BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008682.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 = 2,300,433 number of mapped reads = 1,991,418 (86.57%) number of supplementary alignments = 13,097 (0.57%) number of secondary alignments = 0 number of mapped bases = 127,982,486 bp number of sequenced bases = 127,891,029 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,991 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9529 >>>>>>> ACTG content number of A's = 34,125,665 bp (26.68%) number of C's = 24,318,747 bp (19.02%) number of T's = 39,568,016 bp (30.94%) number of G's = 29,837,192 bp (23.33%) number of N's = 41,409 bp (0.03%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,101,776 number of insertions = 7,800 mapped reads with insertion percentage = 0.39% number of deletions = 51,868 mapped reads with deletion percentage = 2.56% homopolymer indels = 41.52% >>>>>>> Coverage mean coverageData = 0.0413X std coverageData = 0.3816X There is a 3.48% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% 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 12800619 0.051356417683709604 0.7361300117133758 chr2 243199373 11028628 0.045348093886738765 0.4085717462757038 chr3 198022430 10768174 0.05437855701498057 0.2868137201557663 chr4 191154276 6275465 0.03282932054316169 0.21729372138885805 chr5 180915260 6498437 0.035919783660040616 0.21646550251863722 chr6 171115067 4867426 0.028445338480918222 0.202784482048755 chr7 159138663 8047125 0.05056675008008582 0.4932638952934563 chr8 146364022 8403848 0.057417443748573674 0.366532637566044 chr9 141213431 2849015 0.02017524097973372 0.24649274557245313 chr10 135534747 8476925 0.0625442935308685 0.7110044631098322 chr11 135006516 5834465 0.04321617335862515 0.32811977272722803 chr12 133851895 4825727 0.036052735749463986 0.21719828971687136 chr13 115169878 3029558 0.02630512467852054 0.1822345691902367 chr14 107349540 5332121 0.04967064600369969 0.2569434705295633 chr15 102531392 2584681 0.02520867950373677 0.18351277984290149 chr16 90354753 3549815 0.03928752923490367 0.2542132321884028 chr17 81195210 4146816 0.051072175316745905 0.30820353872003814 chr18 78077248 1269632 0.016261228879378534 0.4039021346584273 chr19 59128983 3215942 0.05438858977161843 0.4984866188569225 chr20 63025520 3723321 0.059076402701635784 0.2820782188347452 chr21 48129895 1368309 0.028429503118591885 0.20383787702239592 chr22 51304566 2131140 0.04153899284519822 0.2334602710845987 chrMT 16571 7209 0.4350371130287852 0.8151268017428583 chrX 155270560 6606266 0.04254680346357996 0.2571320706386971 chrY 59373566 341822 0.005757141149312137 0.18782454897999412