BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472655.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 = 21,369,974 number of mapped reads = 21,168,363 (99.06%) number of supplementary alignments = 139,289 (0.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,609,049 number of mapped paired reads (second in pair) = 10,559,314 number of mapped paired reads (both in pair) = 21,038,050 number of mapped paired reads (singletons) = 130,313 number of mapped bases = 2,083,334,165 bp number of sequenced bases = 2,083,071,030 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,594,652 duplication rate = 49.79% >>>>>>> Insert size mean insert size = 23,197.2361 std insert size = 1,561,661.3621 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.6134 >>>>>>> ACTG content number of A's = 560,744,750 bp (26.92%) number of C's = 483,853,468 bp (23.23%) number of T's = 561,034,701 bp (26.93%) number of G's = 477,042,108 bp (22.9%) number of N's = 396,003 bp (0.02%) GC percentage = 46.13% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 13,491,682 number of insertions = 139,312 mapped reads with insertion percentage = 0.65% number of deletions = 107,207 mapped reads with deletion percentage = 0.5% homopolymer indels = 47.5% >>>>>>> Coverage mean coverageData = 0.673X std coverageData = 34.5842X There is a 3.83% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 0.89% 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 0.43% of reference with a coverageData >= 6X There is a 0.39% 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 0.32% 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 0.27% of reference with a coverageData >= 15X There is a 0.26% 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 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% 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 0.21% 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 0.2% 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 0.19% 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 0.18% of reference with a coverageData >= 37X There is a 0.18% 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 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% 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 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% 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 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 249672793 1.0016937650879514 38.53302169824709 chr2 243199373 176161876 0.7243516865481392 46.98343905001432 chr3 198022430 239492057 1.2094188370479042 50.32345146263529 chr4 191154276 56641455 0.29631278036385644 19.953042715531225 chr5 180915260 64052584 0.3540474363522458 17.395211593967414 chr6 171115067 156056273 0.9119960955863694 44.8293193946092 chr7 159138663 93557514 0.5878993340543524 24.94901487205555 chr8 146364022 135694292 0.9271014156744066 43.290579092993276 chr9 141213431 175439144 1.242368680922426 38.18956761331478 chr10 135534747 35809931 0.26421218021678233 16.367984734275684 chr11 135006516 42624001 0.315718102080347 24.63881430562036 chr12 133851895 50767880 0.37928398398842245 21.23167430819277 chr13 115169878 48307494 0.419445560235811 16.626102275622667 chr14 107349540 31447012 0.2929403516773337 16.143716051405505 chr15 102531392 41063707 0.40049887355474506 32.880428094308265 chr16 90354753 153752470 1.7016533706865427 67.31074084765663 chr17 81195210 60512684 0.7452740623492445 28.97089530229775 chr18 78077248 8589938 0.11001845249463711 5.991411486515243 chr19 59128983 72493983 1.2260312848607593 53.88111578721664 chr20 63025520 78787356 1.2500865681076492 38.21518194308999 chr21 48129895 15633610 0.32482119481041877 20.432650523351313 chr22 51304566 21742715 0.4237968799892002 18.923051159315932 chrMT 16571 13660 0.8243316637499246 1.1852092077613696 chrX 155270560 73630634 0.474208594340099 26.36062256691343 chrY 59373566 1389102 0.02339596715481095 1.0918179471398606