BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004101.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 = 3,778,443 number of mapped reads = 3,096,510 (81.95%) number of supplementary alignments = 28,206 (0.75%) number of secondary alignments = 0 number of mapped bases = 207,631,522 bp number of sequenced bases = 207,549,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 200,290 duplication rate = 5.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9112 >>>>>>> ACTG content number of A's = 57,432,533 bp (27.67%) number of C's = 38,219,220 bp (18.41%) number of T's = 67,312,397 bp (32.43%) number of G's = 44,557,448 bp (21.47%) number of N's = 27,668 bp (0.01%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,948,547 number of insertions = 17,018 mapped reads with insertion percentage = 0.54% number of deletions = 50,049 mapped reads with deletion percentage = 1.6% homopolymer indels = 47.07% >>>>>>> Coverage mean coverageData = 0.0671X std coverageData = 0.5659X There is a 4.87% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 18909400 0.07586500657103679 1.169633517351585 chr2 243199373 19626021 0.08069930755948125 0.6301387857301377 chr3 198022430 12882442 0.06505546871634693 0.3496670182038578 chr4 191154276 14518425 0.07595134832348716 0.39466689155814555 chr5 180915260 11448784 0.06328257771069173 0.3267135545357091 chr6 171115067 10732844 0.06272296290542317 0.4021082506244264 chr7 159138663 9929404 0.06239466772446115 0.5621764517384761 chr8 146364022 9343523 0.06383756658449848 0.6178919648122877 chr9 141213431 11735227 0.08310276803627836 0.5299727591601577 chr10 135534747 9687184 0.07147380442596023 0.7406989500879463 chr11 135006516 8068493 0.05976373021876959 0.3982901480130646 chr12 133851895 10535714 0.0787117283621573 0.37261569146061146 chr13 115169878 8440810 0.07329008371442401 0.35604665843746264 chr14 107349540 5647683 0.05261022077970711 0.31876430837190967 chr15 102531392 6018303 0.0586971744224442 0.32006313639332773 chr16 90354753 5132656 0.05680560047571598 0.35617493335124933 chr17 81195210 4381615 0.05396395920399738 0.33316145011682435 chr18 78077248 6386321 0.0817949039392372 0.9006652925869882 chr19 59128983 3189360 0.053939030204527616 0.7078130024137902 chr20 63025520 3883378 0.0616159612804464 0.3389316328743008 chr21 48129895 2652400 0.055109199801911056 0.3463237654020814 chr22 51304566 2002536 0.03903231536935718 0.2540384586805178 chrMT 16571 55198 3.3309999396536116 2.9376626160372217 chrX 155270560 11901912 0.07665272798655456 0.3880638029817313 chrY 59373566 521889 0.008789921764173638 0.21626827795411105