BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008658.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 = 2,203,954 number of mapped reads = 1,682,455 (76.34%) number of supplementary alignments = 7,594 (0.34%) number of secondary alignments = 0 number of mapped bases = 101,963,060 bp number of sequenced bases = 101,910,114 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,212 duplication rate = 2.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3968 >>>>>>> ACTG content number of A's = 27,034,636 bp (26.53%) number of C's = 17,435,493 bp (17.11%) number of T's = 32,688,808 bp (32.08%) number of G's = 24,732,494 bp (24.27%) number of N's = 18,683 bp (0.02%) GC percentage = 41.38% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 837,724 number of insertions = 8,568 mapped reads with insertion percentage = 0.51% number of deletions = 32,706 mapped reads with deletion percentage = 1.92% homopolymer indels = 47.34% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.3496X There is a 2.93% of reference with a coverageData >= 1X There is a 0.23% 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 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 8546211 0.034287621694631606 0.5837745876236363 chr2 243199373 10589135 0.04354096340536207 0.44180971068093516 chr3 198022430 7491208 0.03783009833784991 0.21732313562115346 chr4 191154276 6645290 0.03476401438176565 0.21922088585276694 chr5 180915260 6243615 0.034511267872041305 0.20715623024929788 chr6 171115067 5475645 0.031999782929693736 0.2591118700412507 chr7 159138663 5591932 0.035138739352108296 0.5082952149143175 chr8 146364022 5120756 0.03498643949535631 0.367675342015461 chr9 141213431 4060162 0.0287519534880503 0.40127294018143 chr10 135534747 4749495 0.03504263744263307 0.35527033766000365 chr11 135006516 4303084 0.03187315788520904 0.3361717664250034 chr12 133851895 4667000 0.03486689523521501 0.21686869560226335 chr13 115169878 3084053 0.026778295276131143 0.17948215226194505 chr14 107349540 2972401 0.027688996152195902 0.23016182212252556 chr15 102531392 2443751 0.023834173635329168 0.17882339284888388 chr16 90354753 2488456 0.027540952936919653 0.2292638322505557 chr17 81195210 2720720 0.03350838060521058 0.2536458662135505 chr18 78077248 2535291 0.03247157225623526 0.6592696798769396 chr19 59128983 1755597 0.0296909723612192 0.4191101341093879 chr20 63025520 1973730 0.03131636200700923 0.2087292284602321 chr21 48129895 1280517 0.02660543930129081 0.20201158566740948 chr22 51304566 1029746 0.0200712349852058 0.1534493670509321 chrMT 16571 57230 3.4536238006155333 2.6528683921423513 chrX 155270560 5827848 0.03753350280954741 0.276042637967012 chrY 59373566 310187 0.005224328281040085 0.11210782956906422