BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16362021.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 94,721,674 number of mapped reads = 43,964,229 (46.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,354,933 number of mapped paired reads (second in pair) = 39,609,296 number of mapped paired reads (both in pair) = 7,762,832 number of mapped paired reads (singletons) = 36,201,397 number of mapped bases = 1,722,499,250 bp number of sequenced bases = 1,722,151,864 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,491,297 duplication rate = 3.96% >>>>>>> Insert size mean insert size = 314,157.2897 std insert size = 5,616,504.0632 median insert size = 256 >>>>>>> Mapping quality mean mapping quality = 44.8437 >>>>>>> ACTG content number of A's = 512,447,549 bp (29.76%) number of C's = 345,112,565 bp (20.04%) number of T's = 491,227,339 bp (28.52%) number of G's = 373,360,347 bp (21.68%) number of N's = 4,064 bp (0%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 8,476,997 number of insertions = 65,728 mapped reads with insertion percentage = 0.15% number of deletions = 319,687 mapped reads with deletion percentage = 0.73% homopolymer indels = 45.4% >>>>>>> Coverage mean coverageData = 0.5564X std coverageData = 4.6007X There is a 39.43% of reference with a coverageData >= 1X There is a 11.32% of reference with a coverageData >= 2X There is a 2.61% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 142494002 0.571689656893573 6.548554845626815 chr2 243199373 148861659 0.6120972153986598 13.088401763886571 chr3 198022430 117576436 0.5937531218054439 1.044175251782877 chr4 191154276 114574316 0.5993813918135946 1.7505381232997101 chr5 180915260 106791867 0.590286673440372 0.8964241960616381 chr6 171115067 102151851 0.5969775355901301 1.6796381072978752 chr7 159138663 97007418 0.6095779377007836 2.8937301308365515 chr8 146364022 86665233 0.5921211498273804 2.4299573593351984 chr9 141213431 72218922 0.511416807088272 1.3912778559628145 chr10 135534747 85277745 0.6291947038496335 5.553802185781752 chr11 135006516 79274733 0.58719190264861 1.5108405860164773 chr12 133851895 79643293 0.5950105749343332 1.0147857123001374 chr13 115169878 56049556 0.4866685367158243 0.7815828562763447 chr14 107349540 53364830 0.4971127961982883 1.5309968676636823 chr15 102531392 49702009 0.48474918783897913 0.8006709328309438 chr16 90354753 52304719 0.5788817661866664 2.857131185864004 chr17 81195210 48607117 0.5986451294355911 1.4273950707211878 chr18 78077248 44959630 0.5758352292334894 2.620842154718689 chr19 59128983 36483958 0.6170232625174696 5.186647912362272 chr20 63025520 36105301 0.5728679588839568 1.054811748064091 chr21 48129895 22782503 0.4733545128240982 1.5749692167157654 chr22 51304566 21404816 0.4172107410478826 1.1663805921358037 chrMT 16571 2313557 139.61480900368113 48.6101078054895 chrX 155270560 52349523 0.33715034582215714 1.1559754401029687 chrY 59373566 13534256 0.2279508695839492 2.5425597795304355