BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240063.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 = 2,818,179 number of mapped reads = 2,512,425 (89.15%) number of supplementary alignments = 16,116 (0.57%) number of secondary alignments = 0 number of mapped bases = 172,148,605 bp number of sequenced bases = 172,082,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,421 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5717 >>>>>>> ACTG content number of A's = 49,712,336 bp (28.89%) number of C's = 31,932,448 bp (18.56%) number of T's = 54,738,379 bp (31.81%) number of G's = 35,682,142 bp (20.74%) number of N's = 16,947 bp (0.01%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,335,806 number of insertions = 12,687 mapped reads with insertion percentage = 0.5% number of deletions = 37,692 mapped reads with deletion percentage = 1.48% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.0556X std coverageData = 0.6344X There is a 4.55% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 13530983 0.054286657123313646 1.2896426563839545 chr2 243199373 13784775 0.05668096438719026 0.570937298162428 chr3 198022430 11634103 0.05875144043025833 0.2819635521871447 chr4 191154276 12130940 0.06346151524227478 0.32115988580508226 chr5 180915260 11188371 0.06184315795140775 0.2934130075540931 chr6 171115067 10470364 0.0611890243423158 0.38391043819656523 chr7 159138663 10172479 0.06392210923627026 0.6688625471679495 chr8 146364022 8356950 0.057097023474799016 1.4196154311974507 chr9 141213431 8067893 0.05713261793065562 0.5685404833214484 chr10 135534747 8283707 0.06111869600494403 0.4399611257651492 chr11 135006516 7388725 0.05472865472656149 0.4251058564860094 chr12 133851895 7805213 0.058312308540719573 0.29955999556574303 chr13 115169878 6084340 0.05282926495763068 0.2672669368551956 chr14 107349540 5165582 0.04811927466107447 0.29602634674389733 chr15 102531392 5023176 0.04899159079006749 0.26299183241778246 chr16 90354753 4145858 0.04588422703120001 0.30214589642010775 chr17 81195210 3528000 0.04345083903348486 0.28886069950369736 chr18 78077248 4925022 0.06307883699999263 1.095981386878479 chr19 59128983 2787196 0.04713756027226107 0.7526831117187841 chr20 63025520 3346870 0.05310340953950082 0.2870572178995952 chr21 48129895 2133150 0.04432068675819883 0.2799759268042427 chr22 51304566 1675441 0.032656761973193574 0.20593234937548155 chrMT 16571 128190 7.735803512159797 4.869476794790749 chrX 155270560 9973200 0.06423110730070143 0.35698667918007987 chrY 59373566 418077 0.007041466904649116 0.16338143200866095