BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716190.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 = 1,732,823 number of mapped reads = 1,529,781 (88.28%) number of supplementary alignments = 5,439 (0.31%) number of secondary alignments = 0 number of mapped bases = 87,036,965 bp number of sequenced bases = 87,010,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,884 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0966 >>>>>>> ACTG content number of A's = 21,744,807 bp (24.99%) number of C's = 16,122,788 bp (18.53%) number of T's = 26,837,101 bp (30.84%) number of G's = 22,304,675 bp (25.63%) number of N's = 678 bp (0%) GC percentage = 44.16% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 455,143 number of insertions = 6,050 mapped reads with insertion percentage = 0.39% number of deletions = 16,966 mapped reads with deletion percentage = 1.1% homopolymer indels = 40.56% >>>>>>> Coverage mean coverageData = 0.0281X std coverageData = 0.239X There is a 2.55% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% 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 7357741 0.029519449020750887 0.30524959751297015 chr2 243199373 6848634 0.02816057424621732 0.35503705852889206 chr3 198022430 4990577 0.0252020793806035 0.1756311821694553 chr4 191154276 5301000 0.02773152717755579 0.19409206897190381 chr5 180915260 4952275 0.027373450973676848 0.17806989110542437 chr6 171115067 4633039 0.027075575992381782 0.2090968939008703 chr7 159138663 4963863 0.031192061730467097 0.3238633771949185 chr8 146364022 4492503 0.03069403900365624 0.23342952690095892 chr9 141213431 2887444 0.020447375150880655 0.17929631789226597 chr10 135534747 3836713 0.028307965926995828 0.2967531250411412 chr11 135006516 3065491 0.022706244785992404 0.20242054435369672 chr12 133851895 4354467 0.03253197872170581 0.19639605168967247 chr13 115169878 2612109 0.022680487687935208 0.1637263273124005 chr14 107349540 2937870 0.027367327330885628 0.1888865299790716 chr15 102531392 3209455 0.031302169388278664 0.194464667139183 chr16 90354753 3063673 0.03390715926145025 0.21396788722396018 chr17 81195210 3909603 0.048150660611629675 0.2493982071804548 chr18 78077248 1610321 0.020624715153894767 0.27182023205812583 chr19 59128983 2366347 0.04002008625786782 0.29992218234555795 chr20 63025520 2786091 0.044205759825543686 0.2392477297795033 chr21 48129895 1067870 0.022187249733247913 0.1708228827163682 chr22 51304566 824149 0.016063852874225657 0.138223969647172 chrMT 16571 39887 2.407036388872126 2.1841918058691827 chrX 155270560 4666938 0.030056811799996086 0.1999272658474222 chrY 59373566 258905 0.0043606105787885475 0.12770970506864857