BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525009.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 = 1,440,028 number of mapped reads = 1,318,282 (91.55%) number of supplementary alignments = 4,781 (0.33%) number of secondary alignments = 0 number of mapped bases = 75,959,163 bp number of sequenced bases = 75,935,457 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,233 duplication rate = 1.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0375 >>>>>>> ACTG content number of A's = 18,456,370 bp (24.31%) number of C's = 13,488,933 bp (17.76%) number of T's = 25,044,196 bp (32.98%) number of G's = 18,945,264 bp (24.95%) number of N's = 694 bp (0%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 375,054 number of insertions = 5,023 mapped reads with insertion percentage = 0.38% number of deletions = 14,268 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.49% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.2326X There is a 2.25% 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 7970781 0.03197898150873614 0.429267622601458 chr2 243199373 7051604 0.02899515698998122 0.2780501838940438 chr3 198022430 4136143 0.020887244944928714 0.15535095298047016 chr4 191154276 4773435 0.024971635999395586 0.17888722433347495 chr5 180915260 3263944 0.018041286290609207 0.14540878307328237 chr6 171115067 6059424 0.03541139951165142 0.24696156428534288 chr7 159138663 4737134 0.029767335672538607 0.30235739948827534 chr8 146364022 5276373 0.03604965843313598 0.23655077714478276 chr9 141213431 2092711 0.01481948979768079 0.17179363005984527 chr10 135534747 3802463 0.028055263201251263 0.22932847648261448 chr11 135006516 3148980 0.023324651974575804 0.21179016179396104 chr12 133851895 3189893 0.023831511686853595 0.16698099994806406 chr13 115169878 1457661 0.01265661668930482 0.12062686426386444 chr14 107349540 1733943 0.016152309548788005 0.14124608368847702 chr15 102531392 2095768 0.020440256970275017 0.16257863012999094 chr16 90354753 2412688 0.026702391627366852 0.18294045529591915 chr17 81195210 1908256 0.023502076046111587 0.2072738376172633 chr18 78077248 1482609 0.0189890017639966 0.27073311970652725 chr19 59128983 1868178 0.0315949624907298 0.2826616259576892 chr20 63025520 1835032 0.029115697895074885 0.18360030866938729 chr21 48129895 1312816 0.027276519094837002 0.1826999396916121 chr22 51304566 1015707 0.019797594623449304 0.1494241494896693 chrMT 16571 8823 0.5324361836944059 0.7972750780081674 chrX 155270560 3119401 0.02009009950115463 0.17299226214147578 chrY 59373566 205396 0.003459384602231909 0.09540899402195736