BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716729.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 = 1,995,783 number of mapped reads = 1,720,960 (86.23%) number of supplementary alignments = 47,605 (2.39%) number of secondary alignments = 0 number of mapped bases = 131,205,354 bp number of sequenced bases = 131,156,287 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,036 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5183 >>>>>>> ACTG content number of A's = 34,054,604 bp (25.96%) number of C's = 25,808,637 bp (19.68%) number of T's = 39,413,203 bp (30.05%) number of G's = 31,863,700 bp (24.29%) number of N's = 16,143 bp (0.01%) GC percentage = 43.97% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 939,293 number of insertions = 9,950 mapped reads with insertion percentage = 0.57% number of deletions = 27,830 mapped reads with deletion percentage = 1.59% homopolymer indels = 42.09% >>>>>>> Coverage mean coverageData = 0.0424X std coverageData = 0.358X There is a 3.69% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12566836 0.05041847418305931 0.484909328689812 chr2 243199373 10523873 0.04327261567405439 0.5841129775665092 chr3 198022430 10602508 0.05354195481794664 0.2664305439480176 chr4 191154276 5437669 0.028446494181485118 0.20598200943893039 chr5 180915260 8906808 0.04923193322663882 0.25163186335439347 chr6 171115067 8616640 0.050355822845220284 0.2942333593027599 chr7 159138663 6168258 0.03876027285713717 0.47164218973920086 chr8 146364022 8369522 0.05718291890065716 0.4538654367994897 chr9 141213431 6730052 0.047658724473594864 0.34642995435359253 chr10 135534747 7139697 0.052677982274169144 0.36995899339284744 chr11 135006516 5845599 0.04329864345214271 0.3080309916123009 chr12 133851895 4625089 0.03455378050493794 0.20663731733383076 chr13 115169878 3913265 0.03397819870921458 0.2035031673727109 chr14 107349540 2655042 0.02473268166775563 0.20585079005069232 chr15 102531392 2960632 0.028875371164374712 0.1890122777429798 chr16 90354753 3367606 0.037270933605451834 0.23759212444247432 chr17 81195210 4033963 0.0496822780555651 0.28753425947790134 chr18 78077248 4071970 0.05215309330574766 0.6201575183471915 chr19 59128983 2340524 0.039583363035349345 0.4504453380281803 chr20 63025520 2296415 0.03643627216403768 0.23342739771473975 chr21 48129895 3125440 0.06493760271033211 0.29953257473395806 chr22 51304566 1895040 0.0369370632625564 0.21819208395924175 chrMT 16571 6618 0.39937239756200593 1.1988053569504529 chrX 155270560 4731317 0.030471436439721736 0.2355334096142958 chrY 59373566 274971 0.004631202377165623 0.1399610097270906