BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716130.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 = 1,082,959 number of mapped reads = 999,042 (92.25%) number of supplementary alignments = 20,054 (1.85%) number of secondary alignments = 0 number of mapped bases = 78,451,677 bp number of sequenced bases = 78,415,585 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,992 duplication rate = 1.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3665 >>>>>>> ACTG content number of A's = 20,059,645 bp (25.58%) number of C's = 16,045,336 bp (20.46%) number of T's = 24,257,479 bp (30.93%) number of G's = 18,047,352 bp (23.02%) number of N's = 5,773 bp (0.01%) GC percentage = 43.48% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 522,840 number of insertions = 7,266 mapped reads with insertion percentage = 0.72% number of deletions = 18,902 mapped reads with deletion percentage = 1.86% homopolymer indels = 42.42% >>>>>>> Coverage mean coverageData = 0.0253X std coverageData = 0.2367X There is a 2.34% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.01% 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 6209276 0.02491177745149931 0.36933016813162123 chr2 243199373 6533959 0.026866676995914787 0.2863846574417312 chr3 198022430 5097129 0.02574015983946869 0.16810529768346028 chr4 191154276 5006182 0.02618922320105463 0.20119230490237014 chr5 180915260 4669314 0.025809398278508956 0.16962286309292046 chr6 171115067 4518794 0.026407925843257275 0.18158759072609376 chr7 159138663 4634412 0.029121848283971068 0.3296722521476044 chr8 146364022 3917210 0.02676347606790964 0.2816557838801678 chr9 141213431 3292615 0.023316585233312544 0.21725523864397997 chr10 135534747 3792034 0.027978316143534764 0.2452324490126541 chr11 135006516 4004332 0.029660286915336738 0.2560260304790845 chr12 133851895 3565919 0.026640780842138993 0.17173406313151032 chr13 115169878 2472730 0.021470284096332896 0.15309744356232433 chr14 107349540 2242189 0.02088680584937765 0.16112195105919472 chr15 102531392 2250152 0.02194598118788829 0.1561721705018773 chr16 90354753 2295943 0.025410317927602545 0.17615278867973327 chr17 81195210 2131521 0.02625180721867706 0.18473133374817424 chr18 78077248 2043585 0.026173886149265916 0.34398337495311226 chr19 59128983 1515525 0.02563083149933426 0.2689978169940227 chr20 63025520 1689036 0.026799239419206696 0.17939791480864425 chr21 48129895 1022050 0.021235242669862462 0.16860418914175657 chr22 51304566 898532 0.017513684844346993 0.13984006507241026 chrMT 16571 30437 1.836763019733269 1.770674017138098 chrX 155270560 4385849 0.028246494377298568 0.19744861773645211 chrY 59373566 232952 0.003923496863907416 0.136864650048207