BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089533.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 11,407,991 number of mapped reads = 9,648,132 (84.57%) number of supplementary alignments = 338 (0%) number of secondary alignments = 0 number of mapped bases = 454,805,033 bp number of sequenced bases = 454,714,243 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,950,845 duplication rate = 21.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1607 >>>>>>> ACTG content number of A's = 143,651,580 bp (31.59%) number of C's = 85,955,335 bp (18.9%) number of T's = 127,123,414 bp (27.96%) number of G's = 97,971,336 bp (21.55%) number of N's = 12,578 bp (0%) GC percentage = 40.45% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 2,250,356 number of insertions = 18,942 mapped reads with insertion percentage = 0.2% number of deletions = 60,512 mapped reads with deletion percentage = 0.63% homopolymer indels = 47.03% >>>>>>> Coverage mean coverageData = 0.1469X std coverageData = 1.1792X There is a 5.04% of reference with a coverageData >= 1X There is a 2.52% of reference with a coverageData >= 2X There is a 1.62% of reference with a coverageData >= 3X There is a 1.13% of reference with a coverageData >= 4X There is a 0.83% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% 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% 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 26149427 0.10491218394998503 1.156041488158949 chr2 243199373 43888330 0.18046234847817638 1.4432825178924524 chr3 198022430 33938339 0.17138633739622325 1.1914073562948295 chr4 191154276 29428551 0.153951832079341 1.1600509626477111 chr5 180915260 31168642 0.17228310093908053 1.1982126644009317 chr6 171115067 26421843 0.15440979840775798 1.1913578019988458 chr7 159138663 25832912 0.16232957794800626 1.2606673407046438 chr8 146364022 23085794 0.15772861174858943 1.3404693252022337 chr9 141213431 21405657 0.1515837186903277 1.1646420403282454 chr10 135534747 20401429 0.1505254516024588 1.1857806757831744 chr11 135006516 22384670 0.16580436754623015 1.2540887218250873 chr12 133851895 23515310 0.17568156207276706 1.2118811187728902 chr13 115169878 9761805 0.08476005331880268 0.7912918116466718 chr14 107349540 15378866 0.1432597289191924 1.2089172652725104 chr15 102531392 12881409 0.1256338058884444 0.9803454806117474 chr16 90354753 11195125 0.12390189368344574 0.9845773237419218 chr17 81195210 12012583 0.14794694169766912 1.063211111982625 chr18 78077248 13109549 0.16790485494570712 1.3289985971501719 chr19 59128983 9002046 0.15224422175500635 1.2380383748579582 chr20 63025520 9780288 0.1551798065291647 1.1428255083605292 chr21 48129895 4420897 0.09185345199693455 0.9030472940982478 chr22 51304566 5334679 0.10398058917407078 0.888788209410861 chrMT 16571 22699 1.3698026673103614 3.8488258231476906 chrX 155270560 23201451 0.14942595041841802 1.1553386082875456 chrY 59373566 1082732 0.018235926742213866 0.3918431564751758