BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237312.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 = 1,040,865 number of mapped reads = 923,088 (88.68%) number of supplementary alignments = 5,059 (0.49%) number of secondary alignments = 0 number of mapped bases = 64,647,402 bp number of sequenced bases = 64,617,951 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,860 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4728 >>>>>>> ACTG content number of A's = 18,845,845 bp (29.17%) number of C's = 11,912,689 bp (18.44%) number of T's = 20,448,004 bp (31.64%) number of G's = 13,410,387 bp (20.75%) number of N's = 1,026 bp (0%) GC percentage = 39.19% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 549,865 number of insertions = 5,735 mapped reads with insertion percentage = 0.62% number of deletions = 17,405 mapped reads with deletion percentage = 1.86% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 0.0209X std coverageData = 0.2425X There is a 1.9% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5547409 0.022256349764520747 0.2868028846922887 chr2 243199373 4514499 0.0185629549299866 0.2494795155127066 chr3 198022430 5266546 0.026595704335109917 0.17342963606421252 chr4 191154276 3237705 0.01693765406534772 0.15183417675422337 chr5 180915260 3652047 0.020186506102359746 0.152170876006662 chr6 171115067 6870295 0.04015014645086747 0.2938971474474363 chr7 159138663 4296045 0.02699560822626743 0.38316736329710965 chr8 146364022 3691439 0.025220945349534053 0.46447854625591317 chr9 141213431 3222456 0.022819755721394518 0.26308770570435297 chr10 135534747 2786510 0.020559377293853657 0.21162578768027104 chr11 135006516 2142671 0.015870871002996625 0.19295021918187863 chr12 133851895 2177779 0.016270064760756656 0.14036698840354417 chr13 115169878 1884853 0.016365850452667842 0.13554588878461213 chr14 107349540 2265650 0.02110535359536706 0.1685945233894082 chr15 102531392 1813439 0.01768667102461654 0.14163507525069416 chr16 90354753 1374545 0.015212758093644503 0.15896193837849015 chr17 81195210 1757274 0.021642582117836755 0.18707417899498582 chr18 78077248 2024736 0.02593247139038507 0.45355305927523865 chr19 59128983 783388 0.013248798816648005 0.21917355322900198 chr20 63025520 622879 0.009882964868834086 0.11082009458769473 chr21 48129895 980861 0.02037945439108064 0.1668608854243402 chr22 51304566 519821 0.01013206115026877 0.10608992183919506 chrMT 16571 5429 0.32762054191056666 0.5910703667563497 chrX 155270560 3063533 0.019730288858364392 0.16443241221988233 chrY 59373566 145593 0.002452151854918062 0.0825024061246222