BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818996.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,641,396 number of mapped reads = 2,603,643 (98.57%) number of supplementary alignments = 38,320 (1.45%) number of secondary alignments = 0 number of mapped bases = 240,948,584 bp number of sequenced bases = 240,802,771 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,354,377 duplication rate = 43.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1248 >>>>>>> ACTG content number of A's = 70,253,247 bp (29.17%) number of C's = 52,109,020 bp (21.64%) number of T's = 68,184,972 bp (28.32%) number of G's = 50,242,580 bp (20.86%) number of N's = 12,952 bp (0.01%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,519,382 number of insertions = 36,157 mapped reads with insertion percentage = 1.35% number of deletions = 78,251 mapped reads with deletion percentage = 2.94% homopolymer indels = 41.57% >>>>>>> Coverage mean coverageData = 0.0778X std coverageData = 0.9238X There is a 3.02% of reference with a coverageData >= 1X There is a 1.68% of reference with a coverageData >= 2X There is a 1.04% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 24103698 0.09670466578295907 1.658200082671026 chr2 243199373 20209025 0.08309653413456786 1.2997302675559463 chr3 198022430 13034782 0.06582477550649186 0.5286534685619018 chr4 191154276 14142098 0.0739826400744496 0.6288211534849355 chr5 180915260 11933467 0.06596163861467517 0.5511692259772922 chr6 171115067 10258573 0.05995131334635775 0.5932222212659353 chr7 159138663 12310895 0.07735954775490353 1.1276389821078894 chr8 146364022 20377347 0.13922374311359112 0.8733313947737344 chr9 141213431 10438010 0.07391655259760667 0.8642351509276169 chr10 135534747 13163602 0.09712344835084984 1.0831934205690341 chr11 135006516 8370864 0.06200340730220755 0.6136409765427917 chr12 133851895 10387722 0.07760608843079883 0.5882059184530417 chr13 115169878 5380575 0.04671859598566215 0.4392014105033043 chr14 107349540 6082385 0.05665962797791216 0.5174465357324319 chr15 102531392 6572300 0.0641003684022938 0.5216318091017585 chr16 90354753 8083058 0.08945913448515541 1.0704850469286242 chr17 81195210 8210053 0.10111499188191027 0.7448534171790081 chr18 78077248 5124378 0.06563215445298481 0.9524958849466066 chr19 59128983 4953788 0.08377935402677228 1.4361997275911376 chr20 63025520 6471939 0.10268759385087184 0.7127393682416903 chr21 48129895 3497840 0.07267499752492708 0.6024691818336448 chr22 51304566 1901328 0.0370596254532199 0.4430639425740747 chrMT 16571 45471 2.7440106209643353 3.978396897380865 chrX 155270560 15001303 0.09661395566551702 0.7572142268313125 chrY 59373566 894083 0.015058603689055833 0.9469392891497017