BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514766.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 12,934,265 number of mapped reads = 4,748,172 (36.71%) number of supplementary alignments = 925,292 (7.15%) number of secondary alignments = 0 number of mapped bases = 433,355,761 bp number of sequenced bases = 432,734,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,884,243 duplication rate = 24.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0752 >>>>>>> ACTG content number of A's = 133,029,773 bp (30.74%) number of C's = 81,863,964 bp (18.92%) number of T's = 131,707,384 bp (30.44%) number of G's = 86,105,453 bp (19.9%) number of N's = 28,076 bp (0.01%) GC percentage = 38.82% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 3,146,338 number of insertions = 314,148 mapped reads with insertion percentage = 6.25% number of deletions = 188,714 mapped reads with deletion percentage = 3.62% homopolymer indels = 34.97% >>>>>>> Coverage mean coverageData = 0.14X std coverageData = 18.0509X There is a 1.52% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.08% of reference with a coverageData >= 29X There is a 0.07% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 24409404 0.09793116623769615 5.085127205710481 chr2 243199373 36679973 0.15082264624095063 6.061120163538501 chr3 198022430 26273510 0.13267946464448496 2.96523355446702 chr4 191154276 39898995 0.20872666745890633 4.014046119055811 chr5 180915260 16266172 0.08991044757639571 2.3941004281028397 chr6 171115067 22202179 0.12974999448762745 2.7430633412333623 chr7 159138663 15239651 0.0957633469623909 4.646836535692614 chr8 146364022 12975639 0.0886532005795796 1.8486113186990965 chr9 141213431 17248157 0.12214246816225292 3.493140179477975 chr10 135534747 39358666 0.29039539211299076 54.68392122014245 chr11 135006516 17931607 0.132820307724999 2.628282682253063 chr12 133851895 15945620 0.11912883265492805 9.556493088153532 chr13 115169878 14935349 0.12968103517483973 3.50159598035044 chr14 107349540 47811516 0.4453816569684416 54.401613171258845 chr15 102531392 23630144 0.23046740650902311 45.0104972655213 chr16 90354753 6713490 0.07430145927132356 2.2186745033831525 chr17 81195210 6265292 0.07716332034857722 2.40076483445262 chr18 78077248 6626814 0.0848750970321085 2.092480965199573 chr19 59128983 3414143 0.05774060074735261 1.6880537088030867 chr20 63025520 5589079 0.08867961739942803 2.1225316213470884 chr21 48129895 5498076 0.11423411582343988 3.9807380576240585 chr22 51304566 869337 0.016944632179521798 0.9492271125684955 chrMT 16571 14845721 895.8856435942309 1060.7985633985427 chrX 155270560 10645674 0.06856208929754616 1.9598479735423027 chrY 59373566 2081553 0.03505858145693994 1.545991571313206