BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085040.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 = 3,491,833 number of mapped reads = 3,171,148 (90.82%) number of supplementary alignments = 20,868 (0.6%) number of secondary alignments = 0 number of mapped bases = 210,048,473 bp number of sequenced bases = 209,981,704 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 201,171 duplication rate = 5.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1008 >>>>>>> ACTG content number of A's = 59,703,491 bp (28.43%) number of C's = 39,778,054 bp (18.94%) number of T's = 65,598,099 bp (31.24%) number of G's = 44,879,748 bp (21.37%) number of N's = 22,312 bp (0.01%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,777,322 number of insertions = 14,426 mapped reads with insertion percentage = 0.45% number of deletions = 38,859 mapped reads with deletion percentage = 1.21% homopolymer indels = 46.27% >>>>>>> Coverage mean coverageData = 0.0679X std coverageData = 0.5092X There is a 5.03% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 20764388 0.08330726686534515 0.7582677390242992 chr2 243199373 23518033 0.09670268763398497 0.6226980451530553 chr3 198022430 11688956 0.05902844440400009 0.31387629579914167 chr4 191154276 13428439 0.07024922110557442 0.3466411895099338 chr5 180915260 10237142 0.05658528749868861 0.3055727627924402 chr6 171115067 18175014 0.10621515871539237 0.562067217619475 chr7 159138663 17783219 0.11174669099739766 0.67042799474307 chr8 146364022 10996596 0.07513182440422415 0.8777337410727931 chr9 141213431 6768774 0.04793293351820055 0.4476074944560475 chr10 135534747 10326704 0.07619229923378984 0.5677051382561245 chr11 135006516 11165392 0.08270261562782644 0.5390996294966134 chr12 133851895 7882805 0.05889199402070475 0.32388231731681355 chr13 115169878 4144761 0.035988238174568525 0.23978464727207274 chr14 107349540 6531212 0.06084061468731026 0.33567057244418586 chr15 102531392 3445158 0.033601006801897315 0.2435990641123179 chr16 90354753 5280795 0.05844512684352089 0.32806292146624694 chr17 81195210 2900338 0.03572055543670618 0.2935389768464444 chr18 78077248 5546568 0.07103949155584992 0.8029913173884403 chr19 59128983 2613908 0.0442068824353025 0.4900816678040499 chr20 63025520 5340233 0.08473128028138444 0.3796055473490895 chr21 48129895 2379249 0.04943391212467844 0.2958601673673496 chr22 51304566 1191591 0.02322582750237084 0.18976954692710826 chrMT 16571 7066 0.42640757950636654 0.8304812553667542 chrX 155270560 7550331 0.048626932240084665 0.34098253344996354 chrY 59373566 381801 0.006430487938016052 0.12299369211776977