BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617369.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,294,393 (94.67%) number of supplementary alignments = 91,578 (0.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,250,212 number of mapped paired reads (second in pair) = 15,044,181 number of mapped paired reads (both in pair) = 29,708,776 number of mapped paired reads (singletons) = 585,617 number of mapped bases = 2,969,691,091 bp number of sequenced bases = 2,968,812,018 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,604,151 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 62,800.8695 std insert size = 2,390,941.6021 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.4255 >>>>>>> ACTG content number of A's = 899,040,300 bp (30.28%) number of C's = 589,529,757 bp (19.86%) number of T's = 887,606,167 bp (29.9%) number of G's = 591,510,593 bp (19.92%) number of N's = 1,125,201 bp (0.04%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 30,074,949 number of insertions = 300,094 mapped reads with insertion percentage = 0.96% number of deletions = 364,881 mapped reads with deletion percentage = 1.17% homopolymer indels = 41.4% >>>>>>> Coverage mean coverageData = 0.9593X std coverageData = 9.862X There is a 53.03% of reference with a coverageData >= 1X There is a 24.01% of reference with a coverageData >= 2X There is a 9.25% of reference with a coverageData >= 3X There is a 3.26% of reference with a coverageData >= 4X There is a 1.12% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% 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 0.02% 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 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 192810050 0.7735589553455917 20.004674202260812 chr2 243199373 293129722 1.205306240653836 8.868410225278566 chr3 198022430 235917677 1.1913684576035148 1.4976127959014724 chr4 191154276 162391816 0.8495327407690321 9.383064517758635 chr5 180915260 185872203 1.0273992531088865 1.4808247058356045 chr6 171115067 139488950 0.8151763164140303 3.702020954975262 chr7 159138663 240928110 1.5139508241312798 10.990121854296348 chr8 146364022 124867905 0.8531325068396931 7.761865638441062 chr9 141213431 125266873 0.887074778319068 15.049837170265127 chr10 135534747 125027756 0.9224775105087997 20.269506139377707 chr11 135006516 159460818 1.1811342350320335 5.563249442307636 chr12 133851895 130888307 0.9778592002750502 1.376417733824718 chr13 115169878 129241352 1.1221801589474636 1.3240805117007206 chr14 107349540 86053448 0.8016191592437192 1.3799001789369822 chr15 102531392 66669031 0.6502304289402411 1.0737816858764804 chr16 90354753 74797959 0.8278253939778907 7.928794484247698 chr17 81195210 92937133 1.1446134938255594 7.222043507811715 chr18 78077248 53843694 0.6896207970854711 15.57568927892883 chr19 59128983 55344028 0.9359881599857721 9.755076242523128 chr20 63025520 85247642 1.3525892686010366 2.4336949077185146 chr21 48129895 47130232 0.9792298944346336 3.1863879137939106 chr22 51304566 26499056 0.5165048272701498 0.9353512058753204 chrMT 16571 2027714 122.36521634180194 21.95911195580171 chrX 155270560 123622727 0.7961762165345446 3.0669225378856186 chrY 59373566 10226888 0.17224648423508873 8.451800243168824