BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084266.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,216,440 number of mapped reads = 1,824,322 (82.31%) number of supplementary alignments = 12,090 (0.55%) number of secondary alignments = 0 number of mapped bases = 116,408,347 bp number of sequenced bases = 116,368,947 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,173 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.023 >>>>>>> ACTG content number of A's = 33,588,836 bp (28.86%) number of C's = 21,720,351 bp (18.67%) number of T's = 35,643,895 bp (30.63%) number of G's = 25,414,629 bp (21.84%) number of N's = 1,236 bp (0%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 970,056 number of insertions = 9,052 mapped reads with insertion percentage = 0.49% number of deletions = 25,071 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.46% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.2793X There is a 3.31% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 9409094 0.03774953082263334 0.37899211007258876 chr2 243199373 10286951 0.042298427307211846 0.3651130922306001 chr3 198022430 7319563 0.036963302591529655 0.21322511099373923 chr4 191154276 7610751 0.039814704432769264 0.22569843364412637 chr5 180915260 7606864 0.04204655815103712 0.2270467449785956 chr6 171115067 7203161 0.0420954222575853 0.25877898652282866 chr7 159138663 6538968 0.04108975076660032 0.3502094164142376 chr8 146364022 6353929 0.04341182288636479 0.30101842820409963 chr9 141213431 4784597 0.03388202500369813 0.2728245780983299 chr10 135534747 5113597 0.037729048182751246 0.2766680230956197 chr11 135006516 5420559 0.0401503509652823 0.25643791356495876 chr12 133851895 5146742 0.038451020809230976 0.21830093840586948 chr13 115169878 3792606 0.03293053761852557 0.20142883500998607 chr14 107349540 3468662 0.03231184781974846 0.21121980447408317 chr15 102531392 3209786 0.03130539766786742 0.20027365259363256 chr16 90354753 2973389 0.03290794231931551 0.220787719778718 chr17 81195210 2783750 0.03428465792501799 0.22000150135542965 chr18 78077248 3048025 0.03903858138032734 0.5133255650736596 chr19 59128983 1950383 0.03298522824246783 0.29585281569725025 chr20 63025520 2391364 0.037942788889326104 0.22261359041256343 chr21 48129895 1575890 0.03274243586029016 0.20752303110619377 chr22 51304566 1142144 0.02226203414331582 0.16364132311304716 chrMT 16571 5562 0.33564661155029873 0.6485853031070419 chrX 155270560 6994965 0.04505016920142492 0.252397160217503 chrY 59373566 277045 0.004666133747129151 0.09299764368914878