BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238647.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 = 3,940,198 number of mapped reads = 3,044,310 (77.26%) number of supplementary alignments = 27,610 (0.7%) number of secondary alignments = 0 number of mapped bases = 185,322,270 bp number of sequenced bases = 185,234,835 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,481,318 duplication rate = 22.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.6199 >>>>>>> ACTG content number of A's = 46,304,821 bp (25%) number of C's = 32,387,369 bp (17.48%) number of T's = 62,462,350 bp (33.72%) number of G's = 44,076,127 bp (23.79%) number of N's = 4,168 bp (0%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,278,582 number of insertions = 13,570 mapped reads with insertion percentage = 0.44% number of deletions = 52,703 mapped reads with deletion percentage = 1.71% homopolymer indels = 41.26% >>>>>>> Coverage mean coverageData = 0.0599X std coverageData = 1.9401X There is a 1.16% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 6162354 0.024723525162250248 4.252914267481878 chr2 243199373 8313445 0.03418366132054131 3.1743921960384336 chr3 198022430 3762784 0.019001807017518167 0.5091196640089726 chr4 191154276 22309546 0.11670963614750632 1.2711351736715342 chr5 180915260 14577572 0.08057679600935819 1.1007481247760311 chr6 171115067 4198317 0.024535051609452952 0.929813203211676 chr7 159138663 3394724 0.021331862012690155 0.7429929284756672 chr8 146364022 13821309 0.09443105492140684 2.315718038722865 chr9 141213431 5209971 0.03689430221407197 1.619437846100513 chr10 135534747 2741925 0.02023042105947931 0.5590097584077126 chr11 135006516 16645525 0.12329423418348193 1.4112647289541396 chr12 133851895 19549924 0.14605638567911197 1.496316521611324 chr13 115169878 1900092 0.0164981680366111 0.7589355874243633 chr14 107349540 18950271 0.176528665143791 1.6727991002428488 chr15 102531392 2840095 0.027699760479210113 0.711000296891005 chr16 90354753 2047121 0.02265648382658962 0.6335958328641311 chr17 81195210 3190499 0.03929417757525352 0.7637104145664758 chr18 78077248 2670788 0.034206994590792954 3.406177862910554 chr19 59128983 4590768 0.07763989446596772 2.037749881458375 chr20 63025520 20390653 0.32353010336130505 2.226904097866249 chr21 48129895 1095280 0.022756750248468235 0.5627480040944849 chr22 51304566 2731534 0.05324153799488334 0.873206944938526 chrMT 16571 34185 2.0629412829642146 4.886872592941164 chrX 155270560 3741638 0.024097536583882997 0.6705725062345826 chrY 59373566 451950 0.00761197331485867 0.41264184134096493