BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004088.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,055,198 number of mapped reads = 2,735,834 (89.55%) number of supplementary alignments = 21,410 (0.7%) number of secondary alignments = 0 number of mapped bases = 182,330,318 bp number of sequenced bases = 182,217,562 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,427 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8222 >>>>>>> ACTG content number of A's = 51,674,158 bp (28.36%) number of C's = 32,821,199 bp (18.01%) number of T's = 57,500,569 bp (31.56%) number of G's = 40,027,930 bp (21.97%) number of N's = 193,706 bp (0.11%) GC percentage = 39.98% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,715,033 number of insertions = 15,071 mapped reads with insertion percentage = 0.55% number of deletions = 67,274 mapped reads with deletion percentage = 2.42% homopolymer indels = 44.65% >>>>>>> Coverage mean coverageData = 0.0589X std coverageData = 0.5467X There is a 4.93% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 10639179 0.042684663963184266 0.935302244210888 chr2 243199373 17652383 0.0725839988082535 0.6286837314004746 chr3 198022430 9068350 0.04579455973750044 0.24751715089331294 chr4 191154276 14506069 0.07588670943463488 0.3282570313497099 chr5 180915260 11085834 0.061276389841299184 0.28991252690646774 chr6 171115067 12382154 0.07236156474753914 0.35246203354442296 chr7 159138663 13043616 0.0819638405533167 0.9149235376576278 chr8 146364022 10687574 0.07302049953232359 0.9057819487112926 chr9 141213431 6093911 0.043153905098446334 0.501306683141547 chr10 135534747 7364979 0.05434015382048118 0.47352897914302255 chr11 135006516 9909307 0.07339873136197367 0.5243841600243694 chr12 133851895 9393633 0.07017930526870762 0.315024082343417 chr13 115169878 5017235 0.043563778021888676 0.2368124052198996 chr14 107349540 5042655 0.046974164956831675 0.3048722888710654 chr15 102531392 4165081 0.04062249540121332 0.23603755346348 chr16 90354753 5634427 0.0623589441941145 0.3741514956925694 chr17 81195210 4108073 0.05059501662721237 0.3101492224493798 chr18 78077248 5616009 0.07192887997281872 0.9049029844376125 chr19 59128983 2302982 0.03894844597614676 0.7235506789327018 chr20 63025520 4623294 0.07335590408456764 0.3393507534898671 chr21 48129895 2249313 0.04673421789098023 0.2726195311595166 chr22 51304566 1029598 0.02006835025171054 0.15705231773617492 chrMT 16571 30841 1.8611429605938086 1.8077752612441522 chrX 155270560 10219856 0.0658196634313678 0.35938828209159834 chrY 59373566 463965 0.00781433609697622 0.16507081002550403