BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549037.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,175,614 number of mapped reads = 7,072,380 (86.51%) number of secondary alignments = 0 number of mapped bases = 280,283,118 bp number of sequenced bases = 280,257,455 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 311,559 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4233 >>>>>>> ACTG content number of A's = 79,155,664 bp (28.24%) number of C's = 59,756,175 bp (21.32%) number of T's = 80,702,697 bp (28.8%) number of G's = 60,642,692 bp (21.64%) number of N's = 227 bp (0%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 699,412 number of insertions = 7,623 mapped reads with insertion percentage = 0.11% number of deletions = 19,426 mapped reads with deletion percentage = 0.27% homopolymer indels = 42.7% >>>>>>> Coverage mean coverageData = 0.0905X std coverageData = 0.5128X There is a 6.76% of reference with a coverageData >= 1X There is a 1.54% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.15% 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 0.01% 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% 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 23653572 0.09489874851705986 0.6456220857665587 chr2 243199373 24458587 0.10057010714414959 0.5131054905472643 chr3 198022430 18707925 0.0944737674413954 0.3947710847118982 chr4 191154276 18820547 0.0984573685393258 0.4249078346630885 chr5 180915260 17318081 0.09572482166512654 0.3991312052844292 chr6 171115067 17282457 0.10099903709823518 0.4284142800220104 chr7 159138663 15380023 0.09664542047836609 0.5398494869997515 chr8 146364022 14044467 0.09595573289178949 1.0559236036841086 chr9 141213431 11518416 0.08156742541012264 0.46887543000365106 chr10 135534747 13312992 0.09822567492600255 0.4837885371847695 chr11 135006516 13565171 0.10047789841491798 0.448500312419612 chr12 133851895 13278421 0.09920233852497942 0.4121091860069163 chr13 115169878 9532296 0.08276726662851897 0.3727375561562082 chr14 107349540 8481293 0.07900632829912452 0.40441401708219404 chr15 102531392 7855520 0.07661575490948178 0.35661134646701775 chr16 90354753 8146737 0.090163900951619 0.4146492195884123 chr17 81195210 7251552 0.08931009600196858 0.388981290946326 chr18 78077248 7023120 0.08995091630278772 0.7495997190623008 chr19 59128983 5540824 0.09370741248839 0.6363664737217594 chr20 63025520 5584059 0.08859996712442833 0.3918058545286254 chr21 48129895 3670944 0.0762715979330518 0.4319928586046607 chr22 51304566 3244452 0.06323904971732926 0.4279361965866333 chrMT 16571 12828 0.7741234687103977 1.3125909341803534 chrX 155270560 10328166 0.06651722000616214 0.3639588658721145 chrY 59373566 2270668 0.03824375312070695 0.34332073182812095