BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173923.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,864,898 number of mapped reads = 2,799,921 (97.73%) number of supplementary alignments = 256,412 (8.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,399,649 number of mapped paired reads (second in pair) = 1,400,272 number of mapped paired reads (both in pair) = 2,756,680 number of mapped paired reads (singletons) = 43,241 number of mapped bases = 331,614,701 bp number of sequenced bases = 331,445,066 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,084,274 duplication rate = 64.15% >>>>>>> Insert size mean insert size = 801,772.3041 std insert size = 8,400,720.6364 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.8611 >>>>>>> ACTG content number of A's = 99,940,261 bp (30.15%) number of C's = 65,026,275 bp (19.62%) number of T's = 99,510,977 bp (30.02%) number of G's = 66,963,784 bp (20.2%) number of N's = 3,769 bp (0%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 3,290,461 number of insertions = 33,901 mapped reads with insertion percentage = 1.17% number of deletions = 66,915 mapped reads with deletion percentage = 2.33% homopolymer indels = 44.11% >>>>>>> Coverage mean coverageData = 0.1071X std coverageData = 1.6533X There is a 2.46% of reference with a coverageData >= 1X There is a 1.92% of reference with a coverageData >= 2X There is a 1.44% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.84% of reference with a coverageData >= 5X There is a 0.66% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 28836925 0.11569449610318122 1.3535092887537938 chr2 243199373 34396062 0.14143154061503274 4.497379423804139 chr3 198022430 21419235 0.10816570122889614 0.8968298007195059 chr4 191154276 20361037 0.1065162518258289 1.028546468183453 chr5 180915260 24208725 0.13381250979049528 1.002294163310102 chr6 171115067 19399847 0.11337310816703242 0.9318488229915424 chr7 159138663 24248921 0.15237605081550798 1.7091093313632775 chr8 146364022 12413197 0.08481043927584882 0.9148402039027501 chr9 141213431 13954274 0.09881690361308479 0.9497037426747607 chr10 135534747 17290887 0.1275753073121537 1.8368562349610784 chr11 135006516 15689004 0.11620923541201522 0.9318394539905537 chr12 133851895 11108156 0.08298841043677417 0.7827100824231148 chr13 115169878 9227353 0.08011949964903149 0.7775610744151111 chr14 107349540 7961963 0.07416858050812328 0.7368903126080744 chr15 102531392 10898525 0.10629451904837106 0.8804434499191494 chr16 90354753 13287499 0.14705921447209314 1.3608430581257316 chr17 81195210 7650985 0.09422951181479794 0.9030616394834993 chr18 78077248 5557343 0.07117749590764265 1.0918288899050497 chr19 59128983 5867669 0.09923507393996613 1.388413664342147 chr20 63025520 7706599 0.12227743618775379 0.9435154177612453 chr21 48129895 4665142 0.09692815660620079 0.8677353714696527 chr22 51304566 2733491 0.0532796827479254 0.5907946425315522 chrMT 16571 1292222 77.9809305413071 66.24137300260185 chrX 155270560 11005987 0.07088263866633829 0.7187978232547031 chrY 59373566 433653 0.007303805872128348 0.37829099419143486