BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054609.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 = 17,401,510 number of mapped reads = 12,117,376 (69.63%) number of supplementary alignments = 313 (0%) number of secondary alignments = 0 number of mapped bases = 570,832,466 bp number of sequenced bases = 570,712,453 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,756,932 duplication rate = 15.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5394 >>>>>>> ACTG content number of A's = 175,278,745 bp (30.71%) number of C's = 104,137,653 bp (18.25%) number of T's = 177,119,518 bp (31.03%) number of G's = 113,997,221 bp (19.97%) number of N's = 179,316 bp (0.03%) GC percentage = 38.22% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 3,354,299 number of insertions = 24,087 mapped reads with insertion percentage = 0.2% number of deletions = 81,674 mapped reads with deletion percentage = 0.67% homopolymer indels = 48.7% >>>>>>> Coverage mean coverageData = 0.1844X std coverageData = 1.3509X There is a 7.58% of reference with a coverageData >= 1X There is a 3.04% of reference with a coverageData >= 2X There is a 1.74% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.83% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 51875251 0.20812486160265173 1.4975159575201964 chr2 243199373 41975826 0.1725984137302854 1.3668806074934785 chr3 198022430 44298628 0.2237051024977322 1.4278530823584004 chr4 191154276 34299105 0.17943153413947172 1.2841734215129121 chr5 180915260 29520361 0.1631723106165837 1.1016691126614642 chr6 171115067 29514154 0.17248132801771338 1.2681458793166545 chr7 159138663 38227459 0.24021478048989264 1.6939367412076822 chr8 146364022 31030199 0.2120070122150647 1.478333717535306 chr9 141213431 28673265 0.20304913489425805 1.4703222989924085 chr10 135534747 24417400 0.18015601563782016 1.3157976908453004 chr11 135006516 25779967 0.19095350182949689 1.3588474846861767 chr12 133851895 20905600 0.15618456503734968 1.1187715930142912 chr13 115169878 16114106 0.139915976988358 1.0411250180553033 chr14 107349540 13181048 0.122786255069188 1.150572291454891 chr15 102531392 14435760 0.1407935630094635 1.0116597522939608 chr16 90354753 14948405 0.16544126903871897 1.323007938395415 chr17 81195210 9846834 0.12127358251798351 0.9135461266014725 chr18 78077248 22042489 0.28231641822211767 1.8879021973286596 chr19 59128983 9422222 0.15935031387230184 1.2715112684204382 chr20 63025520 9328366 0.14800934605537566 1.1329898519824573 chr21 48129895 7442704 0.154637860730841 1.2607693084657041 chr22 51304566 5222316 0.1017904722164495 0.816546898911342 chrMT 16571 45904 2.770140607084666 6.9810352318367395 chrX 155270560 46658748 0.3004996439762953 1.7916290787363742 chrY 59373566 1626349 0.027391802607914774 0.573613597581293