BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716882.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 = 1,383,121 number of mapped reads = 1,159,780 (83.85%) number of supplementary alignments = 2,177 (0.16%) number of secondary alignments = 0 number of mapped bases = 66,465,321 bp number of sequenced bases = 66,445,394 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,016 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5641 >>>>>>> ACTG content number of A's = 16,695,266 bp (25.13%) number of C's = 11,631,479 bp (17.51%) number of T's = 21,128,565 bp (31.8%) number of G's = 16,989,440 bp (25.57%) number of N's = 644 bp (0%) GC percentage = 43.07% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 313,864 number of insertions = 3,579 mapped reads with insertion percentage = 0.31% number of deletions = 12,740 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.75% >>>>>>> Coverage mean coverageData = 0.0215X std coverageData = 0.2068X There is a 1.96% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 7733487 0.031026951784404982 0.28573737010184547 chr2 243199373 6821630 0.028049537775740895 0.29106443173027985 chr3 198022430 4181012 0.021113830387800007 0.1585415261515742 chr4 191154276 2913137 0.015239716636001384 0.13759549977128685 chr5 180915260 4967451 0.02745733555035656 0.17803121906055733 chr6 171115067 2483992 0.014516500759106151 0.14376442135327067 chr7 159138663 4099607 0.025761225604867623 0.325450224839573 chr8 146364022 2960569 0.02022743676721319 0.1708364846954231 chr9 141213431 1894870 0.013418482835389788 0.16667100132589202 chr10 135534747 3014527 0.022241728167316385 0.23957400726044403 chr11 135006516 2829596 0.02095895875129464 0.2024355778984901 chr12 133851895 2642895 0.019744920309122258 0.15128101161636795 chr13 115169878 2007676 0.017432301178611997 0.141462233624874 chr14 107349540 1503030 0.014001270988212898 0.13149835580257682 chr15 102531392 2964879 0.028916792624838254 0.1840264090546966 chr16 90354753 1940168 0.021472782953653805 0.1729905575148793 chr17 81195210 2440570 0.030058053917219992 0.19676279496221494 chr18 78077248 2171039 0.027806295119418144 0.3159293312763187 chr19 59128983 1001765 0.01694202993479526 0.21882745726427721 chr20 63025520 1717540 0.02725150066195408 0.17796809891957077 chr21 48129895 810169 0.01683296836612671 0.1441882620722242 chr22 51304566 812136 0.015829702175046173 0.13508749351308214 chrMT 16571 543 0.03276808882988353 0.17802904590071922 chrX 155270560 2410024 0.015521448496096105 0.15356468342162338 chrY 59373566 143009 0.002408630803815961 0.06737676673158448