BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714181.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 1,940,634 number of mapped reads = 1,849,974 (95.33%) number of supplementary alignments = 84,917 (4.38%) number of secondary alignments = 0 number of mapped bases = 241,113,422 bp number of sequenced bases = 236,563,908 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,756,071 duplication rate = 43.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.5254 >>>>>>> ACTG content number of A's = 72,384,255 bp (30.6%) number of C's = 46,357,304 bp (19.6%) number of T's = 67,695,862 bp (28.62%) number of G's = 50,124,814 bp (21.19%) number of N's = 1,673 bp (0%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0408 number of mismatches = 8,832,911 number of insertions = 268,512 mapped reads with insertion percentage = 14.09% number of deletions = 755,280 mapped reads with deletion percentage = 38.78% homopolymer indels = 24.97% >>>>>>> Coverage mean coverageData = 0.0779X std coverageData = 13.8432X There is a 0.1% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% 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 0.03% 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 0.02% 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 0.02% 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 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 15666342 0.0628537731907998 16.461172579830283 chr2 243199373 17560966 0.07220810556941691 11.400979901873866 chr3 198022430 13417849 0.06775923818327045 8.652295011581845 chr4 191154276 13015944 0.06809130442888968 9.808137415189112 chr5 180915260 14887174 0.08228810549204085 11.990716759641973 chr6 171115067 12377737 0.07233575170794282 10.166237416355559 chr7 159138663 10722365 0.06737749832672654 9.977005285346777 chr8 146364022 16207116 0.11073155669362515 19.687528542588993 chr9 141213431 10010666 0.0708903248728515 14.798956191317926 chr10 135534747 10637724 0.0784870613290037 12.677878662071821 chr11 135006516 11313368 0.08379868124291127 12.001404371654974 chr12 133851895 9924454 0.07414503918678178 14.451787214938944 chr13 115169878 8560474 0.07432910539333905 13.809644405615801 chr14 107349540 5767626 0.05372753343889503 6.826178348572987 chr15 102531392 7145067 0.06968662826697992 13.870724527223512 chr16 90354753 4007705 0.04435522058258518 7.435957040335579 chr17 81195210 3055123 0.037626887103315576 8.712994112008845 chr18 78077248 6287829 0.08053343529730966 9.914861950644001 chr19 59128983 1332761 0.022539893845290728 3.5235418659357287 chr20 63025520 2276492 0.036120162118456145 4.924896738224414 chr21 48129895 1661611 0.03452347028806109 5.147407859149857 chr22 51304566 802225 0.015636522488076402 2.4697608519447005 chrMT 16571 11615 0.7009232997405105 6.1345869530329145 chrX 155270560 41589933 0.2678545952304159 33.163849195203284 chrY 59373566 2873256 0.048392848763707405 8.54500827463352