BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230396.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 = 2,779,672 number of mapped reads = 2,470,278 (88.87%) number of supplementary alignments = 19,867 (0.71%) number of secondary alignments = 0 number of mapped bases = 158,837,729 bp number of sequenced bases = 158,764,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,048 duplication rate = 2.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6308 >>>>>>> ACTG content number of A's = 43,846,148 bp (27.62%) number of C's = 28,944,760 bp (18.23%) number of T's = 49,210,377 bp (31%) number of G's = 36,701,400 bp (23.12%) number of N's = 61,487 bp (0.04%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,357,586 number of insertions = 13,225 mapped reads with insertion percentage = 0.53% number of deletions = 44,413 mapped reads with deletion percentage = 1.78% homopolymer indels = 45.35% >>>>>>> Coverage mean coverageData = 0.0513X std coverageData = 0.4874X There is a 4.54% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.05% 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 0.01% 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 13695548 0.05494689620051137 0.9703608528332631 chr2 243199373 12736194 0.052369353764740174 0.5744813760151842 chr3 198022430 11380909 0.057472827699367186 0.2641270934601518 chr4 191154276 11531080 0.06032342169525938 0.29535915219269987 chr5 180915260 9593005 0.05302485262989977 0.25596013369547815 chr6 171115067 7304812 0.04268947280954517 0.27577214835098846 chr7 159138663 9210525 0.057877355674403275 0.7075494746889575 chr8 146364022 9067065 0.06194872808291644 0.5802855566076153 chr9 141213431 6354053 0.04499609530767651 0.46550371632805265 chr10 135534747 7065341 0.052129370190214026 0.4315628452141103 chr11 135006516 6873761 0.050914290685051086 0.40727736135358666 chr12 133851895 6833294 0.05105115620514749 0.2567938367788411 chr13 115169878 4793466 0.04162083075229098 0.22314231935169315 chr14 107349540 5539945 0.05160660213355362 0.27671056962838253 chr15 102531392 3907363 0.03810894325905573 0.24034944909070927 chr16 90354753 4303765 0.04763186060615981 0.30166776945804163 chr17 81195210 3760927 0.046319567373494075 0.25669730140398744 chr18 78077248 4368809 0.0559549563017385 0.8963410319629592 chr19 59128983 2908271 0.04918520245815829 0.6362245076602328 chr20 63025520 3355752 0.05324433657984892 0.27508271257883865 chr21 48129895 1977998 0.04109707698302687 0.2451431893560765 chr22 51304566 1806214 0.03520571638789421 0.2046805030165624 chrMT 16571 3558 0.2147124494598998 0.45391978429032914 chrX 155270560 9992665 0.06435646912073996 0.3323541459870455 chrY 59373566 473409 0.007973396780648142 0.16591630026961657