BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524950.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 = 1,414,478 number of mapped reads = 1,312,465 (92.79%) number of supplementary alignments = 3,270 (0.23%) number of secondary alignments = 0 number of mapped bases = 76,844,846 bp number of sequenced bases = 76,820,209 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,899 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.337 >>>>>>> ACTG content number of A's = 19,678,165 bp (25.62%) number of C's = 12,849,531 bp (16.73%) number of T's = 24,585,841 bp (32%) number of G's = 19,705,739 bp (25.65%) number of N's = 933 bp (0%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 364,989 number of insertions = 5,004 mapped reads with insertion percentage = 0.38% number of deletions = 14,390 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.18% >>>>>>> Coverage mean coverageData = 0.0248X std coverageData = 0.2309X There is a 2.27% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 8160225 0.03273903578358587 0.4132793351620118 chr2 243199373 6728537 0.027666753071768815 0.2556619859354218 chr3 198022430 4417006 0.02230558427143834 0.1607252111052599 chr4 191154276 5148988 0.026936295162970875 0.18467509139730628 chr5 180915260 3483679 0.01925586045090945 0.15016620973151049 chr6 171115067 5332741 0.03116464899026104 0.24000921526178867 chr7 159138663 4875293 0.030635503076961255 0.3101648362879571 chr8 146364022 4827176 0.03298061869330155 0.2584185290325077 chr9 141213431 2139208 0.015148757344476673 0.1807409431649289 chr10 135534747 3881870 0.028641142481344653 0.2271146836111517 chr11 135006516 3246759 0.024048905906141598 0.20722480029172288 chr12 133851895 4234084 0.031632604080801395 0.19112725935271935 chr13 115169878 1548251 0.013443193887901835 0.12433804213201807 chr14 107349540 1776939 0.016552832923177874 0.13998381709152538 chr15 102531392 2114454 0.020622503593826173 0.16349279794155383 chr16 90354753 2372228 0.026254601127624132 0.18291759673962374 chr17 81195210 1881769 0.02317586222142907 0.20703008180533466 chr18 78077248 1546881 0.019812186515590302 0.278018852090049 chr19 59128983 1735520 0.029351426524619913 0.2740264653217067 chr20 63025520 1797244 0.028516131243343967 0.1807034414353173 chr21 48129895 1134970 0.023581393643181642 0.16984440018448993 chr22 51304566 940704 0.018335677958955934 0.1431120121082787 chrMT 16571 67650 4.082433166374993 3.294314122723919 chrX 155270560 3261690 0.02100649343958056 0.17293917941294362 chrY 59373566 190980 0.0032165829487149212 0.07967528241720773