BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354871.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 27,272,112 number of mapped reads = 26,983,295 (98.94%) number of supplementary alignments = 1,369,907 (5.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,504,762 number of mapped paired reads (second in pair) = 13,478,533 number of mapped paired reads (both in pair) = 26,937,064 number of mapped paired reads (singletons) = 46,231 number of mapped bases = 3,314,037,866 bp number of sequenced bases = 3,312,527,016 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,763,347 duplication rate = 65.59% >>>>>>> Insert size mean insert size = 493,597.563 std insert size = 8,108,405.5973 median insert size = 150 >>>>>>> Mapping quality mean mapping quality = 53.594 >>>>>>> ACTG content number of A's = 913,861,687 bp (27.59%) number of C's = 706,336,089 bp (21.32%) number of T's = 934,959,717 bp (28.22%) number of G's = 757,339,598 bp (22.86%) number of N's = 29,925 bp (0%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 17,594,984 number of insertions = 517,298 mapped reads with insertion percentage = 1.79% number of deletions = 539,268 mapped reads with deletion percentage = 1.91% homopolymer indels = 43.77% >>>>>>> Coverage mean coverageData = 1.0705X std coverageData = 73.3211X There is a 26.33% of reference with a coverageData >= 1X There is a 22.04% of reference with a coverageData >= 2X There is a 13.79% of reference with a coverageData >= 3X There is a 11.61% of reference with a coverageData >= 4X There is a 7.03% of reference with a coverageData >= 5X There is a 5.96% of reference with a coverageData >= 6X There is a 3.57% of reference with a coverageData >= 7X There is a 3.03% of reference with a coverageData >= 8X There is a 1.81% of reference with a coverageData >= 9X There is a 1.53% of reference with a coverageData >= 10X There is a 0.92% of reference with a coverageData >= 11X There is a 0.77% of reference with a coverageData >= 12X There is a 0.47% of reference with a coverageData >= 13X There is a 0.39% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% 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 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 267387525 1.0727657324472624 29.99390699467099 chr2 243199373 330458928 1.3587984373627477 256.7601087823384 chr3 198022430 212721066 1.0742271266946881 2.9448875552909772 chr4 191154276 215746661 1.1286520265965696 12.80515590841051 chr5 180915260 196958721 1.088679423725782 2.431963631453422 chr6 171115067 183391023 1.071740941433287 4.249071338753058 chr7 159138663 178210773 1.1198458604619546 19.592045018586 chr8 146364022 163585225 1.117660083158961 6.010237588512102 chr9 141213431 140676919 0.9962007013341386 16.235041889313617 chr10 135534747 182415860 1.3458973734609916 35.07427713166564 chr11 135006516 153813123 1.1393014763820732 6.43303290212793 chr12 133851895 145617621 1.0879010790246937 2.4299521070089942 chr13 115169878 101776160 0.883704678405581 2.139963156873051 chr14 107349540 99192473 0.9240139547873237 9.021860987415764 chr15 102531392 98191552 0.9576730607539201 2.2458801491172027 chr16 90354753 103748220 1.148232013870925 6.602384321913484 chr17 81195210 90693661 1.116982898375409 6.002256403758833 chr18 78077248 90702046 1.161696247285765 14.32882200167267 chr19 59128983 67091881 1.1346699637976185 15.985535759118523 chr20 63025520 71282575 1.131011295107125 4.727644748429826 chr21 48129895 46940318 0.9752840308502647 7.318207433196077 chr22 51304566 43313348 0.844239633563999 3.263197809463199 chrMT 16571 4054873 244.69694043811478 55.81390335296067 chrX 155270560 88895172 0.5725178810458338 2.8722496460584375 chrY 59373566 37172142 0.6260722490544024 16.616740516616595