BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082975.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 5,678,238 number of mapped reads = 4,970,802 (87.54%) number of supplementary alignments = 33,683 (0.59%) number of secondary alignments = 0 number of mapped bases = 333,309,329 bp number of sequenced bases = 333,180,679 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 464,965 duplication rate = 6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6303 >>>>>>> ACTG content number of A's = 93,003,356 bp (27.91%) number of C's = 58,560,534 bp (17.58%) number of T's = 109,589,455 bp (32.89%) number of G's = 71,936,111 bp (21.59%) number of N's = 91,223 bp (0.03%) GC percentage = 39.17% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 3,198,979 number of insertions = 30,367 mapped reads with insertion percentage = 0.61% number of deletions = 80,368 mapped reads with deletion percentage = 1.6% homopolymer indels = 49.28% >>>>>>> Coverage mean coverageData = 0.1077X std coverageData = 0.8542X There is a 6.73% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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% 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 39100354 0.15687164125460695 1.5173559689271285 chr2 243199373 20568227 0.08457351985031639 0.8835989185290007 chr3 198022430 22562422 0.1139387189622913 0.5458924026128453 chr4 191154276 28867352 0.1510159887817524 0.7151177713601293 chr5 180915260 11969334 0.06615989165314191 0.31730833177680284 chr6 171115067 19501168 0.113965230192149 0.8504268344736393 chr7 159138663 17109726 0.1075145767688145 0.8000258698720519 chr8 146364022 21867176 0.14940267219494693 1.4093590866539119 chr9 141213431 6433314 0.04555738044492383 0.6953165376356102 chr10 135534747 17848914 0.13169253195271025 0.7707250272754266 chr11 135006516 19825328 0.1468471936569343 0.8319755838534855 chr12 133851895 11819032 0.08829932516084288 0.5143170347903864 chr13 115169878 10236880 0.08888504683490243 0.5228671525806365 chr14 107349540 10953768 0.10203833197608485 0.6144338868030338 chr15 102531392 8042521 0.07843959633357947 0.4748097728727498 chr16 90354753 13841476 0.1531903473854884 0.6845557093502427 chr17 81195210 10193840 0.12554730753205762 0.6965683535514045 chr18 78077248 9301113 0.11912705990866891 1.498543600080147 chr19 59128983 6820208 0.11534458490517248 1.0680557253578222 chr20 63025520 6602925 0.10476589483117316 0.5486983981136048 chr21 48129895 4893206 0.10166666683980922 0.49771393763516836 chr22 51304566 4727936 0.0921542928557275 0.4999384005840476 chrMT 16571 645395 38.94725725665319 21.7147190617483 chrX 155270560 9036447 0.05819807051639409 0.39401956814624717 chrY 59373566 541267 0.009116295962415328 0.17327877802421626