BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173965.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 7,241,752 number of mapped reads = 7,093,456 (97.95%) number of supplementary alignments = 1,070,671 (14.78%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,543,554 number of mapped paired reads (second in pair) = 3,549,902 number of mapped paired reads (both in pair) = 6,995,660 number of mapped paired reads (singletons) = 97,796 number of mapped bases = 806,590,314 bp number of sequenced bases = 805,983,651 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,807,694 duplication rate = 65.65% >>>>>>> Insert size mean insert size = 1,110,574.1465 std insert size = 9,800,699.9432 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 52.4358 >>>>>>> ACTG content number of A's = 240,610,934 bp (29.85%) number of C's = 160,001,774 bp (19.85%) number of T's = 238,805,623 bp (29.63%) number of G's = 166,559,267 bp (20.67%) number of N's = 6,053 bp (0%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 6,873,849 number of insertions = 89,292 mapped reads with insertion percentage = 1.21% number of deletions = 261,463 mapped reads with deletion percentage = 3.6% homopolymer indels = 40.74% >>>>>>> Coverage mean coverageData = 0.2606X std coverageData = 4.557X There is a 5.54% of reference with a coverageData >= 1X There is a 4.2% of reference with a coverageData >= 2X There is a 3.15% of reference with a coverageData >= 3X There is a 2.54% of reference with a coverageData >= 4X There is a 1.91% of reference with a coverageData >= 5X There is a 1.58% of reference with a coverageData >= 6X There is a 1.18% of reference with a coverageData >= 7X There is a 1.01% of reference with a coverageData >= 8X There is a 0.76% of reference with a coverageData >= 9X There is a 0.68% of reference with a coverageData >= 10X There is a 0.5% of reference with a coverageData >= 11X There is a 0.46% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 65324365 0.26208305816016403 2.1602415212783566 chr2 243199373 73088039 0.30052725094813465 14.858073141677531 chr3 198022430 54856001 0.27701912859063493 1.5827434779864638 chr4 191154276 55382744 0.2897279891348075 2.14445977447494 chr5 180915260 47480011 0.262443372659664 1.5267589814189133 chr6 171115067 47226238 0.2759911142132212 1.8640810785850628 chr7 159138663 45088264 0.2833268996359483 2.217463380370941 chr8 146364022 41625687 0.28439835439886996 2.5501062895206936 chr9 141213431 35210124 0.24933976712172654 2.1440358407639573 chr10 135534747 39408476 0.290762899347132 2.665365631269225 chr11 135006516 37310078 0.2763576092875399 1.6439007540019666 chr12 133851895 35557673 0.2656493806083209 1.6037637964095341 chr13 115169878 26430247 0.22948923328719684 1.4355156647809089 chr14 107349540 24499426 0.22822106177632434 1.4477156111259608 chr15 102531392 23543256 0.22961997824042027 1.4778116599695725 chr16 90354753 25526523 0.2825144461409794 2.0375103630540248 chr17 81195210 22488460 0.27696781620492145 1.7028167815272996 chr18 78077248 22809475 0.29213984335103615 2.8065759229838863 chr19 59128983 15725752 0.26595674747187853 1.89005199123582 chr20 63025520 16902797 0.26818972695504933 1.6702737300440416 chr21 48129895 11741342 0.24395112434797542 1.89555482808244 chr22 51304566 10203026 0.1988716949676565 1.5363372140466207 chrMT 16571 673352 40.63436123348018 35.932470653306645 chrX 155270560 22199845 0.14297523625856698 1.141993141258953 chrY 59373566 6289113 0.10592446140088672 1.527525480341015