BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238268.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,912,581 number of mapped reads = 1,487,545 (77.78%) number of supplementary alignments = 18,877 (0.99%) number of secondary alignments = 0 number of mapped bases = 94,809,041 bp number of sequenced bases = 94,773,763 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,796 duplication rate = 4.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1002 >>>>>>> ACTG content number of A's = 26,397,503 bp (27.85%) number of C's = 18,382,241 bp (19.4%) number of T's = 28,997,772 bp (30.6%) number of G's = 20,975,961 bp (22.13%) number of N's = 20,286 bp (0.02%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 794,371 number of insertions = 7,571 mapped reads with insertion percentage = 0.5% number of deletions = 21,728 mapped reads with deletion percentage = 1.45% homopolymer indels = 46.3% >>>>>>> Coverage mean coverageData = 0.0306X std coverageData = 0.2903X There is a 2.34% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 7188884 0.028841990327478462 0.46552398424485636 chr2 243199373 7699512 0.03165925925310671 0.3518408182690698 chr3 198022430 6671747 0.033691875208278176 0.23203159058311246 chr4 191154276 5994201 0.03135792264463914 0.23119288594691287 chr5 180915260 5632325 0.03113239314361873 0.22342840519643262 chr6 171115067 6471265 0.03781820685609175 0.2782125854543092 chr7 159138663 5453864 0.0342711437760414 0.34501847098841826 chr8 146364022 4735442 0.03235386630739076 0.31279224582710474 chr9 141213431 3348416 0.02371173886427276 0.23813173813893146 chr10 135534747 4139793 0.030544145258927586 0.3018203892003611 chr11 135006516 4862679 0.0360181059705296 0.2776267001467303 chr12 133851895 4136078 0.030900406751805793 0.22344356086972417 chr13 115169878 2709764 0.02352840905154037 0.1959372143057081 chr14 107349540 3339543 0.031109057383944077 0.2420369768112767 chr15 102531392 2708768 0.0264189137313185 0.22093748643623995 chr16 90354753 2153316 0.02383179554483426 0.21218252414943045 chr17 81195210 2430809 0.02993783746602786 0.23244796825882963 chr18 78077248 2226920 0.0285220093822979 0.367782324433015 chr19 59128983 2005564 0.0339184592435828 0.3793433122607254 chr20 63025520 1738139 0.027578336521459877 0.2131705671562416 chr21 48129895 1184571 0.024611958949837726 0.2027934018795356 chr22 51304566 1184549 0.023088568764035543 0.18996460067368923 chrMT 16571 44381 2.6782330577514935 2.3734799726960047 chrX 155270560 6485458 0.04176875513297563 0.27889709781211497 chrY 59373566 263053 0.004430473318715605 0.10506307891302066