BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234110.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 = 5,435,760 number of mapped reads = 5,087,557 (93.59%) number of supplementary alignments = 30,695 (0.56%) number of secondary alignments = 0 number of mapped bases = 347,379,997 bp number of sequenced bases = 347,249,972 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 399,929 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6641 >>>>>>> ACTG content number of A's = 92,312,583 bp (26.58%) number of C's = 66,110,113 bp (19.04%) number of T's = 99,427,370 bp (28.63%) number of G's = 89,321,827 bp (25.72%) number of N's = 78,079 bp (0.02%) GC percentage = 44.76% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 2,347,840 number of insertions = 25,797 mapped reads with insertion percentage = 0.5% number of deletions = 79,100 mapped reads with deletion percentage = 1.54% homopolymer indels = 46.35% >>>>>>> Coverage mean coverageData = 0.1122X std coverageData = 25.4432X There is a 8.31% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% 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 31976448 0.1282903443598642 1.9116875890440301 chr2 243199373 44172361 0.18163024211415216 90.71545864939402 chr3 198022430 28701961 0.14494297943924836 0.47843593637816273 chr4 191154276 16487897 0.08625439799212234 0.4378053129604377 chr5 180915260 18867415 0.1042886874219455 0.4224175940636971 chr6 171115067 20541365 0.12004416303095039 0.5746579671783828 chr7 159138663 15537099 0.09763245905867639 1.356488736241852 chr8 146364022 20113870 0.13742359444044247 1.0822010371250779 chr9 141213431 18045143 0.12778630808849903 1.1109916020193835 chr10 135534747 16578933 0.12232238128573775 0.7411525903390469 chr11 135006516 10194426 0.0755106220206438 0.8444198083823352 chr12 133851895 13225940 0.09881025591755724 0.4402640448383795 chr13 115169878 10565335 0.09173696441703272 0.37376900094816423 chr14 107349540 8405165 0.07829716829713476 0.7083665364578428 chr15 102531392 9134642 0.08909117316967666 0.378073955549231 chr16 90354753 10750649 0.1189826615983334 0.6050372681312896 chr17 81195210 12229478 0.15061821996642413 0.607490508291533 chr18 78077248 9002892 0.11530749649372887 2.278946208712961 chr19 59128983 7776954 0.13152524541137464 1.3667333455571444 chr20 63025520 4935352 0.07830720000406184 0.3869939365077025 chr21 48129895 4992004 0.10371940350171135 0.5961468781371709 chr22 51304566 3277519 0.06388357324765206 0.3892665870817796 chrMT 16571 8464 0.5107718303059562 0.8533432143151475 chrX 155270560 9309937 0.059959447560439014 0.46588101104337165 chrY 59373566 2548748 0.042927318867793794 0.37958162207904195