BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524465.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 = 812,293 number of mapped reads = 738,880 (90.96%) number of supplementary alignments = 1,549 (0.19%) number of secondary alignments = 0 number of mapped bases = 42,545,260 bp number of sequenced bases = 42,531,982 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,537 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0861 >>>>>>> ACTG content number of A's = 10,732,308 bp (25.23%) number of C's = 7,802,820 bp (18.35%) number of T's = 13,782,366 bp (32.4%) number of G's = 10,213,640 bp (24.01%) number of N's = 848 bp (0%) GC percentage = 42.36% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 201,839 number of insertions = 2,546 mapped reads with insertion percentage = 0.34% number of deletions = 7,774 mapped reads with deletion percentage = 1.04% homopolymer indels = 44.69% >>>>>>> Coverage mean coverageData = 0.0137X std coverageData = 0.1578X There is a 1.26% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4209454 0.016888439367218268 0.24818711479138805 chr2 243199373 3359741 0.013814760122757388 0.18567623329620672 chr3 198022430 2336196 0.011797633227710618 0.11600069647670211 chr4 191154276 2412832 0.012622432783036461 0.12954604641925077 chr5 180915260 2353189 0.01300713383713458 0.12180525886038464 chr6 171115067 1823712 0.01065781074672986 0.1284923557052403 chr7 159138663 2148865 0.013503098238295493 0.2021591063249485 chr8 146364022 3866047 0.026413916119358897 0.1883683719298631 chr9 141213431 1803123 0.012768778346586594 0.1407438505903842 chr10 135534747 2218590 0.016369160301011224 0.1603164642620521 chr11 135006516 1465641 0.010856076013397753 0.14739201937199456 chr12 133851895 1934948 0.014455887979770477 0.1286995695445683 chr13 115169878 949558 0.008244846799264648 0.09788699482330555 chr14 107349540 1049679 0.009778141573778518 0.10666521034085956 chr15 102531392 1135243 0.011072150468804715 0.11449762084350437 chr16 90354753 1302502 0.014415423170931583 0.134147840369936 chr17 81195210 1471024 0.0181171278453495 0.14753313110850122 chr18 78077248 989119 0.01266846649103206 0.20885769009839328 chr19 59128983 865806 0.014642666862712657 0.18675971393129134 chr20 63025520 1227371 0.01947419077224591 0.15068864524007505 chr21 48129895 580723 0.012065744170021564 0.12443011313299988 chr22 51304566 341331 0.0066530335720996064 0.0867982929983553 chrMT 16571 3237 0.19534125882565928 0.4496681632876493 chrX 155270560 2556263 0.016463281899672416 0.14601430770996965 chrY 59373566 141066 0.0023759058029292025 0.0769374562946266