BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716157.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 = 695,753 number of mapped reads = 629,516 (90.48%) number of supplementary alignments = 2,606 (0.37%) number of secondary alignments = 0 number of mapped bases = 36,125,689 bp number of sequenced bases = 36,116,164 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,257 duplication rate = 1.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3145 >>>>>>> ACTG content number of A's = 9,020,093 bp (24.98%) number of C's = 6,980,054 bp (19.33%) number of T's = 11,345,128 bp (31.41%) number of G's = 8,770,215 bp (24.28%) number of N's = 674 bp (0%) GC percentage = 43.61% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 175,765 number of insertions = 2,661 mapped reads with insertion percentage = 0.42% number of deletions = 5,628 mapped reads with deletion percentage = 0.89% homopolymer indels = 38.67% >>>>>>> Coverage mean coverageData = 0.0117X std coverageData = 0.129X There is a 1.11% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2943219 0.011808271482701742 0.18062383218854855 chr2 243199373 3033663 0.012473975416046817 0.1367064833019995 chr3 198022430 2394408 0.012091599926331577 0.11452686373770624 chr4 191154276 2352905 0.01230893207955233 0.11936191825208288 chr5 180915260 2145457 0.011858905655609151 0.11362970206029145 chr6 171115067 2076972 0.012137867438639989 0.11811032733109292 chr7 159138663 1984068 0.012467542221339386 0.14135474717082236 chr8 146364022 1820896 0.01244087156883404 0.1278533949912321 chr9 141213431 1520282 0.01076584563687855 0.12841087013458388 chr10 135534747 1694815 0.01250465314256277 0.12665997988553532 chr11 135006516 1648520 0.012210669890925858 0.130866029545514 chr12 133851895 1644946 0.01228929930353246 0.11581838726257677 chr13 115169878 1142822 0.009922924464676432 0.10293743369945735 chr14 107349540 1099070 0.010238236698545703 0.10804247921436451 chr15 102531392 1038549 0.01012908319824625 0.10500675791493284 chr16 90354753 1045146 0.011567139140981328 0.11487137665686273 chr17 81195210 950022 0.011700468537491312 0.11476690868722605 chr18 78077248 989363 0.012671591601179385 0.1906591473076885 chr19 59128983 704579 0.01191596682797673 0.1455595974157232 chr20 63025520 805552 0.012781362216448194 0.11861825139191048 chr21 48129895 484267 0.010061667493768685 0.10993052094929295 chr22 51304566 430976 0.008400343938198405 0.09482198900361781 chrMT 16571 473 0.028543841651077182 0.17739945554463368 chrX 155270560 2072509 0.013347726703632679 0.12791788464471684 chrY 59373566 102210 0.001721473155242183 0.050596098485999566