BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524611.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 = 1,139,271 number of mapped reads = 1,048,317 (92.02%) number of supplementary alignments = 5,185 (0.46%) number of secondary alignments = 0 number of mapped bases = 61,215,563 bp number of sequenced bases = 61,198,678 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,886 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7358 >>>>>>> ACTG content number of A's = 16,137,357 bp (26.37%) number of C's = 12,147,463 bp (19.85%) number of T's = 18,879,918 bp (30.85%) number of G's = 14,032,053 bp (22.93%) number of N's = 1,887 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 289,637 number of insertions = 4,762 mapped reads with insertion percentage = 0.45% number of deletions = 10,103 mapped reads with deletion percentage = 0.96% homopolymer indels = 41.16% >>>>>>> Coverage mean coverageData = 0.0198X std coverageData = 0.1969X There is a 1.83% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4432271 0.017782386989519276 0.3180946284497036 chr2 243199373 4798796 0.01973194231878221 0.20375580075663963 chr3 198022430 3772881 0.019052796190815353 0.1451366640916622 chr4 191154276 3897921 0.02039149257639416 0.1632575788132512 chr5 180915260 3398195 0.018783351940571513 0.1452205185675978 chr6 171115067 3126675 0.018272353538569458 0.1493807525458166 chr7 159138663 3887378 0.024427615054174484 0.24936191294489635 chr8 146364022 2618168 0.01788805721668403 0.1856779764031389 chr9 141213431 2787047 0.019736415865428552 0.1924010740367192 chr10 135534747 2400425 0.017710771983807223 0.20007820461640122 chr11 135006516 2360571 0.01748486717485547 0.16965573365997824 chr12 133851895 4535774 0.03388651314947764 0.2091124252972341 chr13 115169878 2281542 0.019810231977496755 0.14819295201781027 chr14 107349540 2178255 0.02029123739142245 0.16061667986265027 chr15 102531392 1580607 0.015415834791358338 0.13040838040669753 chr16 90354753 1721969 0.01905786848866711 0.15285628235843082 chr17 81195210 1807210 0.02225759376692295 0.16187089925731984 chr18 78077248 1928509 0.024700012479948064 0.3419173780614969 chr19 59128983 1024742 0.017330621093212442 0.24274770119677178 chr20 63025520 1822848 0.0289223793790198 0.18277904422635988 chr21 48129895 732713 0.015223656731434797 0.13967064440354798 chr22 51304566 616799 0.012022302264480709 0.11536070011340979 chrMT 16571 7432 0.4484943576126969 0.7254434336183818 chrX 155270560 3320247 0.021383622239785828 0.16770695067557534 chrY 59373566 176588 0.0029741855154868076 0.08466899398403392