BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068183.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 = 1,707,015 number of mapped reads = 1,526,128 (89.4%) number of supplementary alignments = 11,039 (0.65%) number of secondary alignments = 0 number of mapped bases = 103,645,221 bp number of sequenced bases = 103,596,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 125,622 duplication rate = 6.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9517 >>>>>>> ACTG content number of A's = 29,700,887 bp (28.67%) number of C's = 19,552,038 bp (18.87%) number of T's = 32,377,737 bp (31.25%) number of G's = 21,847,488 bp (21.09%) number of N's = 118,665 bp (0.11%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 857,167 number of insertions = 7,377 mapped reads with insertion percentage = 0.48% number of deletions = 26,845 mapped reads with deletion percentage = 1.74% homopolymer indels = 48.24% >>>>>>> Coverage mean coverageData = 0.0335X std coverageData = 0.3761X There is a 1.85% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 5116286 0.0205266730308367 0.673226858364826 chr2 243199373 12968698 0.05332537596632702 0.4023084434021628 chr3 198022430 10323396 0.05213245792408466 0.38034633857694483 chr4 191154276 3106657 0.016252092629097138 0.21565290646135998 chr5 180915260 10268676 0.05675959009759597 0.4021855378244043 chr6 171115067 3514574 0.020539243338519104 0.23843221513255852 chr7 159138663 2367258 0.014875442305305782 0.22894929631210215 chr8 146364022 5297825 0.036196224506593565 0.5036425018958579 chr9 141213431 1542590 0.010923819278918306 0.1779138266273645 chr10 135534747 6228820 0.04595736619481054 0.3703188632252727 chr11 135006516 6263833 0.04639652355742593 0.36721420521118275 chr12 133851895 2288853 0.017099892384788425 0.21309665020891339 chr13 115169878 4267328 0.03705246609708139 0.32984391118136064 chr14 107349540 4060589 0.037825863063782106 0.32510107224443746 chr15 102531392 6076005 0.05925994840682549 0.4108483959429786 chr16 90354753 1234517 0.013663000108029734 0.20617622087919898 chr17 81195210 6036844 0.07434975536118449 0.5131164691021106 chr18 78077248 1180169 0.015115402120730485 0.24627521060982327 chr19 59128983 1879742 0.03179053493952365 0.5523003961594689 chr20 63025520 3791392 0.06015645725731418 0.4021561811151412 chr21 48129895 1481911 0.03078982407919236 0.29047994498605884 chr22 51304566 499419 0.00973439673965861 0.152463551933425 chrMT 16571 43427 2.62066260334319 2.902612102409212 chrX 155270560 3463930 0.022308994055280022 0.24547408343474647 chrY 59373566 342482 0.005768257207256172 0.1324932449173623