BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525235.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 = 2,319,500 number of mapped reads = 2,146,574 (92.54%) number of supplementary alignments = 7,812 (0.34%) number of secondary alignments = 0 number of mapped bases = 125,546,985 bp number of sequenced bases = 125,506,765 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,415 duplication rate = 3.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3099 >>>>>>> ACTG content number of A's = 32,496,190 bp (25.89%) number of C's = 25,102,495 bp (20%) number of T's = 38,868,342 bp (30.97%) number of G's = 29,036,987 bp (23.14%) number of N's = 2,751 bp (0%) GC percentage = 43.14% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 609,429 number of insertions = 8,124 mapped reads with insertion percentage = 0.38% number of deletions = 25,240 mapped reads with deletion percentage = 1.17% homopolymer indels = 45.11% >>>>>>> Coverage mean coverageData = 0.0406X std coverageData = 0.3852X There is a 3.52% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% 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 14305197 0.05739282390794926 0.6713268115234758 chr2 243199373 10040517 0.04128512699742857 0.5040975164893542 chr3 198022430 7695753 0.03886303687920606 0.22234848040159552 chr4 191154276 7070795 0.03698999126757698 0.23432942095702686 chr5 180915260 5559422 0.03072942547798345 0.19823120832744204 chr6 171115067 7502538 0.04384498765383413 0.26980693461905964 chr7 159138663 9156949 0.05754069330091079 0.694785127698017 chr8 146364022 8080279 0.05520672969754821 0.4562843039072615 chr9 141213431 4109127 0.029098698125959423 0.2575271043601474 chr10 135534747 8424185 0.062155168224130745 0.39080390464531545 chr11 135006516 5721192 0.042377154596004836 0.29894142012452873 chr12 133851895 5473265 0.0408904558280628 0.23130958242562025 chr13 115169878 3855171 0.03347377862117732 0.2083592634871989 chr14 107349540 2705734 0.025204896080598015 0.1851880455014081 chr15 102531392 3292387 0.03211101435158512 0.20495832800517752 chr16 90354753 3292583 0.03644061757326701 0.24250046128371716 chr17 81195210 2164910 0.026663026057817944 0.1959120233733263 chr18 78077248 2654838 0.0340027097266543 0.5100299344040552 chr19 59128983 1714692 0.028999179640887787 0.42102066926348214 chr20 63025520 2268507 0.03599346740812293 0.21732429469575418 chr21 48129895 1689729 0.03510768099535642 0.23057108477767727 chr22 51304566 977444 0.0190517935577118 0.15429763594307358 chrMT 16571 470778 28.409751976344214 15.203428099900757 chrX 155270560 6938351 0.04468555404192527 0.25923932654323667 chrY 59373566 382642 0.006444652490638679 0.17714112975334315