BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084762.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 = 1,454,452 number of mapped reads = 1,296,817 (89.16%) number of supplementary alignments = 13,298 (0.91%) number of secondary alignments = 0 number of mapped bases = 87,824,595 bp number of sequenced bases = 87,790,040 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,691 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0161 >>>>>>> ACTG content number of A's = 24,463,389 bp (27.87%) number of C's = 16,553,839 bp (18.86%) number of T's = 27,331,978 bp (31.13%) number of G's = 19,405,657 bp (22.1%) number of N's = 35,177 bp (0.04%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 731,498 number of insertions = 6,700 mapped reads with insertion percentage = 0.51% number of deletions = 20,776 mapped reads with deletion percentage = 1.59% homopolymer indels = 46.97% >>>>>>> Coverage mean coverageData = 0.0284X std coverageData = 0.2452X There is a 2.48% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7258571 0.029121576391177777 0.3966272443648899 chr2 243199373 7792866 0.03204311715063509 0.2893802765474005 chr3 198022430 5280501 0.026666176149843228 0.18215725361996213 chr4 191154276 5708956 0.02986569863600645 0.20417622681822523 chr5 180915260 5360999 0.029632652325735264 0.19210105168238042 chr6 171115067 5560128 0.03249350333363689 0.21455853157800817 chr7 159138663 4225226 0.026550593805101906 0.2550237385220888 chr8 146364022 4804383 0.032824890532182835 0.2745373491309624 chr9 141213431 3420943 0.02422533731936589 0.2232162468215107 chr10 135534747 3847839 0.0283900555774085 0.2481180090114293 chr11 135006516 4427333 0.03279347642746369 0.23494707550887328 chr12 133851895 3834584 0.028647961988136215 0.19000825178246758 chr13 115169878 2631883 0.02285218188735079 0.16924501529956215 chr14 107349540 2925630 0.027253307280124348 0.18969478230851333 chr15 102531392 2292814 0.022362068389747407 0.1694489872579303 chr16 90354753 2219728 0.02456680945162896 0.1822597621080665 chr17 81195210 3030022 0.0373177432511105 0.22328038738312583 chr18 78077248 2046108 0.026206200300502396 0.3944776578600477 chr19 59128983 1565547 0.026476812564153185 0.315306152879557 chr20 63025520 1507855 0.023924515021851465 0.17654882577352227 chr21 48129895 1013262 0.02105265344958679 0.17232905744548013 chr22 51304566 1090567 0.021256724011660094 0.16064215948927763 chrMT 16571 5139 0.3101200893126546 0.5746066161495262 chrX 155270560 5758175 0.03708478284614933 0.2271938803436988 chrY 59373566 215536 0.0036301676742811774 0.089257176463553