BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237330.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 = 3,429,242 number of mapped reads = 3,033,869 (88.47%) number of supplementary alignments = 32,748 (0.95%) number of secondary alignments = 0 number of mapped bases = 185,696,509 bp number of sequenced bases = 185,594,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 764,848 duplication rate = 19.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7757 >>>>>>> ACTG content number of A's = 48,147,351 bp (25.94%) number of C's = 31,465,983 bp (16.95%) number of T's = 62,816,037 bp (33.85%) number of G's = 43,145,329 bp (23.25%) number of N's = 19,408 bp (0.01%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,179,557 number of insertions = 14,100 mapped reads with insertion percentage = 0.46% number of deletions = 58,128 mapped reads with deletion percentage = 1.89% homopolymer indels = 42.21% >>>>>>> Coverage mean coverageData = 0.06X std coverageData = 0.8311X There is a 3.03% of reference with a coverageData >= 1X There is a 1.38% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 10246400 0.04110882435875656 1.0069704228510488 chr2 243199373 6872346 0.028258074497585155 1.2353643876274374 chr3 198022430 20297713 0.10250209029350867 0.5525538608145267 chr4 191154276 5700990 0.029824025490279904 0.5341094226838928 chr5 180915260 13470963 0.07446007042192018 0.47663692624159915 chr6 171115067 26248250 0.15339531731592052 1.2977697993485924 chr7 159138663 12586258 0.07908988150792746 1.1383324070888585 chr8 146364022 9643440 0.0658866835457692 1.19469468860561 chr9 141213431 7266662 0.05145871712443557 0.6282819598809786 chr10 135534747 10710196 0.07902177291849742 0.9737328905577853 chr11 135006516 4594773 0.03403371286168143 0.43441968439245343 chr12 133851895 7518253 0.0561684464758605 0.4342508477163812 chr13 115169878 7739666 0.06720217242914853 0.48612043294103663 chr14 107349540 4361900 0.040632684592779814 0.3774918083511263 chr15 102531392 4618074 0.045040586204076895 0.38502736636742707 chr16 90354753 5638925 0.06240872574794156 0.48886216580151737 chr17 81195210 3701784 0.04559116233580774 0.4372942837604005 chr18 78077248 5026252 0.06437537347627827 1.6656303637660062 chr19 59128983 2156119 0.036464672494028856 0.707323135814171 chr20 63025520 4026216 0.06388231306937253 0.4610699434271063 chr21 48129895 3178948 0.0660493441757976 0.5502656949597974 chr22 51304566 2075546 0.040455385588877214 0.33787482092270577 chrMT 16571 23769 1.43437330275783 2.3931095476681037 chrX 155270560 7328332 0.04719717633529499 0.4286675839702288 chrY 59373566 664734 0.011195790396015627 0.47389524183716336