BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525012.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 = 1,876,243 number of mapped reads = 1,726,064 (92%) number of supplementary alignments = 6,082 (0.32%) number of secondary alignments = 0 number of mapped bases = 100,142,784 bp number of sequenced bases = 100,109,813 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,978 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7413 >>>>>>> ACTG content number of A's = 24,509,358 bp (24.48%) number of C's = 18,725,758 bp (18.71%) number of T's = 32,180,025 bp (32.14%) number of G's = 24,693,684 bp (24.67%) number of N's = 988 bp (0%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 493,991 number of insertions = 6,507 mapped reads with insertion percentage = 0.38% number of deletions = 20,149 mapped reads with deletion percentage = 1.16% homopolymer indels = 42.28% >>>>>>> Coverage mean coverageData = 0.0323X std coverageData = 0.2986X There is a 2.91% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10618311 0.04260094100226936 0.6099163891008685 chr2 243199373 9519021 0.03914081225859081 0.3271721842012465 chr3 198022430 5446293 0.027503414638432627 0.180236926210933 chr4 191154276 6333387 0.03313233233663054 0.21799224129753506 chr5 180915260 4335730 0.023965529497069513 0.17211675836736418 chr6 171115067 6651464 0.038871293548919335 0.30065469417320423 chr7 159138663 6265100 0.03936881133656376 0.38370090521658023 chr8 146364022 5947539 0.04063525256227244 0.2942215775127902 chr9 141213431 2779763 0.0196848343696146 0.2118796355970781 chr10 135534747 5144693 0.03795848012318199 0.2991161934655006 chr11 135006516 4196956 0.031087062494079915 0.2522368175480694 chr12 133851895 5380610 0.04019823551993791 0.2202655558119735 chr13 115169878 2769533 0.024047372872965968 0.17232244682930623 chr14 107349540 2271631 0.021161068785203924 0.16210009444709564 chr15 102531392 2791588 0.027226666346244474 0.1877680526465878 chr16 90354753 2860442 0.03165790293289828 0.20262192818071292 chr17 81195210 2585815 0.03184689096807558 0.2597865251438411 chr18 78077248 1963028 0.025142125910995225 0.36907418706596085 chr19 59128983 2493100 0.0421637558014485 0.345542573130483 chr20 63025520 2449912 0.03887174592133472 0.21666037909447308 chr21 48129895 1455412 0.030239251508859515 0.20100463546481762 chr22 51304566 1383967 0.026975513251588562 0.17641846262968533 chrMT 16571 30298 1.828374871763925 1.7416549069326743 chrX 155270560 4193309 0.02700646535956333 0.2077556510981162 chrY 59373566 275882 0.004646545905630799 0.12846939790750075