BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174023.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 = 7,511,000 number of mapped reads = 7,294,176 (97.11%) number of supplementary alignments = 760,088 (10.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,653,479 number of mapped paired reads (second in pair) = 3,640,697 number of mapped paired reads (both in pair) = 7,148,678 number of mapped paired reads (singletons) = 145,498 number of mapped bases = 855,066,876 bp number of sequenced bases = 854,588,696 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,640,398 duplication rate = 64.49% >>>>>>> Insert size mean insert size = 796,057.9847 std insert size = 8,315,566.9961 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.5773 >>>>>>> ACTG content number of A's = 257,323,955 bp (30.11%) number of C's = 167,051,959 bp (19.55%) number of T's = 256,879,327 bp (30.06%) number of G's = 173,323,234 bp (20.28%) number of N's = 10,221 bp (0%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 8,863,941 number of insertions = 90,612 mapped reads with insertion percentage = 1.2% number of deletions = 192,136 mapped reads with deletion percentage = 2.57% homopolymer indels = 43.03% >>>>>>> Coverage mean coverageData = 0.2762X std coverageData = 4.0937X There is a 5.76% of reference with a coverageData >= 1X There is a 4.53% of reference with a coverageData >= 2X There is a 3.48% of reference with a coverageData >= 3X There is a 2.85% of reference with a coverageData >= 4X There is a 2.17% of reference with a coverageData >= 5X There is a 1.76% of reference with a coverageData >= 6X There is a 1.3% of reference with a coverageData >= 7X There is a 1.06% of reference with a coverageData >= 8X There is a 0.79% of reference with a coverageData >= 9X There is a 0.66% of reference with a coverageData >= 10X There is a 0.49% of reference with a coverageData >= 11X There is a 0.42% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 69303621 0.2780479371403452 3.044355325136094 chr2 243199373 77166646 0.3172978821783393 12.529787709270899 chr3 198022430 65051617 0.32850630607855885 1.697692606882618 chr4 191154276 45170153 0.23630207989697286 1.8515218341539026 chr5 180915260 55386861 0.306148088337048 1.5853990814787402 chr6 171115067 50794921 0.29684657166981093 1.940618410777241 chr7 159138663 48076877 0.30210682994113125 2.525077445226415 chr8 146364022 47273588 0.32298639620602937 2.46475343604522 chr9 141213431 32112926 0.22740702334468454 2.069912823685177 chr10 135534747 33293126 0.24564273543816775 3.948646006788283 chr11 135006516 31744558 0.23513352496260254 1.465993499171889 chr12 133851895 40606723 0.30337054996494445 1.5896629613615954 chr13 115169878 20538780 0.1783346510100497 1.2037211445846043 chr14 107349540 27313807 0.2544380441686103 1.4683987541688186 chr15 102531392 30335304 0.29586357317766643 1.5581926300992932 chr16 90354753 29070576 0.3217382045192465 2.3805157605095695 chr17 81195210 34972278 0.43071848696493303 2.177093896185808 chr18 78077248 16378367 0.2097713151979947 3.449590707567445 chr19 59128983 13232186 0.2237851105945793 2.222591898473392 chr20 63025520 37580594 0.5962758260463381 2.5603856683587725 chr21 48129895 11294691 0.23467100852806763 1.496112914750841 chr22 51304566 7038697 0.1371943581006026 1.0137861642627493 chrMT 16571 1252624 75.59133425864462 54.79722289362861 chrX 155270560 28542138 0.18382195568818713 1.2402023114304033 chrY 59373566 1535217 0.02585691080101202 1.1035511921861672