BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231763.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 = 2,131,678 number of mapped reads = 1,988,887 (93.3%) number of supplementary alignments = 13,022 (0.61%) number of secondary alignments = 0 number of mapped bases = 134,091,174 bp number of sequenced bases = 134,032,625 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,609 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6909 >>>>>>> ACTG content number of A's = 38,032,881 bp (28.38%) number of C's = 25,825,685 bp (19.27%) number of T's = 39,640,440 bp (29.58%) number of G's = 30,524,118 bp (22.77%) number of N's = 9,501 bp (0.01%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 862,589 number of insertions = 9,648 mapped reads with insertion percentage = 0.48% number of deletions = 34,183 mapped reads with deletion percentage = 1.7% homopolymer indels = 45.78% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 3.1146X There is a 3.78% of reference with a coverageData >= 1X There is a 0.35% 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 0.01% 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 12642727 0.05072295085676035 1.071096933799035 chr2 243199373 8818950 0.036262223422755285 10.997136857213308 chr3 198022430 13777395 0.06957492138643082 0.287476807404086 chr4 191154276 4663016 0.02439399263032965 0.19200314019612727 chr5 180915260 6698071 0.0370232505538781 0.21349235083533008 chr6 171115067 11545825 0.06747404072839477 0.3694110077863848 chr7 159138663 7205559 0.04527849401373945 0.5700362837724301 chr8 146364022 7767176 0.053067522290416426 0.5049294114409327 chr9 141213431 5978167 0.04233426634892824 0.3682705043045217 chr10 135534747 6546484 0.04830114892972796 0.4184082078249941 chr11 135006516 4550032 0.03370231404238296 0.31151218898288763 chr12 133851895 4503698 0.033646875152570685 0.2080814233575706 chr13 115169878 4375556 0.037992190978964134 0.21064977809449667 chr14 107349540 5198082 0.04842202397886381 0.2770943922792767 chr15 102531392 2458763 0.023980587330756222 0.16891847795762616 chr16 90354753 3478391 0.03849704508627233 0.2526411295841042 chr17 81195210 3353254 0.041298667741606926 0.24053107404249668 chr18 78077248 2973966 0.03809004641147188 0.8199357170315716 chr19 59128983 4099270 0.0693275918511908 0.655891124437724 chr20 63025520 3165098 0.05021930798825618 0.25688448246291745 chr21 48129895 2640442 0.054860747151017054 0.2739793134419528 chr22 51304566 1467992 0.028613281710637605 0.18307310363943438 chrMT 16571 197255 11.903626817934947 6.751169351078291 chrX 155270560 5677321 0.03656405309544836 0.24356723907414052 chrY 59373566 308684 0.0051990139854493495 0.11403038351024783