BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472686.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 = 20,846,184 number of mapped reads = 20,682,000 (99.21%) number of supplementary alignments = 125,787 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,364,743 number of mapped paired reads (second in pair) = 10,317,257 number of mapped paired reads (both in pair) = 20,569,498 number of mapped paired reads (singletons) = 112,502 number of mapped bases = 2,037,755,366 bp number of sequenced bases = 2,037,507,989 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,895,393 duplication rate = 49.82% >>>>>>> Insert size mean insert size = 21,388.6274 std insert size = 1,462,264.3108 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 54.8141 >>>>>>> ACTG content number of A's = 552,041,004 bp (27.09%) number of C's = 469,700,643 bp (23.05%) number of T's = 550,937,131 bp (27.04%) number of G's = 464,437,069 bp (22.79%) number of N's = 392,142 bp (0.02%) GC percentage = 45.85% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 12,688,132 number of insertions = 127,628 mapped reads with insertion percentage = 0.61% number of deletions = 108,896 mapped reads with deletion percentage = 0.52% homopolymer indels = 48.28% >>>>>>> Coverage mean coverageData = 0.6583X std coverageData = 30.0702X There is a 3.94% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% 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 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 212892498 0.8541302611238027 27.407411449737367 chr2 243199373 124144415 0.5104635487690998 24.530059945505812 chr3 198022430 187201306 0.9453540490337382 32.173403109745884 chr4 191154276 73175711 0.3828096997422124 21.197548348924098 chr5 180915260 71074890 0.39286287956029803 15.498816395271136 chr6 171115067 185586573 1.084571781162906 41.21496080182478 chr7 159138663 111839021 0.7027771811806663 30.519789317648108 chr8 146364022 86672345 0.592169741003701 24.288705537058444 chr9 141213431 143855829 1.0187120869543917 48.30214364984936 chr10 135534747 40989539 0.3024282695565883 13.246289880358159 chr11 135006516 54844630 0.4062369108169564 17.999014425851907 chr12 133851895 81111635 0.6059804756593099 31.11884397489793 chr13 115169878 99347321 0.8626154922209781 55.116133439536746 chr14 107349540 29057080 0.2706772660600129 13.198084657079711 chr15 102531392 28602193 0.27896035001651004 14.803298073839924 chr16 90354753 113192397 1.252755314377319 46.34568301681964 chr17 81195210 93401044 1.150327020522516 36.2430672936831 chr18 78077248 9311580 0.11926111944929206 4.873778820749385 chr19 59128983 79355948 1.3420820716635697 52.88586724171507 chr20 63025520 70136452 1.1128262329291372 36.02349897328114 chr21 48129895 14718157 0.3058007294634655 20.04428827031258 chr22 51304566 15293881 0.2980998026569409 9.058521344256375 chrMT 16571 2533 0.15285740148452115 0.4735354747827459 chrX 155270560 109196750 0.7032675737113333 27.120005751098486 chrY 59373566 2751638 0.04634449613486244 3.155456183630754