135006516 94516794 0.7000906089599409 3.516976367868294 chr12 133851895 93195186 0.6962560074326927 1.526616215779862 chr13 115169878 65850038 0.5717644156920961 1.2645543325208148 chr14 107349540 63775711 0.5940939383624746 2.903486819842863 chr15 102531392 58539145 0.5709387521043311 1.2705434348098945 chr16 90354753 63319413 0.7007867422314795 4.676352434808579 chr17 81195210 56790093 0.6994266410543184 4.069848567203483 chr18 78077248 57091141 0.7312135412354698 8.581941539192245 chr19 59128983 40291690 0.6814203112541273 9.28491786758512 chr20 63025520 42752299 0.678333141876497 3.5126387132140278 chr21 48129895 29108909 0.6047989300620747 5.3800091158571 chr22 51304566 24439552 0.4763621234024278 1.9862123589543512 chrMT 16571 9791692 590.8932472391527 132.76937167887056 chrX 155270560 56709464 0.3652299830695529 1.549599991841901 chrY 59373566 26054024 0.4388152128170978 12.92073289709511