BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717049.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 = 1,040,352 number of mapped reads = 896,066 (86.13%) number of supplementary alignments = 3,166 (0.3%) number of secondary alignments = 0 number of mapped bases = 50,532,661 bp number of sequenced bases = 50,517,752 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,364 duplication rate = 1.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.1898 >>>>>>> ACTG content number of A's = 11,424,829 bp (22.62%) number of C's = 10,041,279 bp (19.88%) number of T's = 15,527,804 bp (30.74%) number of G's = 13,522,401 bp (26.77%) number of N's = 1,439 bp (0%) GC percentage = 46.64% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 262,022 number of insertions = 3,289 mapped reads with insertion percentage = 0.36% number of deletions = 8,678 mapped reads with deletion percentage = 0.96% homopolymer indels = 38.16% >>>>>>> Coverage mean coverageData = 0.0163X std coverageData = 0.1571X There is a 1.49% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.02% 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 5055626 0.020283303526854604 0.1925217739493404 chr2 243199373 4297192 0.017669420553974864 0.17639758411949158 chr3 198022430 3475642 0.017551759161828284 0.14820887093447596 chr4 191154276 3366376 0.017610780519500387 0.15842052062759202 chr5 180915260 2892945 0.01599060797856411 0.13578118170670458 chr6 171115067 2129665 0.012445806423346695 0.12228735101249824 chr7 159138663 2985173 0.018758313936569897 0.18404894143545658 chr8 146364022 3086706 0.0210892400866109 0.1631085762037926 chr9 141213431 2226271 0.0157652921838575 0.14191652628160034 chr10 135534747 2707177 0.01997404399921151 0.2356597531521403 chr11 135006516 2045974 0.015154631499415925 0.15513735813008128 chr12 133851895 2334984 0.01744453449837225 0.142579610425257 chr13 115169878 940954 0.008170139765191034 0.09793933788055238 chr14 107349540 1655422 0.015420857881645324 0.1348828293897875 chr15 102531392 1040776 0.010150803375418916 0.10869302679918975 chr16 90354753 1384733 0.015325513645087382 0.1440687567109113 chr17 81195210 2050726 0.025256736204019917 0.1783861276427562 chr18 78077248 1340600 0.017170174850425057 0.17272457966058305 chr19 59128983 1370869 0.023184383198337776 0.1935353571122681 chr20 63025520 1212694 0.01924131685069794 0.15492284193381411 chr21 48129895 670286 0.013926604244617613 0.13737163168633 chr22 51304566 574889 0.01120541590781608 0.11530250956865937 chrMT 16571 2672 0.16124554945386518 0.4338968893782742 chrX 155270560 1529045 0.009847616959712131 0.11407064865610604 chrY 59373566 155264 0.0026150357888222514 0.09040951122506952