BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240184.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 = 1,468,637 number of mapped reads = 1,137,215 (77.43%) number of supplementary alignments = 9,947 (0.68%) number of secondary alignments = 0 number of mapped bases = 74,110,381 bp number of sequenced bases = 74,073,916 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,636 duplication rate = 7.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6202 >>>>>>> ACTG content number of A's = 21,297,540 bp (28.75%) number of C's = 13,706,704 bp (18.5%) number of T's = 23,351,005 bp (31.52%) number of G's = 15,661,868 bp (21.14%) number of N's = 56,799 bp (0.08%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 679,985 number of insertions = 5,280 mapped reads with insertion percentage = 0.46% number of deletions = 20,927 mapped reads with deletion percentage = 1.82% homopolymer indels = 48.19% >>>>>>> Coverage mean coverageData = 0.0239X std coverageData = 0.2889X There is a 1.46% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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% 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 6135571 0.02461607106688011 0.4396527122463538 chr2 243199373 7205151 0.02962651963744989 0.3132897044317296 chr3 198022430 5383157 0.02718458206981906 0.24899735892865954 chr4 191154276 4417998 0.02311221120682647 0.2350461965439532 chr5 180915260 5798322 0.03204993321182525 0.2712717812528076 chr6 171115067 3773913 0.022054825832490833 0.24867777866066343 chr7 159138663 4381016 0.02752955138249465 0.373927545874234 chr8 146364022 3970906 0.027130342182042525 0.37655582231406093 chr9 141213431 2523864 0.017872690877399615 0.23809977649844877 chr10 135534747 3284981 0.02423718694070385 0.27645903300311375 chr11 135006516 2951843 0.02186444837966191 0.26125666821214594 chr12 133851895 3483427 0.026024487736987213 0.25674226048316634 chr13 115169878 2332352 0.020251406361653002 0.2179555645172596 chr14 107349540 2210467 0.020591303884488002 0.22953081884558327 chr15 102531392 1985195 0.01936182627853136 0.21622253844088526 chr16 90354753 2045054 0.022633607332200885 0.2325884570353801 chr17 81195210 1604657 0.01976295153371732 0.22363459010359815 chr18 78077248 1666847 0.02134869046613938 0.3658251547827331 chr19 59128983 1254089 0.02120937882527085 0.319342668409059 chr20 63025520 1416511 0.022475197348629572 0.22824249092930832 chr21 48129895 1090218 0.022651576530553413 0.23261225532981963 chr22 51304566 591657 0.011532248416252075 0.15620100506216553 chrMT 16571 19307 1.1651077183030596 1.662745506289998 chrX 155270560 4374569 0.02817384699327419 0.26609286217052464 chrY 59373566 209309 0.003525289351830409 0.09809626382122703