BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240058.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,214,657 number of mapped reads = 1,812,212 (81.83%) number of supplementary alignments = 8,191 (0.37%) number of secondary alignments = 0 number of mapped bases = 110,428,828 bp number of sequenced bases = 110,367,434 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,237 duplication rate = 5.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.3998 >>>>>>> ACTG content number of A's = 28,429,587 bp (25.76%) number of C's = 19,604,641 bp (17.76%) number of T's = 34,661,710 bp (31.41%) number of G's = 27,602,053 bp (25.01%) number of N's = 69,443 bp (0.06%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,086,054 number of insertions = 8,114 mapped reads with insertion percentage = 0.44% number of deletions = 35,480 mapped reads with deletion percentage = 1.94% homopolymer indels = 47.22% >>>>>>> Coverage mean coverageData = 0.0357X std coverageData = 0.3797X There is a 2.76% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 7099401 0.028482982194856798 0.3521575342814868 chr2 243199373 13864570 0.05700906967387617 0.5795439758880553 chr3 198022430 5397619 0.027257614200573137 0.21205968720184426 chr4 191154276 6339920 0.033166508919737686 0.27118747195540605 chr5 180915260 6442426 0.03561018567477393 0.24585679450087747 chr6 171115067 5581704 0.032619593925063306 0.2949690750619192 chr7 159138663 5089820 0.03198355386459417 0.7174552704092252 chr8 146364022 7207541 0.0492439391970248 0.4131766897435288 chr9 141213431 3413985 0.024176064385830268 0.3726122279889604 chr10 135534747 6517853 0.048089904207369055 0.3544101309784899 chr11 135006516 6739285 0.04991822024353254 0.5552143177734179 chr12 133851895 7097501 0.05302503188318701 0.3012753613299787 chr13 115169878 1694993 0.014717329126631531 0.1519229970146059 chr14 107349540 4873653 0.04539984987359983 0.28618631885176565 chr15 102531392 2427070 0.02367148199841079 0.28987195393543735 chr16 90354753 3083547 0.03412711448616322 0.2592719442794589 chr17 81195210 3037815 0.037413721819304364 0.31834072239392247 chr18 78077248 2565280 0.03285566622430135 0.5586531252845464 chr19 59128983 2081708 0.03520622027272142 0.3379266935344124 chr20 63025520 1965896 0.031192063151561464 0.234793075791974 chr21 48129895 1662439 0.034540673733030165 0.25521127055788895 chr22 51304566 1350189 0.026317131305622972 0.20533830844797338 chrMT 16571 20643 1.2457304930299922 1.7319340870101785 chrX 155270560 4593469 0.02958364418856994 0.2804029570319176 chrY 59373566 280501 0.0047243414687270086 0.10785991531066583