BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004006.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 = 4,819,137 number of mapped reads = 4,175,653 (86.65%) number of supplementary alignments = 28,160 (0.58%) number of secondary alignments = 0 number of mapped bases = 282,777,375 bp number of sequenced bases = 282,659,155 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 215,893 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.486 >>>>>>> ACTG content number of A's = 76,981,545 bp (27.23%) number of C's = 54,396,200 bp (19.24%) number of T's = 88,398,031 bp (31.27%) number of G's = 62,845,481 bp (22.23%) number of N's = 37,898 bp (0.01%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 2,763,013 number of insertions = 24,723 mapped reads with insertion percentage = 0.59% number of deletions = 70,311 mapped reads with deletion percentage = 1.67% homopolymer indels = 45.33% >>>>>>> Coverage mean coverageData = 0.0913X std coverageData = 0.9815X There is a 7.4% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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% 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 21172918 0.08494629989307027 2.198874005470346 chr2 243199373 24838127 0.10213071972023546 1.0347101515827872 chr3 198022430 19555685 0.0987548986243629 0.4196835275274095 chr4 191154276 14607440 0.07641701930852962 0.4234653768463171 chr5 180915260 18618532 0.10291299915772721 0.3967010974164582 chr6 171115067 17906559 0.10464630212838008 0.48784323858682743 chr7 159138663 20124241 0.12645727078906022 1.6115378372257607 chr8 146364022 11699580 0.07993480802269837 0.7781884176459569 chr9 141213431 8029907 0.05686362085487463 0.7526141281741315 chr10 135534747 11742954 0.08664164917059977 1.161219036195884 chr11 135006516 12127075 0.08982584959084493 0.6245738736724008 chr12 133851895 11724174 0.08759064636328084 0.36302675625457415 chr13 115169878 7724086 0.06706689400157219 0.2993482977221602 chr14 107349540 8720510 0.08123472163923572 0.41469585698628486 chr15 102531392 9005478 0.08783142239988315 0.34896728240311053 chr16 90354753 6797992 0.07523668400709368 0.5824354125046026 chr17 81195210 7643142 0.09413291744673116 0.4690190439206556 chr18 78077248 8600380 0.11015219183954844 1.8027417251814855 chr19 59128983 5952531 0.10067027535379731 1.4139735073918327 chr20 63025520 6762247 0.10729379146732942 0.42006137593299775 chr21 48129895 4514245 0.09379295342323103 0.4320599981670542 chr22 51304566 3581246 0.0698036506146451 0.30791071558427807 chrMT 16571 26035 1.5711182185746184 1.565387669477008 chrX 155270560 20431911 0.13158908552915632 0.5682568259741732 chrY 59373566 870380 0.01465938562625664 0.28961535186371967