BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240044.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 = 1,961,429 number of mapped reads = 1,684,541 (85.88%) number of supplementary alignments = 12,303 (0.63%) number of secondary alignments = 0 number of mapped bases = 109,447,022 bp number of sequenced bases = 109,402,369 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,038 duplication rate = 4.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8106 >>>>>>> ACTG content number of A's = 30,883,630 bp (28.23%) number of C's = 19,849,583 bp (18.14%) number of T's = 34,839,062 bp (31.84%) number of G's = 23,756,224 bp (21.71%) number of N's = 73,870 bp (0.07%) GC percentage = 39.86% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 972,777 number of insertions = 7,552 mapped reads with insertion percentage = 0.44% number of deletions = 25,467 mapped reads with deletion percentage = 1.5% homopolymer indels = 46.9% >>>>>>> Coverage mean coverageData = 0.0354X std coverageData = 0.6201X There is a 2.68% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 7795000 0.031273743546661015 1.6732401403235146 chr2 243199373 6222391 0.025585555271970213 0.31603351731954754 chr3 198022430 5633072 0.02844663607046939 0.20976753071590395 chr4 191154276 10133229 0.053010736730785976 0.2926159375261817 chr5 180915260 8248073 0.045590808647098094 0.27158766396103406 chr6 171115067 12088641 0.07064626868889343 0.5718779826572378 chr7 159138663 3770159 0.02369103100985585 0.31864643975193846 chr8 146364022 10808585 0.07384728058374893 0.8027947141835556 chr9 141213431 2695940 0.01909124352342944 0.3415854702945273 chr10 135534747 2981493 0.021997997310608475 0.27784517117645463 chr11 135006516 3336071 0.02471044434625659 0.2841495543626977 chr12 133851895 2873007 0.0214640741544974 0.1926472545874195 chr13 115169878 3056383 0.026538041483381618 0.20234825841262483 chr14 107349540 2911439 0.027121112954932084 0.22467347804947335 chr15 102531392 4389449 0.04281078130686063 0.2578833271015248 chr16 90354753 2606690 0.028849506123933513 0.2468508664138786 chr17 81195210 1855973 0.02285815875099036 0.20699404038361052 chr18 78077248 5600651 0.07173217734313586 0.743557429767976 chr19 59128983 2705248 0.0457516409507669 1.493151846252549 chr20 63025520 1664275 0.026406366817758903 0.2088467854813634 chr21 48129895 1070593 0.022243825796835835 0.19505533465051375 chr22 51304566 2305194 0.04493155638427972 0.2602154752297125 chrMT 16571 57529 3.471667370707863 2.816005972688066 chrX 155270560 4351483 0.028025164590119337 0.2437599242708639 chrY 59373566 286454 0.004824604942879799 0.13027911696766034