BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525015.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 = 1,410,226 number of mapped reads = 1,295,951 (91.9%) number of supplementary alignments = 4,234 (0.3%) number of secondary alignments = 0 number of mapped bases = 74,557,674 bp number of sequenced bases = 74,533,114 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,595 duplication rate = 1.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6173 >>>>>>> ACTG content number of A's = 18,487,368 bp (24.8%) number of C's = 14,452,061 bp (19.39%) number of T's = 23,318,992 bp (31.29%) number of G's = 18,274,025 bp (24.52%) number of N's = 668 bp (0%) GC percentage = 43.91% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 378,180 number of insertions = 5,579 mapped reads with insertion percentage = 0.43% number of deletions = 14,803 mapped reads with deletion percentage = 1.13% homopolymer indels = 41.95% >>>>>>> Coverage mean coverageData = 0.0241X std coverageData = 0.246X There is a 2.22% of reference with a coverageData >= 1X There is a 0.13% 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 7766293 0.031158570313050495 0.4731812839797469 chr2 243199373 6948445 0.028570982376669204 0.28193516475098357 chr3 198022430 4032309 0.02036289020390266 0.15514741101758964 chr4 191154276 4692645 0.024548993086610314 0.17952369751765354 chr5 180915260 3215883 0.017775631530474543 0.14646576922471582 chr6 171115067 6031836 0.0352501746675528 0.27940767034841707 chr7 159138663 4633848 0.029118304204931018 0.3239519518363928 chr8 146364022 5140165 0.03511904722049795 0.2321107739626924 chr9 141213431 2106876 0.014919798953117994 0.18687091583068316 chr10 135534747 3767628 0.027798244239169163 0.24040665565440336 chr11 135006516 3111588 0.023047687564946864 0.2148920774196021 chr12 133851895 3176436 0.023730975194635833 0.16710896595230315 chr13 115169878 1417032 0.01230384215567199 0.1223681693089824 chr14 107349540 1680466 0.01565415184825198 0.1372189272929842 chr15 102531392 2067708 0.02016658468852154 0.16751472737246678 chr16 90354753 2382671 0.026370178888099 0.18501759368333923 chr17 81195210 1907018 0.023486828841258002 0.21789856478764638 chr18 78077248 1463238 0.018740901318653035 0.3091034370305973 chr19 59128983 1908332 0.032274054163928374 0.3034341058289433 chr20 63025520 1787514 0.0283617493358246 0.1810506235075161 chr21 48129895 954452 0.019830751760418344 0.15671001401288703 chr22 51304566 992040 0.019336290652960598 0.1471972954239165 chrMT 16571 21632 1.305413071027699 1.4416360115240017 chrX 155270560 3142619 0.020239632033271473 0.18422055943249144 chrY 59373566 209000 0.003520085015611156 0.08861168217822524