BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237321.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 = 2,822,829 number of mapped reads = 2,573,513 (91.17%) number of supplementary alignments = 27,812 (0.99%) number of secondary alignments = 0 number of mapped bases = 158,433,158 bp number of sequenced bases = 158,338,158 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 551,994 duplication rate = 16.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1417 >>>>>>> ACTG content number of A's = 40,778,772 bp (25.75%) number of C's = 27,765,385 bp (17.54%) number of T's = 52,677,476 bp (33.27%) number of G's = 37,099,719 bp (23.43%) number of N's = 16,806 bp (0.01%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,061,000 number of insertions = 9,662 mapped reads with insertion percentage = 0.37% number of deletions = 54,922 mapped reads with deletion percentage = 2.11% homopolymer indels = 40.84% >>>>>>> Coverage mean coverageData = 0.0512X std coverageData = 0.7943X There is a 2.93% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 12480037 0.0500702343285235 1.6699176636409039 chr2 243199373 10582451 0.043513479781874274 1.3517679911767906 chr3 198022430 12175848 0.061487216372407914 0.42682190459029457 chr4 191154276 10169031 0.05319803047460994 0.37469763099314213 chr5 180915260 6079175 0.03360233404302103 0.29944426287182524 chr6 171115067 13198549 0.07713259405730764 0.6466199497576691 chr7 159138663 7781388 0.04889690445620999 0.4987354789219733 chr8 146364022 11984276 0.08187993084803313 0.884252823203821 chr9 141213431 4660951 0.03300642840410839 0.428840102439766 chr10 135534747 9206071 0.06792406525833557 1.0752953539010304 chr11 135006516 6934451 0.05136382454310576 0.40458509149510724 chr12 133851895 9113425 0.06808588701713936 0.4259667024044501 chr13 115169878 3545602 0.030785844889060315 0.36423083239685355 chr14 107349540 6370372 0.05934233160197985 0.39276239416187114 chr15 102531392 4824025 0.047049249072908327 0.39187935145860997 chr16 90354753 3853890 0.042652875161974045 0.3861921511611412 chr17 81195210 3731385 0.045955728176575936 0.3612283591602744 chr18 78077248 4334336 0.055513432030801085 1.1233867343326551 chr19 59128983 3068250 0.05189079609233259 1.0760303897749297 chr20 63025520 4539770 0.07203066313455248 0.4356283737952227 chr21 48129895 2267668 0.04711558169823558 0.3497828087231367 chr22 51304566 819891 0.015980858311909315 0.19196703319722436 chrMT 16571 24635 1.4866332749984914 2.087828760751985 chrX 155270560 6303359 0.04059597002805941 0.34424884184280113 chrY 59373566 384322 0.0064729479108598595 0.1847195106720522