BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230366.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 = 3,013,709 number of mapped reads = 2,891,186 (95.93%) number of supplementary alignments = 23,482 (0.78%) number of secondary alignments = 0 number of mapped bases = 209,756,105 bp number of sequenced bases = 209,650,032 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 189,349 duplication rate = 4.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1683 >>>>>>> ACTG content number of A's = 62,811,734 bp (29.96%) number of C's = 42,813,846 bp (20.42%) number of T's = 61,439,196 bp (29.31%) number of G's = 42,461,449 bp (20.25%) number of N's = 123,807 bp (0.06%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,831,630 number of insertions = 19,458 mapped reads with insertion percentage = 0.67% number of deletions = 61,982 mapped reads with deletion percentage = 2.12% homopolymer indels = 47.19% >>>>>>> Coverage mean coverageData = 0.0678X std coverageData = 0.893X There is a 2.53% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 0.92% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 18814379 0.0754837798378043 1.938895042594279 chr2 243199373 29006219 0.1192693000898485 0.9666180818105067 chr3 198022430 5439972 0.027471494012067218 0.34367572918739525 chr4 191154276 20298649 0.10618987670461529 0.7700097734975407 chr5 180915260 14898708 0.08235185909690537 0.6092914292052087 chr6 171115067 5762544 0.03367642663518345 0.412250908316121 chr7 159138663 11832763 0.07435504846487243 1.3023203661262133 chr8 146364022 12977826 0.088668142776235 0.823362065051803 chr9 141213431 10367613 0.07341803769359587 0.7449694994778773 chr10 135534747 9448112 0.06970988775299075 0.8054581712495099 chr11 135006516 3840397 0.028446012190996767 0.4084404163165086 chr12 133851895 9505137 0.07101234539862136 0.5679084979208384 chr13 115169878 4133831 0.0358933348874434 0.3938018982561355 chr14 107349540 4822979 0.044927803137302685 0.5014195434013492 chr15 102531392 379242 0.00369878914742521 0.09874537836134754 chr16 90354753 6833437 0.07562897106254056 0.6246820052495425 chr17 81195210 4618948 0.056886951828808624 0.5106686572326065 chr18 78077248 5385588 0.06897768732832386 1.4410844571927781 chr19 59128983 6221352 0.10521662447669698 1.1060985982383043 chr20 63025520 4662788 0.07398253913652755 0.5977948876321781 chr21 48129895 3538371 0.07351711446700641 0.6602549903386583 chr22 51304566 3138666 0.061177127977264247 0.5078583905455955 chrMT 16571 5103 0.3079476193349828 0.8956658558634346 chrX 155270560 13209731 0.08507556744820138 0.6494911644265083 chrY 59373566 613750 0.010337091762350942 0.3775770360495207