BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089696.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 24,404,189 number of mapped reads = 19,569,747 (80.19%) number of supplementary alignments = 866 (0%) number of secondary alignments = 0 number of mapped bases = 908,339,978 bp number of sequenced bases = 908,143,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,646,259 duplication rate = 10% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9771 >>>>>>> ACTG content number of A's = 293,305,753 bp (32.3%) number of C's = 180,728,984 bp (19.9%) number of T's = 242,269,670 bp (26.68%) number of G's = 191,810,441 bp (21.12%) number of N's = 29,089 bp (0%) GC percentage = 41.02% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 5,073,294 number of insertions = 43,540 mapped reads with insertion percentage = 0.22% number of deletions = 132,522 mapped reads with deletion percentage = 0.68% homopolymer indels = 44.09% >>>>>>> Coverage mean coverageData = 0.2934X std coverageData = 1.597X There is a 14.82% of reference with a coverageData >= 1X There is a 6.12% of reference with a coverageData >= 2X There is a 3.06% of reference with a coverageData >= 3X There is a 1.71% of reference with a coverageData >= 4X There is a 1.02% of reference with a coverageData >= 5X There is a 0.65% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 75625008 0.303409506851339 1.8154250682730684 chr2 243199373 88893593 0.3655173609349725 2.3230239388826424 chr3 198022430 83996905 0.424178740761842 1.2988551056868332 chr4 191154276 41413681 0.2166505603044946 0.8566167678357406 chr5 180915260 37450476 0.20700562241128803 0.8205981581708163 chr6 171115067 54188541 0.31667895732407947 1.36845886274163 chr7 159138663 61989312 0.3895301797276002 2.595624695148659 chr8 146364022 74461424 0.5087413080244543 3.105627631998124 chr9 141213431 31232667 0.22117348738591303 1.361292009516262 chr10 135534747 37838368 0.27917835711900507 1.3634960083775207 chr11 135006516 44078799 0.3264938634517463 1.4022710286017281 chr12 133851895 26841331 0.20053007841241247 0.8445166539669838 chr13 115169878 26828139 0.23294406025158765 0.8859814646861554 chr14 107349540 31801945 0.29624668163459295 1.130563567621317 chr15 102531392 22800872 0.22237942502526445 0.8465536626216208 chr16 90354753 17233820 0.19073506846950264 0.8737269479450118 chr17 81195210 20878754 0.2571426812000363 1.068309400077153 chr18 78077248 45432534 0.5818921025495161 2.1598539104819814 chr19 59128983 13016636 0.22013969020911453 1.775904054709468 chr20 63025520 19968712 0.31683533908169265 1.0857208694854545 chr21 48129895 14480645 0.300865917118664 1.119796879424279 chr22 51304566 6935051 0.13517414804756364 0.650926978393285 chrMT 16571 786827 47.48216764226661 42.75893495254785 chrX 155270560 28220839 0.18175267095062966 1.142026678271054 chrY 59373566 1945099 0.0327603533195227 0.46646269735682927