BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524288.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,559,092 number of mapped reads = 1,439,212 (92.31%) number of supplementary alignments = 5,126 (0.33%) number of secondary alignments = 0 number of mapped bases = 83,986,279 bp number of sequenced bases = 83,961,263 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,715 duplication rate = 3.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2729 >>>>>>> ACTG content number of A's = 21,064,531 bp (25.09%) number of C's = 16,096,350 bp (19.17%) number of T's = 26,545,384 bp (31.62%) number of G's = 20,244,790 bp (24.11%) number of N's = 10,208 bp (0.01%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 414,428 number of insertions = 6,827 mapped reads with insertion percentage = 0.47% number of deletions = 15,652 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.24% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.2755X There is a 2.43% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6700512 0.026882629110881934 0.5259508829151569 chr2 243199373 7138959 0.029354347883125506 0.3007791745203531 chr3 198022430 5518106 0.027866065475512042 0.18130472248889115 chr4 191154276 5345417 0.02796388923049778 0.20320586165774335 chr5 180915260 4976192 0.027505650988202984 0.182327256948233 chr6 171115067 4895190 0.028607591872666597 0.2012714050132551 chr7 159138663 4381817 0.02753458472879089 0.3439248115501395 chr8 146364022 4529747 0.030948500445006903 0.2807372153196214 chr9 141213431 3532922 0.025018314299013102 0.23991627137313107 chr10 135534747 4118762 0.030388974718047763 0.26494587981667433 chr11 135006516 3766501 0.02789866083204458 0.25319643132587116 chr12 133851895 3623922 0.027074118001840765 0.18295246501896423 chr13 115169878 2667138 0.023158294914578274 0.1663040715241839 chr14 107349540 2636757 0.024562350243885533 0.1808921224689136 chr15 102531392 2417241 0.023575618674912754 0.16927320861915562 chr16 90354753 2441705 0.027023536880234733 0.19499872621927067 chr17 81195210 2244552 0.02764389672740547 0.19516083771904988 chr18 78077248 2278416 0.02918156131732512 0.4846991556993853 chr19 59128983 1656744 0.02801915263788657 0.3544044150505415 chr20 63025520 1776266 0.028183281946741575 0.18554775194234363 chr21 48129895 1154849 0.02399442176219167 0.18927170746691224 chr22 51304566 969972 0.018906153499086222 0.14985107512941603 chrMT 16571 11496 0.6937420795365398 0.9165513867814196 chrX 155270560 4935387 0.03178572293421238 0.21993525555702725 chrY 59373566 267709 0.004508892054757163 0.1324396169367508