BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524607.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 = 1,427,658 number of mapped reads = 1,335,617 (93.55%) number of supplementary alignments = 2,728 (0.19%) number of secondary alignments = 0 number of mapped bases = 77,627,325 bp number of sequenced bases = 77,602,235 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,636 duplication rate = 3.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4176 >>>>>>> ACTG content number of A's = 18,446,060 bp (23.77%) number of C's = 14,324,018 bp (18.46%) number of T's = 25,045,734 bp (32.27%) number of G's = 19,785,941 bp (25.5%) number of N's = 482 bp (0%) GC percentage = 43.95% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 350,905 number of insertions = 4,668 mapped reads with insertion percentage = 0.35% number of deletions = 14,689 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.87% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2296X There is a 2.23% of reference with a coverageData >= 1X There is a 0.2% 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 7945543 0.03187772599370976 0.36748003875993784 chr2 243199373 6978738 0.028695542730696102 0.2746747669592116 chr3 198022430 5595746 0.028258142272064836 0.18434134315529332 chr4 191154276 3552560 0.01858477913410632 0.1703965461967179 chr5 180915260 4098552 0.022654540031614802 0.1654075529090311 chr6 171115067 5083744 0.029709505358753708 0.2015725543007401 chr7 159138663 4750763 0.02985297796551175 0.31523602155577407 chr8 146364022 6820415 0.0465989859174545 0.2923219653437309 chr9 141213431 2762647 0.019563627768522954 0.2019776764080689 chr10 135534747 3341907 0.024657197316345747 0.23675321494925702 chr11 135006516 3916679 0.029011036770995556 0.2295033000560324 chr12 133851895 2538773 0.0189670306871636 0.1553502759989965 chr13 115169878 1708251 0.01483244603245998 0.13367312031106127 chr14 107349540 1441582 0.013428860524227678 0.13037352293131102 chr15 102531392 1969132 0.019205162063926723 0.1579417350544576 chr16 90354753 2333204 0.02582270353835177 0.18440705980734298 chr17 81195210 1972580 0.02429429026663026 0.17660429445119788 chr18 78077248 2060982 0.026396703941204486 0.3197579106618028 chr19 59128983 1487972 0.02516485020552442 0.26568564972058073 chr20 63025520 1442352 0.022885205865814356 0.170681529664989 chr21 48129895 698405 0.014510835729020394 0.14718394772019217 chr22 51304566 1388753 0.027068799295563675 0.18054954344508195 chrMT 16571 14835 0.8952386699656025 1.0584771434087323 chrX 155270560 3526211 0.022710106796806812 0.18615738567969398 chrY 59373566 196999 0.0033179580286621154 0.10440752012496013