BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237585.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,013,857 number of mapped reads = 1,646,962 (81.78%) number of supplementary alignments = 9,708 (0.48%) number of secondary alignments = 0 number of mapped bases = 103,987,942 bp number of sequenced bases = 103,926,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,269 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9275 >>>>>>> ACTG content number of A's = 26,733,707 bp (25.72%) number of C's = 19,790,436 bp (19.04%) number of T's = 31,304,155 bp (30.12%) number of G's = 26,081,521 bp (25.1%) number of N's = 16,895 bp (0.02%) GC percentage = 44.14% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 973,747 number of insertions = 9,700 mapped reads with insertion percentage = 0.58% number of deletions = 37,205 mapped reads with deletion percentage = 2.23% homopolymer indels = 44.69% >>>>>>> Coverage mean coverageData = 0.0336X std coverageData = 0.315X There is a 2.75% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 9379688 0.03763155318277021 0.4440419519640895 chr2 243199373 8915401 0.03665881572811456 0.42030600510273747 chr3 198022430 7280382 0.036765441167447545 0.24566112069810117 chr4 191154276 5968577 0.031223873851506205 0.24637383223899317 chr5 180915260 5870329 0.03244794828252741 0.22210728630981535 chr6 171115067 5764293 0.033686647827452856 0.2571100947693636 chr7 159138663 6205645 0.03899520633775841 0.44972576883877186 chr8 146364022 5377628 0.036741460958212804 0.295495432788293 chr9 141213431 4295628 0.03041940111206561 0.31910478034936895 chr10 135534747 4546712 0.03354646760804445 0.3254149936052911 chr11 135006516 4666710 0.03456655380989167 0.350172982404377 chr12 133851895 5503033 0.041112850886421894 0.2717577550328485 chr13 115169878 3461190 0.03005291018889505 0.22284514266216468 chr14 107349540 2841806 0.02647245623968207 0.2329855745578049 chr15 102531392 2914940 0.028429732037579283 0.22520470331890058 chr16 90354753 2964393 0.032808379211661395 0.2592418988373 chr17 81195210 2718257 0.033478046303470364 0.24958802051331758 chr18 78077248 2587646 0.03314212611592048 0.4254825064357666 chr19 59128983 2395052 0.04050555038296532 0.36670445001652874 chr20 63025520 2155776 0.03420481100354269 0.24196409342489494 chr21 48129895 1338948 0.027819466466735488 0.23433945837777728 chr22 51304566 1069352 0.02084321305826854 0.18719434648475872 chrMT 16571 98089 5.919316878884799 5.172861984820143 chrX 155270560 5297842 0.03412006757752403 0.26169565549770835 chrY 59373566 370625 0.006242256023497056 0.14864747457454713