BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234143.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 889,693 number of mapped reads = 477,886 (53.71%) number of supplementary alignments = 4,232 (0.48%) number of secondary alignments = 0 number of mapped bases = 30,299,026 bp number of sequenced bases = 30,271,693 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,726 duplication rate = 4.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9759 >>>>>>> ACTG content number of A's = 8,459,097 bp (27.94%) number of C's = 5,056,641 bp (16.7%) number of T's = 10,121,834 bp (33.44%) number of G's = 6,628,313 bp (21.9%) number of N's = 5,808 bp (0.02%) GC percentage = 38.6% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 305,513 number of insertions = 2,747 mapped reads with insertion percentage = 0.57% number of deletions = 15,486 mapped reads with deletion percentage = 3.17% homopolymer indels = 42.26% >>>>>>> Coverage mean coverageData = 0.0098X std coverageData = 0.1508X There is a 0.82% of reference with a coverageData >= 1X There is a 0.12% 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 1768451 0.007095071590614011 0.13637128373385002 chr2 243199373 2038478 0.008381921280693433 0.13238255994036527 chr3 198022430 2719575 0.013733671483578905 0.1378031061558054 chr4 191154276 1934648 0.010120872211092992 0.11968519991098586 chr5 180915260 2343112 0.01295143372648609 0.13456987412953134 chr6 171115067 1473881 0.008613391128204976 0.11311199810894768 chr7 159138663 1975852 0.012415914289791413 0.15321523850132318 chr8 146364022 839885 0.005738329601245858 0.378373253046098 chr9 141213431 1125441 0.007969787236456282 0.11773898012923541 chr10 135534747 1687357 0.01244962666289553 0.14505595646608788 chr11 135006516 1197402 0.00886921635693495 0.11640429320310246 chr12 133851895 1255332 0.009378514962376888 0.11545484621344947 chr13 115169878 1213264 0.010534560086969963 0.12168584189895956 chr14 107349540 1164468 0.01084744284884686 0.12507159759332345 chr15 102531392 880909 0.008591602852714611 0.10917315223934301 chr16 90354753 810111 0.008965892474964765 0.11251100508056316 chr17 81195210 582918 0.007179216606496861 0.0989176986033249 chr18 78077248 1166831 0.014944571304562374 0.21631835595757745 chr19 59128983 404695 0.006844274659687619 0.1230175702820115 chr20 63025520 762275 0.012094703859642888 0.12996229766310938 chr21 48129895 566455 0.011769296400916727 0.1276943226704577 chr22 51304566 290835 0.005668793689824801 0.08663575662940572 chrMT 16571 3847 0.23215255566954318 0.657458277515175 chrX 155270560 1970356 0.012689823492618305 0.13473907261438947 chrY 59373566 122648 0.002065700416242474 0.06204352798905983