BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716119.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 = 945,015 number of mapped reads = 883,350 (93.47%) number of supplementary alignments = 17,983 (1.9%) number of secondary alignments = 0 number of mapped bases = 69,945,667 bp number of sequenced bases = 69,912,568 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,339 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3679 >>>>>>> ACTG content number of A's = 18,413,377 bp (26.34%) number of C's = 14,486,181 bp (20.72%) number of T's = 20,728,100 bp (29.65%) number of G's = 16,280,287 bp (23.29%) number of N's = 4,623 bp (0.01%) GC percentage = 44.01% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 447,004 number of insertions = 6,186 mapped reads with insertion percentage = 0.69% number of deletions = 17,216 mapped reads with deletion percentage = 1.92% homopolymer indels = 43.02% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.2246X There is a 2.07% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 5627027 0.022575779259542947 0.37852774237211434 chr2 243199373 5987609 0.024620166269918795 0.2607603757781693 chr3 198022430 4635467 0.023408797680141587 0.16136542972738932 chr4 191154276 4646346 0.02430678558297069 0.19443723174100255 chr5 180915260 4245272 0.02346552745191312 0.16342264846758534 chr6 171115067 3954107 0.02310788330521473 0.17073500747726128 chr7 159138663 3816602 0.023982870837616625 0.26451798852323183 chr8 146364022 3577762 0.02444427224061935 0.2691154594053008 chr9 141213431 2900818 0.02054208285612719 0.21113684027081073 chr10 135534747 3215913 0.023727590681967333 0.23846242521919386 chr11 135006516 3216028 0.023821279855855252 0.21623688966289106 chr12 133851895 3126135 0.023355179244940835 0.16249482559753772 chr13 115169878 2156256 0.018722395451352306 0.14432689099027743 chr14 107349540 2102634 0.019586800278790204 0.15648085462116265 chr15 102531392 2063956 0.020129991017775316 0.15031773014478594 chr16 90354753 2061260 0.022812967016798774 0.16884524904781964 chr17 81195210 1892274 0.02330524177473031 0.17680322867086867 chr18 78077248 1901260 0.02435101196189702 0.33212060510854674 chr19 59128983 1379124 0.023323993243719414 0.27465992438229747 chr20 63025520 1500275 0.023804246279919627 0.16855497570768846 chr21 48129895 941599 0.019563703598356075 0.1651180951577353 chr22 51304566 837266 0.016319522125964384 0.13571439394244483 chrMT 16571 9815 0.5922998008569187 0.8991699232366269 chrX 155270560 3937603 0.025359623872033436 0.18721905985237752 chrY 59373566 213259 0.003591817274374256 0.13264194429359796