BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173872.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 = 11,457,416 number of mapped reads = 11,130,995 (97.15%) number of supplementary alignments = 1,166,393 (10.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,583,664 number of mapped paired reads (second in pair) = 5,547,331 number of mapped paired reads (both in pair) = 10,910,054 number of mapped paired reads (singletons) = 220,941 number of mapped bases = 1,303,301,830 bp number of sequenced bases = 1,302,570,727 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,744,643 duplication rate = 65.56% >>>>>>> Insert size mean insert size = 760,985.3549 std insert size = 7,830,273.7246 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 52.6563 >>>>>>> ACTG content number of A's = 392,571,199 bp (30.14%) number of C's = 254,677,109 bp (19.55%) number of T's = 391,900,296 bp (30.09%) number of G's = 263,406,277 bp (20.22%) number of N's = 15,846 bp (0%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 13,369,661 number of insertions = 138,572 mapped reads with insertion percentage = 1.2% number of deletions = 293,048 mapped reads with deletion percentage = 2.57% homopolymer indels = 42.5% >>>>>>> Coverage mean coverageData = 0.421X std coverageData = 6.1568X There is a 8.23% of reference with a coverageData >= 1X There is a 6.6% of reference with a coverageData >= 2X There is a 5.17% of reference with a coverageData >= 3X There is a 4.3% of reference with a coverageData >= 4X There is a 3.32% of reference with a coverageData >= 5X There is a 2.72% of reference with a coverageData >= 6X There is a 2.06% of reference with a coverageData >= 7X There is a 1.69% of reference with a coverageData >= 8X There is a 1.27% of reference with a coverageData >= 9X There is a 1.07% of reference with a coverageData >= 10X There is a 0.81% of reference with a coverageData >= 11X There is a 0.7% of reference with a coverageData >= 12X There is a 0.53% of reference with a coverageData >= 13X There is a 0.46% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.15% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 116883475 0.4689395538155951 3.359837639498305 chr2 243199373 96042658 0.3949132632015462 18.65265427016299 chr3 198022430 77264683 0.39018147085660954 1.8735006198090738 chr4 191154276 85080852 0.4450899753872103 3.0971934482495933 chr5 180915260 72712169 0.4019128568811719 1.84775912019563 chr6 171115067 65243219 0.38128272479944736 2.0187430482779245 chr7 159138663 114353835 0.7185798400229113 6.995883924773958 chr8 146364022 118842242 0.8119634892241483 3.745927994478467 chr9 141213431 46335175 0.32812158639499384 2.7017272490746906 chr10 135534747 58305704 0.43019008254761415 7.634629886844209 chr11 135006516 53946693 0.39958584665646807 2.038019143706821 chr12 133851895 51239193 0.38280513697620794 1.8382890271486707 chr13 115169878 32126247 0.27894660963346685 1.5479274658956061 chr14 107349540 41558797 0.38713530584295003 1.8725523299812827 chr15 102531392 35939674 0.3505236132949409 1.7375847749833755 chr16 90354753 30147913 0.3336616171149292 3.0987640246696513 chr17 81195210 31807712 0.39174370015177 2.3558566493628366 chr18 78077248 23060960 0.2953608200944787 3.924106673520245 chr19 59128983 19936476 0.33716926942579073 2.544075859678997 chr20 63025520 48940714 0.7765221770482814 2.730143958758607 chr21 48129895 15585802 0.3238278828574216 2.062170490049198 chr22 51304566 14631265 0.2851844609698092 1.5151089366952324 chrMT 16571 3291763 198.64600808641603 129.0011860991346 chrX 155270560 47371765 0.3050917379315177 1.669475075487605 chrY 59373566 2652844 0.044680557000736656 1.873312907657813