BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716848.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 = 3,333,856 number of mapped reads = 3,137,823 (94.12%) number of supplementary alignments = 54,504 (1.63%) number of secondary alignments = 0 number of mapped bases = 249,401,100 bp number of sequenced bases = 249,290,658 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 196,118 duplication rate = 4.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7845 >>>>>>> ACTG content number of A's = 62,584,751 bp (25.11%) number of C's = 48,821,493 bp (19.58%) number of T's = 76,432,579 bp (30.66%) number of G's = 61,433,618 bp (24.64%) number of N's = 18,217 bp (0.01%) GC percentage = 44.23% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,589,501 number of insertions = 19,997 mapped reads with insertion percentage = 0.63% number of deletions = 57,932 mapped reads with deletion percentage = 1.82% homopolymer indels = 42.75% >>>>>>> Coverage mean coverageData = 0.0806X std coverageData = 0.7034X There is a 6.21% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 23770274 0.0953669599884367 1.5166268357274109 chr2 243199373 19715909 0.08106891377553017 0.7211215736350373 chr3 198022430 15580518 0.0786805716907928 0.3381307194663051 chr4 191154276 15764143 0.08246816827681114 0.4693774717340588 chr5 180915260 14307934 0.07908638552657195 0.34503069003838976 chr6 171115067 11736069 0.0685858306095278 0.36178404611597176 chr7 159138663 13390253 0.08414204786928492 0.8600036813603542 chr8 146364022 11959954 0.08171375613058789 0.7754788577950261 chr9 141213431 10025014 0.0709919299390155 0.5423527242503247 chr10 135534747 10660199 0.07865288596436455 0.6023903573505383 chr11 135006516 17331400 0.12837454452939145 0.949505619114298 chr12 133851895 10717220 0.08006774950776752 0.34453578831881376 chr13 115169878 8474471 0.07358235631716133 0.3347576674306748 chr14 107349540 7324071 0.06822638457509925 0.3478885684530641 chr15 102531392 6921731 0.06750840757140994 0.3152137625550453 chr16 90354753 5599858 0.061976352256754 0.34834164785416544 chr17 81195210 9790252 0.12057671874978831 0.6584228302290583 chr18 78077248 5996553 0.07680282225111212 0.940802707372278 chr19 59128983 4734157 0.08006491503498378 1.060484154038412 chr20 63025520 4963379 0.0787518928840254 0.36737284423944616 chr21 48129895 3219228 0.06688624606390685 0.3860983837263002 chr22 51304566 2870022 0.05594086888874569 0.2902520540473957 chrMT 16571 328565 19.82771106149297 11.96870590209523 chrX 155270560 13492389 0.08689598981287888 0.45757351203735674 chrY 59373566 727537 0.012253550679438726 0.38655588742446356