BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236094.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 = 250,752 number of mapped reads = 211,512 (84.35%) number of supplementary alignments = 1,367 (0.55%) number of secondary alignments = 0 number of mapped bases = 13,832,570 bp number of sequenced bases = 13,825,074 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,814 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4035 >>>>>>> ACTG content number of A's = 3,761,278 bp (27.21%) number of C's = 2,460,188 bp (17.8%) number of T's = 4,478,923 bp (32.4%) number of G's = 3,118,089 bp (22.55%) number of N's = 6,596 bp (0.05%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 115,682 number of insertions = 953 mapped reads with insertion percentage = 0.45% number of deletions = 4,254 mapped reads with deletion percentage = 1.99% homopolymer indels = 46% >>>>>>> Coverage mean coverageData = 0.0045X std coverageData = 0.0765X There is a 0.42% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 1542673 0.006189244358993994 0.10371895820778909 chr2 243199373 978405 0.004023057246944465 0.07375077926962763 chr3 198022430 976692 0.004932229141920943 0.07254515656951742 chr4 191154276 669329 0.003501512045694442 0.06317688236028848 chr5 180915260 742569 0.004104512797870119 0.06625166658357025 chr6 171115067 1175421 0.0068691846989721835 0.09136346535572185 chr7 159138663 932001 0.005856534059231099 0.09551143778245132 chr8 146364022 1247155 0.008520912331857073 0.1142353947654465 chr9 141213431 522682 0.0037013618060168793 0.06841070354229355 chr10 135534747 500541 0.0036930824831214685 0.06904044961744686 chr11 135006516 553050 0.004096468943765648 0.06804173606712959 chr12 133851895 443223 0.0033112941733099855 0.060013238840425344 chr13 115169878 608199 0.005280886031675747 0.07513873883077303 chr14 107349540 466118 0.004342058661825659 0.06833253782348654 chr15 102531392 292554 0.0028533115009303687 0.05510122636189025 chr16 90354753 235842 0.002610178127541337 0.054361940994523614 chr17 81195210 331579 0.004083726121282278 0.06683698639531427 chr18 78077248 406541 0.0052069073950967125 0.09464530843900802 chr19 59128983 217181 0.003673004150942356 0.07512884615854257 chr20 63025520 193789 0.003074770346995947 0.057675597629392644 chr21 48129895 271935 0.005650022714572721 0.07897426395000368 chr22 51304566 101968 0.0019875034124643017 0.045546747434866204 chrMT 16571 31557 1.9043509745941705 1.816936397859892 chrX 155270560 359449 0.0023149848883136635 0.05047703494148535 chrY 59373566 32117 5.409309590736053E-4 0.027159939500502214