BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008701.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 = 1,837,552 number of mapped reads = 1,460,454 (79.48%) number of supplementary alignments = 15,059 (0.82%) number of secondary alignments = 0 number of mapped bases = 93,863,347 bp number of sequenced bases = 93,818,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,937 duplication rate = 5.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5229 >>>>>>> ACTG content number of A's = 27,591,731 bp (29.41%) number of C's = 17,945,762 bp (19.13%) number of T's = 28,470,207 bp (30.35%) number of G's = 19,790,924 bp (21.09%) number of N's = 19,836 bp (0.02%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 781,362 number of insertions = 8,116 mapped reads with insertion percentage = 0.55% number of deletions = 28,090 mapped reads with deletion percentage = 1.9% homopolymer indels = 47.72% >>>>>>> Coverage mean coverageData = 0.0303X std coverageData = 0.3269X There is a 2.12% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 6590793 0.026442433617848437 0.5498897646677346 chr2 243199373 7890768 0.032445675754270965 0.36400878161440026 chr3 198022430 6092737 0.030767913513635805 0.23663783380674203 chr4 191154276 5265903 0.027547921554211006 0.23097075782289414 chr5 180915260 6781919 0.03748671615650333 0.2610471065902944 chr6 171115067 5117478 0.029906647554303327 0.26610784929530396 chr7 159138663 5564699 0.03496761186186414 0.34157231796951726 chr8 146364022 6639626 0.04536378482411477 0.5201301476293145 chr9 141213431 3647588 0.025830319213758075 0.30529786494665584 chr10 135534747 4600647 0.03394440984200162 0.3093088334900524 chr11 135006516 3958313 0.029319421886273993 0.28072584648327004 chr12 133851895 5917411 0.044208645682603145 0.28854693330641734 chr13 115169878 2615817 0.022712683606385342 0.20323748027071944 chr14 107349540 2458931 0.022905836392032978 0.21440481508257153 chr15 102531392 2505271 0.024434184995752325 0.2098871683081091 chr16 90354753 2147572 0.023768223902952842 0.2192678337469483 chr17 81195210 2564817 0.03158827965344261 0.24856765124376196 chr18 78077248 2798399 0.03584141439001538 0.5013597424889343 chr19 59128983 1415793 0.023944145969836822 0.40033435049497396 chr20 63025520 1835813 0.029128089700806912 0.2306475425943457 chr21 48129895 1123676 0.023346736991634826 0.21797160653191275 chr22 51304566 884295 0.01723618517696846 0.17210773666671894 chrMT 16571 43036 2.597067165530143 2.2077722626440472 chrX 155270560 5142888 0.03312210634134378 0.2617082021805529 chrY 59373566 259157 0.004364854891821725 0.10449078243311871