BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716137.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 = 545,596 number of mapped reads = 479,405 (87.87%) number of supplementary alignments = 1,459 (0.27%) number of secondary alignments = 0 number of mapped bases = 27,349,264 bp number of sequenced bases = 27,341,181 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,627 duplication rate = 1.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6458 >>>>>>> ACTG content number of A's = 6,773,887 bp (24.78%) number of C's = 5,245,995 bp (19.19%) number of T's = 8,698,342 bp (31.81%) number of G's = 6,622,725 bp (24.22%) number of N's = 232 bp (0%) GC percentage = 43.41% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 136,350 number of insertions = 1,764 mapped reads with insertion percentage = 0.37% number of deletions = 5,147 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 0.0088X std coverageData = 0.1112X There is a 0.84% 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 3260083 0.013079538124801704 0.15034718609822312 chr2 243199373 2808890 0.01154974194773109 0.14291285005154317 chr3 198022430 1628344 0.008223028068082994 0.09442528811051792 chr4 191154276 1152135 0.006027252040127002 0.08173472603432526 chr5 180915260 2033155 0.011238161999159165 0.10935574958127411 chr6 171115067 1081561 0.0063206649125760505 0.08647809933117688 chr7 159138663 1805247 0.011343861799316486 0.14771076324274188 chr8 146364022 1289574 0.008810730822906739 0.10198794188925538 chr9 141213431 654367 0.004633886418353507 0.08221873314553899 chr10 135534747 1257754 0.009279937638427141 0.12881389152356115 chr11 135006516 1221195 0.009045452295058114 0.10975860092844553 chr12 133851895 1168802 0.00873205418571026 0.09638696041599856 chr13 115169878 793966 0.0068938685512890795 0.08536265643043532 chr14 107349540 397717 0.0037048784745607665 0.06428629646872734 chr15 102531392 1087287 0.010604430299746637 0.10765256010066579 chr16 90354753 867596 0.009602106930666945 0.10645350299740022 chr17 81195210 1063386 0.013096659273373392 0.12126922929569635 chr18 78077248 802556 0.010278999587690386 0.1470995893230257 chr19 59128983 491367 0.008310087119205145 0.1273821269256052 chr20 63025520 660947 0.010486974165385705 0.10628989675924508 chr21 48129895 375223 0.007796048588927942 0.09171218970482974 chr22 51304566 351653 0.0068542242419514865 0.08533573921066144 chrMT 16571 186 0.011224428217971155 0.10534913587282416 chrX 155270560 1031213 0.006641394221802253 0.08793220689226644 chrY 59373566 65060 0.0010957738330892909 0.03717288691089669