BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083618.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 = 1,526,909 number of mapped reads = 1,349,879 (88.41%) number of supplementary alignments = 15,423 (1.01%) number of secondary alignments = 0 number of mapped bases = 89,382,349 bp number of sequenced bases = 89,349,615 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,412 duplication rate = 4.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1038 >>>>>>> ACTG content number of A's = 24,034,686 bp (26.9%) number of C's = 16,620,764 bp (18.6%) number of T's = 28,169,051 bp (31.53%) number of G's = 20,520,802 bp (22.97%) number of N's = 4,312 bp (0%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 623,234 number of insertions = 6,533 mapped reads with insertion percentage = 0.48% number of deletions = 20,118 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.54% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2641X There is a 2.42% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 9560607 0.03835740493501118 0.47327819272670674 chr2 243199373 6951529 0.02858366333041492 0.3619795428120459 chr3 198022430 7800449 0.03939174466246071 0.23253985754309173 chr4 191154276 4777834 0.02499464882491041 0.18494397905180374 chr5 180915260 3849580 0.021278359824373025 0.1691156809826886 chr6 171115067 6302060 0.03682936932724925 0.24989858674380952 chr7 159138663 6026604 0.037870143473556765 0.3705330766150293 chr8 146364022 7449600 0.05089775409424045 0.30691032585949296 chr9 141213431 4098421 0.029022883807702397 0.21193573935008989 chr10 135534747 4258952 0.031423322020883694 0.2372771890847771 chr11 135006516 3326309 0.024638136725193324 0.18822713611675332 chr12 133851895 2547339 0.019031026792709956 0.16018164676093 chr13 115169878 2472023 0.02146414533841913 0.16947898423974886 chr14 107349540 1070043 0.00996783963862351 0.11602480869746987 chr15 102531392 2871267 0.02800378444096419 0.19811861760587618 chr16 90354753 2460961 0.027236652398352525 0.19433564198938313 chr17 81195210 1152250 0.014191108071522938 0.1398759522104934 chr18 78077248 3435845 0.0440057134185877 0.280704762386088 chr19 59128983 2653669 0.04487932762178575 0.37399411147822703 chr20 63025520 1253442 0.01988784860481913 0.16306360394657102 chr21 48129895 1390009 0.028880366350269412 0.19901796844323652 chr22 51304566 564867 0.011010072670724864 0.11920962762978077 chrMT 16571 5802 0.35012974473477765 0.7476371251872325 chrX 155270560 2963846 0.019088267602048965 0.1644241722103312 chrY 59373566 139041 0.0023417997160554583 0.059268379251734345