BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716495.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,446,786 number of mapped reads = 2,178,516 (89.04%) number of supplementary alignments = 9,666 (0.4%) number of secondary alignments = 0 number of mapped bases = 126,062,911 bp number of sequenced bases = 126,025,056 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,452 duplication rate = 3.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7695 >>>>>>> ACTG content number of A's = 32,388,796 bp (25.7%) number of C's = 24,578,451 bp (19.5%) number of T's = 39,511,511 bp (31.35%) number of G's = 29,542,651 bp (23.44%) number of N's = 3,647 bp (0%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 630,339 number of insertions = 8,294 mapped reads with insertion percentage = 0.38% number of deletions = 23,869 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.9% >>>>>>> Coverage mean coverageData = 0.0407X std coverageData = 0.4059X There is a 3.52% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 12795901 0.051337488944511 0.9299064277394973 chr2 243199373 11905494 0.04895363772175514 0.4850799538319381 chr3 198022430 7430835 0.03752521873405957 0.22168982976895785 chr4 191154276 5914086 0.030938810911036067 0.2195013492191904 chr5 180915260 5590927 0.030903567780849444 0.20506023867463888 chr6 171115067 8686554 0.05076440171104278 0.29448546467616876 chr7 159138663 9300346 0.0584417753968437 0.5574137244114943 chr8 146364022 7359829 0.05028441347423481 0.31789380471146367 chr9 141213431 5248210 0.03716509090413645 0.3097249039448462 chr10 135534747 6714622 0.04954170165677146 0.3479597030665618 chr11 135006516 4210537 0.031187657638687603 0.2812662768843661 chr12 133851895 5019575 0.037500963284830595 0.22868671407807503 chr13 115169878 2835707 0.02462195019430341 0.17876437546392823 chr14 107349540 2777319 0.02587173638564264 0.20090326521610918 chr15 102531392 3799158 0.03705360793307088 0.2207492123013495 chr16 90354753 2674730 0.02960253789858736 0.21626800286730816 chr17 81195210 2757215 0.03395785293245747 0.21961607836851593 chr18 78077248 4420217 0.05661338114786013 0.5455925593526552 chr19 59128983 2974442 0.05030429831678316 0.5144106433929453 chr20 63025520 1878313 0.029802419718234774 0.19792726945885666 chr21 48129895 1147987 0.02385184925086581 0.19267274906490714 chr22 51304566 1989787 0.03878381896847154 0.223640599324687 chrMT 16571 124952 7.54040190694587 4.7629899051871165 chrX 155270560 8193168 0.05276704096385046 0.3058014276201418 chrY 59373566 313000 0.005271706267398525 0.13195823747826052