BamQC report ----------------------------------- >>>>>>> Input bam file = SRR620535.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP016866/SRP016866.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 = 9,649,196 number of mapped reads = 5,920,024 (61.35%) number of supplementary alignments = 736 (0.01%) number of secondary alignments = 0 number of mapped bases = 269,234,556 bp number of sequenced bases = 269,169,182 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 367,597 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4587 >>>>>>> ACTG content number of A's = 72,568,613 bp (26.96%) number of C's = 52,050,465 bp (19.34%) number of T's = 82,795,076 bp (30.76%) number of G's = 60,883,284 bp (22.62%) number of N's = 871,744 bp (0.32%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 3,167,209 number of insertions = 16,557 mapped reads with insertion percentage = 0.28% number of deletions = 42,452 mapped reads with deletion percentage = 0.71% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.087X std coverageData = 0.8672X There is a 6.9% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.09% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 22920921 0.09195933357373662 1.4803890583806911 chr2 243199373 22693786 0.09331350537651263 0.9118855916332865 chr3 198022430 19083810 0.09637196149951296 0.44495004145815753 chr4 191154276 16285179 0.08519390379737045 0.4500933848735704 chr5 180915260 15969664 0.08827151452011289 0.39591720563016886 chr6 171115067 14177856 0.08285568447341927 0.7498688945096532 chr7 159138663 13149379 0.08262843706309132 0.8942095339097215 chr8 146364022 12083967 0.08256104768697871 1.003185807838636 chr9 141213431 12395054 0.08777531933205418 0.7936900729596027 chr10 135534747 14835957 0.10946238753077836 0.8119870166934607 chr11 135006516 9945694 0.07366825168645934 0.9200596757963468 chr12 133851895 13380822 0.09996737065246629 0.4472150789043523 chr13 115169878 4132381 0.03588074478988334 0.2706132104765724 chr14 107349540 8491136 0.07909801942327839 0.4007033318045398 chr15 102531392 8122103 0.0792157683765768 0.36667749152975615 chr16 90354753 7477687 0.08275919917572018 0.4277562941909073 chr17 81195210 8250332 0.10161106794354002 0.5920054874930497 chr18 78077248 7302943 0.09353484128948807 2.562628056862487 chr19 59128983 5709184 0.09655474710261802 0.9693765285595032 chr20 63025520 6875039 0.10908341573381704 0.5322957601234841 chr21 48129895 4798277 0.09969431680663338 0.4836832206709432 chr22 51304566 3920139 0.07640916404984305 0.34855639095758406 chrMT 16571 496354 29.95317120270352 24.5504196503712 chrX 155270560 15814764 0.10185294623784444 0.6505211356672017 chrY 59373566 922128 0.015530951939117148 0.2548570818358633