BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717079.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 = 582,696 number of mapped reads = 484,334 (83.12%) number of supplementary alignments = 938 (0.16%) number of secondary alignments = 0 number of mapped bases = 27,720,622 bp number of sequenced bases = 27,711,615 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,273 duplication rate = 1.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2872 >>>>>>> ACTG content number of A's = 6,501,315 bp (23.46%) number of C's = 4,802,068 bp (17.33%) number of T's = 9,340,185 bp (33.7%) number of G's = 7,067,805 bp (25.5%) number of N's = 242 bp (0%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 136,712 number of insertions = 1,845 mapped reads with insertion percentage = 0.38% number of deletions = 5,649 mapped reads with deletion percentage = 1.16% homopolymer indels = 44.38% >>>>>>> Coverage mean coverageData = 0.009X std coverageData = 0.1165X There is a 0.85% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 3186563 0.012784573965013311 0.16253169829165978 chr2 243199373 2828911 0.011632065350760588 0.1480931458046293 chr3 198022430 1778491 0.008981260355203196 0.09878168269602694 chr4 191154276 1212841 0.006344827985956223 0.08342998665668488 chr5 180915260 2044800 0.011302529150940611 0.10978777933365298 chr6 171115067 1048103 0.006125135666749907 0.08632961393514914 chr7 159138663 1883383 0.01183485499058139 0.17818538869855882 chr8 146364022 1230768 0.008408951757283631 0.1036450599233561 chr9 141213431 755128 0.005347423362300431 0.08797884136704844 chr10 135534747 1281389 0.009454320964645324 0.1314878220165536 chr11 135006516 1174073 0.008696417289962509 0.10897268883798827 chr12 133851895 1121022 0.008375092485616286 0.0948421276971135 chr13 115169878 838291 0.007278734809461203 0.08795547576151697 chr14 107349540 582194 0.005423348809878459 0.0774756743150163 chr15 102531392 1152513 0.011240586687831176 0.10989416078168884 chr16 90354753 826268 0.009144709852729053 0.10465024407773763 chr17 81195210 994867 0.012252779443516434 0.11715258191228359 chr18 78077248 889512 0.011392717120357521 0.1599692603502417 chr19 59128983 424257 0.0071751107236192446 0.11448634684753277 chr20 63025520 691349 0.010969350193381982 0.10784077399203328 chr21 48129895 353700 0.007348862905269168 0.0897892932031325 chr22 51304566 299665 0.00584090312741365 0.07860352013943275 chrMT 16571 7205 0.4347957274757106 0.725500681329221 chrX 155270560 1055022 0.006794733013135265 0.09259745036295121 chrY 59373566 60307 0.001015721373380201 0.036524999296205236