BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525199.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 = 1,337,622 number of mapped reads = 943,732 (70.55%) number of supplementary alignments = 3,062 (0.23%) number of secondary alignments = 0 number of mapped bases = 57,174,315 bp number of sequenced bases = 57,154,895 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,653 duplication rate = 1.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6901 >>>>>>> ACTG content number of A's = 15,269,320 bp (26.72%) number of C's = 11,111,448 bp (19.44%) number of T's = 17,717,360 bp (31%) number of G's = 13,055,330 bp (22.84%) number of N's = 1,437 bp (0%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 279,425 number of insertions = 4,537 mapped reads with insertion percentage = 0.48% number of deletions = 11,887 mapped reads with deletion percentage = 1.25% homopolymer indels = 41.78% >>>>>>> Coverage mean coverageData = 0.0185X std coverageData = 0.2001X There is a 1.72% 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 6658875 0.026715580379637248 0.3747177423755394 chr2 243199373 4757208 0.019560938588439537 0.21805970942347788 chr3 198022430 4723363 0.02385266658933536 0.16311218722852147 chr4 191154276 3212166 0.016804049939222913 0.14277970329543788 chr5 180915260 2550633 0.014098495616124366 0.12417234514205572 chr6 171115067 3595162 0.021010201281690757 0.16086203398205992 chr7 159138663 2785594 0.01750419381115449 0.2849277833667332 chr8 146364022 3296706 0.02252401891497625 0.18687022869746384 chr9 141213431 1908573 0.013515520347352795 0.1487360004468802 chr10 135534747 3120634 0.023024604900763936 0.23396157106477017 chr11 135006516 2590762 0.019189903396959 0.16653732698519347 chr12 133851895 2563624 0.01915269111430959 0.14615351367815782 chr13 115169878 1757928 0.015263782774867575 0.12962561807864387 chr14 107349540 2137788 0.019914272571638407 0.1505086315065867 chr15 102531392 1532393 0.014945598319780932 0.12775103478660008 chr16 90354753 1589523 0.0175920241849369 0.1474520261948418 chr17 81195210 1322497 0.016287869690835212 0.13685598796687923 chr18 78077248 1205114 0.015434893401980562 0.25674407022180173 chr19 59128983 1027643 0.01737968332721028 0.27096629096020375 chr20 63025520 1054669 0.0167339991800147 0.13644112638754674 chr21 48129895 719884 0.014957107219951343 0.1358477695867933 chr22 51304566 508490 0.009911203614898527 0.10351691581269719 chrMT 16571 96308 5.811839961378311 3.788408691023547 chrX 155270560 2292057 0.014761697259287273 0.13382749202671837 chrY 59373566 166721 0.002808000449223481 0.10292731380947169