BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231818.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 = 976,793 number of mapped reads = 537,784 (55.06%) number of supplementary alignments = 5,546 (0.57%) number of secondary alignments = 0 number of mapped bases = 34,180,772 bp number of sequenced bases = 34,150,248 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,542 duplication rate = 5.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7176 >>>>>>> ACTG content number of A's = 9,628,240 bp (28.19%) number of C's = 5,758,922 bp (16.86%) number of T's = 11,443,287 bp (33.51%) number of G's = 7,318,322 bp (21.43%) number of N's = 1,477 bp (0%) GC percentage = 38.29% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 318,370 number of insertions = 3,068 mapped reads with insertion percentage = 0.56% number of deletions = 17,363 mapped reads with deletion percentage = 3.15% homopolymer indels = 41.72% >>>>>>> Coverage mean coverageData = 0.011X std coverageData = 0.175X There is a 0.87% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.04% 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 2334969 0.009367956599795191 0.24881146267067222 chr2 243199373 2316047 0.00952324412448218 0.14458836635107894 chr3 198022430 2022428 0.010213125856500195 0.12393420206852251 chr4 191154276 1343926 0.007030582983139755 0.10835916694988221 chr5 180915260 2905869 0.016062044738514594 0.15709173485177738 chr6 171115067 1679587 0.009815541257977008 0.13883227911118973 chr7 159138663 2608868 0.016393678008970076 0.19789443986437985 chr8 146364022 2734597 0.018683532760530454 0.425472368962686 chr9 141213431 1949104 0.013802539788159386 0.15211681945394362 chr10 135534747 1645200 0.012138584653867395 0.1470154997502207 chr11 135006516 1449873 0.010739281650672328 0.1298014515447316 chr12 133851895 931782 0.00696129105979411 0.10469558823521109 chr13 115169878 1604057 0.01392774767027191 0.14698574189254357 chr14 107349540 1379534 0.012850860842067885 0.13959979304679151 chr15 102531392 984955 0.009606374991963438 0.1197704438300401 chr16 90354753 1121024 0.012406917874038127 0.13708378955684117 chr17 81195210 634840 0.00781868782653558 0.10808141366599978 chr18 78077248 629823 0.008066664952125362 0.20462174765506225 chr19 59128983 969442 0.016395377542684948 0.17693404979302155 chr20 63025520 1051018 0.016676070264870484 0.16161120786839137 chr21 48129895 459499 0.009547060096432788 0.12258806459913187 chr22 51304566 281073 0.0054785182277928245 0.0873002744765879 chrMT 16571 23057 1.3914066743105424 1.5364177796098228 chrX 155270560 1026440 0.0066106543313813 0.10369660361904799 chrY 59373566 93760 0.0015791539285344592 0.058337417065579385