BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524491.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 = 1,617,435 number of mapped reads = 1,487,110 (91.94%) number of supplementary alignments = 3,370 (0.21%) number of secondary alignments = 0 number of mapped bases = 86,260,129 bp number of sequenced bases = 86,232,932 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,646 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3076 >>>>>>> ACTG content number of A's = 22,013,413 bp (25.53%) number of C's = 15,933,298 bp (18.48%) number of T's = 27,759,334 bp (32.19%) number of G's = 20,525,051 bp (23.8%) number of N's = 1,836 bp (0%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 406,021 number of insertions = 5,332 mapped reads with insertion percentage = 0.36% number of deletions = 16,039 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.66% >>>>>>> Coverage mean coverageData = 0.0279X std coverageData = 0.2623X There is a 2.46% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 8664409 0.034761835157072686 0.4663489350891628 chr2 243199373 6861393 0.028213037374894875 0.29805336650521 chr3 198022430 4737260 0.023922845507955842 0.1731198001118678 chr4 191154276 4877684 0.02551700177504792 0.19646986363858995 chr5 180915260 4657975 0.025746722526336363 0.17851671819571874 chr6 171115067 3805862 0.0222415364510245 0.2174702431324998 chr7 159138663 4289502 0.026954493139105987 0.34333245272189394 chr8 146364022 7918890 0.054104074838828904 0.29543020078395754 chr9 141213431 3603966 0.025521410920183646 0.2305112346834704 chr10 135534747 4403244 0.03248793462535478 0.2605153255854615 chr11 135006516 3072234 0.02275619052342629 0.254594155179311 chr12 133851895 4095296 0.03059572671720486 0.19479875677633085 chr13 115169878 1955258 0.016977164810402942 0.14533079365154059 chr14 107349540 2136458 0.019901883138018103 0.1606868340495765 chr15 102531392 2268433 0.02212427780167073 0.17302064015313454 chr16 90354753 2647655 0.029302885704308217 0.2029046537706892 chr17 81195210 2937683 0.03618049636179277 0.22052523424069262 chr18 78077248 2007281 0.02570891074439509 0.387952610724934 chr19 59128983 1684233 0.028484051552180426 0.3212222128911185 chr20 63025520 2335892 0.037062637483990614 0.2166648234110418 chr21 48129895 1187045 0.024663361513670455 0.1859505359658103 chr22 51304566 710495 0.013848572464290995 0.12970287212051226 chrMT 16571 8114 0.48965059441192443 0.8078642739402606 chrX 155270560 5136972 0.03308400510695653 0.22226117369379475 chrY 59373566 256895 0.004326757129595349 0.116411271215158