BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716628.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 946,913 number of mapped reads = 854,861 (90.28%) number of supplementary alignments = 4,282 (0.45%) number of secondary alignments = 0 number of mapped bases = 49,592,252 bp number of sequenced bases = 49,578,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,979 duplication rate = 1.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3102 >>>>>>> ACTG content number of A's = 12,728,473 bp (25.67%) number of C's = 10,351,342 bp (20.88%) number of T's = 14,800,621 bp (29.85%) number of G's = 11,697,674 bp (23.59%) number of N's = 684 bp (0%) GC percentage = 44.47% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 236,992 number of insertions = 2,962 mapped reads with insertion percentage = 0.34% number of deletions = 8,609 mapped reads with deletion percentage = 1% homopolymer indels = 42.31% >>>>>>> Coverage mean coverageData = 0.016X std coverageData = 0.167X There is a 1.5% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% 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 5113508 0.020515527622296276 0.2657374560405501 chr2 243199373 4546100 0.018692893587353123 0.19924315791858582 chr3 198022430 4467404 0.022560090793755032 0.15934575483893257 chr4 191154276 2271370 0.01188239179122522 0.11799530579887194 chr5 180915260 2208256 0.012206023969453986 0.11668036714272104 chr6 171115067 3567645 0.02084939136306448 0.1901691304102479 chr7 159138663 2901070 0.018229825143120625 0.20138961090063456 chr8 146364022 3598319 0.024584723423356047 0.17431763291460875 chr9 141213431 1892903 0.013404553565446618 0.1419029153945782 chr10 135534747 2604673 0.01921775085469411 0.17990424163127 chr11 135006516 1687945 0.01250269283298889 0.14365337792676872 chr12 133851895 2229985 0.01666009285860316 0.13802026518051647 chr13 115169878 1123656 0.009756509423410173 0.1042906698800152 chr14 107349540 1117271 0.010407785631871362 0.11464106799816251 chr15 102531392 1523159 0.014855538097054217 0.12903337924179759 chr16 90354753 1094638 0.01211489117788856 0.12311469672130287 chr17 81195210 1140791 0.014049979056646322 0.12752450376422925 chr18 78077248 964827 0.01235733872177462 0.22867427362812223 chr19 59128983 1007085 0.017032002732061197 0.2017447212562326 chr20 63025520 490789 0.007787147174668293 0.09245008938560728 chr21 48129895 464696 0.009655038723853438 0.107051479932335 chr22 51304566 831118 0.01619968873725586 0.13405404593068249 chrMT 16571 3827 0.23094562790416995 0.5145385597951496 chrX 155270560 2624393 0.01690206437073454 0.147786976023731 chrY 59373566 116824 0.0019676096261423814 0.05748043719413131