BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237291.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 = 2,691,510 number of mapped reads = 2,500,426 (92.9%) number of supplementary alignments = 16,439 (0.61%) number of secondary alignments = 0 number of mapped bases = 175,944,355 bp number of sequenced bases = 175,844,962 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,429 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.003 >>>>>>> ACTG content number of A's = 51,756,082 bp (29.43%) number of C's = 33,610,049 bp (19.11%) number of T's = 54,336,948 bp (30.9%) number of G's = 36,138,970 bp (20.55%) number of N's = 2,913 bp (0%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,427,984 number of insertions = 15,048 mapped reads with insertion percentage = 0.6% number of deletions = 55,986 mapped reads with deletion percentage = 2.21% homopolymer indels = 45.9% >>>>>>> Coverage mean coverageData = 0.0568X std coverageData = 0.6795X There is a 4.08% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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 20951795 0.08405914864300378 1.3874633549187623 chr2 243199373 13494480 0.05548731410586326 0.6977778382690856 chr3 198022430 13151656 0.0664149813735747 0.3421382085623568 chr4 191154276 4805383 0.025138768017933327 0.36321137467019554 chr5 180915260 11057490 0.06111971980694166 0.3326750145462802 chr6 171115067 26215332 0.1532029438412925 1.0505638583225136 chr7 159138663 2948016 0.018524825736408256 0.4382094628220188 chr8 146364022 7635868 0.05217038925044025 0.5904157946667068 chr9 141213431 7711631 0.0546097559232875 0.6733511318880238 chr10 135534747 3441631 0.02539297911553264 0.6620306405372 chr11 135006516 5112086 0.03786547606339238 0.47039820730504067 chr12 133851895 5019033 0.037496914033230536 0.27470801940298456 chr13 115169878 5063563 0.043966035980345486 0.27173259100076425 chr14 107349540 3207995 0.0298836399298963 0.29667107078696264 chr15 102531392 2572449 0.02508937945561102 0.20384068110599812 chr16 90354753 7486801 0.08286006824676949 0.4797476899422907 chr17 81195210 7105328 0.08750920158960115 0.5750589176810743 chr18 78077248 3036324 0.038888716979368944 1.3905002660426609 chr19 59128983 4082443 0.06904301059938744 0.9202397735058547 chr20 63025520 4864138 0.07717727676027107 0.37723959189280565 chr21 48129895 2887799 0.060000110118669486 0.4259823224448773 chr22 51304566 3385024 0.06597900077743568 0.3290965195683867 chrMT 16571 102599 6.191479089976465 4.894407250289298 chrX 155270560 10144492 0.0653342913170404 0.3953966486498542 chrY 59373566 460999 0.007764381206276207 0.33168107797627433