BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472500.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 = 14,151,610 number of mapped reads = 13,936,649 (98.48%) number of supplementary alignments = 58,892 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,991,257 number of mapped paired reads (second in pair) = 6,945,392 number of mapped paired reads (both in pair) = 13,840,004 number of mapped paired reads (singletons) = 96,645 number of mapped bases = 1,369,199,863 bp number of sequenced bases = 1,369,012,914 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,427,281 duplication rate = 43.94% >>>>>>> Insert size mean insert size = 28,900.499 std insert size = 1,643,611.7734 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 54.3238 >>>>>>> ACTG content number of A's = 384,164,661 bp (28.06%) number of C's = 302,878,043 bp (22.12%) number of T's = 381,796,897 bp (27.89%) number of G's = 299,960,110 bp (21.91%) number of N's = 213,203 bp (0.02%) GC percentage = 44.03% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 8,094,350 number of insertions = 73,816 mapped reads with insertion percentage = 0.53% number of deletions = 73,090 mapped reads with deletion percentage = 0.52% homopolymer indels = 43.5% >>>>>>> Coverage mean coverageData = 0.4423X std coverageData = 21.6478X There is a 4.24% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.18% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.15% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.14% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.14% of reference with a coverageData >= 25X There is a 0.13% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.12% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 78361388 0.3143879348649647 18.27522024133337 chr2 243199373 131567393 0.5409857409459686 27.177204796258533 chr3 198022430 142869710 0.7214824603455275 29.953643486721298 chr4 191154276 80187811 0.41949263536223486 18.329062199136402 chr5 180915260 77507063 0.4284163922932759 18.3882337844534 chr6 171115067 113364907 0.6625068673818185 24.811683771179876 chr7 159138663 30177839 0.18963235225873426 14.014494741569505 chr8 146364022 51710776 0.35330250763401405 19.285900303593902 chr9 141213431 64381446 0.4559158823922351 17.421400242349115 chr10 135534747 27570959 0.20342354717347869 8.682382642364605 chr11 135006516 100719876 0.7460371468292686 26.800129397863106 chr12 133851895 103686573 0.7746365712640826 35.71131681789307 chr13 115169878 41980513 0.36450948571813196 15.757501034943926 chr14 107349540 67482412 0.6286232060239848 32.03428147906803 chr15 102531392 27807070 0.2712054275045832 10.35960039870742 chr16 90354753 33086285 0.366182009262977 24.68535471424147 chr17 81195210 25459547 0.31355971614581696 12.422306128588092 chr18 78077248 21660427 0.27742303366020277 12.528496786070132 chr19 59128983 35322858 0.5973865303923797 22.12906766955169 chr20 63025520 15654659 0.2483860347364052 9.8846655129729 chr21 48129895 4704309 0.09774193357371753 4.796130987573524 chr22 51304566 9901023 0.19298522084759473 11.783048867938081 chrMT 16571 3709 0.2238247540884678 0.6472569992764139 chrX 155270560 80952568 0.5213645651822213 25.355693573223522 chrY 59373566 3078742 0.05185374919202259 1.4728781402206157