BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063545.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,058,143 number of mapped reads = 945,621 (89.37%) number of supplementary alignments = 6,698 (0.63%) number of secondary alignments = 0 number of mapped bases = 61,713,838 bp number of sequenced bases = 61,686,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,562 duplication rate = 3.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1193 >>>>>>> ACTG content number of A's = 16,821,133 bp (27.27%) number of C's = 10,906,935 bp (17.68%) number of T's = 20,102,684 bp (32.59%) number of G's = 13,854,406 bp (22.46%) number of N's = 1,572 bp (0%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 497,021 number of insertions = 4,622 mapped reads with insertion percentage = 0.49% number of deletions = 16,751 mapped reads with deletion percentage = 1.75% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.0199X std coverageData = 0.2214X There is a 1.77% of reference with a coverageData >= 1X There is a 0.17% 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 6856361 0.02750789936848342 0.3968009021232575 chr2 243199373 6691801 0.0275157000507563 0.2806923442484467 chr3 198022430 4221953 0.021320579693926592 0.16098963227616717 chr4 191154276 3262896 0.017069437672427478 0.14662448778337842 chr5 180915260 2770232 0.015312318043265117 0.13554406963021665 chr6 171115067 4551698 0.026600217501594994 0.19460648081203688 chr7 159138663 4263288 0.026789768869680652 0.32498934428266174 chr8 146364022 2359355 0.01611977429808536 0.2735580845109786 chr9 141213431 1927297 0.013648113967289698 0.1844763623361411 chr10 135534747 3249403 0.02397468598956399 0.1972985222944419 chr11 135006516 3131694 0.023196613710111592 0.19066848575599682 chr12 133851895 2568175 0.019186691380051062 0.1563908926704263 chr13 115169878 1121108 0.009734385583008084 0.11036618392915426 chr14 107349540 1567785 0.014604487359703638 0.1392422042537018 chr15 102531392 1007418 0.009825459114024318 0.11560964783044375 chr16 90354753 1164045 0.012883052206451164 0.13210861197474302 chr17 81195210 1505156 0.018537497470602023 0.15435340574435838 chr18 78077248 1391352 0.017820197761068628 0.2825787626045431 chr19 59128983 1304546 0.022062716688362457 0.2730888294992347 chr20 63025520 744336 0.011810073125933749 0.12324742425369525 chr21 48129895 963009 0.02000854146887293 0.15749556715362178 chr22 51304566 648583 0.012641818274030424 0.1222469820744992 chrMT 16571 10545 0.636352664293042 1.0300622043212095 chrX 155270560 4294812 0.02766018232947701 0.19623139364207465 chrY 59373566 136990 0.002307255723868767 0.06407578847413112