BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716643.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 = 1,407,992 number of mapped reads = 1,251,087 (88.86%) number of supplementary alignments = 5,273 (0.37%) number of secondary alignments = 0 number of mapped bases = 70,794,666 bp number of sequenced bases = 70,775,920 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,475 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1859 >>>>>>> ACTG content number of A's = 16,567,351 bp (23.41%) number of C's = 14,178,539 bp (20.03%) number of T's = 22,819,992 bp (32.24%) number of G's = 17,208,434 bp (24.31%) number of N's = 1,604 bp (0%) GC percentage = 44.35% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 350,883 number of insertions = 4,419 mapped reads with insertion percentage = 0.35% number of deletions = 11,229 mapped reads with deletion percentage = 0.89% homopolymer indels = 42.02% >>>>>>> Coverage mean coverageData = 0.0229X std coverageData = 0.199X There is a 2.1% of reference with a coverageData >= 1X There is a 0.14% 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 7836045 0.03143841715844712 0.3083484861743735 chr2 243199373 5833801 0.02398773042889383 0.2217513328730293 chr3 198022430 4530481 0.02287862541632279 0.16373466047824559 chr4 191154276 4409277 0.023066588371792426 0.17279714614253425 chr5 180915260 4392995 0.02428205890426269 0.17028442628942136 chr6 171115067 3680335 0.0215079540599426 0.16758219229694063 chr7 159138663 3026638 0.019018872868122563 0.16685684767300174 chr8 146364022 4389533 0.029990519118147766 0.20662984610901244 chr9 141213431 2546037 0.018029708519722888 0.19337551896611999 chr10 135534747 3328584 0.024558897800576556 0.21247128693856013 chr11 135006516 2204732 0.0163305599264557 0.16942756151781155 chr12 133851895 3133747 0.023412048069995573 0.16611215251299344 chr13 115169878 2147662 0.018647775245537727 0.14539504768047978 chr14 107349540 2414526 0.022492187670296492 0.171981257660287 chr15 102531392 2014852 0.019651074277817277 0.15010894248573325 chr16 90354753 2090923 0.023141261865881033 0.1759089625981858 chr17 81195210 1594804 0.01964160201075901 0.1535399571522501 chr18 78077248 1680485 0.021523363630849283 0.3469052728714445 chr19 59128983 1393362 0.023564788861665353 0.23786466249313745 chr20 63025520 2264878 0.03593588755792892 0.2087804731961519 chr21 48129895 891142 0.018515353087722296 0.15771233670520188 chr22 51304566 867344 0.01690578573454846 0.13908867220171414 chrMT 16571 6232 0.37607869169030234 0.6675436186003546 chrX 155270560 3912505 0.0251979834425792 0.1868619739960498 chrY 59373566 203746 0.003431594457371821 0.08192803716147193