BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751232.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,861,118 number of mapped reads = 4,541,480 (93.42%) number of supplementary alignments = 171,943 (3.54%) number of secondary alignments = 0 number of mapped bases = 446,664,974 bp number of sequenced bases = 446,526,003 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,661 duplication rate = 1.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.1748 >>>>>>> ACTG content number of A's = 130,211,539 bp (29.16%) number of C's = 92,979,273 bp (20.82%) number of T's = 130,946,763 bp (29.33%) number of G's = 92,385,875 bp (20.69%) number of N's = 2,553 bp (0%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 1,724,872 number of insertions = 180,485 mapped reads with insertion percentage = 3.86% number of deletions = 63,423 mapped reads with deletion percentage = 1.37% homopolymer indels = 51.23% >>>>>>> Coverage mean coverageData = 0.1443X std coverageData = 1.4158X There is a 11.43% of reference with a coverageData >= 1X There is a 2.08% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 54032173 0.21677848898920096 4.000698143009402 chr2 243199373 33359967 0.13717127058547146 0.5934887154718297 chr3 198022430 24562256 0.12403774663304556 0.4510364848228042 chr4 191154276 20082200 0.10505755047823256 0.4775624605373782 chr5 180915260 35820802 0.19799768134539894 0.5188862324413598 chr6 171115067 24565298 0.14356011092816273 0.9106582502684063 chr7 159138663 24913090 0.15654957463102476 0.8093354675100912 chr8 146364022 22807244 0.15582548011696482 0.5477862670568286 chr9 141213431 18998724 0.13453907227847187 0.6505035928960591 chr10 135534747 22302512 0.16455198754309108 1.895463832435908 chr11 135006516 20562310 0.15230605610176623 0.7004854534847591 chr12 133851895 23814287 0.17791520247061127 0.4912439881991209 chr13 115169878 12637102 0.1097257565906252 0.38167062607582164 chr14 107349540 9588884 0.08932394121111278 0.3691986271266311 chr15 102531392 10898664 0.10629587473073612 0.37436717435494127 chr16 90354753 13028131 0.14418866265950614 0.947524231747876 chr17 81195210 13794902 0.16989797797185327 0.7152947768549943 chr18 78077248 9256235 0.11855227018247365 1.33977842204341 chr19 59128983 9461449 0.16001372795469862 2.75517433662338 chr20 63025520 8277142 0.13133000727324423 0.43147749884212405 chr21 48129895 5619628 0.11675961478827244 0.4558712227051253 chr22 51304566 6876575 0.1340343664538552 0.4323291156449338 chrMT 16571 1738545 104.91491159254119 39.429520178832604 chrX 155270560 18616458 0.11989689481380114 0.4675796497826997 chrY 59373566 1050396 0.017691307273004286 0.678795899987122