BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240244.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 = 3,506,183 number of mapped reads = 2,804,026 (79.97%) number of supplementary alignments = 30,677 (0.87%) number of secondary alignments = 0 number of mapped bases = 185,425,333 bp number of sequenced bases = 185,352,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 470,530 duplication rate = 11.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8124 >>>>>>> ACTG content number of A's = 52,513,056 bp (28.33%) number of C's = 34,168,188 bp (18.43%) number of T's = 58,875,263 bp (31.76%) number of G's = 39,778,886 bp (21.46%) number of N's = 17,441 bp (0.01%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,478,679 number of insertions = 14,029 mapped reads with insertion percentage = 0.5% number of deletions = 41,944 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 0.0599X std coverageData = 0.748X There is a 2.47% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% 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 0.01% 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 15795627 0.06337246798674977 1.438760324758187 chr2 243199373 20600418 0.08470588450077954 0.7831098316866587 chr3 198022430 13938762 0.07038981392158454 0.5229324005562833 chr4 191154276 7940585 0.04154019029111334 0.4235113489455841 chr5 180915260 8007593 0.04426156754272691 0.42427830789897736 chr6 171115067 18530487 0.1082925502989167 0.8171771873454675 chr7 159138663 9520564 0.05982558745010947 0.5875567273349152 chr8 146364022 8002142 0.05467287582463401 1.2217091970590988 chr9 141213431 7474548 0.0529308575471125 0.6575613440577952 chr10 135534747 13207014 0.0974437499780038 0.8378131699158441 chr11 135006516 4718948 0.034953483282243944 0.4355994613796053 chr12 133851895 13241071 0.09892329876988294 0.6356650552798476 chr13 115169878 4330569 0.0376015766900439 0.38049258406502007 chr14 107349540 2857583 0.026619424731582454 0.3920551976719457 chr15 102531392 3284866 0.03203766120721349 0.35139248207389995 chr16 90354753 4923233 0.05448781427137541 0.48724115079372843 chr17 81195210 5770113 0.07106469704308911 0.5843571414600153 chr18 78077248 3985638 0.051047367858047456 1.2312265052498705 chr19 59128983 5139464 0.08691953994879296 0.8721056530372048 chr20 63025520 2092262 0.033197060492321205 0.3608394918814132 chr21 48129895 3103818 0.06448836009303573 0.5284334411495878 chr22 51304566 2885815 0.05624869724070953 0.44490378849875106 chrMT 16571 58092 3.5056423873031197 3.8132775863327137 chrX 155270560 5585063 0.03596987735472842 0.4216275376239468 chrY 59373566 431058 0.007260099553393845 0.19561516899933964