BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237605.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 = 1,783,615 number of mapped reads = 1,552,710 (87.05%) number of supplementary alignments = 8,988 (0.5%) number of secondary alignments = 0 number of mapped bases = 100,390,944 bp number of sequenced bases = 100,329,862 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,651 duplication rate = 4.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8552 >>>>>>> ACTG content number of A's = 27,240,068 bp (27.15%) number of C's = 17,476,249 bp (17.42%) number of T's = 32,886,397 bp (32.78%) number of G's = 22,541,857 bp (22.47%) number of N's = 185,291 bp (0.18%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 910,508 number of insertions = 8,288 mapped reads with insertion percentage = 0.53% number of deletions = 37,061 mapped reads with deletion percentage = 2.35% homopolymer indels = 45.54% >>>>>>> Coverage mean coverageData = 0.0324X std coverageData = 0.2965X There is a 2.74% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10543188 0.04229954556462268 0.4992802075341018 chr2 243199373 9450262 0.03885808537836979 0.4346108421015535 chr3 198022430 5534851 0.027950626603259036 0.1941385987468051 chr4 191154276 4608267 0.02410757999470543 0.19169954393433355 chr5 180915260 5684102 0.031418587906846554 0.20358445625152768 chr6 171115067 6160767 0.03600365010522422 0.2690751089013279 chr7 159138663 5935330 0.03729659334890856 0.3293873621440287 chr8 146364022 4776998 0.03263778854068386 0.3943955260388693 chr9 141213431 4029469 0.028534601641397695 0.2272991147072069 chr10 135534747 5665982 0.04180464512174136 0.32974662257190523 chr11 135006516 5073666 0.03758089720647261 0.2565086039255096 chr12 133851895 5379101 0.04018696186557538 0.2308414311358161 chr13 115169878 3652329 0.031712536849261924 0.2094889051914325 chr14 107349540 2933412 0.027325799439848555 0.19811526414327663 chr15 102531392 1882496 0.018360191579179966 0.1566436031525499 chr16 90354753 2110213 0.023354753678536424 0.1911739804533455 chr17 81195210 2496404 0.03074570531931625 0.21533770287743853 chr18 78077248 1583579 0.020282208204879353 0.3422122437805552 chr19 59128983 1478862 0.025010780246296473 0.34295444646729123 chr20 63025520 1953977 0.0310029492814974 0.20444637587941517 chr21 48129895 1417247 0.029446293203008234 0.2039252403303859 chr22 51304566 672605 0.01311004170661925 0.12879915614581877 chrMT 16571 12466 0.752278076157142 1.2011535187571527 chrX 155270560 7084852 0.045629074822683705 0.25640236639892844 chrY 59373566 270519 0.004556219513579494 0.10857508373290344