BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524802.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 = 1,518,812 number of mapped reads = 1,383,966 (91.12%) number of supplementary alignments = 5,385 (0.35%) number of secondary alignments = 0 number of mapped bases = 78,919,381 bp number of sequenced bases = 78,895,010 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,148 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5537 >>>>>>> ACTG content number of A's = 18,917,047 bp (23.98%) number of C's = 13,831,744 bp (17.53%) number of T's = 26,372,191 bp (33.43%) number of G's = 19,765,342 bp (25.05%) number of N's = 8,686 bp (0.01%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 397,730 number of insertions = 6,024 mapped reads with insertion percentage = 0.43% number of deletions = 14,947 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.85% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.2332X There is a 2.26% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6278527 0.025189614271813588 0.2936807267117826 chr2 243199373 6777023 0.0278661203620784 0.38588493459490025 chr3 198022430 5123455 0.025873104375095286 0.18114628460484564 chr4 191154276 4964988 0.02597372187478558 0.20395657895463098 chr5 180915260 4699875 0.025978322668856125 0.17894612800420223 chr6 171115067 4549913 0.026589785924579043 0.1999809803262008 chr7 159138663 4325047 0.027177851808394292 0.2727155880669213 chr8 146364022 3933740 0.0268764136585424 0.21390147646262841 chr9 141213431 3354465 0.02375457473305071 0.20231814997717615 chr10 135534747 3846875 0.028382943010178786 0.2765422945598506 chr11 135006516 3598241 0.026652350616913928 0.2077003340139173 chr12 133851895 3576254 0.026717993047464885 0.18371279086234338 chr13 115169878 2455306 0.021318994537790514 0.16184952695606586 chr14 107349540 2369464 0.022072418754658846 0.16749639385162887 chr15 102531392 2278804 0.02222542731108147 0.1667390993230156 chr16 90354753 2416644 0.026746174603565126 0.20073979150380802 chr17 81195210 2220229 0.027344334721223086 0.19012414948012013 chr18 78077248 2080210 0.026642972867076464 0.301336312617605 chr19 59128983 1719834 0.0290861420701249 0.2466815417108449 chr20 63025520 1714336 0.02720066411193434 0.19180669524862162 chr21 48129895 1011133 0.02100841898782451 0.1788543550274485 chr22 51304566 1000106 0.01949350862845229 0.15768561332719647 chrMT 16571 22333 1.347715889204031 1.4769128659674549 chrX 155270560 4335016 0.02791911100211141 0.1995381067549639 chrY 59373566 267563 0.004506433047999845 0.12555180381499942