BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174015.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 = 3,544,476 number of mapped reads = 3,453,751 (97.44%) number of supplementary alignments = 339,820 (9.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,729,048 number of mapped paired reads (second in pair) = 1,724,703 number of mapped paired reads (both in pair) = 3,392,454 number of mapped paired reads (singletons) = 61,297 number of mapped bases = 409,298,072 bp number of sequenced bases = 409,072,022 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,688,235 duplication rate = 64.55% >>>>>>> Insert size mean insert size = 904,564.2017 std insert size = 8,788,752.1794 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 52.7129 >>>>>>> ACTG content number of A's = 123,451,947 bp (30.18%) number of C's = 79,961,720 bp (19.55%) number of T's = 122,989,442 bp (30.07%) number of G's = 82,663,923 bp (20.21%) number of N's = 4,990 bp (0%) GC percentage = 39.75% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 4,220,188 number of insertions = 42,498 mapped reads with insertion percentage = 1.19% number of deletions = 89,317 mapped reads with deletion percentage = 2.52% homopolymer indels = 43.47% >>>>>>> Coverage mean coverageData = 0.1322X std coverageData = 2.0121X There is a 2.75% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 1.68% of reference with a coverageData >= 3X There is a 1.39% of reference with a coverageData >= 4X There is a 1.06% of reference with a coverageData >= 5X There is a 0.86% of reference with a coverageData >= 6X There is a 0.64% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.15% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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% 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 33020640 0.13247966993029076 1.7092698228598704 chr2 243199373 39228239 0.1613007406889984 5.571990573098294 chr3 198022430 30873682 0.155910024940104 1.1493553950403954 chr4 191154276 25993809 0.1359834032695141 1.2278551236676332 chr5 180915260 27262455 0.15069184876941835 1.1293785576282362 chr6 171115067 28602417 0.16715311808281616 1.2374280719481916 chr7 159138663 29467962 0.1851716072290993 1.9703719119484124 chr8 146364022 16068255 0.10978281944178878 1.0971032112488424 chr9 141213431 16504016 0.11687284901391568 1.1240922769114632 chr10 135534747 19398727 0.1431273339817427 2.1298670578422474 chr11 135006516 18823335 0.13942538151269676 1.1004890269427814 chr12 133851895 14515850 0.10844710117850778 0.9650542345612212 chr13 115169878 12130954 0.10533096162522634 0.9456408269288855 chr14 107349540 11879043 0.1106576050535475 0.9650446528044816 chr15 102531392 12400067 0.12093922415488127 0.9880199968096286 chr16 90354753 15716450 0.17394159663078268 1.6671774102320884 chr17 81195210 9092390 0.11198185213142499 1.0078456316450253 chr18 78077248 6210720 0.07954583645161264 1.3163171227195933 chr19 59128983 7062750 0.11944649885150231 1.5792754893109042 chr20 63025520 11802113 0.18725927211707258 1.2500024579347866 chr21 48129895 5706681 0.11856832432316755 1.0308559634642491 chr22 51304566 3135083 0.06110729013865939 0.6739528739836645 chrMT 16571 1076438 64.95914549514211 53.47103849734936 chrX 155270560 12779240 0.08230304572869448 0.8355221878044301 chrY 59373566 546756 0.00920874451098322 0.4956911927356917