BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156411.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 = 14,553,040 number of mapped reads = 14,228,151 (97.77%) number of supplementary alignments = 1,966,476 (13.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,112,979 number of mapped paired reads (second in pair) = 7,115,172 number of mapped paired reads (both in pair) = 14,012,000 number of mapped paired reads (singletons) = 216,151 number of mapped bases = 1,616,449,561 bp number of sequenced bases = 1,615,376,915 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,732,421 duplication rate = 67.01% >>>>>>> Insert size mean insert size = 1,134,337.7094 std insert size = 9,862,170.6652 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.5547 >>>>>>> ACTG content number of A's = 480,223,580 bp (29.73%) number of C's = 322,223,253 bp (19.95%) number of T's = 476,885,541 bp (29.52%) number of G's = 336,032,110 bp (20.8%) number of N's = 12,431 bp (0%) GC percentage = 40.75% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 13,525,770 number of insertions = 174,898 mapped reads with insertion percentage = 1.18% number of deletions = 456,512 mapped reads with deletion percentage = 3.13% homopolymer indels = 41.21% >>>>>>> Coverage mean coverageData = 0.5222X std coverageData = 9.5561X There is a 10.23% of reference with a coverageData >= 1X There is a 7.98% of reference with a coverageData >= 2X There is a 6.17% of reference with a coverageData >= 3X There is a 5.03% of reference with a coverageData >= 4X There is a 3.88% of reference with a coverageData >= 5X There is a 3.21% of reference with a coverageData >= 6X There is a 2.46% of reference with a coverageData >= 7X There is a 2.11% of reference with a coverageData >= 8X There is a 1.62% of reference with a coverageData >= 9X There is a 1.44% of reference with a coverageData >= 10X There is a 1.1% of reference with a coverageData >= 11X There is a 1% of reference with a coverageData >= 12X There is a 0.76% of reference with a coverageData >= 13X There is a 0.7% of reference with a coverageData >= 14X There is a 0.53% of reference with a coverageData >= 15X There is a 0.48% of reference with a coverageData >= 16X There is a 0.37% of reference with a coverageData >= 17X There is a 0.34% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.19% of reference with a coverageData >= 21X There is a 0.17% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% 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 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 132074581 0.5298866677648117 4.277500161967494 chr2 243199373 150204832 0.6176201449335151 32.2563746360886 chr3 198022430 108404735 0.5474366464445467 2.276961778244429 chr4 191154276 107535305 0.5625576746187985 3.5661239557346742 chr5 180915260 100432951 0.555138085090224 2.30718656808456 chr6 171115067 96784833 0.5656125711010591 3.1743866944843497 chr7 159138663 88597259 0.5567299443756166 3.8494812446918245 chr8 146364022 82520139 0.5638007064331697 4.099998499614466 chr9 141213431 70255933 0.4975159409589021 3.7405080549194762 chr10 135534747 79552424 0.5869522447996306 4.523084507374888 chr11 135006516 73827053 0.5468406650831579 2.5619709889180866 chr12 133851895 74363563 0.5555660082361927 2.4497756879061545 chr13 115169878 50158572 0.4355181482435885 2.0485057064304772 chr14 107349540 49789805 0.4638101383573698 2.1931930254119765 chr15 102531392 47572949 0.46398423031260516 2.2185534116250594 chr16 90354753 48720848 0.5392173226349255 3.1193666955782287 chr17 81195210 45964072 0.5660933939329672 2.7486145947511615 chr18 78077248 43655552 0.5591328218945422 4.799282273766557 chr19 59128983 31181377 0.5273450585138595 3.1279157679140734 chr20 63025520 36683781 0.5820464630835255 2.530859172350578 chr21 48129895 21827724 0.4535169669495435 3.0041208497346914 chr22 51304566 20561141 0.4007662982667079 2.400589884315609 chrMT 16571 1785206 107.73073441554523 88.1406184388485 chrX 155270560 43131357 0.27778193754179803 1.6546713781494706 chrY 59373566 10863569 0.18296979164094676 2.6442560565148097