BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094049.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 = 402,962 number of mapped reads = 383,919 (95.27%) number of supplementary alignments = 9,221 (2.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 192,805 number of mapped paired reads (second in pair) = 191,114 number of mapped paired reads (both in pair) = 381,466 number of mapped paired reads (singletons) = 2,453 number of mapped bases = 51,712,425 bp number of sequenced bases = 50,513,653 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 365,780 duplication rate = 50.24% >>>>>>> Insert size mean insert size = 314,559.7415 std insert size = 5,078,406.7935 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 41.9337 >>>>>>> ACTG content number of A's = 13,895,701 bp (27.51%) number of C's = 11,274,570 bp (22.32%) number of T's = 13,578,116 bp (26.88%) number of G's = 11,764,545 bp (23.29%) number of N's = 721 bp (0%) GC percentage = 45.61% >>>>>>> Mismatches and indels general error rate = 0.0438 number of mismatches = 2,105,243 number of insertions = 44,452 mapped reads with insertion percentage = 11.3% number of deletions = 169,594 mapped reads with deletion percentage = 41.05% homopolymer indels = 32.13% >>>>>>> Coverage mean coverageData = 0.0167X std coverageData = 5.8895X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% 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% of reference with a coverageData >= 7X There is a 0% 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 578707 0.0023217875954660108 0.8765807998128325 chr2 243199373 2214626 0.009106215911173422 3.324817749236752 chr3 198022430 1816572 0.009173566853007511 4.802611207844038 chr4 191154276 627135 0.003280779342859168 1.5626472078170874 chr5 180915260 492024 0.002719637912246872 1.0904394342717882 chr6 171115067 1876581 0.010966778279086318 5.504145315956583 chr7 159138663 1205962 0.0075780578852795814 2.6159285810675224 chr8 146364022 756148 0.005166214959575243 3.2537434782604917 chr9 141213431 1025410 0.0072614197724577625 3.4997860074978875 chr10 135534747 335960 0.0024787739486465416 0.8103352559934219 chr11 135006516 1965340 0.01455737143827932 4.079974515877879 chr12 133851895 1408602 0.010523586535700522 5.656936657575512 chr13 115169878 1443746 0.012535795166857778 4.770859920359389 chr14 107349540 325065 0.0030280986765290284 1.208726120977687 chr15 102531392 918121 0.008954535602130517 3.491467806306759 chr16 90354753 257580 0.002850763146903849 0.6505573727254085 chr17 81195210 1922675 0.023679660413465278 6.251511570218906 chr18 78077248 293076 0.003753667137448287 1.4546367888985812 chr19 59128983 595071 0.010063947827413166 3.760716651055186 chr20 63025520 389677 0.0061828446635585075 1.7367688182144232 chr21 48129895 138307 0.0028736194001669855 0.5976850595048766 chr22 51304566 75379 0.0014692454468867352 0.4106743673668908 chrMT 16571 6404517 386.4894695552471 1604.3652891662541 chrX 155270560 24397381 0.15712818321773298 13.744136957629804 chrY 59373566 248763 0.004189793821715206 1.6428907395564831