BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472773.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,755,740 number of mapped reads = 13,621,457 (99.02%) number of supplementary alignments = 46,617 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,835,691 number of mapped paired reads (second in pair) = 6,785,766 number of mapped paired reads (both in pair) = 13,542,040 number of mapped paired reads (singletons) = 79,417 number of mapped bases = 1,343,680,397 bp number of sequenced bases = 1,343,496,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,283,890 duplication rate = 46.62% >>>>>>> Insert size mean insert size = 21,164.4842 std insert size = 1,421,673.742 median insert size = 257 >>>>>>> Mapping quality mean mapping quality = 55.212 >>>>>>> ACTG content number of A's = 369,868,687 bp (27.53%) number of C's = 304,156,449 bp (22.64%) number of T's = 367,097,816 bp (27.32%) number of G's = 302,117,001 bp (22.49%) number of N's = 256,170 bp (0.02%) GC percentage = 45.13% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 8,654,155 number of insertions = 73,868 mapped reads with insertion percentage = 0.54% number of deletions = 74,722 mapped reads with deletion percentage = 0.54% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.434X std coverageData = 14.6503X There is a 3.87% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 117730338 0.47233719028527515 14.610008255711152 chr2 243199373 105518523 0.4338766243447511 15.327134324161271 chr3 198022430 143770390 0.7260308339817868 15.712759940627224 chr4 191154276 48482153 0.25362839908430823 10.88873603442111 chr5 180915260 62482725 0.34537011969029036 10.164006264961897 chr6 171115067 104303287 0.609550572188947 22.705539433464832 chr7 159138663 52258061 0.32838067138970495 9.29530878066742 chr8 146364022 74227690 0.5071443718593631 17.993970476283124 chr9 141213431 75628087 0.5355587387434839 14.72643755323115 chr10 135534747 40876648 0.3015953392379889 13.89818631228399 chr11 135006516 68686002 0.5087606438195916 16.098241594669776 chr12 133851895 72350409 0.5405258476168754 17.096693840838068 chr13 115169878 33182397 0.2881169762114361 12.015179260175685 chr14 107349540 33252737 0.3097613366578003 14.580993009745661 chr15 102531392 26986755 0.26320480463193163 8.917483596419345 chr16 90354753 46396263 0.513490009761855 14.296675989198317 chr17 81195210 39441615 0.4857628300979824 10.375486037108967 chr18 78077248 26941358 0.34506029208406525 14.522948803123722 chr19 59128983 44275484 0.7487949522148892 23.05539641824945 chr20 63025520 26630908 0.422541662488465 14.558679500549 chr21 48129895 6663041 0.1384387188046016 6.512153848991959 chr22 51304566 16045846 0.3127566852431809 9.519475496305509 chrMT 16571 2952 0.1781425381690906 0.6009039299399958 chrX 155270560 75091278 0.48361568348822853 16.16063234293752 chrY 59373566 2455450 0.041355946179820156 1.8517395735200965