BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240256.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 = 1,722,639 number of mapped reads = 1,410,366 (81.87%) number of supplementary alignments = 6,437 (0.37%) number of secondary alignments = 0 number of mapped bases = 87,236,124 bp number of sequenced bases = 87,187,339 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,346 duplication rate = 6.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8024 >>>>>>> ACTG content number of A's = 24,004,596 bp (27.53%) number of C's = 15,016,738 bp (17.22%) number of T's = 28,641,975 bp (32.85%) number of G's = 19,501,806 bp (22.37%) number of N's = 22,224 bp (0.03%) GC percentage = 39.59% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 784,344 number of insertions = 5,874 mapped reads with insertion percentage = 0.41% number of deletions = 28,377 mapped reads with deletion percentage = 1.99% homopolymer indels = 49.6% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.3039X There is a 2.19% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 5589801 0.022426427575480343 0.4621503495203127 chr2 243199373 8211757 0.03376553524256002 0.305359211993822 chr3 198022430 6405607 0.032347886045030354 0.2238311087187206 chr4 191154276 5915196 0.03094461773902458 0.22145685774071053 chr5 180915260 4959412 0.02741290038220104 0.207091443489492 chr6 171115067 4705345 0.027498133755807723 0.27077099746550926 chr7 159138663 5989434 0.03763657358363002 0.6064798708168193 chr8 146364022 6788171 0.0463786858767792 0.4122576882711539 chr9 141213431 2951931 0.020904038511747512 0.2429699216487536 chr10 135534747 4482012 0.03306909924729486 0.27911499538975343 chr11 135006516 4315792 0.031967286675259436 0.2913239850653474 chr12 133851895 3944444 0.029468719886259362 0.21222763635568664 chr13 115169878 1646427 0.014295639003802712 0.14549751006342546 chr14 107349540 3115820 0.029024996287827596 0.22027619982222282 chr15 102531392 2220891 0.021660595420376228 0.18714224352261027 chr16 90354753 2147781 0.023770537007610434 0.1962106915341457 chr17 81195210 2201585 0.027114715264607358 0.24020535864594633 chr18 78077248 1836543 0.023522127726632987 0.3773915879992046 chr19 59128983 1453614 0.024583781527241895 0.31092565452654186 chr20 63025520 1664724 0.02641349091606067 0.20402242842489018 chr21 48129895 1685477 0.03501933673447657 0.23854376322224008 chr22 51304566 717608 0.013987215095046315 0.14316894448788245 chrMT 16571 15109 0.911773580351216 1.3349441124151544 chrX 155270560 4110690 0.026474368354181245 0.21923209679136513 chrY 59373566 160953 0.0027108528397974275 0.06887658621981411