BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524815.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 = 1,279,040 number of mapped reads = 1,176,907 (92.01%) number of supplementary alignments = 3,989 (0.31%) number of secondary alignments = 0 number of mapped bases = 68,263,192 bp number of sequenced bases = 68,240,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,095 duplication rate = 2.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9364 >>>>>>> ACTG content number of A's = 16,034,487 bp (23.5%) number of C's = 13,402,605 bp (19.64%) number of T's = 21,243,002 bp (31.13%) number of G's = 17,552,623 bp (25.72%) number of N's = 8,094 bp (0.01%) GC percentage = 45.36% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 343,731 number of insertions = 3,880 mapped reads with insertion percentage = 0.33% number of deletions = 13,753 mapped reads with deletion percentage = 1.16% homopolymer indels = 42.74% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.2029X There is a 2% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5450349 0.02186694251004494 0.2508798369225098 chr2 243199373 5729436 0.023558596921218214 0.30647706980708384 chr3 198022430 4462250 0.022534063439177066 0.16299306658868548 chr4 191154276 4358717 0.022802089972604116 0.1858139033728502 chr5 180915260 4057035 0.02242505690233096 0.16170200818783947 chr6 171115067 3823378 0.02234390031825777 0.17205041739044824 chr7 159138663 3752026 0.023577086355186985 0.24972843552752544 chr8 146364022 3410626 0.023302352267963775 0.18699973492157476 chr9 141213431 2909675 0.020604803519008046 0.18068898613969997 chr10 135534747 3314738 0.02445673949573979 0.2470632564981625 chr11 135006516 3088400 0.02287593289200945 0.18896205011339157 chr12 133851895 3082382 0.023028303035978685 0.16476684855995782 chr13 115169878 2121433 0.018420033404915128 0.14672161788510443 chr14 107349540 2065216 0.01923823800269661 0.1532328360370568 chr15 102531392 1994733 0.019454851446862244 0.15120911851345836 chr16 90354753 2095988 0.023197318684496874 0.17826394952403674 chr17 81195210 1967645 0.02423351081917271 0.17407923355613472 chr18 78077248 1795091 0.022991217620784994 0.2681064910440192 chr19 59128983 1514894 0.025620159913793884 0.21797223408298824 chr20 63025520 1504971 0.023878755780198244 0.17192502203200996 chr21 48129895 911994 0.018948597332281734 0.16590713506031948 chr22 51304566 865628 0.01687233841915747 0.14065990701755435 chrMT 16571 10828 0.6534306921730735 0.8821940812700673 chrX 155270560 3752076 0.02416476117558924 0.1767685146565929 chrY 59373566 223683 0.003767383619841867 0.10892184155010039