BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094093.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 718,124 number of mapped reads = 666,335 (92.79%) number of supplementary alignments = 49,106 (6.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 334,369 number of mapped paired reads (second in pair) = 331,966 number of mapped paired reads (both in pair) = 661,478 number of mapped paired reads (singletons) = 4,857 number of mapped bases = 82,359,957 bp number of sequenced bases = 80,769,677 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 655,129 duplication rate = 55.06% >>>>>>> Insert size mean insert size = 1,728,685.7139 std insert size = 11,553,687.3899 median insert size = 147 >>>>>>> Mapping quality mean mapping quality = 41.4639 >>>>>>> ACTG content number of A's = 23,379,639 bp (28.95%) number of C's = 17,094,817 bp (21.16%) number of T's = 22,080,777 bp (27.34%) number of G's = 18,213,714 bp (22.55%) number of N's = 730 bp (0%) GC percentage = 43.72% >>>>>>> Mismatches and indels general error rate = 0.0356 number of mismatches = 2,784,248 number of insertions = 49,224 mapped reads with insertion percentage = 7.3% number of deletions = 222,387 mapped reads with deletion percentage = 32.36% homopolymer indels = 27.49% >>>>>>> Coverage mean coverageData = 0.0266X std coverageData = 5.4093X There is a 0.02% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 1858161 0.007454990453163204 2.7209059278245062 chr2 243199373 3764218 0.015477909969776115 4.188243623751005 chr3 198022430 1998062 0.010090079189514036 3.490799387616252 chr4 191154276 3454569 0.01807215131300542 4.889583095992602 chr5 180915260 1472072 0.008136803937932046 3.3313212255898157 chr6 171115067 1828917 0.010688228874667126 3.1454298618569863 chr7 159138663 2295681 0.014425664742451681 4.336284206652048 chr8 146364022 1749115 0.01195044366845836 3.3450037315695282 chr9 141213431 1981902 0.014034798148909787 5.4582598363081 chr10 135534747 1730512 0.012768032097333683 4.231971753946754 chr11 135006516 2153678 0.015952400401177673 3.914364275846972 chr12 133851895 2256013 0.016854546586733046 4.361942122736797 chr13 115169878 1787685 0.015522157625277679 4.088402445963624 chr14 107349540 457790 0.004264480313562592 1.4911558670867477 chr15 102531392 844837 0.008239788649314348 2.1937226241555035 chr16 90354753 434217 0.00480569074213506 1.9274162406166486 chr17 81195210 998673 0.012299654129843374 3.439250340855651 chr18 78077248 542279 0.006945416416316312 1.9137525571365674 chr19 59128983 196608 0.003325069873094215 1.4164268678205625 chr20 63025520 463742 0.007358003551577202 2.6047336186559016 chr21 48129895 450344 0.009356845677722754 2.653321072619632 chr22 51304566 141073 0.002749716272816731 0.7955762698754217 chrMT 16571 72675 4.385673767425019 27.546759553292198 chrX 155270560 48534740 0.3125817283070274 18.329030373834946 chrY 59373566 892394 0.015030156686226325 3.0708738431249594