BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038473.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,108,262 number of mapped reads = 13,895,315 (98.49%) number of supplementary alignments = 122,768 (0.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,020,501 number of mapped paired reads (second in pair) = 6,874,814 number of mapped paired reads (both in pair) = 13,734,944 number of mapped paired reads (singletons) = 160,371 number of mapped bases = 2,041,333,544 bp number of sequenced bases = 2,040,579,090 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,444,625 duplication rate = 7.44% >>>>>>> Insert size mean insert size = 72,798.0516 std insert size = 2,676,670.6445 median insert size = 268 >>>>>>> Mapping quality mean mapping quality = 54.4098 >>>>>>> ACTG content number of A's = 594,864,041 bp (29.15%) number of C's = 428,948,678 bp (21.02%) number of T's = 589,685,659 bp (28.9%) number of G's = 427,035,551 bp (20.93%) number of N's = 45,161 bp (0%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 22,487,445 number of insertions = 257,511 mapped reads with insertion percentage = 1.74% number of deletions = 271,303 mapped reads with deletion percentage = 1.86% homopolymer indels = 43.67% >>>>>>> Coverage mean coverageData = 0.6594X std coverageData = 7.4449X There is a 38.77% of reference with a coverageData >= 1X There is a 15.75% of reference with a coverageData >= 2X There is a 5.3% of reference with a coverageData >= 3X There is a 2.05% of reference with a coverageData >= 4X There is a 0.72% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% 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 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 169885872 0.6815865546028068 18.866941061000745 chr2 243199373 178233503 0.7328699116341884 5.481914212165867 chr3 198022430 136544635 0.6895412555032275 1.0727744076332466 chr4 191154276 136010705 0.7115232148926661 5.362257232330174 chr5 180915260 124011457 0.6854670910568849 1.1658095341184882 chr6 171115067 120381077 0.703509510357729 5.641614551543173 chr7 159138663 111487271 0.7005668446516985 5.361396548952701 chr8 146364022 103741462 0.7087907300060393 5.648694951938362 chr9 141213431 89238722 0.6319421698634318 10.139992091629555 chr10 135534747 104955098 0.7743777911062172 12.271406550782205 chr11 135006516 94793586 0.7021408211141453 3.8450918456789 chr12 133851895 91387421 0.6827502965124251 1.093393105928268 chr13 115169878 65500825 0.5687322600098612 0.9844299534743172 chr14 107349540 61649781 0.574290127372693 1.041557130133917 chr15 102531392 58193713 0.5675697156242646 0.9769417083553963 chr16 90354753 65064144 0.7200965288455827 4.874334126840149 chr17 81195210 57976448 0.7140377862191625 3.7314307125870263 chr18 78077248 57505302 0.7365180442835281 8.778877684294933 chr19 59128983 42292890 0.7152649657444641 8.675294071399728 chr20 63025520 43508437 0.6903304724816233 2.0550304336916665 chr21 48129895 28939582 0.6012808047887909 2.959765982836501 chr22 51304566 25513653 0.4972979013212976 2.0897892348573737 chrMT 16571 738595 44.5715406432925 9.617058830652077 chrX 155270560 54271894 0.34953112811598025 1.2531522402707542 chrY 59373566 19507471 0.32855481511755585 6.508326914952761