BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525225.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 = 559,898 number of mapped reads = 514,843 (91.95%) number of supplementary alignments = 1,220 (0.22%) number of secondary alignments = 0 number of mapped bases = 29,751,654 bp number of sequenced bases = 29,742,234 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,124 duplication rate = 1.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7394 >>>>>>> ACTG content number of A's = 7,214,181 bp (24.26%) number of C's = 5,335,351 bp (17.94%) number of T's = 9,248,728 bp (31.1%) number of G's = 7,943,313 bp (26.71%) number of N's = 661 bp (0%) GC percentage = 44.65% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 152,892 number of insertions = 2,044 mapped reads with insertion percentage = 0.4% number of deletions = 5,874 mapped reads with deletion percentage = 1.13% homopolymer indels = 41.82% >>>>>>> Coverage mean coverageData = 0.0096X std coverageData = 0.1245X There is a 0.91% 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 2472399 0.009919329348431193 0.20292811982746548 chr2 243199373 2545247 0.010465680764727958 0.1478409084787102 chr3 198022430 1978716 0.009992383186086546 0.10353471545017268 chr4 191154276 1891830 0.009896875129280393 0.1066978183996794 chr5 180915260 1727841 0.009550554220799284 0.10100969228859275 chr6 171115067 1648493 0.009633827277173669 0.1059401756804807 chr7 159138663 1651751 0.010379319323551186 0.15336397358365206 chr8 146364022 1479594 0.010109000694173326 0.11254649856303188 chr9 141213431 1212315 0.008584983676234026 0.10477893790984304 chr10 135534747 1469353 0.010841153523531497 0.1257706947318251 chr11 135006516 1356153 0.010045092934625466 0.11373854806844501 chr12 133851895 1324654 0.009896415736213521 0.10337586522444449 chr13 115169878 928598 0.008062854768327531 0.09326704158940177 chr14 107349540 914052 0.008514726751507272 0.09660290791931599 chr15 102531392 855283 0.00834166964201559 0.09450639368082646 chr16 90354753 903201 0.00999616478393782 0.10812743007150617 chr17 81195210 820296 0.010102763451193734 0.10494017120655703 chr18 78077248 796884 0.010206353584593555 0.15991642788436614 chr19 59128983 643351 0.010880467874781476 0.1531877239039413 chr20 63025520 658697 0.01045127434093364 0.10652900736947624 chr21 48129895 396880 0.008246018404985093 0.0969410787666444 chr22 51304566 380531 0.0074170981194929125 0.0889745734549961 chrMT 16571 5238 0.3160943817512522 0.6608955462151997 chrX 155270560 1587884 0.010226561944518008 0.10811694347542221 chrY 59373566 102413 0.0017248921851855756 0.06341592306126254