BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173963.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,762,146 number of mapped reads = 5,617,101 (97.48%) number of supplementary alignments = 543,736 (9.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,811,365 number of mapped paired reads (second in pair) = 2,805,736 number of mapped paired reads (both in pair) = 5,516,714 number of mapped paired reads (singletons) = 100,387 number of mapped bases = 664,464,908 bp number of sequenced bases = 664,100,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,402,485 duplication rate = 65.73% >>>>>>> Insert size mean insert size = 837,677.6806 std insert size = 8,454,032.4944 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.697 >>>>>>> ACTG content number of A's = 200,381,026 bp (30.17%) number of C's = 129,483,597 bp (19.5%) number of T's = 200,065,149 bp (30.13%) number of G's = 134,162,439 bp (20.2%) number of N's = 8,291 bp (0%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 6,562,987 number of insertions = 68,406 mapped reads with insertion percentage = 1.18% number of deletions = 146,919 mapped reads with deletion percentage = 2.55% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 0.2146X std coverageData = 3.2704X There is a 4.31% of reference with a coverageData >= 1X There is a 3.43% of reference with a coverageData >= 2X There is a 2.67% of reference with a coverageData >= 3X There is a 2.22% of reference with a coverageData >= 4X There is a 1.71% of reference with a coverageData >= 5X There is a 1.39% of reference with a coverageData >= 6X There is a 1.05% of reference with a coverageData >= 7X There is a 0.86% of reference with a coverageData >= 8X There is a 0.64% of reference with a coverageData >= 9X There is a 0.53% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 60761856 0.24377815291380958 1.80572516300084 chr2 243199373 50470579 0.20752758684127035 9.490734300054863 chr3 198022430 41965693 0.21192393710146876 1.3513318585220966 chr4 191154276 40564384 0.21220756788092984 1.6571489006918354 chr5 180915260 34525754 0.19083936866353893 1.2786172200622303 chr6 171115067 32254122 0.18849375782905195 1.3181150424992123 chr7 159138663 57375795 0.3605396320314693 3.4537924032509606 chr8 146364022 65772789 0.4493781197130535 2.4345611583262805 chr9 141213431 22915390 0.1622748618012121 1.5391059695839482 chr10 135534747 30591506 0.22570969199507193 4.4971206828628105 chr11 135006516 27004530 0.2000239010685973 1.344148858537989 chr12 133851895 24755013 0.1849433136527503 1.2495032695079589 chr13 115169878 17321003 0.15039525352280048 1.139510538755447 chr14 107349540 22066167 0.20555436939925406 1.3281339640061236 chr15 102531392 15608355 0.15223001166315972 1.1261113849892797 chr16 90354753 14964474 0.16561911247768007 1.6472895629856568 chr17 81195210 15866803 0.1954155054220563 1.4280956374863623 chr18 78077248 11726845 0.1501954192852699 1.9495544021787528 chr19 59128983 9892158 0.16729795606327272 1.483447154078917 chr20 63025520 24495910 0.3886665274637956 1.8550522404120326 chr21 48129895 7907798 0.16430116874345976 1.2908242401530665 chr22 51304566 6839633 0.13331431358370716 1.0352193798754192 chrMT 16571 2575830 155.44203729406794 129.43279173951663 chrX 155270560 25030713 0.16120707621586475 1.1829457217104309 chrY 59373566 1211808 0.020409890825826428 0.8703902225345851