BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063538.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 = 3,797,237 number of mapped reads = 3,578,553 (94.24%) number of supplementary alignments = 38,454 (1.01%) number of secondary alignments = 0 number of mapped bases = 234,002,315 bp number of sequenced bases = 233,919,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 908,312 duplication rate = 17.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9394 >>>>>>> ACTG content number of A's = 62,178,547 bp (26.58%) number of C's = 41,882,084 bp (17.9%) number of T's = 76,248,413 bp (32.6%) number of G's = 53,583,562 bp (22.91%) number of N's = 26,791 bp (0.01%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,186,441 number of insertions = 16,301 mapped reads with insertion percentage = 0.45% number of deletions = 47,259 mapped reads with deletion percentage = 1.31% homopolymer indels = 46.32% >>>>>>> Coverage mean coverageData = 0.0756X std coverageData = 0.8558X There is a 3.61% of reference with a coverageData >= 1X There is a 1.75% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 25165864 0.10096610351073107 1.1613798756795806 chr2 243199373 22507173 0.09254618020746296 1.2645872692938613 chr3 198022430 14972036 0.07560777837136934 0.5034124389399818 chr4 191154276 13794727 0.07216541156526365 0.5296000394451719 chr5 180915260 8022988 0.04434666263089139 0.3805614930286642 chr6 171115067 17694077 0.1034045529140926 0.6655143357570742 chr7 159138663 15039347 0.09450467106161373 0.8041153621081721 chr8 146364022 8357438 0.057100357627504934 2.043647627833183 chr9 141213431 7768558 0.055012883300031144 0.5861159297989548 chr10 135534747 13110585 0.09673227928776079 0.6875190876824022 chr11 135006516 11275575 0.08351874660627491 0.5811666633728907 chr12 133851895 9323145 0.06965269337427012 0.48655795376043187 chr13 115169878 4964127 0.04310265050380621 0.4098494161478803 chr14 107349540 5190482 0.048351227215319224 0.4200389044252665 chr15 102531392 4196707 0.04093094727515257 0.36993781504254286 chr16 90354753 6067456 0.0671514867624064 0.47103415743174565 chr17 81195210 6062483 0.07466552522002222 0.4975177574495025 chr18 78077248 6310565 0.08082463408546367 0.9848323450579239 chr19 59128983 4091683 0.06919927914200723 0.807628103836919 chr20 63025520 3551336 0.05634758745346329 0.4474649178538759 chr21 48129895 4076950 0.08470722822063086 0.5480541332921095 chr22 51304566 2516379 0.04904785667614847 0.3900840101391616 chrMT 16571 1088283 65.67394846418442 49.85363840303066 chrX 155270560 18115068 0.11666775723614316 0.6747714144218058 chrY 59373566 739283 0.01245138282581848 0.3136025991442521