BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234021.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 = 1,754,021 number of mapped reads = 1,117,268 (63.7%) number of supplementary alignments = 15,573 (0.89%) number of secondary alignments = 0 number of mapped bases = 73,172,249 bp number of sequenced bases = 73,134,192 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,722 duplication rate = 10.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.9507 >>>>>>> ACTG content number of A's = 19,998,863 bp (27.35%) number of C's = 13,778,395 bp (18.84%) number of T's = 22,963,655 bp (31.4%) number of G's = 16,374,995 bp (22.39%) number of N's = 18,284 bp (0.03%) GC percentage = 41.23% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 573,754 number of insertions = 5,735 mapped reads with insertion percentage = 0.51% number of deletions = 21,567 mapped reads with deletion percentage = 1.91% homopolymer indels = 44.52% >>>>>>> Coverage mean coverageData = 0.0236X std coverageData = 0.3039X There is a 1.25% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 1954326 0.007840806944268355 0.14240765948607545 chr2 243199373 6756644 0.02778232491578011 0.4369497650451919 chr3 198022430 583556 0.002946918689968606 0.07678818188668876 chr4 191154276 1087948 0.005691465672470753 0.12861655976938097 chr5 180915260 2772218 0.015323295558373572 0.20391834677396967 chr6 171115067 3286459 0.01920613454804655 0.2401757283279088 chr7 159138663 4106721 0.02580592875786571 0.29727428656493277 chr8 146364022 2845635 0.0194421754821687 0.3678384899868635 chr9 141213431 2384456 0.016885475999800614 0.29287246729346034 chr10 135534747 3510334 0.0258998823379218 0.2853430386361468 chr11 135006516 4450980 0.03296863093630236 0.3681127839576271 chr12 133851895 6284557 0.046951572855953964 0.36653605560535435 chr13 115169878 1461272 0.012687970373642317 0.19706429286877464 chr14 107349540 3777881 0.035192335244287026 0.32471790947739576 chr15 102531392 3938231 0.03841000227520563 0.332618517660893 chr16 90354753 1882023 0.020829263956927645 0.251648571309636 chr17 81195210 4142111 0.0510142285487038 0.3919478181960358 chr18 78077248 4059620 0.05199491662411052 0.6430001158233497 chr19 59128983 238349 0.004031001175853134 0.12041973679046701 chr20 63025520 2282466 0.03621494911902353 0.32918723793491833 chr21 48129895 2083020 0.04327913036170139 0.3548959342469652 chr22 51304566 2104572 0.0410211441999139 0.3364381260474066 chrMT 16571 11488 0.6932593084303904 1.2438060548591128 chrX 155270560 6868358 0.04423477315983146 0.36615493040151675 chrY 59373566 299024 0.0050363153191775615 0.10905584877725336