BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716835.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 = 877,451 number of mapped reads = 780,743 (88.98%) number of supplementary alignments = 4,166 (0.47%) number of secondary alignments = 0 number of mapped bases = 45,549,791 bp number of sequenced bases = 45,536,685 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,245 duplication rate = 1.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6974 >>>>>>> ACTG content number of A's = 11,429,940 bp (25.1%) number of C's = 8,039,280 bp (17.65%) number of T's = 14,352,210 bp (31.52%) number of G's = 11,714,777 bp (25.73%) number of N's = 478 bp (0%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 226,612 number of insertions = 3,154 mapped reads with insertion percentage = 0.4% number of deletions = 8,393 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.05% >>>>>>> Coverage mean coverageData = 0.0147X std coverageData = 0.1582X There is a 1.38% of reference with a coverageData >= 1X There is a 0.06% 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 3455782 0.013864687622984899 0.20366631746410352 chr2 243199373 4625614 0.019019843443428615 0.1938109346138816 chr3 198022430 3277354 0.016550418051126836 0.13688275813535875 chr4 191154276 2594186 0.01357116384882753 0.12869129388266365 chr5 180915260 2155335 0.011913505803766912 0.11405852950248674 chr6 171115067 2583640 0.015098845737529355 0.13383692053400748 chr7 159138663 2246429 0.01411617364159959 0.24567591825389154 chr8 146364022 3893258 0.02659982929411437 0.20282835717639053 chr9 141213431 1954414 0.013840142443674498 0.13524373226666528 chr10 135534747 2086246 0.015392702212370678 0.19732002899559445 chr11 135006516 1579483 0.011699309387407642 0.12959270923903607 chr12 133851895 2146032 0.0160328847043966 0.13654460068060773 chr13 115169878 1225165 0.010637894398047378 0.10722017193142486 chr14 107349540 1335257 0.012438404486875304 0.11766759476369854 chr15 102531392 1102409 0.010751916837333097 0.11106795757715182 chr16 90354753 1424395 0.015764472290682927 0.1341500645126425 chr17 81195210 1825760 0.022486055519777583 0.16055807023118013 chr18 78077248 1100807 0.0140989472374846 0.1849975906780399 chr19 59128983 933025 0.01577948668591171 0.18941588910292123 chr20 63025520 1070294 0.01698191462759847 0.13925655388411734 chr21 48129895 509469 0.010585292155738134 0.11093495815827795 chr22 51304566 704645 0.013734547525458066 0.12183551422999835 chrMT 16571 3904 0.2355922998008569 0.5337133107856666 chrX 155270560 1603288 0.010325769418233566 0.11260590458723213 chrY 59373566 113600 0.0019133093673369729 0.06142864704246613